Download 第三章芽胞杆菌物资组学(Bacillus chemomics)

1 芽胞杆菌研究文献学（第二卷）刘波、王阶平、朱育菁、唐建阳主编福建省农业科学院农业生物资源研究所 1 芽胞杆菌研究文献学（第二卷）主编：刘波、王阶平、朱育菁、唐建阳编委： 1 目录第一章芽胞杆菌分类学(Bacillus taxonomy) ............................................................................................... 1 第一节 Alicyclobacillus ........................................................................................................................ 1 第二节 Amphibacillus .......................................................................................................................... 3 第三节 Aneurinibacillus ....................................................................................................................... 3 第四节 Anoxybacillus ........................................................................................................................... 4 第五节 Bacillus..................................................................................................................................... 5 第六节 Brevibacillus........................................................................................................................... 56 第七节 Caldalkalibacillus ................................................................................................................... 56 第八节 Caldibacillus ........................................................................................................................... 56 第九节 Cerasibacillus ......................................................................................................................... 57 第十节 Domibacillus .......................................................................................................................... 57 第十一节 Edaphobacillus................................................................................................................... 58 第十二节 Fictibacillus ........................................................................................................................ 58 第十三节 Filobacillus ......................................................................................................................... 59 第十四节 Geobacillus ........................................................................................................................ 59 第十五节 Gracilibacillus..................................................................................................................... 61 第十六节 Halobacillus ....................................................................................................................... 61 第十七节 Jeotgalibacillus................................................................................................................... 62 第十八节 Lentibacillus ....................................................................................................................... 63 第十九节 Lysinibacillus ...................................................................................................................... 63 第二十节 Natronobacillus ................................................................................................................. 64 第二十一节 Oceanobacillus .............................................................................................................. 65 第二十二节 Ornithinibacillus ............................................................................................................ 65 第二十三节 Paenibacillus .................................................................................................................. 66 第二十四节 Paraliobacillus ................................................................................................................ 71 第二十五节 Pelagibacillus ................................................................................................................. 72 第二十六节 Pontibacillus .................................................................................................................. 72 第二十七节 Psychrobacillus .............................................................................................................. 72 第二十八节 Rummeliibacillus ........................................................................................................... 73 第二十九节 Salinibacillus .................................................................................................................. 74 第三十节 Salsuginibacillus ................................................................................................................. 74 第三十一节 Sulfobacillus ................................................................................................................... 74 第三十二节 Tenuibacillus .................................................................................................................. 75 第三十三节 Texcoconibacillus ........................................................................................................... 75 第三十四节 Thermobacillus .............................................................................................................. 76 第三十五节 Tuberibacillus................................................................................................................. 76 第三十六节 Ureibacillus .................................................................................................................... 77 第三十七节 Virgibacillus ................................................................................................................... 77 第二章芽胞杆菌基因组学(Bacillus genomics) .......................................................................................... 79 第三章芽胞杆菌物资组学(Bacillus chemomics) ................................................................................... 229 2 第一节芽胞杆菌物资组学--GC-MS 分析 ...................................................................................... 229 第二节芽胞杆菌物资组学--LC-MS 分析 ....................................................................................... 331 第三节芽胞杆菌物质组学--LC-MS-MS 分析 ................................................................................. 370 第四节芽胞杆菌物资组学--TLC 分析 ............................................................................................ 383 第四章芽胞杆菌代谢组学(Bacillus metabolomics)................................................................................. 421 第五章芽胞杆菌酶学(Bacillus enzymology) ............................................................................................ 437 第一节 2014 年芽胞杆菌酶学研究 ................................................................................................ 437 第二节 2013 年芽胞杆菌酶学研究 ................................................................................................ 474 第三节 2012 年芽胞杆菌酶学研究 ................................................................................................ 612 第四节 2011 年芽胞杆菌酶学研究 ................................................................................................ 735 第五节 2010 年芽胞杆菌酶学研究 ................................................................................................ 857 第六章芽胞杆菌发酵技术(Bacillus fermentation) .................................................................................. 906 第一节 2014 年芽胞杆菌发酵技术研究 ........................................................................................ 906 第二节 2013 年芽胞杆菌发酵技术研究 ........................................................................................ 923 第三节 2012 年芽胞杆菌发酵技术研究 ...................................................................................... 1000 第四节 2011 年芽胞杆菌发酵技术研究 ...................................................................................... 1039 第五节 2010 年芽胞杆菌发酵技术研究 ...................................................................................... 1064 第六节 2009 年芽胞杆菌发酵技术研究 ...................................................................................... 1071 第七节 2008 年芽胞杆菌发酵技术研究 ...................................................................................... 1077 第八节 2007 年芽胞杆菌发酵技术研究 ...................................................................................... 1091 第九节 2006 年芽胞杆菌发酵技术研究 ...................................................................................... 1139 第十节 2005 年芽胞杆菌发酵技术研究 ...................................................................................... 1151 第十一节 2004 年芽胞杆菌发酵技术研究 .................................................................................. 1170 第七章芽胞杆菌益生菌(Bacillus probiotic) ........................................................................................... 1173 第一节 2014 年芽胞杆菌益生菌研究 .......................................................................................... 1173 第二节 2013 年芽胞杆菌益生菌研究 .......................................................................................... 1188 第三节 2012 年芽胞杆菌益生菌研究 .......................................................................................... 1215 第四节 2011 年芽胞杆菌益生菌研究 .......................................................................................... 1233 第五节 2010 年芽胞杆菌益生菌研究 .......................................................................................... 1248 第六节 2009 年芽胞杆菌益生菌研究 .......................................................................................... 1264 第七节 2008 年芽胞杆菌益生菌研究 .......................................................................................... 1274 第八节 2007 年芽胞杆菌益生菌研究 .......................................................................................... 1285 第九节 2006 年芽胞杆菌益生菌研究 .......................................................................................... 1289 第十节 2006 年芽胞杆菌益生菌研究 .......................................................................................... 1293 第十一节 2005 年芽胞杆菌益生菌研究 ...................................................................................... 1299 第十二节 2004 年芽胞杆菌益生菌研究 ...................................................................................... 1305 第十三节 2003 年芽胞杆菌益生菌研究 ...................................................................................... 1309 第十四节 2002 年芽胞杆菌益生菌研究 ...................................................................................... 1314 第十五节 2001 年芽胞杆菌益生菌研究 ...................................................................................... 1316 第十六节 2000 年芽胞杆菌益生菌研究 ...................................................................................... 1320 第十七节 1999 年芽胞杆菌益生菌研究 ...................................................................................... 1322 第十八节 1998 年芽胞杆菌益生菌研究 ...................................................................................... 1325 第十九节 1997 年芽胞杆菌益生菌研究 ...................................................................................... 1327 第二十节 1996 年芽胞杆菌益生菌研究 ...................................................................................... 1328 3 第二十一节 1995 年芽胞杆菌益生菌研究 .................................................................................. 1329 索引 ....................................................................................................................................................... 1332 1 第一章芽胞杆菌分类学(Bacillus taxonomy) 第一节 1. 2. 3. Alicyclobacillus Alicyclobacillus pomorum Int J Syst Evol Microbiol. 2003 Sep;53(Pt 5):1537-44. Alicyclobacillus pomorum sp. nov., a novel thermo-acidophilic, endospore-forming bacterium that does not possess omega-alicyclic fatty acids, and emended description of the genus Alicyclobacillus. Goto K(1), Mochida K, Asahara M, Suzuki M, Kasai H, Yokota A. Author information: (1)Microbiological and Analytical Group, Food Research Laboratories, Mitsui Norin Co. Ltd, 223-1, Miyahara, Fujieda, Shizuoka 426-0133, Japan. [email protected] A thermo-acidophilic endospore-forming bacterium was isolated from a mixed fruit juice. The organism, strain 3A(T), was rod-shaped, grew aerobically at 30-60 degrees C (optimum 45-50 degrees C), pH 3.0-6.0 (optimum pH 4.0-4.5) and produced acid from various sugars. It contained menaquinone-7 as the major isoprenoid quinone. The G+C content of the DNA was 53.1 mol%. The predominant cellular fatty acids of the strain were iso-C(15 : 0), anteiso-C(15 : 0), iso-C(16 : 0), iso-C(17 : 0) and anteiso-C(17 : 0), but omega-alicyclic fatty acids, which are characteristic of the genus Alicyclobacillus, were not found in the strain. Phylogenetic analyses based on both 16S rRNA and gyrB (DNA gyrase B subunit gene) gene sequences showed that strain 3A(T) falls into the Alicyclobacillus cluster, validated by significant bootstrap values. However, strain 3A(T) did not show a close relationship to the other species of the cluster. The level of 16S rDNA similarity between strain 3A(T) and other strains of the cluster was between 92.5 and 95.5 %. The level of gyrB sequence similarity between strain 3A(T) and other strains of the cluster was between 68.5 and 74.4 %. DNA-DNA hybridization values between strain 3A(T) and phylogenetically related strains of the genera Alicyclobacillus, Bacillus and Sulfobacillus were under 13 %, indicating that strain 3A(T) represents a distinct species. On the basis of these results, strain 3A(T) should be classified as a novel Alicyclobacillus species. The name Alicyclobacillus pomorum is proposed for this organism. The type strain of Alicyclobacillus pomorum is strain 3A(T) (=DSM 14955(T)=IAM 14988(T)). PMID: 13130044 [PubMed - indexed for MEDLINE] Alicyclobacillus sendaiensis Int J Syst Evol Microbiol. 2003 Jul;53(Pt 4):1081-4. Alicyclobacillus sendaiensis sp. nov., a novel acidophilic, slightly thermophilic species isolated from soil in Sendai, Japan. Tsuruoka N(1), Isono Y, Shida O, Hemmi H, Nakayama T, Nishino T. Author information: (1)Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 07, Sendai, Miyagi 980-8579, Japan. An acidophilic, slightly thermophilic bacterium, designated strain NTAP-1T, that produces a thermostable extracellular acid collagenase activity with potential industrial applications was isolated from soil of Aoba-yama Park, Sendai, Japan. The temperature range for growth was 40-65 degrees C, with an optimum at 55 degrees C, and the pH range for growth was 2.5-6.5, with an optimum at pH 5.5. Analysis of the 16S rDNA sequence of strain NTAP-1T showed that it is most closely related to strains of the genus Alicyclobacillus. Consistently, the major constituents of the cell-membrane lipid of strain NTAP-1T were omega-alicyclic fatty acids. However, DNA-DNA reassociation studies showed only low similarities (less than 33%) to any type strain of Alicyclobacillus. On the basis of the phenotypic and genotypic properties, a novel species is proposed, Alicyclobacillus sendaiensis sp. nov., represented by strain NTAP-1T (=JCM 11817T=ATCC BAA-609T). PMID: 12892130 [PubMed - indexed for MEDLINE] Alkalibacillus haloalkaliphilus Int J Syst Evol Microbiol. 2005 Sep;55(Pt 5):1891-6. Reclassification of Bacillus haloalkaliphilus Fritze 1996 as Alkalibacillus haloalkaliphilus gen. nov., comb. nov. and the description of Alkalibacillus salilacus sp. nov., a novel halophilic bacterium isolated from a salt lake in China. Jeon CO(1), Lim JM, Lee JM, Xu LH, Jiang CL, Kim CJ. Author information: (1)Environmental Biotechnology National Core Research Center, Gyeongsang National University, Korea. A spore-forming, halophilic bacterium, designated strain BH163(T), was isolated from a salt lake in China. Cells were motile, strictly aerobic rods that contained type A1gamma peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. The isolate showed Gram- and catalase-positive reactions and formed a terminal endospore with a swollen sporangium. The major cellular fatty acids were anteiso-C(15:0), iso-C(15:0), anteiso-C(17:0) and iso-C(16:0). The genomic DNA G+C content of the strain was 41.0 mol%. Comparative analysis of 16S rRNA gene sequences showed that strain BH163(T) formed a distinct line within the phyletic group classically defined as the genus Bacillus and was most closely related to the taxa [Bacillus] haloalkaliphilus DSM 5271(T) and Filobacillus milosensis DSM 13259(T), with 16S rRNA gene sequence similarities of 95.9 and 94.5%, respectively. On the basis of physiological and mo- 2 4. 5. 6. lecular properties, it is proposed that [Bacillus] haloalkaliphilus DSM 5271(T) is reclassified in the new genus Alkalibacillus as Alkalibacillus haloalkaliphilus gen. nov., comb. nov. Strain BH163(T) (=KCTC 3916(T)=DSM 16460(T)) was assigned as the type strain of the novel species Alkalibacillus salilacus. PMID: 16166684 [PubMed - indexed for MEDLINE] Alkalibacillus halophilus Syst Appl Microbiol. 2007 Jun;30(4):268-72. Epub 2006 Oct 4. Alkalibacillus halophilus sp. nov., a new halophilic species isolated from hypersaline soil in Xin-Jiang province, China. Tian XP(1), Dastager SG, Lee JC, Tang SK, Zhang YQ, Park DJ, Kim CJ, Li WJ. Author information: (1)Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China. A halophilic, Gram-positive, spore-forming motile Bacillus-like strain YIM 012(T), was isolated from one of the hypersaline soil samples collected in Xin-jiang province, China. Its optimum growth occurred at 10-20% of NaCl concentration (w/v), pH 7.0-8.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 012(T) is a member of the genus of Alkalibacillus, which is well supported by its chemotaxonomic and molecular characteristics. Based on its phenotypic evidence and genotypic data, Alkalibacillus halophilus sp. nov. was proposed and strain YIM 012(T) (=DSM 17369(T)=KCTC 3990(T)) was assigned as the type strain of the novel species. PMID: 17027220 [PubMed - indexed for MEDLINE] Alkalilactibacillus ikkensis Extremophiles. 2012 Feb 2. [Epub ahead of print] Alkalilactibacillus ikkensis, gen. nov., sp. nov., a novel enzyme-producing bacterium from a cold and alkaline environment in Greenland. Schmidt M(1), Priemé A, Johansen A, Stougaard P. Author information: (1)Department of Agriculture and Ecology, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark. Three novel Gram-positive, endospore-forming bacteria were isolated from a cold and alkaline environment. Phylogenetic analysis showed that the strains were almost identical, and that they were related to Natronobacillus azotifigens 24KS-1(T) (95.8% identity), Paraliobacillus quinghaiensis YIM-C158(T) (95.1%), Paraliobacillus ryukyuensis O15-7(T) (94.5%), and Halolactibacillus miurensis M23-1(T) (93.9%). The isolates produced amylase, α-galactosidase, β-galactosidase, and β-glucuronidase, and showed optimal growth at pH 10, at 20°C, and at 2-8% (w/v) NaCl. Major fatty acids were C(14:0) (10.6-11.6%), anteiso-C(15:0) (25.7-32.7%), C(16:1) ω11c (12.2-16.0%), and C(16:0) (14.0-20.4%). The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol, and meso-diaminopimelic acid was found in the cell-wall peptidoglycan. The G+C content was 38.4%. DNA-DNA hybridization between strain GCM68(T) and H. miurensis M23-1(T) was 32.4%, while hybridization to N. azotifigens 24KS-1(T), Amphibacillus tropicus Z-7792(T), and Paraliobacillus ryukyuensis O15-7(T) was below 30%. The phylogenetic analysis and G+C content place strain GCM68(T) in relation to species belonging to Bacillus rRNA group 1, but phylogenetic and physiologic data combined with chemotaxonomic analyses support our proposal for a new genus, Alkalilactibacillus, gen. nov., with the novel species Alkalilactibacillus ikkensis, sp. nov. (type strain is GCM68(T) = DSM 19937 = LMG 24405). PMID: 22297696 [PubMed - as supplied by publisher] Alteribacillus bidgolensis Int J Syst Evol Microbiol. 2012 Nov;62(Pt 11):2691-7. doi: 10.1099/ijs.0.034173-0. Epub 2012 Jan 6. Alteribacillus bidgolensis gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Bacillus persepolensis as Alteribacillus persepolensis comb. nov. Didari M(1), Amoozegar MA, Bagheri M, Schumann P, Spröer C, Sánchez-Porro C, Ventosa A. Author information: (1)Extremophiles Laboratory, Department of Microbiology, Faculty of Biology, College of Science, University of Tehran, Tehran, Iran. A novel Gram-stain-positive, moderately halophilic bacterium, designated strain P4B(T), was isolated from water of the hypersaline Aran-Bidgol lake in Iran and characterized taxonomically by using a polyphasic approach. Cells of strain P4B(T) were non-motile rods producing ellipsoidal endospores at a central position in non-swollen sporangia. Strain P4B(T) was strictly aerobic and catalase- and oxidase-positive. It was able to grow at NaCl concentrations of 0.5-12.5% (w/v), with optimum growth occurring at 5-7.5% (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain P4B(T) was shown to belong to the phylum Firmicutes and shared highest similarity with Bacillus persepolensis HS136(T) (97.1%) and Bacillus salarius BH169(T) (95.1%). However, it shared only 91.3% 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10(T), indicating that strain P4B(T) might not be a member of the genus Bacillus. The DNA G+C content of this new isolate was 38.9 mol%. DNA-DNA hybridization experiments revealed a low level of relatedness between strain P4B(T) and B. persepolensis HS136(T) (6%). The major cellular fatty acids of strain P4B(T) were iso-C(15:0) and anteiso-C(15:0), as for B. persepolensis HS136(T) but in contrast to B. salarius DSM 16461(T) and B. subtilis subsp. subtilis DSM 10(T). Its polar lipid pattern consisted of phosphatidylglycerol, an aminoglycolipid and an unknown phospholipid. This polar lipid profile was similar to that obtained for B. persepolensis DSM 21632(T) but different from those of B. salarius DSM 16461(T) and B. subtilis subsp. subtilis DSM 10(T). The isoprenoid quinones were MK-7 (88%) and MK-8 (2%). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All these features indicate placement of strain P4B(T) within the Firmicutes, closely related to B. persepolensis but with features clearly distinct from those of the genus Bacillus and other related genera. On the basis of these data, strain P4B(T) is considered to represent a novel species of a new genus, for which the name Alteribacillus bidgolensis gen. nov., sp. nov. is proposed. The type strain of Alteribacillus bidgolensis is P4B(T) (=CCM 7963(T)=CECT 7998(T)=DSM 25260(T)=IBRC-M 10614(T)=KCTC 13821(T)). It is also suggested to transfer B. persepolensis to this new genus, as Alteribacillus persepolensis comb. nov. The type strain of Alteribacillus persepolensis is HS136(T) (=CCM 7595(T)=DSM 21632(T)=JCM 15720(T)=LMG 25222(T)). PMID: 22228653 [PubMed - indexed for MEDLINE] 3 第二节 7. 8. Amphibacillus Amphibacillus fermentum Mikrobiologiia. 2001 Nov-Dec;70(6):825-37. [Amphibacillus fermentum sp. nov., Amphibacillus tropicus sp. nov.--new alkaliphilic, facultatively anaerobic, saccharolytic Bacilli from Lake Magadi]. [Article in Russian] Zhilina TN(1), Garnova ES, Turova TP, Kostrikina NA, Zavarzin GA. Author information: (1)Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7, k. 2, Moscow, 117312 Russia. New alkaliphilic, saccharolytic, rod-shaped, gram-positive bacteria resistant to heating and drying and phylogenetically affiliated to the Bacillus lineage were isolated under strictly anaerobic conditions from sediments of the alkaline and highly mineralized Lake Magadi. Strain Z-7792 forms endospores; in strain Z-7984, endospore formation was not revealed. The strains are capable of both anaerobic growth (at the expense of fermentation of glucose and certain monoand disaccharides with the formation of formate, ethanol, and acetate) and aerobic growth. Among polysaccharides, the strains hydrolyze starch, glycogen, and xylan. Yeast extract or methionine are required for growth. The strains are strict alkaliphiles exhibiting obligate requirement for Na+ and carbonate ions but not for Cl- ion. Growth occurs at a total mineralization as high as 3.3-3.6 M Na+, with an optimum at 1-1.7 M Na+. Strain Z-7792 is an obligate alkaliphile with a pH growth range of 8.5-11.5 and an optimum of 9.5-9.7. Strain Z-7984 grows in a pH range of 7.0-10.5 with an optimum at 8.0-9.5. Both strains are mesophiles having a growth optimum at 37-38 degrees C. They belong to bacilli with a low G + C content. The G + C contents of the DNA of strains Z-7792 and Z-7984 are 39.2 and 41.5 mol%, respectively. These isolates of facultatively anaerobic, strictly alkaliphilic, Na(+)-dependent bacilli can be considered representatives of the ecological group adapted to the life at drying-up shoars of soda lakes. Because of their independence of NaCl and lack of obligate dependence on sodium carbonates, the isolates are to be assigned to athalassophilic organisms. According to their physiological and phylogenetic characteristics, they taxonomically belong to group 1 of the species of bacilli, occupying a position intermediate between the genera Amphibacillus and Gracilibacillus. The isolates are described as new species of Amphibacillus: A. fermentum (type strain, Z-7984T) and A. tropicus (type strain, Z-7792T). PMID: 11785140 [PubMed - indexed for MEDLINE] Amphibacillus jilinensis Int J Syst Evol Microbiol. 2010 Nov;60(Pt 11):2540-3. doi: 10.1099/ijs.0.018259-0. Epub 2009 Dec 4. Amphibacillus jilinensis sp. nov., a facultatively anaerobic, alkaliphilic bacillus from a soda lake. Wu XY(1), Zheng G, Zhang WW, Xu XW, Wu M, Zhu XF. Author information: (1)College of Life Sciences, Zhejiang University, Hangzhou, PR China. A facultatively anaerobic, alkaliphilic, spore-forming, Gram-positive-staining rod, designated Y1(T), was isolated under strictly anaerobic conditions from sediment of a soda lake in Jilin province, China. The strain was not dependent on Na(+) but was highly halotolerant and grew optimally in medium JY with 0.5 M Na(+) (0.06 M NaHCO(3) and 0.44 M NaCl). The optimum pH for growth was 9.0, with a range of pH 7.5-10.5. No growth occurred at pH 7.0 or 11.0. The strain was mesophilic, with a temperature range of 15-45 °C and optimum growth at 32 °C. Strain Y1(T) was able to use certain mono- and oligosaccharides. Soluble starch and casein were hydrolysed. The methyl red test, Voges-Proskauer test and tests for catalase and oxidase activities were negative. The predominant fatty acids were anteiso-C(15 : 0) and iso-C(15 : 0). Comparative 16S rRNA gene sequence analysis revealed 93.4-96.8 % sequence similarity to members of the genus Amphibacillus. The DNA G+C content was 37.7 mol% (T(m) method). The DNA-DNA relatedness of strain Y1(T) with respect to Amphibacillus tropicus DSM 13870(T) and Amphibacillus sediminis DSM 21624(T) was 48 and 37 %, respectively. On the basis of its phylogenetic position and the DNA-DNA relatedness data as well as its physiological and biochemical properties, strain Y1(T) represents a novel species of the genus Amphibacillus, for which the name Amphibacillus jilinensis sp. nov. is proposed. The type strain is Y1(T) (=CGMCC 1.5123(T) =JCM 16149(T)). PMID: 19965990 [PubMed - indexed for MEDLINE] 第三节 9. Aneurinibacillus Aneurinibacillus danicus Int J Syst Evol Microbiol. 2004 Mar;54(Pt 2):419-27. Reclassification of Brevibacillus brevis strains NCIMB 13288 and DSM 6472 (=NRRL NRS-887) as Aneurinibacillus danicus sp. nov. and Brevibacillus limnophilus sp. nov. Goto K(1), Fujita 4 R, Kato Y, Asahara M, Yokota A. Author information: (1)Microbiological and Analytical Group, Food Research Laboratories, Mitsui Norin Co. Ltd, 223-1, Miyahara, Fujieda, Shizuoka 426-0133, Japan. [email protected] Comparison of the hypervariable region (269-279 bases in length) at the 5' end of the 16S rDNA sequences of 29 bacterial strains that were identified previously as Brevibacillus brevis showed that 13 strains clustered with Aneurinibacillus species, eight strains clustered with Bacillus species and eight strains clustered with Brevibacillus species. Based on DNA-DNA hybridization results, 27 strains, not including [Brevibacillus brevis] NCIMB 13288 and [Brevibacillus brevis] DSM 6472, were reidentified as Aneurinibacillus migulanus, Aneurinibacillus thermoaerophilus, Bacillus methanolicus, Bacillus oleronius, Brevibacillus agri, Brevibacillus brevis and Brevibacillus parabrevis. [Brevibacillus brevis] NCIMB 13288, which was located in the Aneurinibacillus cluster, showed low DNA-DNA relatedness (<14 %) and low 16S rDNA sequence similarity (96.8-97.9 %) to other Aneurinibacillus species. [Brevibacillus brevis] DSM 6472, which was located in the Brevibacillus cluster, also showed low DNA-DNA relatedness (<12 %) and low 16S rDNA sequence similarity (95.4-98.8 %) to other Brevibacillus species. These genotypic and phylogenetic data, plus phenotypic and chemotaxonomic characteristics, suggest that [Brevibacillus brevis] NCIMB 13288 (=IAM 15048) and [Brevibacillus brevis] DSM 6472 (=NRRL NRS-887) represent novel species of the genera Aneurinibacillus and Brevibacillus, respectively, for which the names Aneurinibacillus danicus sp. nov. and Brevibacillus limnophilus sp. nov. are proposed. PMID: 15023954 [PubMed - indexed for MEDLINE] 第四节 Anoxybacillus 10. Anoxybacillus contaminans Int J Syst Evol Microbiol. 2004 May;54(Pt 3):941-6. Anoxybacillus contaminans sp. nov. and Bacillus gelatini sp. nov., isolated from contaminated gelatin batches. De Clerck E(1), Rodríguez-Díaz M, Vanhoutte T, Heyrman J, Logan NA, De Vos P. Author information: (1)Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium. [email protected] Aerobic, endospore-forming bacteria that are attributed to the genus Bacillus or related genera constitute a hazard to the quality of gelatin. During repetitive extragenic palindromic DNA (rep)-PCR screening of gelatin isolates, a group of five isolates (group 1) and a group of 66 isolates (group 2) that did not match any pattern in our database were found. On the basis of 16S rDNA sequence analysis, representative strains of the different rep-PCR fingerprint types of group 1 were shown to be related most closely to Anoxybacillus species, but with sequence similarity of <97 %. Likewise, representative strains of group 2 were shown to be related most closely to Bacillus species, with 16S rDNA sequence similarity of <97 %. DNA-DNA reassociation values of isolates that displayed the most divergent rep-PCR profiles revealed that strains within each group belonged to a single species, according to recommendations for species delineation. A mean fatty acid profile could be calculated for each group. Isolates within a single group had similar patterns of results in API and other phenotypic tests; no correlation of patterns of results with rep-PCR groups was seen. Physiological characterization of group 1 isolates allows their distinction from other Anoxybacillus species. Despite the weak reaction of group 2 isolates in API tests, physiological characterization allows distinction between Bacillus species that react weakly in API tests. Two novel species are therefore proposed, with the names Anoxybacillus contaminans sp. nov. (type strain, LMG 21881(T)=DSM 15866(T)) and Bacillus gelatini sp. nov. (type strain, LMG 21880(T)=DSM 15865(T)). PMID: 15143046 [PubMed - indexed for MEDLINE] 11. Anoxybacillus pushchinensis Int J Syst Evol Microbiol. 2000 Nov;50 Pt 6:2109-17. Anoxybacillus pushchinensis gen. nov., sp. nov., a novel anaerobic, alkaliphilic, moderately thermophilic bacterium from manure, and description of Anoxybacillus flavitherms comb. nov. Pikuta E(1), Lysenko A, Chuvilskaya N, Mendrock U, Hippe H, Suzina N, Nikitin D, Osipov G, Laurinavichius K. Author information: (1)Institute of Microbiology, Russian Academy of Sciences, Moscow. [email protected] A new strictly anaerobic, alkaliphilic, moderately thermophilic, fermentative, spore-forming bacterium, strain K1T, was isolated from manure samples (pH 6-8). Cells were Gram-positive, straight, non-motile rods that grew at temperatures of 37-66 degrees C (optimum at 62 degrees C) and in a pH range of 8.0-10.5 (optimum at 9.5-9.7). The bacterium fermented D-glucose, sucrose, D-fructose, D-trehalose and starch as carbon and energy sources. It required vitamins and its growth is stimulated by yeast extract. The major metabolic products were H2 and acetate. Cells were catalase-negative and could reduce nitrate to nitrite. The G+C content of the DNA was 42.2 mol%. Based on the phenotypic properties and 16S rDNA sequencing and DNA-DNA hybridization data, strain K1T (= DSM 12423T = ATCC 700785T = VKM B-2193T) was assigned to the new genus Anoxybacillus gen. nov., as a representative of a new species, Anoxybacillus pushchinensis sp. nov. 'Bacillus flavothermus' strain d.y., which was found to be closely related to strain K1T, is described as Anoxybacillus flavithermus comb. nov. (type strain = d.y.T = DSM 2641T). PMID: 11155986 [PubMed - indexed for MEDLINE] 5 第五节 Bacillus 12. Bacillus abyssalis Antonie Van Leeuwenhoek. 2013 May;103(5):963-9. doi: 10.1007/s10482-013-9875-7. Epub 2013 Jan 12. Bacillus abyssalis sp. nov., isolated from a sediment of the South China Sea. You ZQ(1), Li J, Qin S, Tian XP, Wang FZ, Zhang S, Li WJ. Author information: (1)Key Laboratory of Marine Bio-resources Sustainable Utilization CAS, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, People's Republic of China. A Gram-positive bacterium, designated SCSIO 15042(T), was isolated from a sediment of the South China Sea and was subjected to a polyphasic taxonomic study. The isolate grew at 20-60 °C, pH 6.0-10.0 and it could grow with up to 10 % (w/v) NaCl. The cell-wall diamino acid was found to be meso-diaminopimelic acid. Polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and an unknown polar lipid. The only menaquinone was determined to be MK-7. The major fatty acids were identified as C16:1 ω7c/C16:1 ω6c, C16:0, iso-C15:0, anteiso-C15:0, and iso-C16:0. The DNA G+C content of strain SCSIO 15042(T) was determined to be 43.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain SCSIO 15042(T) to the genus Bacillus. Levels of 16S rRNA gene sequence similarities between strain SCSIO 15042(T) and Bacillus herbersteinensis D-1-5a(T), Bacillus infantis SMC 4352-1(T), Bacillus novalis LMG 21837(T) and Bacillus drentensis LMG 21831(T) were 96.2, 96.2, 96.1 and 96.1 %, respectively. Based on the evidence of the present polyphasic study, strain SCSIO 15042(T) is considered to represent a novel species of the genus Bacillus, for which the name Bacillus abyssalis sp. nov. is proposed. The type strain is SCSIO 15042(T) (=DSM 25875(T) = CCTCC AB 2012074(T) = NBRC 109102(T)). PMID: 23314911 [PubMed - indexed for MEDLINE] 13. Bacillus acidiceler Int J Syst Evol Microbiol. 2007 Sep;57(Pt 9):2031-6. Bacillus acidiceler sp. nov., isolated from a forensic specimen, containing Bacillus anthracis pX02 genes. Peak KK(1), Duncan KE, Veguilla W, Luna VA, King DS, Heller L, Heberlein-Larson L, Reeves F, Cannons AC, Amuso P, Cattani J. Author information: (1)USF Center for Biological Defense, College of Public Health, University of South Florida, 3602 Spectrum Blvd, Tampa, FL 33612-9401, USA. [email protected] Research at the Center for Biological Defense identified plasmid-borne forms of Bacillus anthracis pXO2 genes in a Gram-positive, endospore-forming rod, isolated from a forensic specimen considered a credible threat of harbouring anthrax. Conventional, commercial and molecular-based methods indicated that the isolate (CBD 119(T)) was not B. anthracis and considered not to be a member of the Bacillus cereus group. Based on the 16S rRNA gene sequence similarities, strain CBD 119(T) was most closely related to Bacillus luciferensis LMG 18422(T) (99.3 %). Phenotyping and fatty acid methyl ester analysis of the isolate were conducted alongside B. luciferensis JCM 12212(T). The major cellular fatty acids (anteiso-C(15 : 0), iso-C(15 : 0), and >7 iso or anteiso forms) supported inclusion of the isolate in the genus Bacillus. Strain CBD 119(T) was inconsistent with B. luciferensis JCM 12212(T) for 18 of 96 traits evaluated including motility, degree of endospore-driven swelling and pH optimum; the two were linked by fatty acid methyl ester analysis as separate but closely related species. DNA-DNA relatedness between strain CBD 119(T) and B. luciferensis JCM 12212(T) resulted in less than 20 % hybridization. The results of biochemical and physiological characterization, chemotaxonomic analysis and DNA-DNA hybridization differentiated strain CBD 119(T) both phenotypically and genotypically from the only species with validly published name with greater than 97 % 16S rRNA gene sequence similarity. The isolate has an accelerated doubling time when grown in aerated broth at pH 5.9 relative to that at pH 7.1. Therefore, it is proposed that strain CBD 119(T) represents a novel species, Bacillus acidiceler sp. nov. The type strain is strain CBD 119(T) (=NRRL B-41736(T)=DSM 18954(T)). PMID: 17766868 [PubMed - indexed for MEDLINE] 14. Bacillus acidicola Int J Syst Evol Microbiol. 2005 Sep;55(Pt 5):2125-30. Bacillus acidicola sp. nov., a novel mesophilic, acidophilic species isolated from acidic Sphagnum peat bogs in Wisconsin. Albert RA(1), Archambault J, Rosselló-Mora R, Tindall BJ, Matheny M. Author information: (1)Semco BioScience, 630 East Keefe, Milwaukee, WI 53212, USA. [email protected] A mesophilic, acidophilic, spore-forming bacterium, strain 105-2(T), was isolated from an acidic Sphagnum peat bog in Wisconsin, USA. Strain 105-2(T) has 16S rRNA gene sequence similarity to Bacillus sporothermodurans DSM 10599(T) and Bacillus oleronius DSM 9356(T) of 97.4 and 97.8%, respectively. The primary lipoquinone is MK-7 and the major fatty acids are 15:0 iso, 15:0 anteiso and 17:0 anteiso. The predominant polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and a glycolipid. The DNA G+C content was found to be 43.2 mol%. The phenotypic, chemotaxonomic and molecular analyses identified strain 105-2(T) as a novel Bacillus species, for which the name Bacillus acidicola is proposed. The type strain is 105-2(T) (=DSM 14745(T)=ATCC BAA-366(T)=NRRL B-23453(T)). PMID: 16166720 [PubMed - indexed for MEDLINE] 15. Bacillus acidiproducens Int J Syst Evol Microbiol. 2009 Sep;59(Pt 9):2226-31. doi: 10.1099/ijs.0.003913-0. Epub 2009 Jul 15. Bacillus acidiproducens sp. nov., vineyard soil isolates that produce lactic acid. Jung MY(1), Kim JS, Chang YH. Author information: (1)Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 52 Oeundong, Daejeon 305-806, Republic of Korea. Two novel spore-forming lactic acid bacteria, strains SL213T and SL1213, were isolated from vineyard soils in Korea. Cells of both isolates were rod-shaped bacilli and contained subterminal, ellipsoidal spores. Strains were facultatively anaerobic, catalase-positive, oxidase-negative and motile with single flagella. meso-Diaminopimelic acid, 6 16. 17. 18. 19. glucose and galactose were detected in whole-cell hydrolysates. Major fatty acids found in the strains were anteiso-C15:0, iso-C15:0, iso-C16:0, C16:0 and anteiso-C17:0. The G+C contents of the DNA were 46.1 and 46.3 mol%. 16S rRNA gene sequences from the two strains were almost identical (99.9%) and placed them in the genus Bacillus, according to phylogenetic analysis. The type strains most closely related to SL213T were Bacillus coagulans ATCC 7050T and Bacillus badius ATCC 14574T, with 16S rRNA gene sequence similarities of 96.9 and 95.9%, respectively. Levels of DNA-DNA relatedness between strain SL213T and strain SL1213, B. coagulans ATCC 7050T and B. badius ATCC 14574T were 92.5, 49.0 and 27.5%, respectively. On the basis of 16S rRNA gene sequences and chemotaxonomic and phenotypic evidence given in this study, we report that SL213T represents a novel species, for which the name Bacillus acidiproducens sp. nov. is proposed. The type strain is SL213T (=KCTC 13078T=JCM 14638T). PMID: 19605722 [PubMed - indexed for MEDLINE] Bacillus aeolius Syst Appl Microbiol. 2003 Jun;26(2):172-6. Bacillus aeolius sp. nov. a novel thermophilic, halophilic marine Bacillus species from Eolian Islands (Italy). Gugliandolo C(1), Maugeri TL, Caccamo D, Stackebrandt E. Author information: (1)Dipartimento di Biologia Animale ed Ecologia Marina, Sez. Ecologia Microbica e Biotecnologie, Messina, Italy. Phylogenetic relationships of a thermophilic, halophilic, aerobic spore-forming strain 4-1(T), isolated from the water of a shallow sea hot spring at Vulcano Island (Italy), revealed its relatedness to members of the genus Bacillus. Chemotaxonomic and phenotypic properties of strain 4-1(T) are sufficiently different from related moderately thermophilic species, e.g., B. smithii, B. fumarioli, B. oleronius, B. sporothermodurans and B. infernus to describe strain 4-1(T) as a new Bacillus species, for which the name Bacillus aeolius sp. nov. is proposed. Strain 4-1(T) is characterised by the potential biotechnological important properties such as exopolysaccharide production, surfactant activity, and utilisation of hydrocarbons. PMID: 12866842 [PubMed - indexed for MEDLINE] Bacillus aequororis Singh NK(1), Kaur C, Kumar N, Velmurugan S, Citarasu T, Mayilraj S. Bacillus aequororis sp. nov., Isolated From Marine Sediment. Curr Microbiol. 2014 Jul 10. [Epub ahead of print] Author information: (1)MTCC- Microbial Type Culture Collection and Gene Bank, Chandigarh, 160 036, India. The taxonomic position of a bacterium isolated from a marine sediment sample collected from the Bay of Bengal, Kanyakumari coast, India, was analyzed by using a polyphasic taxonomic approach. The isolated strain, designated as M-8(T), had phenotypic characteristics that matched those of the genus Bacillus and it represents a novel species. The diagnostic cell wall amino acid is meso-DAP. The major menaquinone is MK-7, and the strain has a phospholipid pattern of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unknown glycolipid. The almost-complete 16S rRNA gene sequence (1,450 bases) of the novel strain was compared with those of closely related species and confirmed that the strain belongs to the genus Bacillus. 16S rRNA gene sequence analysis revealed that strain M-8(T) differs from the closely related species Bacillus horikoshi 99.5 %, Bacillus halmapalus 98.3 %, and Bacillus cohni 97.4 %. However, the DNA-DNA hybridization showed that it had genomic relatedness value of 60.7 % with B. horikoshi, B. halmapalus (37.6 %), and B. cohnii (29.9 %). The DNA G+C content of strain M-8(T) is 40.6 mol%. Based on the polyphasic data, strain M-8(T) should be recognized as a novel species of the genus Bacillus, for which the name Bacillus aequororis sp. nov. is proposed. The type strain is M-8(T) (=MTCC 11626(T) = JCM 19304(T)). PMID: 25008778 [PubMed - as supplied by publisher] Bacillus aerius Int J Syst Evol Microbiol. 2006 Jul;56(Pt 7):1465-73. Bacillus aerius sp. nov., Bacillus aerophilus sp. nov., Bacillus stratosphericus sp. nov. and Bacillus altitudinis sp. nov., isolated from cryogenic tubes used for collecting air samples from high altitudes. Shivaji S(1), Chaturvedi P, Suresh K, Reddy GS, Dutt CB, Wainwright M, Narlikar JV, Bhargava PM. Author information: (1)Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India. [email protected] Four novel bacterial strains were isolated from cryogenic tubes used to collect air samples at altitudes of 24, 28 and 41 km. The four strains, 24K(T), 28K(T), 41KF2a(T) and 41KF2b(T), were identified as members of the genus Bacillus. Phylogenetic analysis based on 16S rRNA gene sequences indicated that three of the strains, 24K(T), 28K(T) and 41KF2a(T), are very similar to one another (>98 % sequence similarity) and show a similarity of 98-99 % with Bacillus licheniformis and 98 % with Bacillus sonorensis. DNA-DNA hybridization studies showed that strains 24K(T), 28K(T) and 41KF2a(T) exhibit <70 % similarity with each other and with B. licheniformis and B. sonorensis. Differences in phenotypic and chemotaxonomic characteristics between the novel strains and B. licheniformis and B. sonorensis further confirmed that these three isolates are representatives of three separate novel species. Strain 41KF2b(T) showed 100 % 16S rRNA gene sequence similarity to Bacillus pumilus, but differed from its nearest phylogenetic neighbour in a number of phenotypic and chemotaxonomic characteristics and showed only 55 % DNA-DNA relatedness. Therefore, the four isolates represent four novel species for which the names Bacillus aerius sp. nov. (type strain, 24K(T)=MTCC 7303(T)=JCM 13348(T)), Bacillus aerophilus sp. nov. (type strain, 28K(T)=MTCC 7304(T)=JCM 13347(T)), Bacillus stratosphericus sp. nov. (type strain, 41KF2a(T)=MTCC 7305(T)=JCM 13349(T)) and Bacillus altitudinis sp. nov. (type strain, 41KF2b(T)=MTCC 7306(T)=JCM 13350(T)) are proposed. PMID: 16825614 [PubMed - indexed for MEDLINE] Bacillus aidingensis Int J Syst Evol Microbiol. 2008 Dec;58(Pt 12):2828-32. doi: 10.1099/ijs.0.2008/000471-0. Bacillus aidingensis sp. nov., a moderately halophilic bacterium isolated from Ai-Ding salt lake in China. Xue Y(1), Ventosa A, Wang X, Ren P, Zhou P, Ma Y. Author information: (1)State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China. A Gram-positive, halophilic bacterium was isolated from a sediment sample from Ai-Ding salt lake in China. The isolate, designated strain 17-5(T), grew at salinities of 8-33 % (w/v) NaCl (optimally at 12 %, w/v). The genomic DNA G+C con- 7 20. 21. 22. 23. tent of strain 17-5(T) was 48.1 mol%. The predominant isoprenoid quinone was MK-7(H(2)) and the cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and an unidentified glycolipid. The major cellular fatty acids were anteiso-C(15 : 0), anteiso-C(17 : 0), iso-C(16 : 0) and C(16 : 0). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 17-5(T) was a member of the genus Bacillus, being most closely related to Bacillus qingdaonensis JCM 14087(T) (96.0 % sequence similarity) and Bacillus salarius DSM 16461(T) (95.6 %). The levels of 16S rRNA gene sequence similarity with respect to other Bacillus species were less than 91.7 %. Comparative analysis of the 16S rRNA gene sequence data, chemotaxonomy and phenotypic features of the novel isolate and related species of Bacillus indicated that strain 17-5(T) represents a novel species within the genus Bacillus, for which the name Bacillus aidingensis sp. nov. is proposed. The type strain is 17-5(T) (=CGMCC 1.3227(T)=DSM 18341(T)). PMID: 19060067 [PubMed - indexed for MEDLINE] Bacillus algicola Syst Appl Microbiol. 2004 May;27(3):301-7. Bacillus algicola sp. nov., a novel filamentous organism isolated from brown alga Fucus evanescens. Ivanova EP(1), Alexeeva YA, Zhukova NV, Gorshkova NM, Buljan V, Nicolau DV, Mikhailov VV, Christen R. Author information: (1)Industrial Research Institute, Swinburne University of Technology, Hawthorn, Vic, Australia. [email protected] A slightly yellowish, Gram-positive, filamentous with 'cross-like' branching, aerobic, spore-forming bacterium was isolated from enrichment culture during degradation of the thallus of the brown alga Fucus evanescens. The bacterium studied was chemoorganotrophic, tolerant to 3% NaCl, alkalitolerant, and alginolytic. The predominant cellular fatty acid was ai15:0 which accounted more than 65% of total fatty acids, while i14:0, il5:0 i16:0, and ai17:0 made up 25%. DNA base composition was 37 mol% GC. Phylogenetic analysis of 16S rDNA gene revealed that this isolate was a member of the genus Bacillus, with no close relatives at the species level (16S rRNA gene sequence similarity less 97%). On the basis of the significant differences demonstrated in the phenotypic and chemotaxonomic characteristics, it is suggested that the bacterium be classified as a novel species; the name Bacillus algicola sp. nov. is proposed. The type strain is KMM 3737T (= CIP 107850T). PMID: 15214635 [PubMed - indexed for MEDLINE] Bacillus alkalicola Curr Microbiol. 2014 Sep;69(3):311-6. doi: 10.1007/s00284-014-0576-x. Epub 2014 Apr 23. Bacillus alkalicola sp. nov., An Alkaliphilic, Gram-Positive Bacterium Isolated from Zhabuye Lake in Tibet, China. Zhai L(1), Ma Y, Xue Y, Ma Y. Author information: (1)State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China, [email protected]. A Gram-positive, alkaliphilic bacterium, designated strain Zby6(T), was isolated from Zhabuye Lake in Tibet, China. The strain was able to grow at pH 8.0-11.0 (optimum at pH 10.0), in 0-8 % (w/v) NaCl (optimum at 3 %, w/v) and at 10-45 °C (optimum at 37 °C). Cells of the isolate were facultatively anaerobic and spore-forming rods with polar flagellum. The predominant isoprenoid quinone was MK-7, and its cell wall peptidoglycan contained meso-diaminopimelic acid. The major cellular fatty acids were iso-C15:0, C16:0 and anteiso-C15:0. The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethanolamine. The genomic DNA G+C content of the isolate was 38.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Zby6(T) was a member of the genus Bacillus and most closely related to Bacillus cellulosilyticus DSM 2522(T) (97.7 % similarity). The DNA-DNA relatedness value between strain Zby6(T) and B. cellulosilyticus DSM 2522(T) was 59.2 ± 1.8 %. Comparative analysis of genotypic and phenotypic features indicated that strain Zby6(T) represents a novel species of the genus Bacillus, for which the name Bacillus alkalicola sp. nov. is proposed; the type strain is Zby6(T) (=CGMCC 1.10368(T) = JCM 17098(T) = NBRC 107743(T)). PMID: 24756808 [PubMed - in process]$$ Bacillus alkalidiazotrophicus Int J Syst Evol Microbiol. 2008 Oct;58(Pt 10):2459-64. doi: 10.1099/ijs.0.65655-0. Bacillus alkalidiazotrophicus sp. nov., a diazotrophic, low salt-tolerant alkaliphile isolated from Mongolian soda soil. Sorokin ID(1), Kravchenko IK, Tourova TP, Kolganova TV, Boulygina ES, Sorokin DY. Author information: (1)Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, 117811 Moscow, Russia. Strain MS 6(T) was obtained from a microoxic enrichment with a soda soil sample from north-eastern Mongolia in nitrogen-free alkaline medium at pH 10. The isolate had clostridia-like motile cells and formed ellipsoid endospores. It was able to fix dinitrogen gas growing on nitrogen-free alkaline medium. Strain MS 6(T) was a strictly fermentative bacterium without a respiratory chain, although it had a high catalase activity and tolerated aerobic conditions. It was an obligate alkaliphile with a pH range for growth between 7.5 and 10.6 (optimum at 9.0-9.5). Growth and nitrogen fixation at pH 10 were possible at a total salt content of up to 1.2 M Na(+) (optimum at 0.2-0.3 M). The dominant cellular fatty acids included C(16 : 0), C(16 : 1)omega7, anteiso-C(15 : 0) and C(14 : 0). The dominant isoprenoid quinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. 16S rRNA gene sequencing identified strain MS 6(T) as a member of the genus Bacillus. Its closest relative was Bacillus arseniciselenatis E1H(T). The key functional nitrogenase gene nifH was detected in both strain MS 6(T) and its close relative and these strains formed a novel lineage in the nifH gene family. On the basis of these phenotypic and genetic comparisons, strain MS 6(T) is proposed to represent a novel species of the genus Bacillus, Bacillus alkalidiazotrophicus sp. nov. with the type strain MS 6(T) (=NCCB 100213(T)=UNIQEM U377(T)). PMID: 18842875 [PubMed indexed for MEDLINE] Bacillus alkalinitrilicus FEMS Microbiol Lett. 2008 Nov;288(2):235-40. doi: 10.1111/j. 1574- 6968. 2008.01353.x. Epub 2008 Sep 16. Utilization of aliphatic nitriles under haloalkaline conditions by Bacillus alkalinitrilicus sp. nov. isolated from soda solonchak soil. Sorokin DY(1), van Pelt S, Tourova TP. Author information: (1)Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia. [email protected] Enrichment with isobutyronitrile as the sole carbon, energy and nitrogen source at pH 10, using 8 soda solonchak soils as an inoculum, resulted in the selection of a binary culture consisting of two different spore-forming phenotypes. One of them, strain ANL-iso4, was capable of growth with isobutyronitrile as a single substrate, while the other phenotype only utilized products of isobutyronitrile hydrolysis, such as isobutyroamide and isobutyrate. Strain ANL-iso4 is an obligate alkaliphile and a moderately salt-tolerant bacterium. Apart from isobutyronitrile, it grew on other (C3-C6) aliphatic nitriles at pH 10. Resting cells of ANL-iso4 actively hydrolyzed a number of aliphatic and arylaliphatic nitriles and their corresponding amides. The latter, together with the intermediate formation of amides during nitrile hydrolysis, indicated the presence of a nitrile hydratase/amidase system in the novel bacterium. Although present in an alkaliphilic bacterium, both nitrile- and amide-hydrolyzing activities had a pH optimum within the neutral range, probably due to their intracellular localization. On the basis of phenotypic and phylogenetic analyses, strain ANL-iso4 is proposed as a new species Bacillus alkalinitrilicus sp. nov. PMID: 18801047 [PubMed - indexed for MEDLINE] 24. Bacillus alkalisediminis Int J Syst Evol Microbiol. 2011 Aug;61(Pt 8):1880-6. doi: 10.1099/ijs.0.019489-0. Epub 2010 Sep 10. Bacillus alkalisediminis sp. nov., an alkaliphilic and moderately halophilic bacterium isolated from sediment of extremely shallow soda ponds. Borsodi AK(1), Pollák B, Kéki Z, Rusznyák A, Kovács AL, Spröer C, Schumann P, Márialigeti K, Tóth EM. Author information: (1)Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary. [email protected] Alkaliphilic strains characterized by optimal growth at pH 9.0 and 5 % (w/v) NaCl designated K1-25(T) and H3-93 were isolated from extremely shallow soda ponds located in Hungary. Cells of both strains were Gram-stain-positive, non-motile, straight rods and formed central, ellipsoidal endospores with swollen sporangia. The isolates were aerobic, catalase-positive, oxidase-negative and contained a peptidoglycan of type A1γ based on meso-diaminopimelic acid. In both strains, menaquinone-7 (MK-7) was the predominant isoprenoid quinone and the major cellular fatty acids were anteiso-C(15 : 0) and iso-C(15 : 0). The DNA G+C contents of strains K1-25(T) and H3-93 were 39.0 and 36.3 mol%, respectively. 16S rRNA gene sequence-based phylogenetic analysis revealed 99.2 % similarity between strains K1-25(T) and H3-93 and the novel isolates had the highest similarities to Bacillus akibai 1139(T) (97.8 and 98.3 %, respectively), Bacillus wakoensis N-1(T) (97.0 and 97.4 %), Bacillus okhensis Kh10-101(T) (97.1 and 97.4 %) and Bacillus krulwichiae AM31D(T) (96.9 and 97.1 %). DNA-DNA hybridization between our strains and the type strains of closely related Bacillus species was lower than 70 %. Although DNA-DNA hybridization between strains K1-25(T) and H3-93 was 27 %, the phenotypic and chemotaxonomic data did not support the differentiation of these two strains into separate species. Therefore, they represent genomovars of a novel species, for which the name Bacillus alkalisediminis sp. nov. is proposed. The type strain is K1-25(T) ( = DSM 21670(T) = NCAIM B02301(T)). PMID: 20833886 [PubMed - indexed for MEDLINE] 25. Bacillus alkalitelluris Int J Syst Evol Microbiol. 2008 Nov;58(Pt 11):2629-34. doi: 10.1099/ijs.0.65733-0. Bacillus alkalitelluris sp. nov., an alkaliphilic bacterium isolated from sandy soil. Lee JC(1), Lee GS, Park DJ, Kim CJ. Author information: (1)Functional Metabolomics Research Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea. A Gram-positive, alkaliphilic bacterium, designated strain BA288(T), was isolated from sandy soil. Cells were facultatively anaerobic, endospore-forming rods that were motile by means of peritrichous flagella. The strain grew at 15-40 degrees C and pH 7.0-11.0 (optimally at 30 degrees C and pH 9.0-9.5) and at salinities of 0-4 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BA288(T) belonged to the genus Bacillus and that Bacillus herbersteinensis D-1,5a(T), Bacillus humi LMG 22167(T), Bacillus cohnii DSM 6307(T) and Bacillus litoralis SW-211(T) were the closest neighbours (96.2, 96.0, 96.0 and 95.9 % sequence similarity, respectively). The genomic DNA G+C content was 37.9 mol% and the predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0), C(16 : 0) and iso-C(14 : 0). The peptidoglycan type was A1gamma (meso-diaminopimelic acid). Therefore, on the basis of phylogenetic, phenotypic and chemotaxonomic properties, strain BA288(T) represents a novel species of the genus Bacillus, for which the name Bacillus alkalitelluris sp. nov. is proposed. The type strain is BA288(T) (=KCTC 3947(T) =DSM 16976(T)). PMID: 18984705 [PubMed - indexed for MEDLINE] 26. Bacillus alveayuensis Int J Syst Evol Microbiol. 2005 May;55(Pt 3):1211-5. Bacillus alveayuensis sp. nov., a thermophilic bacterium isolated from deep-sea sediments of the Ayu Trough. Bae SS(1), Lee JH, Kim SJ. Author information: (1)Microbiology Laboratory, Korea Ocean Research and Development Institute, Republic of Korea. Two thermophilic, spore-forming strains, TM1(T) and TM5, were isolated from deep-sea sediment (4000 m below sea level) of the Ayu Trough in the western Pacific Ocean. Cells of the two strains were Gram-positive, motile and rod-shaped. Their spores were ellipsoidal, subterminal to terminal and occurred in swollen sporangia. The two strains grew at temperatures up to 65 degrees C and in the pH range 6.5-9.0. The NaCl concentration for optimal growth was 3.0 % (w/v) and growth was inhibited by 5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains TM1(T) and TM5 belonged to the genus Bacillus, and that strain TM1(T) was most closely related to Bacillus aeolius DSM 15084(T) (96.7 %), Bacillus smithii DSM 4216(T) (96.1 %), Bacillus methanolicus NCIMB 13113(T) (95.8 %) and Bacillus pallidus DSM 3670(T) (95.7 %). Between the 16S rRNA gene sequences of strains TM1(T) and TM5 there were only three nucleotide differences, implying that the two strains were of the same species. The cellular fatty acid profiles of the two strains were also very similar, with iso-C(15 : 0), iso-C(16 : 0), C(16 : 0), iso-C(17 : 0) and anteiso-C(17 : 0) as the major components. The G + C content of strain TM1(T) was 38.7 %. On the basis of phenotypic and molecular data, strains TM1(T) and TM5 represent a novel species of the genus Bacillus, for which the name Bacillus alveayuensis sp. nov. is proposed. The type strain is TM1(T) (= KCTC 10634(T) = JCM 9 27. 28. 29. 30. 12523(T)). PMID: 15879257 [PubMed - indexed for MEDLINE] Bacillus arenosi Int J Syst Evol Microbiol. 2005 Jan;55(Pt 1):111-7. Bacillus arenosi sp. nov., Bacillus arvi sp. nov. and Bacillus humi sp. nov., isolated from soil. Heyrman J(1), Rodríguez-Díaz M, Devos J, Felske A, Logan NA, De Vos P. Author information: (1)Vakgroep BFM WE10V, Laboratorium voor Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium. [email protected] A group of nine Gram-positive endospore-forming bacteria was isolated from soil of the Drentse A agricultural research area in The Netherlands. Using (GTG)5-PCR genomic fingerprinting and fatty acid analysis, the nine isolates were divided into three consistent groups. On the basis of 16S rRNA gene sequence similarity of representative strains, the nine isolates were shown to belong to the genus Bacillus. The first group of four isolates was most closely related to Bacillus carboniphilus (95.5 %) and Bacillus sporothermodurans (95.5 %). The second and third groups of three and two isolates, respectively, showed highest sequence similarity to Bacillus neidei (97.0 and 97.1 %, respectively) and Bacillus pycnus (both 96.7 %). A DNA-DNA relatedness study confirmed the consistency of the three groups delineated by (GTG)5-PCR and fatty acid analysis. A small number of phenotypic characters allowed differentiation of the three groups of isolates. The three groups therefore represent novel species, for which the names Bacillus humi, Bacillus arenosi and Bacillus arvi are proposed, with LMG 22167T (=DSM 16318T), LMG 22166T (=DSM 16319T) and LMG 22165T (=DSM 16317T) as the respective type strains. PMID: 15653863 [PubMed - indexed for MEDLINE] Bacillus arsenicoselenatis Arch Microbiol. 1998 Dec;171(1):19-30. Bacillus arsenicoselenatis, sp. nov., and Bacillus selenitireducens, sp. nov.: two haloalkaliphiles from Mono Lake, California that respire oxyanions of selenium and arsenic. Switzer Blum J(1), Burns Bindi A, Buzzelli J, Stolz JF, Oremland RS. Author information: (1)US Geological Survey, ms 480, 345 Middlefield Road, Menlo Park, CA 94025, USA. Two gram-positive anaerobic bacteria (strains E1H and MLS10) were isolated from the anoxic muds of Mono Lake, California, an alkaline, hypersaline, arsenic-rich water body. Both grew by dissimilatory reduction of As(V) to As(III) with the concomitant oxidation of lactate to acetate plus CO2. Bacillus arsenicoselenatis (strain E1H) is a spore-forming rod that also grew by dissimilatory reduction of Se(VI) to Se(IV). Bacillus selenitireducens (strain MLS10) is a short, non-spore-forming rod that grew by dissimilatory reduction of Se(IV) to Se(0). When the two isolates were cocultured, a complete reduction of Se(VI) to Se(0) was achieved. Both isolates are alkaliphiles and had optimal specific growth rates in the pH range of 8.5-10. Strain E1H had a salinity optimum at 60 g l-1 NaCl, while strain MLS10 had optimal growth at lower salinities (24-60 g l-1 NaCl). Both strains have limited abilities to grow with electron donors and acceptors other than those given above. Strain MLS10 demonstrated weak growth as a microaerophile and was also capable of fermentative growth on glucose, while strain E1H is a strict anaerobe. Comparative 16S rRNA gene sequence analysis placed the two isolates with other Bacillus spp. in the low G+C gram-positive group of bacteria. PMID: 9871015 [PubMed - indexed for MEDLINE] Bacillus arsenicus Int J Syst Evol Microbiol. 2005 May;55(Pt 3):1123-7. Bacillus arsenicus sp. nov., an arsenic-resistant bacterium isolated from a siderite concretion in West Bengal, India. Shivaji S(1), Suresh K, Chaturvedi P, Dube S, Sengupta S. Author information: (1)Centre for Cellular and Molecular Biology, Hyderabad, India. [email protected] Strain Con a/3(T) is a Gram-positive, motile, endospore-forming, rod-shaped and arsenic-resistant bacterium, which was isolated from a concretion of arsenic ore obtained from a bore-hole. The bacterium grew in the presence of 20 mM arsenate and 0.5 mM arsenite. Diaminopimelic acid was present in the cell wall peptidoglycan, MK-7 was the major menaquinone, and iso-C(15 : 0), anteiso-C(15 : 0), iso-C(16 : 0) and C(16 : 1)(delta7cis) were the major fatty acids. Based on its phenotypic, chemotaxonomic and phylogenetic characteristics, strain Con a/3(T) was identified as a member of the genus Bacillus. It exhibited maximum similarity (97 %) at the 16S rRNA gene level with Bacillus barbaricus (DSM 14730(T)); however, the DNA-DNA relatedness value with B. barbaricus was 60 %. Strain Con a/3(T) also exhibited a number of phenotypic differences from B. barbaricus (DSM 14730(T)). Strain Con a/3(T) was therefore identified as representing a novel species of the genus Bacillus, for which the name Bacillus arsenicus sp. nov. is proposed. The type strain is Con a/3(T) (= MTCC 4380(T) = DSM 15822(T) = JCM 12167(T)). PMID: 15879243 [PubMed - indexed for MEDLINE] Bacillus asahii Int J Syst Evol Microbiol. 2004 Nov;54(Pt 6):1997-2001. Bacillus asahii sp. nov., a novel bacterium isolated from soil with the ability to deodorize the bad smell generated from short-chain fatty acids. Yumoto I(1), Hirota K, Yamaga S, Nodasaka Y, Kawasaki T, Matsuyama H, Nakajima K. Author information: (1)Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan. [email protected] In a screening campaign to isolate strains with the ability to remove the bad smell associated with animal faeces, strain MA001(T) was isolated from a soil sample obtained from Shizuoka prefecture, Japan. The isolate grew at pH 6-9 but not at pH 10. Cells were Gram-positive, straight rods with peritrichous flagella and produced ellipsoidal spores. The isolate was positive for catalase and oxidase tests but negative for indole production, deamination of phenylalanine and H(2)S production. The isolate did not produce acid from any carbohydrates tested and could not grow in more than 2 % NaCl. The DNA G+C content was 39.4 mol%. The cellular fatty acids profile consisted of significant amount of C(15) branched-chain fatty acids, iso-C(15 : 0) and anteiso-C(15 : 0). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain MA001(T) was closely related to Bacillus simplex and Bacillus psychrosaccharolyticus. DNA-DNA hybridization revealed a low relatedness of the isolate to several phylogenetically close neighbours (less than 9 %). On the basis of the phenotypic characteristics observed, phylogenetic data based on 16S rRNA gene sequencing and DNA-DNA relatedness data, it is concluded that the isolate should be classified as representing a novel spe- 10 31. 32. 33. 34. cies, for which the name Bacillus asahii is proposed. The type strain is MA001(T) (=JCM 12112(T)=NCIMB 13969(T)). PMID: 15545424 [PubMed - indexed for MEDLINE] Bacillus aurantiacus Int J Syst Evol Microbiol. 2008 Apr;58(Pt 4):845-51. doi: 10.1099/ijs.0.65325-0. Bacillus aurantiacus sp. nov., an alkaliphilic and moderately halophilic bacterium isolated from Hungarian soda lakes. Borsodi AK(1), Márialigeti K, Szabó G, Palatinszky M, Pollák B, Kéki Z, Kovács AL, Schumann P, Tóth EM. Author information: (1)Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary. [email protected] Three alkaliphilic and moderately halophilic strains designated K1-5T, K1-10 and B1-1, characterized by optimal growth at pH 9.0-10.0 and at 3-7 % (w/v) NaCl, were isolated from extremely shallow, alkaline soda lakes located in Hungary. Cells of the strains are Gram-positive, straight rods and form a central to subterminal, ellipsoidal endospore. The isolates are strictly aerobic, catalase-positive, oxidase-negative and contain a peptidoglycan of type A1 gamma based on meso-diaminopimelic acid. In strain K1-5T, menaquinone-7 (MK-7) is the predominant isoprenoid quinone and anteiso-C15 : 0 is the major cellular fatty acid. The DNA G+C content of strain K1-5T is 42.9 mol%. 16S rRNA gene-based phylogenetic analysis revealed that the strains exhibit levels of sequence similarity of less than 95.8 % to known Bacillus species. According to the polyphasic characterization, the strains represent a novel species, for which the name Bacillus aurantiacus sp. nov. is proposed. The type strain is K1-5T (=DSM 18675T =CCM 7447T =NCAIM B002265T). PMID: 18398180 [PubMed - indexed for MEDLINE] Bacillus axarquiensis Int J Syst Evol Microbiol. 2005 May;55(Pt 3):1279-85. Bacillus axarquiensis sp. nov. and Bacillus malacitensis sp. nov., isolated from river-mouth sediments in southern Spain. Ruiz-García C(1), Quesada E, Martínez-Checa F, Llamas I, Urdaci MC, Béjar V. Author information: (1)Microbial Exopolysaccharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Spain. Two Gram-positive, rod-shaped, endospore-forming bacteria (strains CR-119(T) and CR-95(T)) were isolated from brackish sediments in the mouth of the river Velez in Malaga, southern Spain, and subjected to a polyphasic taxonomic study. Phenotypic tests showed that these strains were related to other Bacillus species at a similarity level of less than 87.6 %. Both strains are halotolerant, aerobic, chemoheterotrophic, motile with peritrichous flagella and biosurfactant producers. Their endospores are oval, subterminal and non-deforming structures. The predominant menaquinone in both strains is MK-7. The fatty-acid profiles of both strains contain large quantities of branched and saturated fatty acids. The major fatty acids (%) are 15 : 0 anteiso (32.4), 15 : 0 iso (16.8), 17 : 0 iso (13.4), 16 : 0 (11.5) and 17 : 0 anteiso (10.2) in strain CR-119(T) and 15 : 0 anteiso (37.5), 17 : 0 iso (16.0) and 17 : 0 anteiso (15.8) in strain CR-95(T). The G + C contents of strains CR-119(T) and CR-95(T) are 41.0 and 42.5 mol%, respectively. RAPD analysis confirmed the low degree of similarity between the two strains and also amongst other Bacillus species. 16S rRNA gene analysis of strain CR-119(T) showed the highest sequence similarity to be 97.4 %, with Bacillus mojavensis and Bacillus subtilis subsp. spizizenii. In the case of strain CR-95(T), the maximum similarity value was 99.5 %, with B. mojavensis. DNA-DNA hybridization of strains CR-119(T) and CR-95(T) with the above species produced values lower than 46.9 %. Therefore, on the basis of phenotypic characteristics, phylogenetic data and genomic distinctiveness, we conclude that these Bacillus strains merit classification as novel species, for which we propose the names Bacillus axarquiensis sp. nov. (type strain CR-119(T) = CECT 5688(T) = LMG 22476(T)) and Bacillus malacitensis sp. nov. (type strain CR-95(T) = CECT 5687(T) = LMG 22477(T)). PMID: 15879268 [PubMed indexed for MEDLINE] Bacillus barbaricus Int J Syst Evol Microbiol. 2003 May;53(Pt 3):725-30. Bacillus barbaricus sp. nov., isolated from an experimental wall painting. Täubel M(1), Kämpfer P, Buczolits S, Lubitz W, Busse HJ. Author information: (1)Institut für Mikrobiologie und Genetik, Universität Wien, A-1030 Wien, Austria. In a project concerning bacterial colonization of experimental wall paintings, a large number of isolates have been acquired with high similarities in their whole-cell protein patterns obtained after SDS-PAGE. Of this group, four strains, designated V2-BIII-A2(T), V2-BI-A9, V2-BI-04 and V2-BII-A8, were chosen for further characterization. Banding patterns obtained after ERIC-PCR were barely distinguishable among these four strains, indicating their affiliation within a single species. The isolates also displayed nearly identical biochemical and physiological features. The chemotaxonomic characteristics, including polar lipids, quinone systems, cell-wall diamino acid composition and fatty acid profiles, were in good agreement with those of numerous previously described Bacillus species. 16S rDNA analysis of strain V2-BIII-A2(T) showed that this bacterium belongs to the genus Bacillus, with highest sequence similarities to Bacillus megaterium (94.6%), Bacillus flexus (94.4%) and the alkaliphilic Bacillus cohnii (94.2%). Based on almost identical biochemical, physiological and chemotaxonomic traits, ERIC-PCR-generated genomic fingerprints and comparative 16S rDNA sequence analysis, it is demonstrated that the four isolates represent a novel species of the genus Bacillus, for which the name Bacillus barbaricus sp. nov. is proposed. The type strain is V2-BIII-A2(T) (= CCM 4982(T) = DSM 14730(T)). PMID: 12807193 [PubMed - indexed for MEDLINE] Bacillus beijingensis Int J Syst Evol Microbiol. 2009 Apr;59(Pt 4):729-34. doi: 10.1099/ijs.0.65861-0. Bacillus beijingensis sp. nov. and Bacillus ginsengi sp. nov., isolated from ginseng root. Qiu F(1), Zhang X, Liu L, Sun L, Schumann P, Song W. Author information: (1)College of Life Sciences, Capital Normal University, Beijing 100048, PR China. Four alkaligenous, moderately halotolerant strains, designated ge09, ge10(T), ge14(T) and ge15, were isolated from the internal tissue of ginseng root and their taxonomic positions were investigated by using a polyphasic approach. Cells of the four strains were Gram-positive-staining, non-motile, short rods. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains ge09 and ge10(T) formed one cluster and strains ge14(T) 11 35. 36. 37. 38. and ge15 formed another separate cluster within the genus Bacillus. 16S rRNA gene sequence similarities with type strains of other Bacillus species were less than 97 %. Levels of DNA-DNA relatedness among the four strains showed that strains ge09 and ge10(T) and strains ge14(T) and ge15 belonged to two separate species; the mean level of DNA-DNA relatedness between ge10(T) and ge14(T) was only 28.7 %. Their phenotypic and physiological properties supported the view that the two strains represent two different novel species of the genus Bacillus. The DNA G+C contents of strains ge10(T) and ge14(T) were 49.9 and 49.6 mol%, respectively. Strains ge10(T) and ge14(T) showed the peptidoglycan type A4alpha l-Lys-d-Glu. The lipids present in strains ge10(T) and ge14(T) were diphosphatidylglycerol, phosphatidylglycerol, a minor amount of phosphatidylcholine and two unknown phospholipids. Their predominant respiratory quinone was MK-7. The fatty acid profiles of the four novel strains contained large quantities of branched and saturated fatty acids. The predominant cellular fatty acids were iso-C(15 : 0) (42.5 %), anteiso-C(15 : 0) (22.2 %), anteiso-C(17 : 0) (7.3 %) and C(16 : 1)omega7c alcohol (5.7 %) in ge10(T) and iso-C(15 : 0) (50.7 %) and anteiso-C(15 : 0) (20.1 %) in ge14(T). On the basis of their phenotypic properties and phylogenetic distinctiveness, two novel species of the genus Bacillus are proposed, Bacillus beijingensis sp. nov. (type strain ge10(T) =DSM 19037(T) =CGMCC 1.6762(T)) and Bacillus ginsengi sp. nov. (type strain ge14(T) =DSM 19038(T) =CGMCC 1.6763(T)). PMID: 19329597 [PubMed - indexed for MEDLINE] Bacillus benzoevorans Ann Microbiol (Paris). 1984 Sep-Oct;135B(2):209-17. [Biochemical characterization of Bacillus benzoevorans sp. nov., a new filamentous, sheathed mesophilic species, degrading various aromatic acids and phenols]. [Article in French] Pichinoty F, Asselineau J, Mandel M. The eleven strains studied were prototrophic and did not grow in media containing only 1% Bacto-peptone or Bacto-tryptone; they grew rapidly in media containing 0.4% yeast extract and 0.2% sodium acetate or benzoate. The maximal growth temperature ranged from 39 to 45 degrees C. Six aliphatic acids, four aromatic acids and five phenols were used as sole carbon and energy sources by the 11 strains. Carbohydrates and amino acids (except for glycine) were not used as carbon and energy sources. Nitrate (but not nitrite) was used anaerobically as a respiratory electron acceptor. Nitrous oxide was used and reduced to N2 by only 3 strains. The mean guanine-plus-cytosine content of the DNA was 41.3 +/- 1.1 mol %. Morphologically and nutritionally, the bacteria described are clearly different from the 5 known species of the first morphological group whose cells have a diameter greater than 1 micrometer: Bacillus megaterium, B. cereus, B. cereus var. mycoides, B. macroides, B. badius, and B. fastidiosus. Strain B1 (=CCM 3364) is the holotype of Bacillus benzoevorans sp. nov. PMID: 6508078 [PubMed - indexed for MEDLINE] Bacillus beringensis Antonie Van Leeuwenhoek. 2011 Mar;99(3):551-7. doi: 10.1007/s10482-010-9523-4. Epub 2010 Oct 21. Bacillus beringensis sp. nov., a psychrotolerant bacterium isolated from the Bering Sea. Yu Y(1), Li HR, Zeng YX, Chen B. Author information: (1)SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, People's Republic of China. [email protected] Psychrotolerant Bacillus-like strains BR035(T) and BR011 were isolated from seawater of the Bering Sea and were characterized by means of a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that these strains were related to the members of the genus Bacillus and had the highest 16S rRNA gene sequence similarity with Bacillus korlensis ZLC-26(T). DNA-DNA hybridization experiments confirmed that strains BR035(T) and BR011 belonged to the same species and were distinct from their closest relatives. The cells were Gram-positive, rods, motile, spore-forming and psychrotolerant. The temperature range for growth was 4-42°C. The main respiratory quinone was MK-7. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unknown aminolipid and two unknown phospholipids. The major cellular fatty acids were iso-C15:0, anteiso-C15:0, iso-C14:0 and C16:1ω7c alcohol. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The genomic DNA G + C content was 37.6-37.8 mol%. On the basis of the phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, a novel species Bacillus beringensis is proposed and the type strain is BR035(T) (=CGMCC 1.9126(T)=DSM 22571(T)). PMID: 20963491 [PubMed - indexed for MEDLINE] Bacillus berkeleyi Arch Microbiol. 2012 Mar;194(3):215-21. doi: 10.1007/s00203-011-0771-0. Epub 2011 Nov 20. Bacillus berkeleyi sp. nov., isolated from the sea urchin Strongylocentrotus intermedius. Nedashkovskaya OI(1), Van Trappen S, Frolova GM, De Vos P. Author information: (1)Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia. [email protected] A bacterial strain, designated KMM 6244(T), was isolated from the sea urchin Strongylocentrotus intermedius and subjected to a polyphasic taxonomic investigation. The bacterium was found to be heterotrophic, aerobic, non-motile and spore-forming. Comparative phylogenetic analysis based on 16S rRNA gene sequencing placed the marine isolate in the genus Bacillus. The nearest neighbor of strain KMM 6244(T) was Bacillus decolorationis LMG 19507(T) with a 16S rRNA gene sequence similarity of 98.0%. Sequence similarities with the other recognized Bacillus species were less than 96.0%. The results of the DNA-DNA hybridization experiments revealed a low relatedness (37%) of the novel isolate with the type strain of B. decolorationis LMG 19507(T). Strain KMM 6244(T) grew at 4-45°C and with 0-12% NaCl. It produced catalase and oxidase and hydrolyzed aesculin, casein, gelatin and DNA. The predominant fatty acids were anteiso-C(15:0), iso-C(15:0), anteiso-C(17:0), C(15:0), iso-C(16:0) and iso-C(14:0). The DNA G + C content was 39.4 mol%. A combination of phylogenetic, genotypic and phenotypic data clearly indicated that strain KMM 6244(T) represents a novel species in the genus Bacillus, for which the name Bacillus berkeleyi sp. nov. is proposed. The type strain is KMM 6244(T) (KCTC 12718(T) = LMG 26357(T)). PMID: 22102083 [PubMed - indexed for MEDLINE] Bacillus bingmayongensis Antonie Van Leeuwenhoek. 2014 Mar;105(3):501-10. doi: 10.1007/s10482-013-0102-3. Epub 2013 Dec 12 39. 40. 41. 42. 27. Bacillus bingmayongensis sp. nov., isolated from the pit soil of Emperor Qin's Terra-cotta warriors in China. Liu B(1), Liu GH, Hu GP, Sengonca C, Lin NQ, Tang JY, Tang WQ, Lin YZ. Author information: (1)Agricultural Bio-Resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, People's Republic of China, [email protected]. Erratum in Antonie Van Leeuwenhoek. 2014 May;105(5):995. Cetin, Sengonca [corrected to Sengonca, Cetin]. A Bacillus-like isolate, strain FJAT-13831(T), isolated from the No. 1 pit soil of Emperor Qin's Terra-cotta Warriors in Xi'an City, China, was studied to determine its taxonomic status. Dominant fatty acids of this organism included iso-C15:0, iso-C17:0, C16:0, iso-C13:0, anteiso-C15:0, and iso-C17:1ω5c. Comparative 16S rRNA gene sequence analysis confirmed the affiliation of this isolate to the genus Bacillus and indicated that it was closely related to Bacillus pseudomycoides DSM 12442(T) (99.72 % similarity). A phylogenetic analysis of the gyrB gene sequence similarities exhibited independent clustering of the isolate FJAT-13831(T) and showed 93.8 % (<95 %) sequence similarity with its closest phylogenetic neighbour B. pseudomycoides DSM 12442(T). Separate standing of the strain FJAT-13831(T) was supported by a whole genome-based phylogenetic analysis with an average nucleotide identity value of 91.47 (<95 %) between isolate FJAT-13831(T) and B. pseudomycoides DSM 12442(T) and was consistent with the results of DNA-DNA hybridization (69.1 % relatedness). These findings support the conclusion that the isolate FJAT-13831(T) represents a novel species, for which the name Bacillus bingmayongensis sp. nov. is proposed. The type strain is FJAT-13831(T) (= CGMCC 1.12043(T) = DSM 25427(T)). PMID: 24370979 [PubMed - in process]$$ Bacillus bogoriensis Int J Syst Evol Microbiol. 2005 Mar;55(Pt 2):899-902. Bacillus bogoriensis sp. nov., a novel alkaliphilic, halotolerant bacterium isolated from a Kenyan soda lake. Vargas VA(1), Delgado OD, Hatti-Kaul R, Mattiasson B. Author information: (1)Department of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, PO Box 124, SE-22 100 Lund, Sweden. Strain LBB3(T) isolated from Bogoria soda lake in Kenya is an alkaliphilic, Gram-positive, strictly aerobic, non-motile, spore-forming bacterium. It was identified as a member of the genus Bacillus on the basis of phenotypic and phylogenetic analyses. The organism grows optimally at 37 degrees C and pH 10. The G+C content of the genomic DNA is 37.5 mol%. 16S rRNA gene sequence analysis showed 95 and 96 % sequence similarity with Bacillus pseudofirmus (DSM 8715(T)) and Bacillus alcalophilus (DSM 485(T)), respectively. Furthermore, DNA-DNA hybridization against these two Bacillus species showed 39.0 and 55.5 % similarity, respectively. Based on our observations, strain LBB3(T) is proposed to represent a novel species of the genus Bacillus, for which the name Bacillus bogoriensis sp. nov. is proposed. The type strain of B. bogoriensis is LBB3(T) (=ATCC BAA-922(T)=LMG 22234(T)). PMID: 15774682 [PubMed - indexed for MEDLINE] Bacillus borbori Curr Microbiol. 2013 Dec;67(6):718-24. doi: 10.1007/s00284-013-0426-2. Epub 2013 Jul 30. Bacillus borbori sp. Nov., isolated from an electrochemically active biofilm. Wang YQ(1), Yuan Y, Yu Z, Yang GQ, Zhou SG. Author information: (1)Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou, 510650, People's Republic of China. A Gram-positive, facultative anaerobic, motile, endospore-forming rod strain, designated DX-4(T), was isolated from an electrochemically active biofilm. Growth occurred at 30-65 °C (optimum 55 °C), at pH 6.0-8.5 (optimum pH 7.0-7.5) and with <6 % (w/v) NaCl. Cells were catalaseand oxidase-positive. The main respiratory quinone was MK-7, the predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannoside, and unidentified aminophospholipid, the DNA G+C content was 38.6 mol% and the major fatty acids (>5 %) were iso-C15:0 (38.9 %), iso-C17:0 (30.5 %), iso-C16:0 (5.6 %), and anteiso-C17:0 (5.2 %). The phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain DX-4(T) is a member of the genus Bacillus. The results of phenotypic, chemotaxonomic, and genotypic analyses clearly indicated that strain DX-4(T) represents a novel species, for which the name Bacillus borbori sp. nov. is proposed. The type strain is DX-4(T) (= CCTCC AB2012196(T) = KCTC 33103(T)). PMID: 23896693 [PubMed - indexed for MEDLINE]$$ Bacillus boroniphilus Extremophiles. 2007 Mar;11(2):217-24. Epub 2006 Oct 27. A novel highly boron tolerant bacterium, Bacillus boroniphilus sp. nov., isolated from soil, that requires boron for its growth. Ahmed I(1), Yokota A, Fujiwara T. Author information: (1)Biotechnology Research Centre, University of Tokyo, Yayoi 1-1-1, Bunkyo-Ku, Tokyo, 113-8657, Japan. [email protected] Three strains of gram-positive, motile, rod-shaped and boron (B)-tolerant bacterium were isolated from naturally B containing soil of Hisarcik area in the Kutahya Province, Turkey. The strains, designated as T-14A, T-15Z(T) and T-17s, produced spherical or ellipsoidal endospores in a terminal bulging sporangium. The strains required B for the growth and can tolerate more than 450 mM B. These also tolerated up to 7.0% (w/v) NaCl in the presence of 50 mM B in agar medium but grew optimally without NaCl. The temperature range for growth was 16-37 degrees C (optimal of 30 degrees C), whereas the pH range was 6.5-9.0 (optimal of 7.5-8.5). The DNA G + C content was 41.1-42.2 mol% and the predominant cellular fatty acid was iso-C(15:0). The major respiratory quinone system was detected as MK-7 and the diamino acid of the peptidoglycan was meso-diaminopimelic acid. Based on phenotypic and chemotaxonomic characteristics, phylogenetic analysis of 16S rRNA gene sequences data and DNA-DNA re-association values, we concluded that the three strains belong to a novel species of the genus Bacillus, the type strain of which is T-15Z(T) and for which we proposed the name, B. boroniphilus sp. nov. (DSM 17376(T) = IAM 15287(T) = ATCC BAA-1204(T)). PMID: 17072687 [PubMed - indexed for MEDLINE] Bacillus butanolivorans Int J Syst Evol Microbiol. 2008 Feb;58(Pt 2):505-9. doi: 10.1099/ijs.0.65332-0. Bacillus butanolivorans sp. nov., a species with industrial application for the remediation of n-butanol. Kuisiene N(1), Raugalas J, Spröer C, Kroppenstedt RM, 13 Chitavichius D. Author information: (1)Department of Plant Physiology and Microbiology, Vilnius University, Chiurlionio 21/27, Vilnius LT-03101, Lithuania. [email protected] Four bacterial strains, designated K9(T), K105, K1012A and K101, were isolated from soil in Lithuania. All these strains could use n-butanol as a sole carbon source. The strains grew in a medium containing 12-120 mM n-butanol. The strains were strictly aerobic, Gram-positive endospore-formers. The best growth was achieved at 25 degrees C and pH 7.0 in medium containing 1 % (w/v) NaCl. The strains showed identical profiles of 16S-23S rRNA internal transcribed spacer PCR and nearly identical 16S rRNA gene PCR-RFLP electrophoretic patterns and physiological characteristics, demonstrating their relationship at the species level. The cellular fatty acid profile of K9(T) consisted of significant amounts of the C(15) branched-chain fatty acids iso-C(15 : 0) (16.78 %) and anteiso-C(15 : 0) (45.80 %). The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. The 16S rRNA gene sequence of K9(T) showed the highest similarity to the sequences of Bacillus simplex DSM 1321(T) and Bacillus muralis LMG 20238(T) (98.3 and 97.7 %, respectively). The DNA G+C content was 37.4 mol%. Studies of DNA-DNA relatedness, morphological, physiological and chemotaxonomic analyses and phylogenetic data based on 16S rRNA gene sequencing allowed strains K9(T), K105, K1012A and K101 to be described as members of a novel species of the genus Bacillus, for which the name Bacillus butanolivorans sp. nov. is proposed. The type strain is K9(T) (=DSM 18926(T) =LMG 23974(T)). PMID: 18218958 [PubMed indexed for MEDLINE] 43. Bacillus canaveralius Int J Syst Evol Microbiol. 2009 Aug;59(Pt 8):2015-9. doi: 10.1099/ijs.0.009167-0. Epub 2009 Jun 30. Bacillus canaveralius sp. nov., an alkali-tolerant bacterium isolated from a spacecraft assembly facility. Newcombe D(1), Dekas A, Mayilraj S, Venkateswaran K. Author information: (1)Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA. Two Gram-positive, rod-shaped, alkali-tolerant (pH 10.5), endospore-forming bacteria (strains KSC SF8bT and KSC SF10a) were isolated from surfaces within the Payload Hazardous Servicing Facility, where robotic spacecraft are assembled and tested before launch, at the Kennedy Space Center at Cape Canaveral. Based on 16S rRNA gene sequence similarities, these strains were shown to belong to the family Bacillaceae and the genus Bacillus. The highest 16S rRNA gene sequence similarity was approximately 97.5%, observed between the novel strains and Bacillus selenatarsenatis SF-1T. Several phenotypic characteristics, such as growth with 10% NaCl and assimilation of melibiose and lactose, were useful in the discrimination of this novel species from the closely related alkali-tolerant species Bacillus firmus and B. selenatarsenatis. DNA-DNA hybridization studies revealed reassociation values of less than 45% between strain KSC SF8bT and its closest genotypic neighbours. The combination of unique phenotypic and genotypic characteristics allowed the differentiation of these alkali- and halotolerant spore-forming strains from related Bacillus species, and a novel species, Bacillus canaveralius sp. nov., is proposed. The type strain is KSC SF8bT (=ATCC BAA-1493T=MTCC 8908T). PMID: 19567559 [PubMed - indexed for MEDLINE] 44. Bacillus cecembensis Int J Syst Evol Microbiol. 2008 Oct;58(Pt 10):2330-5. doi: 10.1099/ijs. 0.65515-0. Bacillus cecembensis sp. nov., isolated from the Pindari glacier of the Indian Himalayas. Reddy GS(1), Uttam A, Shivaji S. Author information: (1)Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India. Strain PN5(T) is a Gram-positive, aerobic, motile, rod-shaped, peritrichously flagellated bacterium that was isolated from the Pindari glacier using nutrient agar medium. Cells of PN5(T) are catalase-positive and oxidase-negative and contain lysine, glutamic acid and alanine in the peptidoglycan (peptidoglycan type A4alpha). Further, the cells are characterized by the presence of iso-C(15 : 0) and iso-C(16 : 1) as the predominant fatty acids and MK-7 as the isoprenoid quinone. Based on the above characteristics, strain PN5(T) was assigned to the genus Bacillus. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain PN5(T) clustered with the type strain of Bacillus silvestris with a sequence similarity of 97.2 %. DNA-DNA hybridization between PN5(T) and B. silvestris DSM 12223(T) resulted in a relatedness of only 15 %, clearly indicating that strain PN5(T) represents a novel species. Further, PN5(T) was different from B. silvestris with respect to various phenotypic and chemotaxonomic characteristics. Therefore, strain PN5(T) is identified as a representative of a novel species of the genus Bacillus, for which the name Bacillus cecembensis sp. nov. is proposed. Bacillus cecembensis is unique among psychrotolerant Bacillus species in containing l-Lys-d-Glu in the cell-wall peptidoglycan. The type strain is PN5(T) (=LMG 23935(T) =MTCC9127(T) =JCM 15113(T)). PMID: 18842851 [PubMed - indexed for MEDLINE] 45. Bacillus chagannorensis Int J Syst Evol Microbiol. 2007 Sep;57(Pt 9):2084-8. Bacillus chagannorensis sp. nov., a moderate halophile from a soda lake in Inner Mongolia, China. Carrasco IJ(1), Márquez MC, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A. Author information: (1)Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain. A Gram-positive, moderately halophilic, spore-forming bacterium, designated strain CG-15(T), was isolated from a soda lake, Lake Chagannor, in the Inner Mongolia Autonomous Region, China. The cells were found to be motile short rods with ellipsoidal, terminal and deforming endospores. Strain CG-15(T), a facultatively anaerobic bacterium, grew at pH 5.8-11.0 (optimally at pH 8.5), at 6-40 degrees C (optimally at 37 degrees C) and at salinities of 3-20 % (w/v) total salts (optimally at 7 % w/v). On the basis of the results of 16S rRNA gene sequence analysis, strain CG-15(T) was shown to belong to the genus Bacillus (phylum Firmicutes), showing the greatest phylogenetic similarity with respect to Bacillus saliphilus (96.0 %). The DNA G+C content of the novel isolate was found to be 53.8 mol%. The major cellular fatty acids of strain CG-15(T) were anteiso-C(15 : 0), iso-C(15 : 0) and anteiso-C(17 : 0), and its polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three different unidentified phospholipids. The analysis of the quinones showed that MK-7 was the major menaquinone. The peptidoglycan type was A1gamma, 14 46. 47. 48. 49. 50. with meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of the data from this polyphasic study, strain CG-15(T) represents a novel species of the genus Bacillus, for which the name Bacillus chagannorensis sp. nov. is proposed. The type strain is CG-15(T) (=CCM 7371(T)=CECT 7153(T)=CGMCC 1.6292(T)=DSM 18086(T)). PMID: 17766876 [PubMed - indexed for MEDLINE] Bacillus cheonanensis Kim HJ(1), Park CS, Lee S, Ahn TY. Erratum to: Bacillus cheonanensis sp. nov. isolated from near poultry farm soil. J Microbiol. 2014 Aug;52(8):720. doi: 10.1007/s12275-014-0702-2. Author information: (1)Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan, 330-714, Republic of Korea. PMID: 25056919 [PubMed - in process] Bacillus chungangensis Int J Syst Evol Microbiol. 2010 Jun;60(Pt 6):1349-52. doi: 10.1099/ijs.0.013607-0. Epub 2009 Aug 10. Bacillus chungangensis sp. nov., a halophilic species isolated from sea sand. Cho SL(1), Jung MY, Park MH, Kim W. Author information: (1)Department of Microbiology and Research Institute for Translational System Biomics, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea. The taxonomic position of a Gram-stain-positive, endospore-forming, halophilic strain, designated CAU 348(T), isolated from sea sand was investigated using a polyphasic approach. Colony morphology, biochemical tests and chemotaxonomic investigations revealed that strain CAU 348(T) had the characteristics of the genus Bacillus. Comparative 16S rRNA gene sequence analysis showed that the organism formed a hitherto unknown subline within the genus Bacillus. Sequence divergence values of more than 4.3 % from other described Bacillus species, together with phenotypic differences, showed that the unidentified bacterium represents a previously unrecognized member of this genus. The genotypic and phenotypic data indicated that strain CAU 348(T) represents a novel species of the genus Bacillus, for which the name Bacillus chungangensis sp. nov. is proposed. The type strain is CAU 348(T) (=KCTC 13566(T) =CCUG 57835(T)). PMID: 19667364 [PubMed - indexed for MEDLINE] Bacillus cibi Int J Syst Evol Microbiol. 2005 Mar;55(Pt 2):733-6. Bacillus cibi sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Yoon JH(1), Lee CH, Oh TK. Author information: (1)Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea. [email protected] A Gram-variable, motile, endospore-forming, halotolerant bacillus, strain JG-30(T), was isolated from the traditional Korean fermented seafood jeotgal, and was subjected to a polyphasic taxonomic study. This organism grew optimally at 37 degrees C and in the presence of 0-1 % (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain JG-30(T) forms a distinct phylogenetic lineage within the evolutionary radiation encompassed by the genus Bacillus. Strain JG-30(T) was characterized chemotaxonomically as having cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as the predominant menaquinone and iso-C(15 : 0) and iso-C(14 : 0) as the major fatty acids. The DNA G+C content was 45 mol%. Strain JG-30(T) exhibited levels of 16S rRNA gene sequence similarity of less than 95.7 % to Bacillus species with validly published names. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain JG-30(T) (=KCTC 3880(T)=DSM 16189(T)) was classified within the genus Bacillus as a novel species, for which the name Bacillus cibi sp. nov. is proposed. PMID: 15774653 [PubMed - indexed for MEDLINE] Bacillus coahuilensis Int J Syst Evol Microbiol. 2008 Apr;58(Pt 4):919-23. doi: 10.1099/ijs.0.64959-0. Bacillus coahuilensis sp. nov., a moderately halophilic species from a desiccation lagoon in the Cuatro Ciénegas Valley in Coahuila, Mexico. Cerritos R(1), Vinuesa P, Eguiarte LE, Herrera-Estrella L, Alcaraz-Peraza LD, Arvizu-Gómez JL, Olmedo G, Ramirez E, Siefert JL, Souza V. Author information: (1)Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Apartado Postal 70-275, México DF 04510, Mexico. A moderately halophilic, Gram-positive and rod-shaped bacterium, strain m4-4T, was isolated from a Chihuahuan desert lagoon in Cuatro Ciénegas, Coahuila, Mexico. Strain m4-4T was found to grow optimally at 30-37 degrees C, pH 7.0-8.0 and 5 % NaCl and to tolerate from 0.5 % to 10 % NaCl. It was shown to be aerobic. The genomic DNA G+C content was about 37 mol%. Strain m4-4T exhibited minimal or no growth on most sugars tested. Its major cellular fatty acids were C14 : 0, C16 : 0 and C18 : 1. Based on phylogenetic analysis of 16S rRNA and recA gene sequences, we observed that the closest relatives of the isolate are moderately halophilic Bacillus species, with 16S rRNA gene sequence similarity ranging from 96.6 to 97.4 % (Bacillus marisflavi, Bacillus aquimaris and Bacillus vietnamensis). Additionally, using genomic data it was determined that the type strain contains a total of nine rRNA operons with three slightly different sequences. On the basis of phenotypic and molecular properties, strain m4-4T represents a novel species within the genus Bacillus, for which the name Bacillus coahuilensis sp. nov. is proposed, with the type strain m4-4T (=NRRL B-41737T =CECT 7197T). PMID: 18398195 [PubMed - indexed for MEDLINE] Bacillus cohnii Int J Syst Bacteriol. 1993 Jan;43(1):150-6. Bacillus cohnii sp. nov., a new, obligately alkaliphilic, oval-spore-forming Bacillus species with ornithine and aspartic acid instead of diaminopimelic acid in the cell wall. Spanka R(1), Fritze D. Author information: (1)DSM-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-3300 Braunschweig, Germany. A group of 20 alkaliphilic Bacillus strains in which all strains revealed the same unique comination of properties--obligate alkaliphily, oval spores distending the sporangium, and ornithine and aspartic acid instead of diaminopimelic acid in the cell wall--was examined. Most of the strains had been isolated by a five-step enrichment and isolation procedure. The G+C content was determined to span a range from 33.5 to 35.0 mol%. Unsaturated fatty acids amounted to 17 to 28% of the total cellular fatty acids. Through DNA-DNA hybridization experiments 11 strains could be grouped in one species. Low homology values with the type strains of validly published Bacillus species with similar G+C contents suggest that these strains belong to a hitherto undescribed species for which the name Bacillus cohnii is proposed. The type strain of the new species is strain RSH (= DSM 6307). PMID: 8323866 [PubMed - in- 15 51. 52. 53. 54. dexed for MEDLINE] Bacillus composti Int J Syst Evol Microbiol. 2013 Aug;63(Pt 8):3030-6. doi: 10.1099/ijs.0.049106-0. Epub 2013 Feb 8. Bacillus composti sp. nov. and Bacillus thermophilus sp. nov., two thermophilic, Fe(III)-reducing bacteria isolated from compost. Yang G(1), Chen M, Yu Z, Lu Q, Zhou S. Author information: (1)Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China. Two novel thermophilic bacteria, designated SgZ-9(T) and SgZ-10(T), were isolated from compost. Cells of the two strains were catalase-positive, endospore-forming and Gram-staining-positive rods. Strain SgZ-9(T) was oxidase-positive and non-motile, and strain SgZ-10(T) was oxidase-negative and motile. The highest 16S rRNA gene sequence similarity for both strains SgZ-9(T) and SgZ-10(T) was observed with Bacillus fortis (97.5 % and 96.9 %, respectively). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SgZ-9(T) formed a cluster with B. fortis R-6514(T) and Bacillus fordii R-7190(T), and SgZ-10(T) formed a cluster with Bacillus farraginis R-6540(T). The DNA-DNA pairing studies showed that SgZ-9(T) displayed 41.6 % and 30.7 % relatedness to the type strains of B. fortis and B. fordii, respectively. The 16S rRNA gene sequence similarity between strains SgZ-9(T) and SgZ-10(T) was 97.2 %, and the level of DNA-DNA relatedness between them was 39.2 %. The DNA G+C content of SgZ-9(T) and SgZ-10(T) was 45.3 and 47.9 mol%, respectively. Chemotaxonomic analysis revealed that both strains contained the menaquinone 7 (MK-7) as the predominant respiratory quinone. The major cellular fatty acids (>5 %) were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C17 : 0 in SgZ-9(T) and iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0, anteiso-C17 : 0 and iso-C16 : 0 in SgZ-10(T). Based on the phenotypic characteristics, chemotaxonomic features, DNA-DNA hybridization with the nearest phylogenetic neighbours and phylogenetic analysis based on the 16S rRNA gene sequences, the two strains were determined to be two distinct novel species in the genus Bacillus, and the names proposed are Bacillus composti sp. nov. SgZ-9(T) ( = CCTCC AB2012109(T) = KACC 16872(T)) and Bacillus thermophilus sp. nov. SgZ-10(T) (CCTCC AB2012110(T) = KACC 16873(T)). PMID: 23396719 [PubMed - indexed for MEDLINE] Bacillus curdlanolyticus Int J Syst Bacteriol. 1995 Jul;45(3):515-21. Bacillus curdlanolyticus sp. nov. and Bacillus kobensis sp. nov., which hydrolyze resistant curdlan. Kanzawa Y(1), Harada A, Takeuchi M, Yokota A, Harada T. Author information: (1)Kobe Women's University, Suma, Japan. Taxonomic characteristics of seven bacterial strains which were isolated from soil and hydrolyze resistant curdlan were studied. These bacteria were aerobic, spore-forming rods, contained menaquinone 7 as a major quinone, contained anteiso-C15:0 and iso-C16:0 as major cellular fatty acids, had guanine-plus-cytosine contents of 50 to 52 mol%, and could be divided into two groups on the basis of physiological and chemotaxonomic characteristics and DNA-DNA hybridization data. We propose the following two new species: Bacillus curdlanolyticus for strains YK9, YK121, YK161, YK201, and YK203, with type strain YK9 (= IFO 15724); and Bacillus kobensis for strains YK205 and YK207, with type strain YK205 (= IFO 15729). PMID: 8590679 [PubMed - indexed for MEDLINE] Bacillus cytotoxicus Int J Syst Evol Microbiol. 2013 Jan;63(Pt 1):31-40. doi: 10.1099/ijs.0.030627-0. Epub 2012 Feb 10. Bacillus cytotoxicus sp. nov. is a novel thermotolerant species of the Bacillus cereus Group occasionally associated with food poisoning. Guinebretière MH(1), Auger S, Galleron N, Contzen M, De Sarrau B, De Buyser ML, Lamberet G, Fagerlund A, Granum PE, Lereclus D, De Vos P, Nguyen-The C, Sorokin A. Author information: (1)INRA, UMR408 Sécurité et Qualité des produits d'Origine Végétale, F-84000 Avignon, France. [email protected] An aerobic endospore-forming bacillus (NVH 391-98(T)) was isolated during a severe food poisoning outbreak in France in 1998, and four other similar strains have since been isolated, also mostly from food poisoning cases. Based on 16S rRNA gene sequence similarity, these strains were shown to belong to the Bacillus cereus Group (over 97% similarity with the current Group species) and phylogenetic distance from other validly described species of the genus Bacillus was less than 95%. Based on 16S rRNA gene sequence similarity and MLST data, these novel strains were shown to form a robust and well-separated cluster in the B. cereus Group, and constituted the most distant cluster from species of this Group. Major fatty acids (iso-C(15:0), C(16:0), iso-C(17:0), anteiso-C(15 : 0), iso-C(16:0), iso-C(13:0)) supported the affiliation of these strains to the genus Bacillus, and more specifically to the B. cereus Group. NVH 391-98(T) taxon was more specifically characterized by an abundance of iso-C(15:0) and low amounts of iso-C(13:0) compared with other members of the B. cereus Group. Genome similarity together with DNA-DNA hybridization values and physiological and biochemical tests made it possible to genotypically and phenotypically differentiate NVH 391-98(T) taxon from the six current B. cereus Group species. NVH 391-98(T) therefore represents a novel species, for which the name Bacillus cytotoxicus sp. nov. is proposed, with the type strain NVH 391-98(T) (= DSM 22905(T) = CIP 110041(T)). PMID: 22328607 [PubMed - indexed for MEDLINE] Bacillus daliensis Int J Syst Evol Microbiol. 2012 Apr;62(Pt 4):949-53. doi: 10.1099/ijs.0.031575-0. Epub 2011 Jun 13. Bacillus daliensis sp. nov., an alkaliphilic, Gram-positive bacterium isolated from a soda lake. Zhai L(1), Liao T, Xue Y, Ma Y. Author information: (1)State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China. A Gram-positive, alkaliphilic bacterium, designated strain DLS13T, was isolated from Dali Lake in Inner Mongolia Autonomous Region, China. The isolate was able to grow at pH 7.5-11.0 (optimum at pH 9), in 0-8 % (w/v) NaCl (optimum at 2 %, w/v) and at 10-45 °C (optimum at 30 °C). Cells of the isolate were facultatively anaerobic, spore-forming rods with peritrichous flagella. The predominant isoprenoid quinone was MK-7 and its cell wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were anteiso-C15:0, an- 16 teiso-C17:0 and iso-C15:0. The genomic DNA G+C content of the isolate was 43.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain DLS13T was a member of the genus Bacillus and most closely related to Bacillus saliphilus DSM 15402T (96.9 % similarity). The DNA-DNA relatedness value between strain DLS13T and B. saliphilus DSM 15402T was 38.7±1.9 %. Comparative analysis of genotypic and phenotypic features indicated that strain DLS13T represents a novel species of 55. 56. 57. 58. the genus Bacillus, for which the name Bacillus daliensis sp. nov. is proposed; the type strain is DLS13T (=CGMCC 1.10369T=JCM 17097T=NBRC 107572T). PMID: 21669916 [PubMed - indexed for MEDLINE] Bacillus daqingensis Kim HJ(1), Park CS, Lee S, Ahn TY. J Microbiol. 2014 Jul;52(7):554-8. doi: 10.1007/s 12275- 014-3458-9. Epub 2014 May 30. Bacillus daqingensis sp. nov. isolated from near poultry farm soil. Author information: (1)Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan, 330-714, Republic of Korea. A novel bacterial strain, designated PFS-5(T), was isolated from the soil environment with feces of a live poultry farm located in Cheonan, Republic of Korea. Strain PFS-5(T) was Gram-staining-positive, motile, strictly aerobic bacterium, rod-shaped, and endospore-forming. The strain contained meso-diaminopimelic acid in their peptidoglycan and MK-7 menaquinone. The major fatty acids were anteiso-C15:0 (44.2%), C16:0 (22.2%), and iso-C15:0 (16.7%). The DNA G+C content was 40.1 mol%. Comparative 16S rRNA gene sequence analysis identified strain PFS-5(T) in the genus Bacillus, exhibiting the highest level of sequence similarity with type strain of B. herbersteinensis D-1,5a(T) (96.9%), B. humi LMG 22167(T) (96.7%), B. alkalitelluris BA288(T) (96.1%), B. litoralis SW-211(T) (96.0%), and B. luteolus YIM93174(T) (95.5%). The major polar lipids of PFS-5(T) were diphosphatidylglycerol and phosphatidylglycerol. On the basis of result from poly-phasic data, strain PFS-5(T) represents a novel species, for which the name Bacillus cheonanensis sp. nov. is proposed (Type strai PFS-5(T) = KACC 17469(T) = JCM19333(T)). PMID: 24879346 [PubMed - in process] Bacillus daqingensis Wang S(1), Sun L, Wei D, Zhou B, Zhang J, Gu X, Zhang L, Liu Y, Li Y, Guo W, Jiang S, Pan Y, Wang Y. Bacillus daqingensis sp. nov., a halophilic, alkaliphilic bacterium isolated from saline-sodic soil in Daqing, China. J Microbiol. 2014 Jul;52(7):548-53. doi: 10.1007/s12275-014-3376-x. Epub 2014 May 30. Author information: (1)Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin, 150086, P. R. China. An alkaliphilic, moderately halophilic, bacterium, designated strain X10-1(T), was isolated from saline-alkaline soil in Daqing, Heilongjiang Province, China. Strain X10-1(T) was determined to be a Gram-positive aerobe with rod-shaped cells. The isolate was catalase-positive, oxidase-negative, non-motile, and capable of growth at salinities of 0-16% (w/v) NaCl (optimum, 3%). The pH range for growth was 7.5-11.0 (optimum, pH 10.0). The genomic DNA G+C content was 47.7 mol%. Its major isoprenoid quinone was MK-7 and its cellular fatty acid profile mainly consisted of anteiso-C15:0, anteiso-C17:0, iso-C15:0, C16:0, and iso-C16:0. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences showed that X10-1(T) is a member of the genus Bacillus, being most closely related to B. saliphilus DSM15402(T) (97.8% similarity) and B. agaradhaerens DSM 8721(T) (96.2%). DNA-DNA relatedness to the type strains of these species was less than 40%. On the basis of the phylogenetic, physiological, and biochemical data, strain X10-1(T) represents a novel species of the genus Bacillus, for which the name Bacillus daqingensis sp. nov. is proposed. The type strain is X10-1(T) (=NBRC 109404(T) = CGMCC 1.12295(T)). PMID: 24879344 [PubMed - in process] Bacillus decisifrondis Int J Syst Evol Microbiol. 2007 May;57(Pt 5):974-8. Bacillus decisifrondis sp. nov., isolated from soil underlying decaying leaf foliage. Zhang L(1), Xu Z, Patel BK. Author information: (1)Microbial Gene Research and Resources Facility, School of Biomolecular and Biomedical Sciences, Faculty of Science, Griffith University, Brisbane, QLD 4111, Australia. An aerobic bacterium, designated strain E5HC-32(T), was isolated from soil underlying the decaying leaf litter of a slash pine forest located in south east Queensland, Australia. The strictly aerobic, motile rod-shaped cells (0.8-1.6 x 2.6-4.8 microm) produced subterminal spherical spores which distended the cells. Strain E5HC-32(T) grew optimally in 1 % trypticase soy broth (TSB) at 30 degrees C (temperature range for growth, 25-40 degrees C) and a pH of 8.4 (pH growth range, pH 7.1-9.1). Electron microscopic examination of negatively stained cells revealed the presence of peritrichous flagella and thin sections showed the presence of a typical Gram-positive type cell-wall ultrastructure. The strain was catalase-positive and oxidase-negative and metabolized pyruvic acid methyl ester, D-galactonic acid lactone, alpha-ketobutyric acid, alpha-ketovaleric acid, L-proline, L-alanine, urocanic acid, inosine, uridine, thymidine, glycerol, alpha-cyclodextrin, alpha-D-lactose, D-psicose, D-raffinose, L-rhamnose, D-sorbitol, turanose, cis-aconitic acid, alpha-hydroxybutyric acid, L-alaninamide and 2-aminoethanol. The G+C content of DNA was 41+/-1 mol% as determined by the thermal denaturation method. 16S rRNA gene sequence analysis revealed that strain E5HC-32(T) was placed equidistantly as a member of the class Bacilli, phylum Firmicutes, with Bacillus sphaericus DSM 28(T) and Bacillus odysseyi ATCC PTA-4993(T) (similarity of 93 %). In addition to its significant phylogenetic separation from its nearest relatives, strain E5HC-32(T) possessed phenotypic traits that also suggested that it represented a novel species, for which the name Bacillus decisifrondis sp. nov. is proposed. The type strain is E5HC-32(T) (=JCM 13601(T)=DSM 17725(T)). PMID: 17473244 [PubMed - indexed for MEDLINE] Bacillus decolorationis Int J Syst Evol Microbiol. 2003 Mar;53(Pt 2):459-63. Bacillus decolorationis sp. nov., isolated from biodeteriorated parts of the mural paintings at the Servilia tomb (Roman necropolis of Carmona, Spain) and the Saint-Catherine chapel (Castle Herberstein, Austria). Heyrman J(1), Balcaen A, Rodriguez-Diaz M, Logan NA, Swings J, De Vos P. Author information: (1)Vakgroep BFM WE10V, Laboratorium voor Microbiologie, Universiteit Gent, Belgium. [email protected] Microbial 17 59. 60. 61. 62. growths causing discoloration on the Roman wall paintings of the Servilia tomb at the necropolis of Carmona (Spain) and the medieval wall paintings of the Saint-Catherine chapel at Castle Herberstein (Austria) were investigated and from four different samples, a group of ten strains with similar characteristics was isolated. The isolates were characterized in a polyphasic taxonomic study, including 16S rDNA sequence analysis, (GTG)5-PCR genomic fingerprinting, DNA-DNA hybridization, DNA base ratio, fatty acid analysis, morphological and biochemical characterization. The data obtained attribute the isolates to a novel species of the genus Bacillus, for which the name Bacillus decolorationis sp. nov. is proposed. The type strain is strain LMG 19507T (=DSM 14890T). PMID: 12710613 [PubMed - indexed for MEDLINE] Bacillus deserti Antonie Van Leeuwenhoek. 2011 Feb;99(2):221-9. doi: 10.1007/s10482-010-9479-4. Epub 2010 Jun 26. Bacillus deserti sp. nov., a novel bacterium isolated from the desert of Xinjiang, China. Zhang L(1), Wu GL, Wang Y, Dai J, Fang CX. Author information: (1)College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China. A Gram-positive, rod-shaped, motile and spore-forming bacterium, designated ZLD-8(T), was isolated from a desert soil sample collected from Xinjiang Province in north-west China, and subjected to a polyphasic taxonomic analysis. This isolate grew optimally at 30°C and pH 7.0. It grew with 0-4% NaCl (optimum, 0-1%). Comparative 16S rRNA gene sequence analysis showed that strain ZLD-8(T) was closely related to members of the genus Bacillus, exhibiting the highest 16S rRNA gene sequence similarity to Bacillus kribbensis DSM 17871(T) (98.0%). The levels of 16S rRNA gene sequence similarity with respect to other Bacillus species with validly published names were less than 96.3%. The DNA G + C content of strain ZLD-8(T) was 40.1 mol%. The strain contained MK-7 as the predominant menaquinone. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids (>5% of total fatty acids) were anteiso-C15:0 (39.56%), iso-C14:0 (25.69%), C16:1 ω7c alcohol (10.13%) and iso-C15:0 (5.27%). These chemotaxonomic results supported the affiliation of strain ZLD-8(T) to the genus Bacillus. However, low DNA-DNA relatedness values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain ZLD-8(T) from recognized Bacillus species. On the basis of the polyphasic evidence presented, strain ZLD-8(T) is considered to represent a novel species of the genus Bacillus, for which the name Bacillus deserti sp. nov. is proposed. The type strain is ZLD-8(T) (=CCTCC AB 207173(T) = KCTC 13246(T)). PMID: 20582469 [PubMed - indexed for MEDLINE] Bacillus dipsosauri J Appl Bacteriol. 1996 Jul;81(1):109-12. Phylogenetic characterization of a novel salt-tolerant Bacillus species: description of Bacillus dipsosauri sp. nov. Lawson PA(1), Deutch CE, Collins MD. Author information: (1)BBSRC Institute of Food Research, Reading Laboratory, UK. The taxonomic position of a novel halophilic endospore-forming bacterium previously isolated from a desert iguana was investigated by 16S rRNA gene sequencing. Comparative sequence analyses showed the unidentified bacterium to be phylogenetically loosely associated with some other spore-forming (Bacillus pantothenticus, Sporosarcina halophila) and non-spore-forming (Marinococcus albus) halotolerant bacteria. Based on the phenotypic and phylogenetic distinctiveness of the unidentified bacterium, it is proposed that it is classified in the genus Bacillus as a new species, Bacillus dipsosauri. PMID: 8675481 [PubMed - indexed for MEDLINE] Bacillus eiseniae Int J Syst Evol Microbiol. 2012 Sep;62(Pt 9):2077-83. doi: 10.1099/ijs.0.034892-0. Epub 2011 Oct 21. Bacillus eiseniae sp. nov., a swarming, moderately halotolerant bacterium isolated from the intestinal tract of an earthworm (Eisenia fetida L.). Hong SW(1), Park JM, Kim SJ, Chung KS. Author information: (1)Division of Biological Science and Technology, Yonsei University, Wonju 220-710, Republic of Korea. A swarming and moderately halotolerant bacterium, designated strain A1-2(T), was isolated from the intestinal tract of the earthworm Eisenia fetida L. Cells were endospore-forming rods that were facultatively anaerobic, catalase-positive, oxidase-negative and motile by peritrichous flagella. The isolate grew optimally at 30 °C and pH 7.0, and could grow with up to 9 % (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain A1-2(T) belonged to the genus Bacillus and exhibited 16S rRNA gene sequence similarities of 96.8, 96.0, 96.0, 96.4 and 96.7 % with Bacillus drentensis LMG 21831(T), B. horneckiae PT-45(T), B. niacini BAC 1015, B. infantis SMC 4352-1(T) and B. shackletonii LMG 18435(T), respectively. DNA-DNA relatedness values between the isolate and the reference strains were ≤ 38.3 %. The DNA G+C content of strain A1-2(T) was 38.5 mol%. The predominant menaquinone was MK-7 and the major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were iso-C(15 : 0) (51.5 %) and anteiso-C(15 : 0) (29.6 %) and the cell-wall diamino acid was meso-diaminopimelic acid. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and phenotypic characteristics, it is concluded that strain A1-2(T) represents a novel species of the genus Bacillus, for which we propose the name Bacillus eiseniae sp. nov. The type strain is A1-2(T) (= KCCM 90092(T) = JCM 16993(T)). PMID: 22021583 [PubMed - indexed for MEDLINE] Bacillus enclensis Antonie Van Leeuwenhoek. 2014 Jan;105(1):199-206. doi: 10.1007 /s10482- 013-0066-3. Epub 2013 Oct 31. Bacillus enclensis sp. nov., isolated from sediment sample. Dastager SG(1), Mawlankar R, Tang SK, Srinivasan K, Ramana VV, Shouche YS. Author information: (1)NCIM-Resource Center, CSIR-National Chemical Laboratory, Pune, 411008, Maharashtra, India, [email protected]. A novel bacterial strain, designated SGD-1123(T) was isolated from Chorao Island, in Goa Province, India. The strain was found to be able to grow at 15-42 °C, pH 5-12 and 0-12 % (w/v) NaCl. The whole cell hydrolysates were found to contain meso-diaminopimelic acid, galactose and arabinose. The major fatty acids were identified as iso-C15:0 and anteiso-C15:0, MK-7 was identified as the predominant menaquinone and the predominant polar lipids were identified as diphosphatidylglycerol, 18 phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminolipid. The genomic DNA G+C content was determined to be 44.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolate within the genus Bacillus and further revealed that strain SGD-1123(T) had highest sequence similarity with Bacillus aquimaris, and forms a separate clade with its closest relatives i.e. B. aquimaris, Bacillus vietnamensis and Bacillus marisflavi, with which it shares 94.5, 94.1 and 94.1 % similarity respectively. The phylogenetic, chemotaxonomic and phenotypic analyses indicated that strain SGD-1123(T) represents a novel species within the genus Bacillus, for which the name Bacillus enclensis is proposed. The type strain is SGD-1123(T) (NCIM 5450(T)=CCTCC AB 2011125(T)). PMID: 24174310 [PubMed - in process]$$ 63. Bacillus endophyticus Int J Syst Evol Microbiol. 2002 Jan;52(Pt 1):101-7. Bacillus endophyticus sp. nov., isolated from the inner tissues of cotton plants (Gossypium sp.). Reva ON(1), Smirnov VV, Pettersson B, Priest FG. Author information: (1)Department of Antibiotics, Institute of Microbiology and Virology, Kiev, Ukraine. Four strains of aerobic, endospore-forming bacteria were isolated from the inner tissues of healthy cotton plants (Gossypium sp., Dushanbe, Tajikistan). The organisms had identical randomly amplified polymorphic DNA patterns that distinguished them from other bacilli that are commonly isolated from plant tissues, e.g. Bacillus amyloliquefaciens, Bacillus licheniformis, Bacillus pumilus and Bacillus subtilis. PCR amplification of 16S-23S rRNA spacer regions suggested that the four strains could be assigned to two highly related taxa, which correlated with differences in cell morphology. However, the cloned spacer region provided a simple and specific hybridization probe for all four strains. The virtually complete 16S rDNA sequences were prepared for representatives of the two groups (strains 2DT(T) and 12DX) and differed by only two bases, thus supporting classification of the four strains in a single taxon at the species level. Phylogenetic analyses indicated that strain 2DT(T) belonged to the genus Bacillus and was most closely related to Bacillus sporothermodurans DSM 10599T with a sequence similarity of 94.8%. It is concluded that the four strains belong to a novel species of Bacillus for which the name Bacillus endophyticus sp. nov. is proposed. The type strain is 2DT(T) (= UCM B-5715T = CIP 106778T). PMID: 11837291 [PubMed - indexed for MEDLINE] 64. Bacillus endoradicis Int J Syst Evol Microbiol. 2012 Feb;62(Pt 2):359-63. doi: 10.1099/ijs. 0.028936-0. Epub 2011 Mar 25. Bacillus endoradicis sp. nov., an endophytic bacterium isolated from soybean root. Zhang YZ(1), Chen WF, Li M, Sui XH, Liu HC, Zhang XX, Chen WX. Author information: (1)State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China. A gram-positive, aerobic, motile rod, designated strain CCBAU 05776(T), was isolated from the inner tissues of a healthy soybean (Glycine max L.) root collected from an agricultural field in the countryside of Shijiazhuang city, Hebei Province, China. Phylogenetic analysis of the 16S rRNA gene indicated that this strain was most closely related to Bacillus muralis LMG 20238(T) and Bacillus simplex NBRC 15720(T) with similarity of 96.5 % and 96.3 %, respectively, lower than the suggested threshold (97.0 %) for separating bacterial species. In phenotypic characterization, the novel strain differed from the two most related species in that it did not hydrolyse casein or starch but could grow on MacConkey agar. It grew between 15 and 45 °C and tolerated up to 7 % NaCl (w/v). Strain CCBAU 05776(T) grew in media with pH 5.5 to 10 (optimal growth at pH 7.0-8.0). The predominant cellular fatty acids were iso-C(15 : 0) (40.81 %) and C(16 : 1)ω7c alcohol (10.61 %). The predominant isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C was 40.8 mol% (T(m)). DNA-DNA relatedness of the novel isolate with B. muralis and B. simplex was 42.4 % and 32.7 %, respectively. Based upon the consensus of phylogenetic and phenotypic analyses, strain CCBAU 05776(T) represents a novel species within the genus Bacillus, for which the name Bacillus endoradicis sp. nov. is proposed. The type strain is CCBAU 05776(T) ( = LMG 25492(T) = HAMBI 3097(T)). PMID: 21441377 [PubMed indexed for MEDLINE] 65. Bacillus farraginis Int J Syst Evol Microbiol. 2004 Jul;54(Pt 4):1355-64. Bacillus farraginis sp. nov., Bacillus fortis sp. nov. and Bacillus fordii sp. nov., isolated at dairy farms. Scheldeman P(1), Rodríguez-Díaz M, Goris J, Pil A, De Clerck E, Herman L, De Vos P, Logan NA, Heyndrickx M. Author information: (1)Ministry of the Flemish Community, Centre for Agricultural Research, Department of Animal Product Quality, Brusselsesteenweg 370, 9090 Melle, Belgium. [email protected] Forty-eight bacterial strains were isolated at dairy farms from raw milk, the milking apparatus, green fodder or feed concentrate after a heat treatment of 30 min at 100 degrees C. In this way, spore-forming bacteria with a very high intrinsic heat resistance were selected for. The aerobic spore-forming isolates were subjected to a polyphasic taxonomical study, including repetitive element sequence-based PCR typing, whole-cell protein profiling, 16S rDNA sequence analysis, DNA-DNA hybridizations, DNA base composition, fatty acid analysis, and morphological and biochemical characteristics. A comparison of the REP- and (GTG)5-PCR and whole-cell protein SDS-PAGE profiles resulted in three clusters of similar strains. Analysis of the 16S rDNA sequences and DNA-DNA relatedness data showed that these clusters represented three novel species. The highest 16S rDNA similarity to a recognized species found for the three groups was around 94% with Bacillus lentus and Bacillus sporothermodurans. Further phenotypic characterization supported the proposal of three novel species in the genus Bacillus, Bacillus farraginis, Bacillus fortis and Bacillus fordii. The respective type strains are R-6540T (=LMG 22081T=DSM 16013T), R-6514T (=LMG 22079T=DSM 16012T) and R-7190T (=LMG 22080T=DSM 16014T); their G+C DNA base contents are 43.7, 44.3 and 41.9 mol%, respectively. Although in variable amounts, a predominance of the branched fatty acids iso-C(15 : 0) and anteiso-C(15 : 0) was observed in all three novel species. PMID: 15280314 [PubMed - indexed for MEDLINE] 66. Bacillus fengqiuensis Zhao F(1), Feng YZ(1), Chen RR(1), Zhang HY(1), Wang JH(1), Lin XG(2). Bacillus fengqiuensis sp. nov., 19 67. 68. 69. 70. isolated from a typical sandy loam soil under long-term NPK fertilization in the North China. Int J Syst Evol Microbiol. 2014 May 28. pii: ijs.0.063081-0. doi: 10.1099/ijs.0.063081-0. [Epub ahead of print] Author information: (1)Institute of Soil Science, Chinese Academy of Sciences. (2)Institute of Soil Science, Chinese Academy of Sciences [email protected]. A Gram-positive, endospore forming, moderately alkaliphilic bacterium, strain NPK15T, was isolated from a typical sandy loam soil under long-term NPK fertilization in the North China and was subjected to a polyphasic taxonomic study. The cell-wall peptidoglycan of strain NPK15T was found to be meso-diaminopimelic acid and the cell-wall sugars were xylose, glucose and traces of mannose. The only respiratory quinone found in strain NPK15T was menaquinone 7 (MK-7). The major cellular fatty acids were iso-C15:0, anteiso-C15:0, C16:0, and C16:1 ω6c /C16:1 ω7c. The major polar lipids were found to be diphosphatidylglyerol, phosphatidylethanolamine, and phosphatidylglycerol. Phylogenetic analysis of this strain based on 16S rRNA gene sequence was most closely to Bacillus thaonhiensis NHI-38T (99.59%), Bacillus songklensis CAU 1033T (99.52%) and Bacillus abyssalis SCSIO 15042T (99.00 %). The DNA-DNA hybridization results indicated that this strain was distinct from other Bacillus species, the degree of similarity being 35.4% with B. abyssalis, 39.7% with B. songklensis and 51.2% with B. thaonhiensis. The DNA G+C content of strain NPK15T was 45.5%. The phenotypic, chemotaxonomic and molecular analyses identified strain NPK15T as a novel Bacillus species, for which the name Bacillus fengqiuensis is proposed. The type strain is NPK15T (=DSM 26745T =CCTCC AB 2013156T). Copyright © 2014, the Society for General Microbiology. PMID: 24871777 [PubMed - as supplied by publisher] Bacillus fumarioli Int J Syst Evol Microbiol. 2000 Sep;50 Pt 5:1741-53. Aerobic endospore-forming bacteria from geothermal environments in northern Victoria Land, Antarctica, and Candlemas Island, South Sandwich archipelago, with the proposal of Bacillus fumarioli sp. nov. Logan NA(1), Lebbe L, Hoste B, Goris J, Forsyth G, Heyndrickx M, Murray BL, Syme N, Wynn-Williams DD, De Vos P. Author information: (1)School of Biological and Biomedical Sciences, Glasgow Galedonian University, UK. [email protected] Aerobic endospore-forming bacteria were isolated from soils taken from active fumaroles on Mount Rittmann and Mount Melbourne in northern Victoria Land, Antarctica, and from active and inactive fumaroles on Candlemas Island, South Sandwich archipelago. The Mt Rittmann and Mt Melbourne soils yielded a dominant, moderately thermophilic and acidophilic, aerobic endospore-former growing at pH 5.5 and 50 degrees C, and further strains of the same organism were isolated from a cold, dead fumarole at Clinker Gulch, Candlemas Island. Amplified rDNA restriction analysis, SDS-PAGE and routine phenotypic tests show that the Candlemas Island isolates are not distinguishable from the Mt Rittmann strains, although the two sites are 5600 km apart, and 16S rDNA sequence comparisons and DNA relatedness data support the proposal of a new species, Bacillus fumarioli, the type strain of which is LMG 17489T. PMID: 11034482 [PubMed - indexed for MEDLINE] Bacillus funiculus Int J Syst Evol Microbiol. 2002 Jul;52(Pt 4):1141-4. Bacillus funiculus sp. nov., novel filamentous isolates from activated sludge. Ajithkumar VP(1), Ajithkumar B, Iriye R, Sakai T. Author information: (1)Laboratory of Ecological and Toxicological Chemistry, Faculty of Agriculture, Shinshu University, Kamiina, Nagano, Japan. A novel filamentous Bacillus strain, NAF001T, was reported previously that produces endospores and spore-like resting cells; the latter outgrow by budding. Phylogenetic analysis based on 16S rDNA gene sequences reported in the same paper speculated on the proposal of a novel species for this isolate. This communication describes the DNA-DNA relatedness of strain NAF001T to various members of the genus Bacillus and its whole-cell fatty acid and quinone profiles, in order to authenticate the creation of a novel species, for which the name Bacillus funiculus sp. nov. is proposed. The type strain is NAF001T (= JCM 11201T = CIP 107128T). Further, features of the binding points between filaments of strain NAF001T that enable it to form extremely long filaments are captured by electron microscopy. PMID: 12148618 [PubMed - indexed for MEDLINE] Bacillus gaemokensis J Microbiol. 2010 Dec;48(6):867-71. doi: 10.1007/s12275-010-0148-0. Epub 2011 Jan 9. Bacillus gaemokensis sp. nov., isolated from foreshore tidal flat sediment from the Yellow Sea. Jung MY(1), Paek WK, Park IS, Han JR, Sin Y, Paek J, Rhee MS, Kim H, Song HS, Chang YH. Author information: (1)Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Daejeon, 305-806, Republic of Korea. Erratum in J Microbiol. 2011 Feb;49(1):169. Jung, Min-Young [corrected to Jung, Min Young].J Microbiol. 2012 Jun;50(3):553. A Gram-positive, rod-shaped, endospore-forming organism, strain BL3-6(T), was isolated from tidal flat sediments of the Yellow Sea in the region of Tae-An. A 16S rRNA gene sequence analysis demonstrated that this isolate belongs to the Bacillus cereus group, and is closely related to Bacillus mycoides (99.0% similarity), Bacillus thuringiensis (99.0%), Bacillus weihenstephanensis (99.0%), Bacillus cereus (98.9%), Bacillus anthracis (98.8%), and Bacillus pseudomycoides (98.1%). The phylogenetic distance from any validly described Bacillus species outside the Bacillus cereus group was less than 95.6%. The DNA G+C content of the strain was 39.4 mol% and the major respiratory quinone was menaquinone-7. The major cellular fatty acids were iso-C(14:0) (17.8%), iso-C(16:0) (15.8%), and iso-C(12:0) (11.3%). The diagnostic amino acid of the cell wall was meso-diaminopimelic acid and the major cell wall sugar was galactose. The results of DNA-DNA hybridization (<55.6%) and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain BL3-6(T) from the published Bacillus species. BL3-6(T) therefore represents a new species, for which the name Bacillus gaemokensis sp. nov. is proposed, with the type strain BL3-6(T) (=KCTC 13318(T) =JCM 15801(T)). PMID: 21221948 [PubMed - indexed for MEDLINE] Bacillus galactosidilyticus Int J Syst Evol Microbiol. 2004 Mar;54(Pt 2):617-21. Bacillus galactosidilyticus sp. nov., an alkali-tolerant beta-galactosidase producer. Heyndrickx M(1), Logan NA, Lebbe L, Rodríguez-Díaz M, Forsyth G, Goris J, Scheldeman P, De Vos P. 20 Author information: (1)Department of Animal Product Quality, Center for Agricultural Research-Ghent, Brusselsesteenweg 370, B-9090 Melle, Belgium. [email protected] A novel Bacillus isolate from raw milk and four strains from diverse origins that were identified previously as Bacillus lentus, Bacillus firmus and Bacillus circulans showed a high degree of similarity in amplified rDNA restriction analysis, SDS-PAGE and routine phenotypic tests, whilst 16S rDNA sequence comparisons and DNA relatedness data showed that this taxon was different from related Bacillus species. On the basis of these data, Bacillus galactosidilyticus sp. nov. is proposed, with the type strain LMG 17892(T) (=DSM 15595(T)=Logan B2188(T)=MB 800(T)). PMID: 15023985 [PubMed - indexed for MEDLINE] 71. Bacillus galliciensis Int J Syst Evol Microbiol. 2010 Apr;60(Pt 4):892-5. doi: 10.1099/ijs.0.011817-0. Epub 2009 Aug 6. Bacillus galliciensis sp. nov., isolated from faeces of wild seahorses (Hippocampus guttulatus). Balcázar JL(1), Pintado J, Planas M. Author information: (1)Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas (CSIC), c/. Eduardo Cabello 6, 36208 Vigo, Spain. [email protected] A Gram-positive-staining, motile, rod-shaped, endospore-forming bacterium (BFLP-1( T)) was isolated from faeces of wild long-snouted seahorses ( Hippocampus guttulatus) captured in north-west Spain (Toralla, Galicia). Strain BFLP-1(T) grew at 10-30 degrees C and pH 5.5-9 (optimally at 20 degrees C and pH 7.2) and with 0-7 % (w/v) NaCl (optimally with 2 % NaCl). The G+C content of the DNA was 48.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BFLP-1(T) was a member of the genus Bacillus and was most closely related to Bacillus herbersteinensis D-1,5a(T) (96.6 %), B. shackletonii LMG 18435(T) (96.0 %) and B. isabeliae CVS-8(T) (95.9 %). Chemotaxonomic data (peptidoglycan type, meso-diaminopimelic acid; major menaquinone, MK-7; predominant fatty acids, anteiso-C(15 : 0 ), anteiso-C(17 : 0) and C(16 : 1 )omega11c; major polar lipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown aminoglycophospholipid) supported the affiliation of strain BFLP-1(T) to the genus Bacillus . Comparative analysis of 16S rRNA gene sequences and chemotaxonomic and phenotypic features indicated that strain BFLP-1(T) represents a novel species within the genus Bacillus, for which the name Bacillus galliciensis sp. nov. is proposed. The type strain is BFLP-1( T) (=DSM 21539(T) =LMG 24668(T)). PMID: 19661512 [PubMed - indexed for MEDLINE] 72. Bacillus ginsengisoli Int J Syst Evol Microbiol. 2013 Mar;63(Pt 3):855-60. doi: 10.1099/ijs. 0.031740-0. Epub 2012 May 18. Bacillus ginsengisoli sp. nov., isolated from soil of a ginseng field. Nguyen NL(1), Kim YJ, Hoang VA, Min JW, Liang ZQ, Yang DC. Author information: (1)Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung Hee University, 1 Seocheon-dong, Giheung-gu Yongin-si, Gyeonggi-do 449-701, Republic of Korea. A novel bacterial strain DCY53(T) was isolated from a soil sample from a ginseng field and was characterized using a polyphasic approach. Cells were Gram-reaction-positive, rod-shaped, endospore-forming and motile with flagella. The strain was aerobic, catalase- and oxidase-positive, optimum growth temperature and pH were 30-37 °C and 6.0-7.5, respectively. On the basis of 16S rRNA gene sequence analysis, strain DCY53(T) was shown to belong to the genus Bacillus and the closest phylogenetic relatives were Bacillus pocheonensis KCTC 13943(T) (98.3 %), Bacillus bataviensis LMG 21833(T) (98.0 %), Bacillus soli LMG 21838(T) (97.9 %), Bacillus drentensis LMG 21831(T) (97.8 %), Bacillus niacini DSM 2923(T) (97.8 %), Bacillus novalis LMG 21837(T) (97.7 %), Bacillus vireti LMG 21834(T) (97.6 %) and Bacillus fumarioli LMG 17489(T) (97.3 %). The DNA G+C content was 43.6 mol% and the predominant respiratory quinone was MK-7. The major fatty acids were iso-C14 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0. The DNA-DNA relatedness with closest relatives was below 55 %. The results of the genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that DCY53(T) represented a novel species within the genus Bacillus, for which we propose the name Bacillus ginsengisoli. The type strain is DCY53(T) ( = KCTC 13945(T) = JCM 17335(T)). PMID: 22611202 [PubMed - indexed for MEDLINE] 73. Bacillus gordonae Ann Inst Pasteur Microbiol. 1986 Jan-Feb;137A(1):65-78. [Bacillus gordonae sp. nov., a new species belonging to the second morphological group, degrading various aromatic compounds]. [Article in French] Pichinoty F(1), Waterbury JB, Mandel M, Asselineau J. Author information: (1)Département de Biologie, UER Scientifique de Luminy, Marseille, France. Thirty strains were isolated from pasteurized soil samples by enrichment culture in aerobiosis at 32 degrees C in a minimal medium containing one of the following compounds as sole source of carbon and energy: quinate, p-hydroxybenzoate, phthalate, isophthalate or trimellitate. These bacteria were rods (0.8 X 2-7 micron), motile by peritrichous flagella. Endospores were oval (1.4-1.8 X 2 micron) and distinctly swelled the sporangia. The Gram reaction was variable but the Gram type was positive. Colonies were smaller on peptone (0.4%) agar than on minimal salts-glucose (0.2%) agar. The following characters were always present: growth in the presence of lysozyme, cytochrome c oxidase, catalase, nitrate assimilation, urease, amylase and L-glutamate dehydrogenase. The cells contained glycogen. In anaerobiosis, glucose was not fermented and nitrate was not used as a respiratory acceptor of electrons. Of 215 substrates tested, 31 (including 9 aromatic compounds) were used as sole carbon and energy sources by all 30 strains, and 38 substrates (including 13 aromatic compounds) were used by only some of them; 146 substrates (including 49 aromatic compounds) were not used by any of the 30 strains. No amino acid could be used as sole carbon and energy source. Numerical analysis of the 30 strains showed an aggregate cluster made of 5 phena. The mean G + C content of the DNA was 55 +/- 0.6 mol %. The described bacteria are clearly different from the 2 known species of the second morphological group which cannot ferment carbohydrates: Bacillus brevis and B. azotoformans. Strain Q1 (ATCC 29948) is the holotype of Bacillus gordonae sp. nov. PMID: 3674781 [PubMed - indexed for MEDLINE] 21 74. Bacillus gottheilii Int J Syst Evol Microbiol. 2013 Mar;63(Pt 3):867-72. doi: 10.1099/ijs.0.036277-0. Epub 2012 May 25. Bacillus gottheilii sp. nov., isolated from a pharmaceutical manufacturing site. Seiler H(1), Wenning M, Schmidt V, Scherer S. Author information: (1)Department of Microbiology (ZIEL), Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany. [email protected] A novel Gram-staining-positive, rod-shaped, motile, strictly aerobic, endospore-forming bacterium, designated WCC 4585(T), was isolated from a pharmaceutical production line. The organism grew optimally at 30 °C, at pH 8 and in the presence of 0.5 % (w/v) NaCl. Oval endospores were formed subterminally and terminally in swollen sporangia. The cell-wall diamino acid was meso-diaminopimelic acid (type A1γ) and the genomic DNA G+C content was 38.7 mol%. The major menaquinone was MK-7. The cellular fatty acid profile contained major amounts of iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0, and the cellular phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. The isolate was most closely related to Bacillus oceanisediminis H2(T), Bacillus infantis SMC 4352-1(T), Bacillus firmus NCIMB 9366(T), Bacillus circulans ATCC 4513(T) and Bacillus horneckiae DSM 23495(T) with which it shared less than 98.0 % 16S rRNA gene sequence similarity. DNA-DNA relatedness values between strain WCC 4585(T) and five type strains of related species were ≤27 % and sequence similarity values based on groEL sequences were ≤88.7 %. On the basis of the characteristics presented, strain WCC 4585(T) is proposed to represent a novel species, Bacillus gottheilii sp. nov. The type strain is WCC 4585(T)( = DSM 23668(T) = CCUG 59876(T) = LMG 25856(T)). PMID: 22634699 [PubMed - indexed for MEDLINE] 75. Bacillus graminis Int J Syst Evol Microbiol. 2011 Jul;61(Pt 7):1567-71. doi: 10.1099/ijs.0.023820-0. Epub 2010 Jul 23. Bacillus graminis sp. nov., an endophyte isolated from a coastal dune plant. Bibi F(1), Chung EJ, Jeon CO, Chung YR. Author information: (1)Division of Applied Life Science (BK 21), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea. A Gram-stain-positive endophytic bacterium, designated strain YC6957(T), was isolated from surface-sterilized roots of a halophyte (Elymus mollis Trin.) inhabiting coastal tidal flats of Namhae Island, located on the southern coast of Korea, and was subjected to a polyphasic taxonomic study. Cells were facultatively anaerobic, endospore-forming rods to coccoid rods, motile by a single flagellum. Strain YC6957(T) was catalase-positive, oxidase-negative and able to grow in the presence of 0-8 % (w/v) NaCl, with optimum growth at 4-5 % (w/v) NaCl. Growth occurred at 15-45 °C (optimal growth at 30-35 °C) and pH 6.0-8.5 (optimal growth at pH 7.0-8.0). The predominant isoprenoid quinone was menaquinone 7 (MK-7). The major cellular fatty acids were C(16 : 0) (11.3 %), iso-C(15 : 0) (19.2 %) and anteiso-C(15 : 0) (36.4 %). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 41.6 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate belonged to the genus Bacillus. Strain YC6957(T) exhibited high 16S rRNA gene sequence similarity to its closest neighbours, Bacillus ruris LMG 22866(T) (96.14 %), Bacillus lentus NCIMB 8773(T) (95.97 %) and Bacillus galactosidilyticus LMG 17892(T) (95.91 %), and less than 95.84 % similarity to all other type strains in the genus Bacillus. On the basis of the phylogenetic, physiological and biochemical data, it is suggested that strain YC6957(T) represents a novel species of the genus Bacillus, for which the name Bacillus graminis sp. nov. is proposed. The type strain is YC6957(T) ( = KACC 13779(T) = DSM 22162(T)). PMID: 20656804 [PubMed - in process] 76. Bacillus hackensackii Diagn Microbiol Infect Dis. 2003 Feb;45(2):143-7. "Bacillus hackensackii" sp. nov., a novel carbon dioxide sensitive bacterium isolated from blood culture. Hong T(1), Heibler N, Tang Yi. Author information: (1)Department of Pathology, Microbiology Laboratory, Hackensack University Medical Center, Hackensack, NJ, USA. [email protected] An endospore-forming, gram-positive bacillus was isolated from a patient's blood culture. This bacillus did not grow in the presence of 5% carbon dioxide although it grew well in ambient air at 37 degrees C. Although the organism thus is an aerobic bacterium, its sensitivity to increased carbon dioxide concentration places it in a distinct category of gaseous atmospheric requirement: capnophobic. Based on its morphology, growth characteristics, biochemical reactions and a complete 16S rRNA gene nucleotide sequence analysis, this microorganism represents a novel Bacillus species. The clinical significance of this isolate is unknown. It is proposed that the bacterium be classified in the genus Bacillus as "Bacillus hackensackii". PMID: 12614987 [PubMed - indexed for MEDLINE] 77. Bacillus haikouensis Li J(1), Yang G, Lu Q, Zhao Y, Zhou S. Bacillus haikouensis sp. nov., a facultatively anaerobic halotolerant bacterium isolated from a paddy soil. Antonie Van Leeuwenhoek. 2014 Aug 7. [Epub ahead of print]. Author information: (1)College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China. A Gram-stain positive, rod-shaped, endospore-forming and facultatively anaerobic halotolerant bacterium, designated as C-89(T), was isolated from a paddy field soil in Haikou, Hainan Province, People's Republic of China. Optimal growth was observed at 37 °C and pH 7.0 in the presence of 4 % NaCl (w/v). The predominant menaquinone was identified as MK-7, the major cellular fatty acids were identified as anteiso-C15:0 and iso-C15:0, and the major cellular polar lipids were identified as phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and two unknown phospholipids. The peptidoglycan type was determined to be based on meso-DAP. Based on 16S rRNA gene sequence similarity, the closest phylogenetic relatives were identified as Bacillus vietnamensis JCM 11124(T) (98.8 % sequence similarity), Bacillus aquimaris JCM 11545(T) (98.6 %) and Bacillus marisflavi JCM 11544(T) (98.5 %). The DNA G+C content of strain C-89(T) was determined to be 45.4 mol%. The DNA-DNA relatedness values of strain C-89(T) with its closest relatives were below 18 %. Therefore, on the basis of phylogenetic, chemotaxonomic, and phenotypic results, strain C-89(T) can be considered to repre- 22 78. 79. 80. 81. sent a novel species within the genus Bacillus, for which the name Bacillus haikouensis sp. nov., is proposed. The type strain is C-89(T) (=KCTC 33545(T) = CCTCC AB 2014076(T)). PMID: 25100188 [PubMed - as supplied by publisher] Bacillus halochares Int J Syst Evol Microbiol. 2010 Jun;60(Pt 6):1432-6. doi: 10.1099/ijs.0.014233-0. Epub 2009 Aug 11. Bacillus halochares sp. nov., a halophilic bacterium isolated from a solar saltern. Pappa A(1), Sánchez-Porro C, Lazoura P, Kallimanis A, Perisynakis A, Ventosa A, Drainas C, Koukkou AI. Author information: (1)Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece. A novel halophilic bacterium, designated strain MSS4(T), was isolated from the solar salterns of Mesolongi, Greece. The micro-organism, a motile, Gram-stain-positive, aerobic rod, proliferated at salinities of 1.0-4.0 M NaCl, with optimal growth at 2.5 M NaCl. Endospores were not observed. Strain MSS4(T) showed optimal growth at 37 degrees C and pH 8.0. The G+C content of its DNA was 47.2 mol%. The polar lipid pattern of strain MSS4(T) consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidic acid and phosphatidylethanolamine. It possessed anteiso-C(15 : 0), C(18 : 0), C(16 : 0) and anteiso-C(17 : 0) as the major fatty acids (altogether representing 84.7 % of the total). The predominant isoprenoid quinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. 16S rRNA gene sequence analysis showed that the new isolate has 96.1 % similarity to Bacillus qingdaonensis CM1(T) and Bacillus aidingensis 17-5(T), 95.5 % to Bacillus salarius BH169(T) and lower similarity to other Bacillus species. These results justify the assignment of strain MSS4(T) to a novel species within the genus Bacillus, for which the name Bacillus halochares sp. nov. is proposed. The type strain is MSS4(T) (=LMG 24571(T) =DSM 21373(T)). PMID: 19671720 [PubMed - indexed for MEDLINE] Bacillus halosaccharovorans Int J Syst Evol Microbiol. 2013 Aug;63(Pt 8):2776-81. doi: 10.1099/ijs.0.046961-0. Epub 2013 Jan 4. Bacillus halosaccharovorans sp. nov., a moderately halophilic bacterium from a hypersaline lake. Mehrshad M(1), Amoozegar MA, Didari M, Bagheri M, Fazeli SA, Schumann P, Spröer C, Sánchez-Porro C, Ventosa A. Author information: (1)Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of living organisms, College of Science, University of Tehran, Tehran, Iran. A novel Gram-stain-positive, moderately halophilic bacterium, designated strain E33(T), was isolated from water of the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using a polyphasic approach. Cells of strain E33(T) were motile rods and produced ellipsoidal endospores at a central or subterminal position in swollen sporangia. Strain E33(T) was a strictly aerobic bacterium, catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5-25 % (w/v), with optimum growth occurring at 5-15 % (w/v) NaCl. The optimum temperature and pH for growth were 40 °C and pH 7.5-8.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain E33(T) was shown to belong to the genus Bacillus within the phylum Firmicutes and showed the closest phylogenetic similarity with the species Bacillus niabensis 4T19(T) (99.2 %), Bacillus herbersteinensis D-1-5a(T) (97.3 %) and Bacillus litoralis SW-211(T) (97.2 %). The DNA G+C content of the type strain of the novel species was 42.6 mol%. The major cellular fatty acids of strain E33(T) were anteiso-C15 : 0 and iso-C15 : 0, and the polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids, an unknown lipid and an unknown phospholipid. The isoprenoid quinones were MK-7 (97 %), MK-6 (2 %) and MK-8 (0.5 %). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All these features confirm the placement of isolate E33(T) within the genus Bacillus. DNA-DNA hybridization experiments revealed low levels of relatedness between strain E33(T) and Bacillus niabensis IBRC-M 10590(T) (22 %), Bacillus herbersteinensis CCM 7228(T) (38 %) and Bacillus litoralis DSM 16303(T) (19 %). On the basis of polyphasic evidence from this study, a novel species of the genus Bacillus, Bacillus halosaccharovorans sp. nov. is proposed, with strain E33(T) (= IBRC-M 10095(T) = DSM 25387(T)) as the type strain. PMID: 23291894 [PubMed - indexed for MEDLINE] Bacillus hemicentroti Int J Syst Evol Microbiol. 2011 Dec;61(Pt 12):2950-5. doi: 10.1099/ijs.0.026732-0. Epub 2011 Jan 29. Bacillus hemicentroti sp. nov., a moderate halophile isolated from a sea urchin. Chen YG(1), Zhang YQ, He JW, Klenk HP, Xiao JQ, Zhu HY, Tang SK, Li WJ. Author information: (1)College of Biology and Environmental Sciences, Jishou University, Jishou, PR China. [email protected] A novel Gram-staining-positive, moderately halophilic, facultatively alkaliphilic, non-motile, catalase-positive, oxidase-negative, endospore-forming, facultatively anaerobic rod, designated JSM 076093(T), was isolated from a sea urchin (Hemicentrotus pulcherrimus) collected from Naozhou Island in the South China Sea. Growth occurred with 0.5-25% (w/v) NaCl (optimum 5-8%) and at pH 6.0-10.5 (optimum pH 8.0) and 5-40 °C (optimum 30-35 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The predominant respiratory quinone was menaquinone 7 and the polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. The major cellular fatty acids (>10% of the total) were anteiso-C(15:0), anteiso-C(17:0), iso-C(16:0) and iso-C(14:0). The genomic DNA G+C content was 38.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 076093(T) belonged to the genus Bacillus and was related most closely to Bacillus hwajinpoensis SW-72(T) (99.1% 16S rRNA gene sequence similarity) and Bacillus algicola KMM 3737(T) (97.3%). The combination of results from the phylogenetic analysis, DNA-DNA hybridization and phenotypic and chemotaxonomic characterization supported the conclusion that strain JSM 076093(T) represents a novel species of the genus Bacillus, for which the name Bacillus hemicentroti sp. nov. is proposed, with JSM 076093(T) (=DSM 23007(T)=KCTC 13710(T)) as the type strain. PMID: 21278416 [PubMed - indexed for MEDLINE] Bacillus herbersteinensis Int J Syst Evol Microbiol. 2005 Sep;55(Pt 5):2119-23. Bacillus herbersteinensis sp. nov. Wieser M(1), Worliczek H, Kämpfer P, Busse HJ. Author information: (1)Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische 23 Universität Wien, A-1210 Wien, Austria. Two bacterial strains, designated D-1,5a(T) and D-1,5b, were isolated from a medieval wall painting in the chapel of Castle Herberstein, Styria (Austria). The Gram-positive, heterotrophic, aerobic, spore-forming rods showed nearly identical whole-cell protein patterns, identical genomic fingerprints and identical physiological profiles, demonstrating their relationship at the species level. Both strains contained meso-diaminopimelic acid in their peptidoglycan, possessed a quinone system comprising menaquinone MK-7 and had fatty acid profiles in which C(15:0) iso and C(15:0) anteiso were predominant. The 16S rRNA gene sequence of D-1,5a(T) showed the highest similarity (99.5%) to the sequence of Bacillus sp. LMG 20243, and Bacillus flexus IFO 15715(T) was the next most closely related established species (96.5%). Other type strains, such as Bacillus fastidiosus DSM 91(T), Bacillus indicus SD/3(T), Bacillus cibi JG-30(T), Bacillus megaterium IAM 13418(T), Bacillus cohnii DSM 6308(T), Bacillus bataviensis LMG 21833(T) and Bacillus soli LMG 21838(T), shared 96.0-96.1% 16S rRNA gene sequence similarity with D-1,5a(T). The combination of physiological and chemotaxonomic traits distinguishes the two strains from those species sharing the highest sequence similarities (96.0-96.5%). On the basis of these characteristics and the phylogenetic position of strain D-1,5a(T) (=DSM 16534(T)=CCM 7228(T)), this strain is assigned as the type strain of a novel species of the genus Bacillus, for which the name Bacillus herbersteinensis sp. nov. is proposed. PMID: 16166719 [PubMed - indexed for MEDLINE] 82. Bacillus horneckiae Int J Syst Evol Microbiol. 2010 May;60(Pt 5):1031-7. doi: 10.1099/ijs.0.008979-0. Epub 2009 Aug 7. Bacillus horneckiae sp. nov., isolated from a spacecraft-assembly clean room. Vaishampayan P(1), Probst A, Krishnamurthi S, Ghosh S, Osman S, McDowall A, Ruckmani A, Mayilraj S, Venkateswaran K. Author information: (1)Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA. Five Gram-stain-positive, motile, aerobic strains were isolated from a clean room of the Kennedy Space Center where the Phoenix spacecraft was assembled. All strains are rod-shaped, spore-forming bacteria, whose spores were resistant to UV radiation up to 1000 J m(-2). The spores were subterminally positioned and produced an external layer. A polyphasic taxonomic study including traditional biochemical tests, fatty acid analysis, cell-wall typing, lipid analyses, 16S rRNA gene sequencing and DNA-DNA hybridization studies was performed to characterize these novel strains. 16S rRNA gene sequencing and lipid analyses convincingly grouped these novel strains within the genus Bacillus as a cluster separate from already described species. The similarity of 16S rRNA gene sequences among the novel strains was >99 %, but the similarity was only about 97 % with their nearest neighbours Bacillus pocheonensis, Bacillus firmus and Bacillus bataviensis. DNA-DNA hybridization dissociation values were <24 % to the closest related type strains. The novel strains had a G+C content 35.6+/-0.5 mol% and could liquefy gelatin but did not utilize or produce acids from any of the carbon substrates tested. The major fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0) and the cell-wall diamino acid was meso-diaminopimelic acid. Based on phylogenetic and phenotypic results, it is concluded that these strains represent a novel species of the genus Bacillus, for which the name Bacillus horneckiae sp. nov. is proposed. The type strain is 1P01SC(T) (=NRRL B-59162(T) =MTCC 9535(T)). PMID: 19666815 [PubMed - indexed for MEDLINE] 83. Bacillus horti Int J Syst Bacteriol. 1998 Apr;48 Pt 2:565-71. Bacillus horti sp. nov., a new gram-negative alkaliphilic bacillus. Yumoto I(1), Yamazaki K, Sawabe T, Nakano K, Kawasaki K, Ezura Y, Shinano H. Author information: (1)Bioscience and Chemistry Division, Hokkaido National Industrial Research Institute, Sapporo, Japan. [email protected] Erratum in Int J Syst Bacteriol 1999 Oct;49 Pt 4:1951. Novel Gram-negative alkaliphilic strains were isolated from soil obtained from Atsuma, Hokkaido, Japan. The isolates were strictly aerobic rods that produced subterminally located ellipsoidal spores. Chemotaxonomic characteristics of the isolates included the presence of meso-diaminopimelic acid in the cell wall and a DNA G + C content of 40.2-40.9 mol%. The major isoprenoid quinone was menaquinone-7 and the cellular fatty acid profile consisted of a significant amount of 15-C branched-chain acids, iso-C15:0 and anteiso-C15:0. The growth rate was higher at pH 8-10 than at pH 7. Comparative sequence analysis of 16S rDNA of 14 alkaliphilic Bacillus strains indicates that the isolated strain has an equidistant relationship to three already defined rRNA groups of alkaliphilic Bacillus species. Based on the morphological and physiological characteristics, as well as phylogenetic position as determined by 16S rDNA analysis and DNA-DNA relatedness data, it is concluded that these isolates should be designated as a new species, for which the name Bacillus horti is proposed. The type strain is K13T (= JCM 9943T). PMID: 9731298 [PubMed - indexed for MEDLINE] 84. Bacillus huizhouensis Li J(1), Yang G, Wu M, Zhao Y, Zhou S. Bacillus huizhouensis sp. nov., isolated from a paddy field soil. Antonie Van Leeuwenhoek. 2014 Aug;106(2):357-63. doi: 10.1007/s10482-014-0208-2. Epub 2014 Jun 6. Author information: (1)College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, Peoples's Republic of China. A Gram-stain positive, facultative aerobic bacterium, designated as strain GSS03(T), was isolated from a paddy field soil. The cells were observed to be endospore forming, rod-shaped and motile with flagella. The organism was found to grow optimally at 35 °C at pH 7.0 and in the presence of 1 % NaCl. The strain was classified as a novel taxon within the genus Bacillus on the basis of phenotypic and phylogenetic analyses. The closest phylogenetic relatives were identified as Bacillus psychrosaccharolyticus DSM 6(T) (97.61 %), Bacillus muralis DSM 16288(T) (97.55 %), Bacillus asahii JCM 12112(T) (97.48 %), Bacillus simplex DSM 1321(T) (97.48 %) and "Bacillus frigoritolerans" DSM 8801(T) (97.38 %). The menaquinone was identified as MK-7, the major cellular fatty acid was identified as anteiso-C15:0 and the major cellular polar lipids as phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and three unknown polar lipids. The DNA G+C content was determined to be 40.2 mol%. The DNA-DNA relatedness with the closest relatives was below 48 %. Therefore, on the basis of all the results, strain 24 85. 86. 87. 88. GSS03(T) is considered to represent a novel species within the genus Bacillus, for which the name Bacillus huizhouensis sp. nov. is proposed. The type strain is GSS03(T) (=KCTC 33172(T) =CCTCC AB 2013237(T)). PMID: 24903955 [PubMed - in process] Bacillus hunanensis Antonie Van Leeuwenhoek. 2011 Mar;99(3):481-8. doi: 10.1007/s10482-010-9512-7. Epub 2010 Sep 26. Bacillus hunanensis sp. nov., a slightly halophilic bacterium isolated from non-saline forest soil. Chen YG(1), Hao DF, Chen QH, Zhang YQ, Liu JB, He JW, Tang SK, Li WJ. Author information: (1)Key Laboratory of Ecotourism's Application Technology of Hunan Province, College of Biology and Environmental Sciences, Jishou University, 416000 Jishou, People's Republic of China. [email protected] A novel Gram-stain-positive, slightly halophilic, catalase- and oxidase-positive, endospore-forming, motile, aerobic, rod-shaped bacterium, designated strain JSM 081003(T), was isolated from non-saline forest soil in Hunan Province, China. Growth occurred with 0.5-15% (w/v) NaCl (optimum 2-4%) at pH 6.5-10.5 (optimum pH 7.5-8.5) and at 5-40 °C (optimum 30 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were iso-C15:0, anteiso-C15:0 and iso-C14:0. Strain JSM 081003(T) contained MK-7 as the predominant respiratory quinone, and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genomic DNA G + C content of strain JSM 081003(T) was 40.9 mol%. A phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 081003(T) should be assigned to the genus Bacillus, and was related most closely to the type strains of Bacillus lehensis (sequence similarity 99.6%), Bacillus oshimensis (99.4%) and Bacillus patagoniensis (96.6%); lower than 96.0% sequence similarity was observed with other Bacillus species. The combination of phylogenetic analysis, DNA-DNA relatedness values, phenotypic characteristics and chemotaxonomic data supports the view that strain JSM 081003(T) represents a new species of the genus Bacillus, for which the name Bacillus hunanensis sp. nov. is proposed. The type strain is JSM 081003(T) (= DSM 23008(T) = KCTC 13711(T)). PMID: 20872176 [PubMed - indexed for MEDLINE] Bacillus hwajinpoensis Int J Syst Evol Microbiol. 2004 May;54(Pt 3):803-8. Bacillus hwajinpoensis sp. nov. and an unnamed Bacillus genomospecies, novel members of Bacillus rRNA group 6 isolated from sea water of the East Sea and the Yellow Sea in Korea. Yoon JH(1), Kim IG, Kang KH, Oh TK, Park YH. Author information: (1)Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea. Two Gram-positive or -variable, endospore-forming, slightly halophilic strains (SW-72(T) and SW-93) were isolated from sea water of the East Sea and the Yellow Sea in Korea, respectively, and subjected to polyphasic taxonomic study. Both strains had cell-wall peptidoglycan that was based on meso-diaminopimelic acid and MK-7 as the predominant menaquinone. The two strains contained large amounts of saturated and branched fatty acids, with anteiso-C(15 : 0) as the major fatty acid. The DNA G+C contents of strains SW-72(T) and SW-93 were 40.9 and 41.0 mol%, respectively. Phylogenetic analysis based on 16S rDNA sequences showed that strains SW-72(T) and SW-93 fall within the radiation of the cluster that comprises members of the genus Bacillus, particularly Bacillus rRNA group 6. There were five nucleotide differences between the 16S rDNA sequences of strains SW-72(T) and SW-93. The mean level of DNA-DNA relatedness between strains SW-72(T) and SW-93 was 21.5 %. Strains SW-72(T) and SW-93 showed 93.1-95.2 % 16S rDNA sequence similarity to the type strains of Bacillus species that are assigned to rRNA group 6. Strains SW-72(T) and SW-93 could not be differentiated clearly by using their phenotypic properties. On the basis of phenotypic properties, phylogeny and genomic data, it is proposed that strain SW-72(T) (=KCCM 41641(T)=JCM 11807(T)) should be placed in the genus Bacillus as the type strain of a novel species, Bacillus hwajinpoensis sp. nov., and that strain SW-93 (=KCCM 41640=JCM 11806) should be placed in the genus Bacillus as an unnamed Bacillus genomospecies. PMID: 15143027 [PubMed - indexed for MEDLINE] Bacillus indicus Int J Syst Evol Microbiol. 2004 Jul;54(Pt 4):1369-75. Bacillus indicus sp. nov., an arsenic-resistant bacterium isolated from an aquifer in West Bengal, India. Suresh K(1), Prabagaran SR, Sengupta S, Shivaji S. Author information: (1)Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, India. Strain Sd/3T (=MTCC 4374T=DSM 15820T), an arsenic-resistant bacterium, was isolated from a sand sample obtained from an arsenic-contaminated aquifer in Chakdah district in West Bengal, India (23 degrees 3' N 88 degrees 35' E). The bacterium was Gram-positive, rod-shaped, non-motile, endospore-forming and yellowish-orange pigmented. It possessed all the characteristics that conform to the genus Bacillus, such as it had A4beta murein type (L-orn-D-Asp) peptidoglycan variant, MK-7 as the major menaquinone and iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. Based on its chemotaxonomic and phylogenetic characteristics, strain Sd/3T was identified as a species of the genus Bacillus. It exhibited maximum similarity (95%) at the 16S rRNA gene level with Bacillus cohnii; however, DNA-DNA similarity with B. cohnii was 60.7%. Strain Sd/3T also exhibited a number of phenotypic differences from B. cohnii (DSM 6307T). These data suggest that Sd/3T represents a novel species of the genus Bacillus. The name Bacillus indicus sp. nov. is proposed. PMID: 15280316 [PubMed indexed for MEDLINE] Bacillus infantis Int J Syst Evol Microbiol. 2006 Nov;56(Pt 11):2541-4. Bacillus infantis sp. nov. and Bacillus idriensis sp. nov., isolated from a patient with neonatal sepsis. Ko KS(1), Oh WS, Lee MY, Lee JH, Lee H, Peck KR, Lee NY, Song JH. Author information: (1)Asian-Pacific Research Foundation for Infectious Diseases (ARFID), Seoul 135-710, Korea. Two Gram-positive bacilli, designated as strains SMC 4352-1T and SMC 4352-2T, were isolated sequentially from the blood of a newborn child with sepsis. They could not be identified by using conventional clinical microbiological methods. 16S rRNA gene sequencing and phylogenetic analysis revealed that both strains belonged to the genus Bacillus but clearly diverged from known Bacillus species. Strain SMC 4352-1T and strain 25 SMC 4352-2T were found to be closely related to Bacillus firmus NCIMB 9366T (98.2% sequence similarity) and Bacillus cibi JG-30T (97.1% sequence similarity), respectively. They also displayed low DNA-DNA reassociation values (less than 40%) with respect to the most closely related Bacillus species. On the basis of their polyphasic characteristics, strain SMC 4352-1T and strain SMC 4352-2T represent two novel species of the genus Bacillus, for which the names Bacillus infantis sp. nov. (type strain SMC 4352-1T=KCCM 90025T=JCM 13438T) and Bacillus idriensis sp. nov. (type strain SMC 4352-2T=KCCM 90024T=JCM 13437T) are proposed. PMID: 17082387 [PubMed - indexed for MEDLINE] 89. Bacillus infernus Int J Syst Bacteriol. 1995 Jul;45(3):441-8. Bacillus infernus sp. nov., an Fe(III)- and Mn(IV)-reducing anaerobe from the deep terrestrial subsurface. Boone DR(1), Liu Y, Zhao ZJ, Balkwill DL, Drake GR, Stevens TO, Aldrich HC. Author information: (1)Department of Environmental Science and Engineering, Oregon Graduate Institute of Science & Technology, Portland 97291-1000, USA. Bacillus infernus sp. nov. was isolated from ca. 2,700 m below the land surface in the Taylorsville Triassic Basin in Virginia. B. infernus was a strict anaerobe that grew on formate or lactate with Fe(III), MnO2, trimethylamine oxide, or nitrate (reduced to nitrite) as an electron acceptor, and it also grew fermentatively on glucose. Type strain TH-23 and five reference strains were gram-positive rods that were thermophilic (growth occurred at 61 degrees C), halotolerant (good growth occurred in the presence of Na+ concentrations up to 0.6 M), and very slightly alkaliphilic (good growth occurred at pH 7.3 to 7.8). A phylogenetic analysis of its 16S rRNA indicated that B. infernus should be classified as a new species of the genus Bacillus. B. infernus is the only strictly anaerobic species in the genus Bacillus. PMID: 8590670 [PubMed - indexed for MEDLINE] 90. Bacillus iranensis Int J Syst Evol Microbiol. 2012 Apr;62(Pt 4):811-6. doi: 10.1099/ijs.0.030874-0. Epub 2011 May 13. Bacillus iranensis sp. nov., a moderate halophile from a hypersaline lake. Bagheri M(1), Didari M, Amoozegar MA, Schumann P, Sánchez-Porro C, Mehrshad M, Ventosa A. Author information: (1)Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Teheran, Iran. A Gram-positive, moderately halophilic rod, designated X5BT, was isolated from saline mud of the hypersaline lake Aran-Bidgol in Iran. Strain X5BT was a strictly aerobic, motile bacterium that produced ellipsoidal endospores at a central-subterminal position in non-swollen sporangia. The isolate grew at pH 7.0-10.0 (optimum pH 7.5), at 25-45 °C (optimum 35 °C) and with 2.5-15 % (w/v) NaCl (optimum 5-7.5 %). On the basis of 16S rRNA gene sequences, strain X5BT belonged to the genus Bacillus and showed highest similarity with Bacillus persepolensis HS136T (95.6 % 16S rRNA gene sequence similarity) and Bacillus salarius BH169T (95.5 %). The DNA G+C content was 42.4 mol%. The major cellular fatty acids were anteiso-C15:0 and iso-C15:0 and the polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, three phospholipids and two glycolipids. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid and the isoprenoid quinones were MK-7 (92 %), MK-6 (6 %) and MK-5 (2 %). On the basis of phylogenetic, chemotaxonomic and phenotypic data, a novel species of the genus Bacillus is proposed, with the name Bacillus iranensis sp. nov. The type strain is X5BT (=IBRC 10446T=DSM 23995T). PMID: 21571930 [PubMed - indexed for MEDLINE] 91. Bacillus isabeliae Int J Syst Evol Microbiol. 2008 Jan;58(Pt 1):226-30. doi: 10.1099/ijs.0.65217-0. Bacillus isabeliae sp. nov., a halophilic bacterium isolated from a sea salt evaporation pond. Albuquerque L(1), Tiago I, Taborda M, Nobre MF, Veríssimo A, da Costa MS. Author information: (1)Centro de Neurociências e Biologia Celular, Department of Zoology, University of Coimbra, 3004-517 Coimbra, Portugal. A low-G+C, Gram-positive isolate, designated strain CVS-8(T), was isolated from a sea salt evaporation pond on the Island of Sal in the Cape Verde Archipelago. This organism was found to be a catalase- and oxidase-positive, non-motile, spore-forming, aerobic, curved rod-shaped organism with an optimum growth temperature of about 35-37 degrees C and an optimum pH between 7.5 and 8.0. Optimal growth occurred in media containing 4-6% (w/v) NaCl and no growth occurred in medium without NaCl. The cell-wall peptidoglycan was of the A1gamma type with meso-diaminopimelic acid, the major respiratory quinone was MK-7, the major fatty acids were iso-15:0, 16:0, anteiso-15:0 and iso-16:0 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminoglycophospholipid. The G+C content of the DNA was 37.9 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain CVS-8(T) represented a novel species of the genus Bacillus, the highest levels of sequence similarity (mean pairwise similarity values of approximately 97.5 %) being found with respect to the type strains of Bacillus shackletonii and Bacillus acidicola. On the basis of the phylogenetic, physiological and biochemical data, strain CVS-8(T) represents a novel species of the genus Bacillus, for which the name Bacillus isabeliae sp. nov. is proposed. The type strain is CVS-8(T) (=LMG 22838(T)=CIP 108578(T)). PMID: 18175713 [PubMed - indexed for MEDLINE] 92. Bacillus jeotgali Int J Syst Evol Microbiol. 2001 May;51(Pt 3):1087-92. Bacillus jeotgali sp. nov., isolated from jeotgal, Korean traditional fermented seafood. Yoon JH(1), Kang SS, Lee KC, Kho YH, Choi SH, Kang KH, Park YH. Author information: (1)Korea Research Institute of Biosciences and Biotechnology (KRIBB), Yusong, Taejon. Two Gram-variable, rod-shaped, endospore-forming bacterial strains, which are motile with peritrichous flagella, were isolated from a Korean traditional fermented seafood, jeotgal. The two isolates (strains YKJ-1OT and YKJ-11) were proven to be members of the same species on the basis of the results of phenotypic and phylogenetic analyses and DNA relatedness. Strains YKJ-10T and YKJ-11 were characterized by having cell wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as the predominant menaquinone, and iso-C15:0 as the major fatty acid. The G+C content of the DNA was 41 mol%. Strains YKJ-10T and YKJ-11 showed only a 1 bp sequence difference in the 16S rDNA sequences. The two strains formed distinct phylogenetic lineages within the radiation of the cluster comprising Bacillus species. Levels of 16S 26 rDNA similarity between strains YKJ-10T and YKJ-11 and Bacillus species were less than 96.6%. Levels of DNA-DNA relatedness were found to be low enough to distinguish strains YKJ-10T and YKJ-11 from some phylogenetically related Bacillus species. On the basis of phenotypic properties, phylogeny and genomic distinctiveness, strains YKJ-10T and YKJ-11 represent a new species of the genus Bacillus, for which a new name, Bacillusjeotgali sp. nov., is proposed. The type strain of the new species is strain YKJ-10T (= KCCM 41040T = JCM 10885T). PMID: 11411677 [PubMed - indexed for MEDLINE] 93. Bacillus kochii Int J Syst Evol Microbiol. 2012 May;62(Pt 5):1092-7. doi: 10.1099/ijs.0.027771-0. Epub 2011 Jun 24. Bacillus kochii sp. nov., isolated from foods and a pharmaceuticals manufacturing site. Seiler H(1), Schmidt V, Wenning M, Scherer S. Author information: (1)Department of Microbiology (ZIEL), Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany. [email protected] Three Gram-staining-positive, strictly aerobic, motile, catalase-positive, endospore-forming rods, designated WCC 4582(T), WCC 4581 and WCC 4583, were isolated from two different food sources and a pharmaceuticals production site. The three isolates were highly similar in their 16S rRNA gene sequences (100 % similarity) and groEL sequences (99.2-100 % similarity), Fourier-transform infrared spectroscopic fingerprints and other features tested. The isolates were most closely related to Bacillus horneckiae; the isolates and the type strain of B. horneckiae shared 97.6 % and 89.6 % 16S rRNA gene and groEL sequence similarities, respectively. The organisms grew optimally at 30 °C, at pH 7 and in the presence of 0.5 % (w/v) NaCl. The cell-wall peptidoglycan of WCC 4582(T) contained meso-diaminopimelic acid (A1γ) and the genomic DNA G+C content was 36.4 mol%. DNA-DNA relatedness between strain WCC 4582(T) and B. horneckiae NRRL B-59162(T) was 17 %. The three isolates are considered to represent a novel species of the genus Bacillus, for which the name Bacillus kochii sp. nov. is proposed. The type strain is WCC 4582(T) ( = DSM 23667(T) = CCUG 59877(T) = LMG 25855(T)). PMID: 21705449 [PubMed - indexed for MEDLINE] 94. Bacillus kokeshiiformis Poudel P(1), Miyamoto H(2), Miyamoto H(3), Okugawa Y(1), Tashiro Y(1), Sakai K(4). Thermotolerant Bacillus kokeshiiformis sp. nov. isolated from marine animal resources compost. Int J Syst Evol Microbiol. 2014 May 16. pii: ijs.0.059329-0. doi: 10.1099/ijs.0.059329-0. [Epub ahead of print] Author information: (1)Laboratory of Soil Microbiology, Kyushu University, Japan; (2)Japan Eco-science Co. Ltd., Japan; (3)Oita Miroku Co.Ltd., Japan. (4)Laboratory of Soil Microbiology, Kyushu University, Japan; [email protected]. A novel Gram-staining positive, endospore forming rod-shaped, facultatively anaerobic, thermotolerant bacterium, designated strain MO-04(T), was isolated from a marine animal resources (MAR) compost. The 16S rRNA gene sequence of strain MO-04(T) showed 99.4% similarity with Bacillus thermolactis R-6488(T),94.1% similarity with Bacillus thermoamylovorans CNCM I-1378(T), 93.3% similarity with B. humi LMG 22167(T), and 93.2% similarity with B. niacini IFO 15566(T) and others were < 93%. DNA-DNA relatedness between strain MO-04(T) and B. thermolactis DSM 23332(T) was 45%. The DNA G+C content of strain MO-04(T) was 33.4 mol%, comparatively lower than that of B. thermolactis R-6488(T) (35.0 mol%). Strain MO-04(T) grew at 35-61°C (optimum 50°C), pH 4.5-9.0 (optimum 7.2), and tolerated up to 8.0% (w/v) NaCl (optimum 2%). The MO-04(T) cell wall peptidoglycan type was meso 2,6-diaminopimelic acid, and the major fatty acids were C16:1, C14:1, C17:0 and C17:1. The major polar lipids were represented by diphosphatidylglycerol and phosphatidylglycerol, and two unidentified phospholipids. The analyzed polyphasic data presented here clearly indicate that the isolate MO-04(T) is considered to be a novel species within the genus Bacillus for which the name Bacillus kokeshiiformis sp. nov. is proposed. The type strain of B. kokeshiiformis is MO-04(T) (= JCM 19325(T) = KCTC 33163(T)). Copyright © 2014, the Society for General Microbiology. PMID: 24835163 [PubMed - as supplied by publisher] 95. Bacillus koreensis Int J Syst Evol Microbiol. 2006 Jan;56(Pt 1):59-63. Bacillus koreensis sp. nov., a spore-forming bacterium, isolated from the rhizosphere of willow roots in Korea. Lim JM(1), Jeon CO, Lee JC, Ju YJ, Park DJ, Kim CJ. Author information: (1)Korea Research Institute of Bioscience and Biotechnology, 52 Oeundong, Yusong, Daejeon 305-333, Republic of Korea. An endospore-forming, rod-shaped bacterium was isolated from the rhizosphere of willow roots in Korea. The bacterium, designated strain BR030T, was a strictly aerobic, motile rod. The cell wall contained type A1gamma peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0), iso-C(14 : 0) and iso-C(16 : 0). The major cellular phospholipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and unknown phospholipids (PL1, PL2). The genomic DNA G+C content was 36 mol%. Comparative 16S rRNA gene sequence analyses showed that strain BR030T formed a distinct phyletic line within the genus Bacillus and was most closely related to Bacillus flexus DSM 1320T, with 16S rRNA gene sequence similarity of 96.8 %. Sequence similarities to other type strains were lower than 96.2 %. On the basis of physiological and molecular properties, the isolate represents a novel species within the genus Bacillus, for which the name Bacillus koreensis sp. nov. is proposed. The type strain is BR030T (= KCTC 3914T = DSM 16467T). PMID: 16403867 [PubMed - indexed for MEDLINE] 96. Bacillus korlensis Int J Syst Evol Microbiol. 2009 Jul;59(Pt 7):1787-92. doi: 10.1099/ijs.0.004879-0. Epub 2009 Jun 19. Bacillus korlensis sp. nov., a moderately halotolerant bacterium isolated from a sand soil sample in China. Zhang L(1), Wang Y, Dai J, Tang Y, Yang Q, Luo X, Fang C. Author information: (1)College of Life Sciences, Wuhan University, Wuhan 430072, PR China. A Gram-positive-staining, rod-shaped, motile, spore-forming and moderately halotolerant bacterium, designated ZLC-26(T), was isolated from a sand soil sample collected from Xinjiang Province, China, and was characterized by using a polyphasic taxonomic approach. This isolate grew optimally at 30-37 degrees C and pH 7-8. It grew with 0-8% NaCl (optimum, 0-2 %). Comparative 16S 27 rRNA gene sequence analysis showed that strain ZLC-26(T) was closely related to members of the genus Bacillus, exhibiting the highest 16S rRNA gene sequence similarities to Bacillus nealsonii DSM 15077(T) (97.1 %), B. shackletonii LMG 18435(T) (97.0 %), B. siralis 171544(T) (97.0 %), B. circulans IAM 12462(T) (96.7 %) and B. pocheonensis Gsoil 420(T) (96.7 %). Strain ZLC-26(T) contained MK-7 as the predominant menaquinone. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major cellular fatty acids were iso-C(15 : 0), C(16 : 1)omega11c and anteiso-C(15 : 0). The DNA G+C content was 38.2 mol%. These chemotaxonomic results supported the affiliation of strain ZLC-26(T) to the genus Bacillus. However, low DNA-DNA relatedness values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain ZLC-26(T) from recognized Bacillus species. On the basis of the evidence presented, strain ZLC-26(T) is considered to represent a novel species of the genus Bacillus, for which the name Bacillus korlensis sp. nov. is proposed. The type strain is ZLC-26(T) (=CCTCC AB 207172(T)=NRRL B-51302(T)). PMID: 19542113 [PubMed - indexed for MEDLINE] 201. Extremophiles. 2009 Jul;13(4):695-705. doi: 10.1007/s00792-009-0257-z. Epub 2009 Jun 18. Enrichment and isolation of Bacillus beveridgei sp. nov., a facultative anaerobic haloalkaliphile from Mono Lake, California, that respires oxyanions of tellurium, selenium, and arsenic. Baesman SM(1), Stolz JF, Kulp TR, Oremland RS. Author information: (1)U.S. Geological Survey, Menlo Park, CA 94025, USA. Mono Lake sediment slurries incubated with lactate and tellurite [Te(IV)] turned progressively black with time because of the precipitation of elemental tellurium [Te(0)]. An enrichment culture was established from these slurries that demonstrated Te(IV)-dependent growth. The enrichment was purified by picking isolated black colonies from lactate/Te(IV) agar plates, followed by repeated streaking and picking. The isolate, strain MLTeJB, grew in aqueous Te(IV)-medium if provided with a small amount of sterile solid phase material (e.g., agar plug; glass beads). Strain MLTeJB grew at high concentrations of Te(IV) (~8 mM) by oxidizing lactate to acetate plus formate, while reducing Te(IV) to Te(0). Other electron acceptors that were found to sustain growth were tellurate, selenate, selenite, arsenate, nitrate, nitrite, fumarate and oxygen. Notably, growth on arsenate, nitrate, nitrite and fumarate did not result in the accumulation of formate, implying that in these cases lactate was oxidized to acetate plus CO(2). Strain MLTeJB is a low G + C Gram positive motile rod with pH, sodium, and temperature growth optima at 8.5-9.0, 0.5-1.5 M, and 40 degrees C, respectively. The epithet Bacillus beveridgei strain MLTeJB(T) is proposed. PMID: 19536453 [PubMed - indexed for MEDLINE] 97. Bacillus kribbensis Int J Syst Evol Microbiol. 2007 Dec;57(Pt 12):2912-6. Bacillus kribbensis sp. nov., isolated from a soil sample in Jeju, Korea. Lim JM(1), Jeon CO, Lee JR, Park DJ, Kim CJ. Author information: (1)Functional Metabolomics Research Center, KRIBB, Daejeon 305-806, Korea. A Gram-positive, endospore-forming bacterium, designated strain BT080(T), was isolated from a soil sample in Jeju, Korea. Cells of the isolate were strictly aerobic rods that were motile by means of peritrichous flagella. The strain grew optimally at 30-33 degrees C and pH 5.5-6.5. Chemotaxonomic data (major isoprenoid quinone, MK-7; DNA G+C content, 43.3 mol%; major fatty acids, anteiso-C(15 : 0), iso-C(14 : 0), iso-C(16 : 0) and iso-C(15 : 0)) supported the affiliation of the isolate to the genus Bacillus. Comparative 16S rRNA gene sequence analyses showed that strain BT080(T) formed a distinct phyletic line within the genus Bacillus. The levels of 16S rRNA gene sequence similarity with respect to related Bacillus species were below 96.4 %. On the basis of physiological, biochemical and phylogenetic properties, strain BT080(T) represents a novel species within the genus Bacillus, for which the name Bacillus kribbensis sp. nov. is proposed. The type strain is BT080(T) (=KCTC 13934(T)=DSM 17871(T)). PMID: 18048748 [PubMed - indexed for MEDLINE] 98. Bacillus krulwichiae Int J Syst Evol Microbiol. 2003 Sep;53(Pt 5):1531-6. Bacillus krulwichiae sp. nov., a halotolerant obligate alkaliphile that utilizes benzoate and m-hydroxybenzoate. Yumoto I(1), Yamaga S, Sogabe Y, Nodasaka Y, Matsuyama H, Nakajima K, Suemori A. Author information: (1)Institute of Biological Resources and Function, Hokkaido Center, National Institute of Advanced Industrial Science and Technology, Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan. [email protected] Obligate alkaliphilic strains, AM31D(T) and AM11D, that utilize benzoate and m-hydroxybenzoate were isolated from soil obtained from Tsukuba, Ibaraki, Japan. The isolates grew at pH 8-10, but not at neutral pH. They were Gram-positive, facultatively anaerobic, straight rods with peritrichous flagella and produced ellipsoidal spores. The isolates reduced nitrate to nitrite and grew in 0-14 % NaCl, but not in higher concentrations. The major isoprenoid quinones were menaquinone-5, -6 and -7, and the cellular fatty acid profile consisted of significant amounts of 15-C branched-chain acids, isoC(15 : 0) and anteisoC(15 : 0). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain AM31D(T) was a member of group 6 (alkaliphiles) in the genus Bacillus. DNA-DNA hybridization revealed a low relatedness of the isolates with several phylogenetically close neighbours, including Bacillus alcalophilus and Bacillus pseudalcaliphilus (less than 19.3 %). Based on phenotypic characteristics, phylogenetic data and DNA-DNA relatedness data, it was concluded that these isolates merited classification as a new species, for which the name Bacillus krulwichiae is proposed. The type strain of this species is AM31D(T) (=NCIMB 13904(T)=JCM 11691(T)=IAM 15000(T)). PMID: 13130043 [PubMed - indexed for MEDLINE] 99. Bacillus kyonggiensis J Microbiol. 2011 Oct;49(5):776-81. doi: 10.1007/s12275-011-1218-7. Epub 2011 Nov 9. Bacillus kyonggiensis sp. nov., isolated from soil of a lettuce field. Dong K(1), Lee S. Author information: (1)Department of Bioengineering, Granduate School of Kyonggi University, Suwon, 443-760, Republic of Korea. A Gram-positive, rod-shaped, motile, endospore-forming bacterial strain, designated NB22(T), was isolated from soil of a lettuce field in Kyonggi province, South Korea, and was characterized by using a polyphasic taxonomic approach. This novel isolate grew optimally at 30-37°C and pH 8-9. It grew in the presence of 0-4% 28 NaCl (optimum, 1-2%). Comparative 16S rRNA gene sequence analysis showed that strain NB22(T) was closely related to members of the genus Bacillus and fell within a coherent cluster comprising B. siralis 171544(T) (98.1%) and B. korlensis ZLC-26(T) (97.3%). The levels of 16S rRNA gene sequence similarity with respect to other Bacillus species with validly published names were less than 96.4%. Strain NB22(T) had a genomic DNA G+C content of 36.3 mol% and the predominant respiratory quinone was MK-7. The peptidoglycan contained meso-diaminopimelic acid. The major cellular fatty acids were iso-C(15:0), anteiso-C(15:0), C(14:0), and C(16:0). These chemotaxonomic results supported the affiliation of strain NB22(T) to the genus Bacillus, and the low DNA-DNA relatedness values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain NB22(T) from recognized Bacillus species. On the basis of the evidence presented, strain NB22(T) is considered to represent a novel species of the genus Bacillus, for which the name Bacillus kyonggiensis sp. nov. is proposed. The type strain is NB22(T) (=KEMB 5401-267(T) =JCM 17569(T)). PMID: 22068494 [PubMed - indexed for MEDLINE] 100. Bacillus lehensis Int J Syst Evol Microbiol. 2007 Feb;57(Pt 2):238-42. Bacillus lehensis sp. nov., an alkalitolerant bacterium isolated from soil. Ghosh A(1), Bhardwaj M, Satyanarayana T, Khurana M, Mayilraj S, Jain RK. Author information: (1)Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India. A Gram-positive, endospore-forming, alkalitolerant bacterial strain, designated MLB2T, was isolated from soil from Leh, India, and was subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genus Bacillus. Growth was observed at pH 7.0-11.0, but not at pH 6.0. The DNA G+C content was 41.4 mol%. The highest level of 16S rRNA gene sequence similarity was with Bacillus oshimensis JCM 12663T (98.8 %). However, DNA-DNA hybridization experiments indicated low levels of genomic relatedness with the type strains of B. oshimensis (62 %), Bacillus patagoniensis (55 %), Bacillus clausii (51 %) and Bacillus gibsonii (34 %), the species with which strain MLB2T formed a coherent cluster (based on the results of the phylogenetic analysis). On the basis of the phenotypic characteristics and genotypic distinctiveness of strain MLB2T, it should be classified within a novel species of Bacillus, for which the name Bacillus lehensis sp. nov. is proposed. The type strain is MLB2T (=MTCC 7633T=JCM 13820T). PMID: 17267957 [PubMed - indexed for MEDLINE] 101. Bacillus ligniniphilus Int J Syst Evol Microbiol. 2014 May;64(Pt 5):1712-7. doi: 10.1099/ ijs. 0.058610-0. Epub 2014 Feb 19. Bacillus ligniniphilus sp. nov., an alkaliphilic and halotolerant bacterium isolated from sediments of the South China Sea. Zhu D(1), Tanabe SH, Xie C, Honda D, Sun J, Ai L. Author information: (1)State Key Laboratory of Dairy Biotechnology, Technology Center of Bright Dairy & Food Co. Ltd, Shanghai 200436, PR China. An alkaliphilic and halotolerant Gram-stain-positive bacterium, which was isolated from sediment samples from the South China Sea, was subjected to a taxonomic study. The isolate, strain L1T, grew well at a wide range of temperatures and pH values, 10.0-45.0 °C and pH 6-11, with optima at 30 °C and pH 9.0, respectively. The growth of strain L1T occurred at total salt concentrations of 0-10% (w/v) with an optimum at 2% (w/v). Phylogenetic analysis based on 16S rRNA sequence comparison indicated that the isolate represented a member of the genus Bacillus. The strains most closely related to strain L1T were Bacillus nanhaiisediminis JCM 16507T, Bacillus halodurans DSM 497T and Bacillus pseudofirmus DSM 8715T, with 16S rRNA similarities of 96.5%, 95.9% and 95.7%, respectively. DNA-DNA hybridization of strain L1T with the type strains of the most closely related species, B. nanhaiisediminis JCM 16507T, B. halodurans DSM 497T and B. pseudofirmus DSM 8715T, showed reassociation values of about 21.7%, 14.3% and 13.9%, respectively. The DNA G+C content of strain L1T was 40.76 mol%. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant cellular fatty acids of strain L1T were iso-C14 : 0 and anteiso-C15:0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on the phenotypic and phylogenetic characteristics, it is proposed that strain L1T (=JCM 18543T=DSM 26145T) should be classified as the type strain of Bacillus ligniniphilus sp. nov. PMID: 24554634 [PubMed - indexed for MEDLINE]$$ 102. Bacillus litoralis Int J Syst Evol Microbiol. 2005 Sep;55(Pt 5):1945-8. Bacillus litoralis sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Yoon JH(1), Oh TK. Author information: (1)Korea Research Institute of Bioscience and Biotechnolog, Yusong, Taejon, South Korea. [email protected] A Gram-variable, motile, endospore-forming, slightly halophilic bacterial strain, designated SW-211(T), was isolated from a tidal flat of the Yellow Sea in Korea, and was characterized taxonomically by using a polyphasic approach. The organism grew optimally at 37 degrees C and in the presence of 2-3% NaCl. Comparative 16S rRNA gene sequence analysis showed that strain SW-211(T) forms a distinct phylogenetic lineage within the radiation of the cluster comprising Bacillus species. Strain SW-211(T) had cell-wall peptidoglycan based on meso-diaminopimelic acid. The predominant menaquinone was MK-7 and the major fatty acids were anteiso-C(15:0) (34.8%), iso-C(15:0) (15.6%), iso-C(16:0) (12.5%) and iso-C(14:0) (10.0%). The DNA G+C content was 35.2 mol%. Strain SW-211(T) exhibited levels of 16S rRNA gene sequence similarity of <96.2% with respect to the type strains of recognized Bacillus species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain SW-211(T) (=KCTC 3898(T)=DSM 16303(T)) was classified in the genus Bacillus as the type strain of a novel species, for which the name Bacillus litoralis sp. nov. is proposed. PMID: 16166692 [PubMed - indexed for MEDLINE] 103. Bacillus locisalis Syst Appl Microbiol. 2011 Sep;34(6):424-8. doi: 10.1016/j.syapm.2011.04.003. Epub 2011 Jul 29. Bacillus locisalis sp. nov., a new haloalkaliphilic species from hypersaline and alkaline lakes of China, Kenya and Tanzania. Márquez MC(1), Carrasco IJ, de la Haba RR, Jones BE, Grant WD, Ventosa A. Author information: (1)Department of Microbiology and Parasitology, Faculty of 29 Pharmacy, University of Sevilla, 41012 Sevilla, Spain. [email protected] A polyphasic taxonomic study was performed on seven Bacillus-like bacteria isolated from three hypersaline and alkaline lakes located in China, Kenya and Tanzania. All strains were moderately halophilic and alkaliphilic, Gram positive, motile rods. The DNA G+C content from the seven isolates ranged from 42.2 to 43.4mol% and their major fatty acid was anteiso-C(15:0). Strain CG1(T), selected as representative strain of the isolates, possesses meso-diaminopimelic acid in the cell wall peptidoglycan, MK-7 as the predominant menaquinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. Comparative 16S rRNA gene sequence analysis indicated that the isolates belonged to the genus Bacillus. The seven isolates shared 97.7-99.9% 16S rRNA gene sequence similarity, and formed a branch that was distinct from the type strains of the recognized species of the genus Bacillus. They were most closely related to Bacillus agaradhaerens DSM 8721(T) (92.6-93.8% 16S rRNA sequence similarity). DNA-DNA hybridization values between the seven isolates were 85-100%. According to the polyphasic characterization, the strains represent a novel species, for which the name Bacillus locisalis sp. nov. is proposed. The type strain is CG1(T) (CCM 7370(T)=CECT 7152(T)=CGMCC 1.6286(T)=DSM 18085(T)). Copyright © 2011 Elsevier GmbH. All rights reserved. PMID: 21640538 [PubMed - indexed for MEDLINE] 104. Bacillus luciferensis Int J Syst Evol Microbiol. 2002 Nov;52(Pt 6):1985-9. Bacillus luciferensis sp. nov., from volcanic soil on Candlemas Island, South Sandwich archipelago. Logan NA(1), Lebbe L, Verhelst A, Goris J, Forsyth G, Rodriguez-Diaz M, Heyndrickx M, De Vos P. Author information: (1)School of Biological and Biomedical Sciences, Glasgow Caledonian University, Cowcaddens Road, Glasgow G4 0BA, UK. [email protected] Aerobic, endospore-forming bacteria were found in soil taken from an active fumarole on Lucifer Hill, Candlemas Island, South Sandwich archipelago. Amplified rDNA restriction analysis, SDS-PAGE, repetitive element primed-PCR (rep-PCR) and routine phenotypic tests suggested that six of the isolates represent a novel taxon, and 16S rDNA sequence comparisons support the proposal of a novel species, Bacillus luciferensis sp. nov., the type strain of which is strain LMG 18422(T) (= CIP 107105(T)). PMID: 12508857 [PubMed - indexed for MEDLINE] 105. Bacillus luteolus Int J Syst Evol Microbiol. 2011 Jun;61(Pt 6):1344-9. doi: 10.1099/ijs.0.021683-0. Epub 2010 Jun 28. Bacillus luteolus sp. nov., a halotolerant bacterium isolated from a salt field. Shi R(1), Yin M, Tang SK, Lee JC, Park DJ, Zhang YJ, Kim CJ, Li WJ. Author information: (1)The Key Laboratory for Microbial Resources of the Ministry of Education, PR China, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China. A novel Gram-stain-positive, motile, strictly aerobic bacterium, designated YIM 93174(T), was isolated from a salt field in Korea. Cells of this strain were rod-shaped and formed pale tangerine colonies and grew at pH 6.0-8.0 (optimal growth at pH 7.0), at 15-45 °C (optimum 28-37 °C) and at salinities of 0-10 % (w/v) NaCl (optimum 0-2 % NaCl). Some phenotypic characters allowed differentiation of strain YIM 93174(T) from its nearest phylogenetic relatives. Comparative 16S rRNA gene sequence analysis showed that strain YIM 93174(T) belongs to the genus Bacillus, exhibiting the highest level of sequence similarity with the type strain of Bacillus humi (95.7 %), followed by those of Bacillus alkalitelluris (94.9 %) and Bacillus litoralis (94.5 %). The major fatty acids were iso-C(15 : 0), anteiso-C(15 : 0) and iso-C(16 : 0). The cell-wall peptidoglycan was of the A1γ type, containing meso-diaminopimelic acid as the diagnostic diamino acid. The genomic DNA G+C content was 36.9 mol% and the predominant respiratory quinone was MK-7. The major polar lipids of strain YIM 93174(T) were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and two unknown phospholipids. On the basis of the evidence from this polyphasic study, strain YIM 93174(T) represents a novel species of the genus Bacillus, for which the name Bacillus luteolus sp. nov. is proposed, with YIM 93174(T) ( = DSM 22388(T) = KCTC 13210(T) = CCTCC AA 208068(T)) as the type strain. PMID: 20584813 [PubMed - indexed for MEDLINE] 106. Bacillus luteus Int J Syst Evol Microbiol. 2014 May;64(Pt 5):1580-6. doi: 10.1099/ijs.0.053504-0. Epub 2014 Jan 29. Bacillus luteus sp. nov., isolated from soil. Subhash Y(1), Sasikala Ch, Ramana ChV. Author information: (1)Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India. Two bacterial strains (JC167T and JC168) were isolated from a soil sample collected from Mandpam, Tamilnadu, India. Colonies of both strains were orange and cells Gram-stain-positive. Cells were small rods, and formed terminal endospores of ellipsoidal to oval shape. Both strains were positive for catalase, oxidase and hydrolysis of starch/gelatin, and negative for chitin hydrolysis, H2S production, indole production and nitrate reduction activity. Major fatty acids of both strains (>5%) were anteiso-C15:0, iso-C16:0, iso-C15:0, anteiso-C17:0, iso-C14:0 and C16:0 with minor (<5 but >1%) amounts of iso-C17:0, anteiso-C17:0 B/iso-C17:0 I and C16:1ω11c. Diphosphatydilglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of both strains. Cell wall amino acids were L-alanine, D-alanine, D-glutamic acid and meso-diaminopimelic acid. β-Carotene and five unidentified carotenoids were present in both strains. Mean genomic DNA G+C content was 53.4±1 mol% and the two strains were closely related (mean DNA-DNA hybridization>90%). 16S rRNA gene sequence comparisons of both strains indicated that they represent species of the genus Bacillus within the family Bacillaceae of the phylum Firmicutes. Both strains had a sequence similarity of 97.6% with Bacillus saliphilus 6AGT and <96.8% with other members of the genus Bacillus. Sequence similarity between strain JC167T and 168 was 100%. Strain JC167T showed 25.8±1% reassociation (based on DNA-DNA hybridization) with B. saliphilus DSM 15402T (=6AGT). Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain JC167T as a representative of a novel species of the genus Bacillus, for which the name Bacillus luteus sp. nov. is proposed. The type strain is JC167T (=KCTC 33100T=LMG 30 107. 108. 109. 110. 111. 27257T). PMID: 24478212 [PubMed - indexed for MEDLINE]$$ Bacillus macauensis Int J Syst Evol Microbiol. 2006 Feb;56(Pt 2):349-53. Bacillus macauensis sp. nov., a long-chain bacterium isolated from a drinking water supply. Zhang T(1), Fan X, Hanada S, Kamagata Y, Fang HH. Author information: (1)Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China. A novel long-chain, Gram-positive, rod-shaped, endospore-forming strain was isolated from the influent of a drinking water treatment plant in Macau, China. This facultatively anaerobic isolate (2.0-5.0 microm in length and 0.8-1.2 microm in diameter) formed long chains over 100 microm in length in both liquid and solid media. It had a growth temperature range of 20-40 degrees C, with an optimum at about 30 degrees C, and a growth pH range of 6.0-10.0, with an optimum at pH 8.5. The G+C content of the DNA extracted was 40.8 mol%. The main fatty acid components were anteiso-C(15:0) (67.2%) and iso-C(15:0) (21.7%), with small quantities of iso-C(14:0), C(14:0), iso-C(16:0) and iso-C(17:0). The main quinone component was MK-7. Phylogenetic analyses based on its 16S rRNA gene sequence revealed that this isolate is a member of the genus Bacillus, with no close relatives at the species level (sequence similarity <96.1%). These phenotypic and genetic properties suggested that this strain represents a novel species, for which the name Bacillus macauensis sp. nov. is proposed. The type strain is ZFHKF-1T (=JCM 13285T=DSM 17262T). PMID: 16449438 [PubMed - indexed for MEDLINE] Bacillus macyae Int J Syst Evol Microbiol. 2004 Nov;54(Pt 6):2241-4. Bacillus macyae sp. nov., an arsenate-respiring bacterium isolated from an Australian gold mine. Santini JM(1), Streimann IC, vanden Hoven RN. Author information: (1)Department of Microbiology, La Trobe University, 3086, Victoria, Australia. A strictly anaerobic arsenate-respiring bacterium isolated from a gold mine in Bendigo, Victoria, Australia, belonging to the genus Bacillus is described. Cells are Gram-positive, motile rods capable of respiring with arsenate and nitrate as terminal electron acceptors using a variety of substrates, including acetate as the electron donor. Reduction of arsenate to arsenite is catalysed by a membrane-bound arsenate reductase that displays activity over a broad pH range. Synthesis of the enzyme is regulated; maximal activity is obtained when the organism is grown with arsenate as the terminal electron acceptor and no activity is detectable when it is grown with nitrate. Mass of the catalytic subunit was determined to be approximately 87 kDa based on ingel activity stains. The closest phylogenetic relative, based on 16S rRNA gene sequence analysis, is Bacillus arseniciselenatis, but DNA-DNA hybridization experiments clearly show that strain JMM-4(T) represents a novel Bacillus species, for which the name Bacillus macyae sp. nov. is proposed. The type strain is JMM-4(T) (=DSM 16346(T)=JCM 12340(T)). PMID: 15545465 [PubMed - indexed for MEDLINE] Bacillus manliponensis J Microbiol. 2011 Dec;49(6):1027-32. doi: 10.1007/s12275-011-1049-6. Epub 2011 Dec 28. Bacillus manliponensis sp. nov., a new member of the Bacillus cereus group isolated from foreshore tidal flat sediment. Jung MY(1), Kim JS, Paek WK, Lim J, Lee H, Kim PI, Ma JY, Kim W, Chang YH. Author information: (1)Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Daejeon 305-806, Republic of Korea. A Gram-positive, endospore-forming, new Bacillus species, strain BL4-6(T), was isolated from tidal flat sediment of the Yellow Sea. Strain BL4-6(T) is a straight rod, with motility by peritrichate flagella. The cell wall contains meso-diaminopimelic acid, and the major respiratory quinone is menaquinone-7. The major fatty acids are iso-C(15:0) and summed feature 3 (containing C(16:1) ω7c/iso-C(15:0) 2OH, and/or iso-C(15:0) 2OH/C(16:1) ω7c). Cells are catalase-positive and oxidase-negative. The G+C content of the genomic DNA is 38.0 mol%. Based on a comparative 16S rRNA gene sequence analysis, the isolate belongs to the genus Bacillus, forms a clade with the Bacillus cereus group, and is closely related to Bacillus mycoides (98.5%), Bacillus cereus (98.5%), Bacillus anthracis (98.4%), Bacillus thuringiensis (98.4%), Bacillus weihenstephanensis (98.1%), and Bacillus pseudomycoides (97.5%). The isolate showed less than 85% similarity of the gyrA gene sequence and below 95% similarity of the rpoB gene sequence to the members of this group. DNA-DNA relatedness between strain BL4-6(T) and B. cereus group was found to be in a range of 22.8-42.3%, and thus BL4-6(T) represents a unique species. On the basis of these studies, strain BL4-6(T) (=KCTC 13319(T) =JCM 15802(T)) is proposed to represent the type strain of a novel species, Bacillus manliponensis sp. nov. PMID: 22203569 [PubMed - indexed for MEDLINE] Bacillus marcorestinctum Int J Mol Sci. 2010 Feb 3;11(2):507-20. doi: 10.3390/ijms11020507. Bacillus marcorestinctum sp. nov., a novel soil acylhomoserine lactone quorum-sensing signal quenching bacterium. Han Y(1), Chen F, Li N, Zhu B, Li X. Author information: (1)Department of Bio & Food Engineering, Dalian College of Light Industry, China. [email protected] A Gram-positive, facultatively anaerobic, endospore-forming and rod-shaped bacterium was isolated from soil samples and designated strain LQQ. This organism strongly quenches the acylhomoserine lactone quorum-sensing signal. The LQQ strain exhibits phenotypic characteristics consistent with its classification in the genus Bacillus. It is positive in catalase and no special growth factor is needed. It uses glucose as sole carbon source. The DNA G + C content is 39.8 mol %. The closest relatives based on the 16S rRNA gene sequence are Bacillus anthracis, Bacillus thuringiensis, and Brevibacillus brevis (syn. Bacillus brevis) with the similarity of 96.5%. The DNA-DNA hybridization data indicates a low level of genomic relatedness with the relative type strains of Bacillus thuringiensis (6.1%), Bacillus anthracis (10.5%) and Brevibacillus brevis (8.7%). On the basis of the phenotypic and phylogenetic data together with the genomic distinctiveness, the LQQ strain represents a novel species of the genus Bacillus, for which the name Bacillus marcorestinctum sp. nov. is proposed. The type strain is LQQ(T). PMCID: PMC2852851 PMID: 20386651 [PubMed - in process] Bacillus marisflavi Int J Syst Evol Microbiol. 2003 Sep;53(Pt 5):1297-303. Bacillus marisflavi sp. nov. and Bacillus aquimaris sp. 31 112. 113. 114. 115. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea. Yoon JH(1), Kim IG, Kang KH, Oh TK, Park YH. Author information: (1)Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea. Two Gram-positive or Gram-variable, endospore-forming, moderately halophilic rods (strains TF-11(T) and TF-12(T)) were isolated from a tidal flat of the Yellow Sea in Korea and were subjected to a polyphasic taxonomic study. Strains TF-11(T) and TF-12(T) had cell-wall peptidoglycan based on meso-diaminopimelic acid. The predominant menaquinone found in the two strains was MK-7. The cellular fatty acid profiles of both strains contained large amounts of branched and saturated fatty acids. The major fatty acids were anteiso-C(15 : 0) and iso-C(15 : 0). The DNA G+C contents of strains TF-11(T) and TF-12(T) were respectively 49 and 38 mol%. Phylogenetic analysis based on 16S rDNA sequences showed that strains TF-11(T) and TF-12(T) fell within the radiation of the cluster comprising Bacillus species. The level of 16S rDNA sequence similarity between strains TF-11(T) and TF-12(T) was 98.3 %. Strains TF-11(T) and TF-12(T) exhibited levels of 16S rDNA sequence similarity of less than 96.0 and 96.3 %, respectively, to Bacillus species. The mean level of DNA-DNA relatedness between the two strains was approximately 7 %. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains TF-11(T) and TF-12(T) should be placed in the genus Bacillus as two distinct novel species, for which the names Bacillus marisflavi sp. nov. (type strain TF-11(T)=KCCM 41588(T)=JCM 11544(T)) and Bacillus aquimaris sp. nov. (type strain TF-12(T)=KCCM 41589(T)=JCM 11545(T)) are proposed. PMID: 13130010 [PubMed - indexed for MEDLINE] Bacillus marismortui Int J Syst Bacteriol. 1999 Apr;49 Pt 2:521-30. Bacillus marismortui sp. nov., a new moderately halophilic species from the Dead Sea. Arahal DR(1), Márquez MC, Volcani BE, Schleifer KH, Ventosa A. Author information: (1)Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Spain. A group of 91 moderately halophilic, Gram-positive, rod-shaped strains were isolated from enrichments prepared from Dead Sea water samples collected 57 years ago. These strains were examined for 117 morphological, physiological, biochemical, nutritional and antibiotic susceptibility characteristics. All strains formed endospores and were motile, strictly aerobic and positive for catalase and oxidase. They grew in media containing 5-25% (w/v) total salts, showing optimal growth at 10% (w/v). Eighteen strains were chosen as representative isolates and were studied in more detail. All these strains had mesodiaminopimelic acid in the cell wall and a DNA G + C content of 39.0-42.8 mol%; they constitute a group with levels of DNA-DNA similarity of 70-100%. The sequences of the 16S rRNA genes of three representative strains (strains 123T, 557 and 832) were almost identical (99.9%), and placed the strains in the low G + C content Gram-positive bacteria. On the basis of their features, these isolates should be regarded as members of a new species of the genus Bacillus, for which the name Bacillus marismortui sp. nov. is proposed. The type strain is strain 123T (= DSM 12325T = ATCC 700626T = CIP 105609T = CECT 5066T). PMID: 10319473 [PubMed - indexed for MEDLINE] Bacillus marmarensis Int J Syst Evol Microbiol. 2010 Jul;60(Pt 7):1590-4. doi: 10.1099/ijs.0.012369-0. Epub 2009 Aug 21. Bacillus marmarensis sp. nov., an alkaliphilic, protease-producing bacterium isolated from mushroom compost. Denizci AA(1), Kazan D, Erarslan A. Author information: (1)Scientific and Technological Research Council of Turkey, Marmara Research Center, Genetic Engineering and Biotechnology Institute, Gebze - Kocaeli, Turkey. [email protected] A Gram-stain-positive, obligately alkaliphilic bacterium designated strain GMBE 72(T) was isolated from mushroom compost from Yalova, located in the Marmara region of Turkey. Cells were aerobic, straight rods and they formed subterminal to terminal ellipsoidal endospores. The isolate was catalase-positive, oxidase-negative and motile and contained a type A1gamma peptidoglycan based on meso-diaminopimelic acid. The strain grew at pH 8.0-12.5. The major cellular fatty acid was anteiso-C(15 : 0). The genomic DNA G+C content was 40.2 mol%. Phylogenetic analyses based on 16S rRNA gene sequencing showed that strain GMBE 72(T) belonged to the genus Bacillus and exhibited 98.2 % sequence similarity to Bacillus pseudofirmus DSM 8715(T). DNA-DNA reassociation was 56 % between GMBE 72(T) and B. pseudofirmus DSM 8715(T). According to our polyphasic characterization, strain GMBE 72(T) represents a novel species of the genus Bacillus, for which the name Bacillus marmarensis sp. nov. is proposed. The type strain is GMBE 72(T) (=DSM 21297(T) =JCM 15719(T)). PMID: 19700450 [PubMed - indexed for MEDLINE] Bacillus massiliensis Int J Syst Evol Microbiol. 2006 Jul;56(Pt 7):1485-8. Bacillus massiliensis sp. nov., isolated from cerebrospinal fluid. Glazunova OO(1), Raoult D, Roux V. Author information: (1)Laboratoire de Bactériologie-Virologie, Hôpital de la Timone, CNRS UMR 6020, IFR48, 264 rue Saint-Pierre, 13385 Marseille Cedex 05, France. An unidentified Gram-negative-staining, aerobic, rod-shaped, spore-forming bacterium was isolated from a sample of cerebrospinal fluid. Based on comparative analysis of 16S rRNA gene sequences and phenotypic characteristics, the novel isolate was included in the Bacillus sphaericus-like group. The isolate was closely related to Bacillus odysseyi and Bacillus silvestris, with 96.2 and 94.4 % 16S rRNA gene sequence similarity, respectively. The major fatty acid was iso-C(15 : 0) (48 %). The name Bacillus massiliensis sp. nov. is proposed for the novel isolate, with strain 4400831(T) (=CIP 108446(T)=CCUG 49529(T)) as the type strain. PMID: 16825616 [PubMed - indexed for MEDLINE] Bacillus massilioanorexius Stand Genomic Sci. 2013 Jul 30;8(3):465-79. doi: 10.4056/sigs. 4087826. eCollection 2013. Non-contiguous finished genome sequence and description of Bacillus massilioanorexius sp. nov. Mishra AK, Pfleiderer A, Lagier JC, Robert C, Raoult D, Fournier PE. Author information: Aix-Marseille Université, URMITE, Faculté de médecine, France. Bacillus massilioanorexius strain AP8(T) sp. nov. is the type strain of B. massilioanorexius sp. nov., a new species within the genus Bacillus. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old Caucasian French female suffering from a 32 severe form of anorexia nervosa since the age of 12 years. B. massilioanorexius is a Gram-positive aerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,616,135 bp long genome (one chromosome but no plasmid) contains 4,432 protein-coding and 87 RNA genes, including 8 rRNA genes. PMCID: PMC3910694 PMID: 24501631 [PubMed]$$ 116. Bacillus massiliogorillae Stand Genomic Sci. 2013 Oct 2;9(1):93-105. doi: 10.4056/sigs.4388124. eCollection 2013. Non-contiguous finished genome sequence and description of Bacillus massiliogorillae sp. nov. Keita MB(1), Diene SM(1), Robert C(1), Raoult D(2), Fournier PE(1), Bittar F(1). Author information: (1)URMITE, Aix-Marseille Université, Faculté de Médecine, Marseille, France. (2)URMITE, Aix-Marseille Université, Faculté de Médecine, Marseille, France ; King Fahad Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia. Strain G2(T) sp. nov. is the type strain of B. massiliogorillae, a proposed new species within the genus Bacillus. This strain, whose genome is described here, was isolated in France from the fecal sample of a wild western lowland gorilla from Cameroon. B. massiliogorillae is a facultative anaerobic, Gram-variable, rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,431,633 bp long genome (1 chromosome but no plasmid) contains 5,179 protein-coding and 98 RNA genes, including 91 tRNA genes. PMCID: PMC3910557 PMID: 24501648 [PubMed]$$ 117. Bacillus massiliosenegalensis Stand Genomic Sci. 2013 Jun 5;8(2):264-78. doi: 10.4056/sigs.3496989. eCollection 2013. Non contiguous-finished genome sequence and description of Bacillus massiliosenegalensis sp. nov. Ramasamy D(1), Lagier JC, Gorlas A, Raoult D, Fournier PE. Author information: (1)Aix-Marseille Université, URMITE, Faculté de médecine, Marseille, France. Bacillus massiliosenegalensis strain JC6(T) sp. nov. is the type strain of Bacillus massiliosenegalensis sp. nov., a new species within the genus Bacillus. This strain was isolated from the fecal flora of a healthy Senegalese patient. B. massiliosenegalensis is an aerobic Gram-positive rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,981,278-bp long genome comprises a 4,957,301-bp chromosome and a 23,977-bp plasmid. The chromosome contains 4,925 protein-coding and 72 RNA genes, including 4 rRNA genes. The plasmid contains 29 protein-coding genes. PMCID: PMC3746431 PMID: 23991258 [PubMed]$$ 118. Bacillus mesonae Liu B(1), Liu G(2), Hu G(2), Chen M(2). Bacillus mesonae sp. nov., isolated from Mesona chinensis root.. Int J Syst Evol Microbiol. 2014 Jul 10. pii: ijs.0.059485-0. doi: 10.1099/ijs.0.059485-0. [Epub ahead of print] Author information: (1)Agricultural Bio-resource Institute [email protected]. (2)Agricultural Bio-resource Institute. A Gram-positive, short rod-shaped and motile, mildly halotolerant, endospore-forming bacterium (FJAT-13985T), was isolated from the internal tissue of Mesona chinensis root. Strain FJAT-13985T grew at 20 - 45 ℃ (optimum at 30 ℃) and pH 5.7 - 9.0 (optimum at pH 7.0) with 0 - 2% (w/v) NaCl (optimum with 1% NaCl). The strain was catalase-positive and oxidase-negative. The cell-wall of strain FJAT-13985T contained meso-diaminopimelic acid and the predominant isoprenoid quinone was MK-7 (97.4%). The major fatty acids of the strain were anteiso-C15:0 (23.3%) and iso-C15:0 (40.8%). The G+C content of the DNA was 41.64 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FJAT-13985T was a member of the genus Bacillus and was most closely related to Bacillus drentensis DSM 5600T (97.85%), Bacillus vireti DSM 15602T (97.69%) and Bacillus novalis DSM 15603T (97.58%). DNA-DNA hybridization resulted in relatedness values of only 12.11% to B. novalis DSM 15603T, 36.63% to B. drentensis DSM 5600T and 32.08% to B. vireti DSM 15602T. Phenotypic, chemotaxonomic and genotypic properties clearly indicated that strain FJAT-13985T represents a novel species within the genus Bacillus, for which the name Bacillus mesonae sp. nov. is proposed. The type strain is FJAT-13985T (= DSM 25968T =CGMCC1.12238T). Copyright © 2014, the Society for General Microbiology. PMID: 25013229 [PubMed - as supplied by publisher] 119. Bacillus mesophilum Manickam N(1), Singh NK, Bajaj A, Kumar RM, Kaur G, Kaur N, Bala M, Kumar A, Mayilraj S. Bacillus mesophilum sp. nov., strain IITR-54T, a novel 4-chlorobiphenyl dechlorinating bacterium. Arch Microbiol. 2014 Jul;196(7):517-23. doi: 10.1007/s00203-014-0988-9. Epub 2014 May 8. Author information: (1)Environmental Biotechnology Division, CSIR-Indian Institute of Toxicological Research (IITR), Lucknow, 226 001, India. The taxonomic position of a Gram-positive, endospore-forming bacterium isolated from soil sample collected from an industrial site was analyzed by a polyphasic approach. The strain designated as IITR-54T matched most of the phenotypic and chemical characteristics of the genus Bacillus and represents a novel species. It was found to biodegrade 4-chlorobiphenyl through dechlorination and was isolated through enrichment procedure from an aged polychlorinated biphenyl-contaminated soil. Both resting cell assay and growth under aerobic liquid conditions using 4-chlorobiphenyl as sole source of carbon along with 0.01% yeast extract, formation of chloride ions was measured. 16S rRNA (1,489 bases) nucleotide sequence of isolated strain was compared with those of closely related Bacillus type strains and confirmed that the strain belongs to the genus Bacillus. Strain IITR-54T differs from all other species of Bacillus by at least 2.1% at the 16S rRNA level, and the moderately related species are Bacillus oceanisediminis (97.9%) followed by Bacillus infantis (97.7%), Bacillus firmus (97.4%), Bacillus drentensis (97.3%), Bacillus circulans (97.2%), Bacillus soli (97.1%), Bacillus horneckiae (97.1%), Bacillus pocheonensis (97.1%) and Bacillus bataviensis (97.1%), respectively. The cell wall peptidoglycan contained meso-diaminopimelic acid and the major isoprenoid quinone was MK-7. Major fatty acids are iso-C15:0 (32.4%) and anteiso-C15:0 (27.4%). Predominant polar lipids are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The results of physiological and biochemical tests allowed the genotypic and 33 phenotypic distinctiveness of strain IITR-54T with its phylogenetic relatives and suggest that the strain IITR-54T should be recognized as a novel species, for which the name Bacillus mesophilum sp. nov. is proposed. The type strain is IITR-54T (=MTCC 11060T=JCM 19208T). PMID: 24807729 [PubMed - in process]$$ 120. Bacillus methanolicus Int J Syst Bacteriol. 1992 Jul;42(3):439-45. Bacillus methanolicus sp. nov., a new species of thermotolerant, methanol-utilizing, endospore-forming bacteria. Arfman N(1), Dijkhuizen L, Kirchhof G, Ludwig W, Schleifer KH, Bulygina ES, Chumakov KM, Govorukhina NI, Trotsenko YA, White D, et al. Author information: (1)Department of Microbiology, University of Groningen, Haren, The Netherlands. The generic position of 14 strains of gram-positive bacteria able to use methanol as a growth substrate was determined. All are obligately aerobic, thermotolerant organisms that are able to grow at temperatures of 35 to 60 degrees C. Nine of the strains produce oval spores at a subterminal-to-central position in slightly swollen rod-shaped cells. DNA-DNA hybridization studies, 5S rRNA sequence analysis, and physiological characteristics revealed that all 14 strains cluster as a well-defined group and form a distinct new genospecies. Analysis of the 16S and 5S rRNA sequences indicated that this new species is distinct from Bacillus brevis but closely related to B. firmus and B. azotoformans. The name proposed for this new species is B. methanolicus. The type strain, PB1, has been deposited in the National Collection of Industrial and Marine Bacteria as NCIMB 13113. PMID: 1380290 [PubMed - indexed for MEDLINE] 121. Bacillus methylotrophicus Int J Syst Evol Microbiol. 2010 Oct;60(Pt 10):2490-5. doi: 10.1099/ijs.0.015487-0. Epub 2009 Dec 4. Bacillus methylotrophicus sp. nov., a methanol-utilizing, plant-growth-promoting bacterium isolated from rice rhizosphere soil. Madhaiyan M(1), Poonguzhali S, Kwon SW, Sa TM. Author information: (1)Department of Agricultural Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea. [email protected] A Gram-positive bacterium, designated strain CBMB205(T), was isolated from the rhizosphere soil of traditionally cultivated, field-grown rice. Cells were strictly aerobic, motile, rod-shaped and formed endospores. The best growth was achieved at 30°C and pH 7.0 in ammonium mineral salts (AMS) medium containing 600 mM methanol. A comparative 16S rRNA gene sequence-based phylogenetic analysis placed strain CBMB205(T) in a clade with the species Bacillus amyloliquefaciens, Bacillus vallismortis, Bacillus subtilis, Bacillus atrophaeus, Bacillus mojavensis and Bacillus licheniformis and revealed pairwise similarities ranging from 98.2 to 99.2 %. DNA-DNA hybridization experiments revealed a low level (<36 %) of DNA-DNA relatedness between strain CBMB205(T) and its closest relatives. The major components of the fatty acid profile were C₁₅:₀ anteiso, C₁₅:₀ iso, C₁₆:₀ iso and C₁₇:₀ anteiso. The diagnostic diamino acid of the cell wall was meso-diaminopimelic acid. The G+C content of the genomic DNA was 45.0 mol%. The lipids present in strain CBMB205(T) were diphosphatidylglycerol, phosphatidylglycerol, a minor amount of phosphatidylcholine and two unknown phospholipids. The predominant respiratory quinone was MK-7. Studies of DNA-DNA relatedness, morphological, physiological and chemotaxonomic analyses and phylogenetic data based on 16S rRNA gene sequencing enabled strain CBMB205(T) to be described as representing a novel species of the genus Bacillus, for which the name Bacillus methylotrophicus sp. nov. is proposed. The type strain is CBMB205(T) (=KACC 13105(T)=NCCB 100236(T)). PMID: 19966000 [PubMed - indexed for MEDLINE] 122. Bacillus migulanu Int J Syst Bacteriol. 1993 Apr;43(2):221-31. Characterization of Bacillus brevis with descriptions of Bacillus migulanus sp. nov., Bacillus choshinensis sp. nov., Bacillus parabrevis sp. nov., and Bacillus galactophilus sp. nov. Takagi H(1), Shida O, Kadowaki K, Komagata K, Udaka S. Author information: (1)Research Laboratory, Higeta Shoyu Co., Ltd., Chiba, Japan. Thirty-five Bacillus brevis strains obtained from culture collections, including protein-producing isolates, were taxonomically studied by using numerical analysis, DNA base composition, and DNA-DNA hybridization. Six DNA relatedness groups were represented, and these groups correlated well with clusters based on the numerical analysis. The B. brevis strains were separated into B. brevis sensu stricto, four new species, and an unidentified species of the genus Bacillus. Bacillus migulanus sp. nov., Bacillus choshinensis sp. nov., Bacillus parabrevis sp. nov., and Bacillus galactophilus sp. nov. are proposed. PMID: 8494737 [PubMed - indexed for MEDLINE] 123. Bacillus mojavensis Int J Syst Bacteriol. 1994 Apr;44(2):256-64. Bacillus mojavensis sp. nov., distinguishable from Bacillus subtilis by sexual isolation, divergence in DNA sequence, and differences in fatty acid composition. Roberts MS(1), Nakamura LK, Cohan FM. Author information: (1)Department of Biology, Wesleyan University, Middletown, Connecticut 06459-0170. A number of Bacillus strains isolated from desert soil samples were shown to belong to a previously unidentified species, for which we propose the name Bacillus mojavensis. The type strain is RO-H-1 (= NRRL B-14698). On the basis of restriction digest data, B. mojavensis is most closely related to Bacillus amyloliquefaciens, Bacillus atrophaeus, and Bacillus subtilis. So far, B. mojavensis can be distinguished from B. subtilis only by differences in whole-cell fatty acid composition, divergence in DNA sequence, and resistance to genetic transformation between taxa (in addition to reduced genome relatedness values). Sequence divergence and sexual isolation may prove to be more useful than metabolic characteristics for delimiting cryptic Bacillus species. PMID: 8186089 [PubMed - indexed for MEDLINE] 124. Bacillus muralis Int J Syst Evol Microbiol. 2005 Jan;55(Pt 1):119-31. Study of mural painting isolates, leading to the transfer of 'Bacillus maroccanus' and 'Bacillus carotarum' to Bacillus simplex, emended description of Bacillus simplex, re-examination of the strains previously attributed to 'Bacillus macroides' and description of Bacillus muralis sp. nov. Heyrman J(1), Logan NA, Rodríguez-Díaz M, Scheldeman P, Lebbe L, Swings J, Heyndrickx M, De Vos P. Author information: (1)Vakgroep BFM WE10V, Laboratorium voor Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium. [email protected] A group of 24 strains was 34 isolated from deteriorated mural paintings situated in Spain (necropolis of Carmona) and Germany (church of Greene-Kreiensen). (GTG)5-PCR genomic fingerprinting was performed on these strains to assess their genomic variability and the strains were delineated into four groups. Representatives were studied by 16S rRNA gene sequencing and were found to be closely related to Bacillus simplex and the species 'Bacillus macroides' (strain NCIMB 8796) and 'Bacillus maroccanus' (names not validly published) according to a fasta search. The close similarity between B. simplex, 'B. macroides' NCIMB 8796, 'B. maroccanus' and the mural painting isolates was confirmed by additional (GTG)5-PCR, ARDRA, FAME and SDS-PAGE analyses. Furthermore, these techniques revealed that strains of 'Bacillus carotarum', another name that has not been validly published, also showed high similarity to this group of organisms. On the other hand, it was shown that the strains labelled 'B. macroides' in different collections do not all belong to the same species. Strain NCIMB 8796 can be allocated to B. simplex, while strain DSM 54 (=ATCC 12905) shares the highest 16S rRNA gene sequence similarity with Bacillus sphaericus and Bacillus fusiformis (both around 98.6 %). On the basis of further DNA-DNA hybridization data and the study of phenotypic characteristics, one group of five mural painting strains was attributed to a novel species in the genus Bacillus, for which the name Bacillus muralis sp. nov. is proposed. Finally, the remaining mural painting strains, one (LMG 18508=NCIMB 8796) of two strains belonging to 'B. macroides' and strains belonging to 'B. maroccanus' and 'B. carotarum' are allocated to the species B. simplex and an emended description of B. simplex is given. PMID: 15653864 [PubMed - indexed for MEDLINE] 125. Bacillus naganoensis Int J Syst Bacteriol. 1990 Apr;40(2):123-5. Description of Bacillus naganoensis sp. nov. Tomimura E(1), Zeman NW, Frankiewicz JR, Teague WM. Author information: (1)Enzyme Bio-Systems Ltd., Arlington Heights, Illinois 60005. A new species, Bacillus naganoensis, is proposed for an obligately aerobic, moderately acidophilic, endospore-forming bacterium that produces a thermostable, aciduric pullulanase (EC 3.2.1.41). The organism was isolated from soil by selection on solid, pullulan-containing medium at pH 4.0 and 30 degrees C. The isolate required a medium pH of less than 6.5 for growth initiation. Fatty acid composition studies revealed that the major fatty acid of cells grown in nutrient broth supplemented with 1% starch was 14-methylpentadecanoic acid (iso-C16) at 45 mol%. The guanine-plus-cytosine content of the DNA of this organism was 45 +/- 2 mol%. A type culture has been deposited with the American Type Culture Collection, Rockville, Md., as strain ATCC 53909. PMID: 2223604 [PubMed - indexed for MEDLINE] 126. Bacillus nanhaiensis Int J Syst Evol Microbiol. 2011 Apr;61(Pt 4):888-93. doi: 10.1099/ijs.0.022889-0. Epub 2010 May 21. Bacillus nanhaiensis sp. nov., isolated from an oyster. Chen YG(1), Zhang L, Zhang YQ, He JW, Klenk HP, Tang SK, Zhang YX, Li WJ. Author information: (1)College of Biology and Environmental Sciences, Jishou University, Jishou 416000, People's Republic of China. A novel Gram-stain-positive, slightly halophilic, facultatively alkaliphilic, catalase-positive, oxidase-negative, endospore-forming, motile, rod-shaped, aerobic bacterium, designated strain JSM 082006(T), was isolated from an oyster collected from Naozhou Island in the South China Sea. The isolate grew in 0-18 % (w/v) NaCl (optimum, 0.5-4.0 %), at pH 6.0-10.5 (optimum, pH 8.0) and at 15-45 °C (optimum, 30 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0) and C(16 : 0). Strain JSM 082006(T) contained MK-7 as the predominant respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genomic DNA G+C content was 40.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 082006(T) should be assigned to the genus Bacillus and that it was most closely related to the type strains of Bacillus barbaricus (sequence similarity 99.1 %) and Bacillus arsenicus (97.5 %), followed by those of Bacillus rigui (96.6 %) and Bacillus solisalsi (96.1 %). Phylogenetic analysis, DNA-DNA relatedness values, phenotypic characteristics and chemotaxonomic data support the view that strain JSM 082006(T) represents a novel species of the genus Bacillus, for which the name Bacillus nanhaiensis sp. nov. is proposed; the type strain is JSM 082006(T) ( = DSM 23009(T) = KCTC 13712(T)). PMID: 20495032 [PubMed - indexed for MEDLINE] 127. Bacillus nanhaiisediminis Int J Syst Evol Microbiol. 2011 May;61(Pt 5):1078-83. doi: 10.1099/ijs.0.023671-0. Epub 2010 Jun 4. Bacillus nanhaiisediminis sp. nov., an alkalitolerant member of Bacillus rRNA group 6. Zhang J(1), Wang J, Song F, Fang C, Xin Y, Zhang Y. Author information: (1)School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China. [email protected] A Gram-stain-positive, rod-shaped bacterium, designated strain NH3(T), was isolated from a sediment sample from the South China Sea and was subjected to a polyphasic taxonomic study. The isolate grew optimally at 37 °C and pH 9. Strain NH3(T) had cell-wall peptidoglycan based on meso-diaminopimelic acid and MK-7 as the predominant menaquinone. The cellular fatty acid profile included significant amounts of iso-C(15 : 0) and iso-C(14 : 0). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content of strain NH3(T) was 40.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain NH3(T) was a member of rRNA group 6 of the genus Bacillus, which includes alkalitolerant, alkaliphilic and halotolerant species. The closest phylogenetic relatives were Bacillus akibai 1139(T) (96.82 % 16S rRNA gene sequence similarity), B. pseudofirmus DSM 8715(T) (96.76 %), B. okhensis Kh10-101(T) (96.76 %) and B. alkalidiazotrophicus MS 6(T) (96.47 %). Strain NH3(T) could be distinguished from these phylogenetically close neighbours based on a number of phenotypic properties. On the basis of phenotypic and chemotaxonomic characteristics and phylogenetic data, we conclude that strain NH3(T) ( = CGMCC 1.10116(T) = JCM 16507(T)) merits classification as the type strain of a novel species, for which the name Bacillus nanhaiisediminis sp. nov. is proposed. PMID: 20525818 [PubMed - indexed for MEDLINE] 35 128. Bacillus naphthovorans Appl Microbiol Biotechnol. 2002 Mar;58(4):547-53. Bacillus naphthovorans sp. nov. from oil-contaminated tropical marine sediments and its role in naphthalene biodegradation. Zhuang WQ(1), Zhuang WQ, Maszenan AM, Tay ST. Author information: (1)Environmental Engineering Research Centre, Division of Environmental and Water Resources Engineering, School of Civil and Environmental Engineering, Nanyang Technological University, Singapore. A Bacillus sp., designated as strain MN-003, was isolated as the dominant cultivatable naphthalene-degrading organism from oil-contaminated tropical marine sediments. Strain MN-003 is strictly aerobic, rod-shaped, Gram-positive, catalase positive, oxidase negative, and forms endospores. Strain MN-003 grew at salinities ranging from 0.28 to 7.00% and temperatures ranging from 15 to 41 degrees C. Phylogenetic analyses reveal that strain MN-003 is most similar to Bacillus sp. VAN14, with a 16S rRNA sequence identity of 97.9%. Based on taxonomic and 16S rRNA data, strain MN-003 was named Bacillus naphthovorans sp. nov. When grown with naphthalene as sole carbon source, strain MN-003 had a maximal specific growth rate (mu(max)) of 0.32 +/- 0.03 h(-1), and a half-saturation constant (K(S)) of 22.3 +/-4.2 microM. A batch study of the tropical marine sediments enriched with naphthalene showed that cells of the Bacillus genus grew to become dominant members of the microbial community. The bacilli comprised 39.5 +/- 6.5% of the microbial fraction after 20 days of enrichment. PMID: 11954805 [PubMed - indexed for MEDLINE] 129. Bacillus nealsonii Int J Syst Evol Microbiol. 2003 Jan;53(Pt 1):165-72. Bacillus nealsonii sp. nov., isolated from a spacecraft-assembly facility, whose spores are gamma-radiation resistant. Venkateswaran K(1), Kempf M, Chen F, Satomi M, Nicholson W, Kern R. Author information: (1)Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA. [email protected] One of the spore-formers isolated from a spacecraft-assembly facility, belonging to the genus Bacillus, is described on the basis of phenotypic characterization, 16S rDNA sequence analysis and DNA-DNA hybridization studies. It is a Gram-positive, facultatively anaerobic, rod-shaped eubacterium that produces endospores. The spores of this novel bacterial species exhibited resistance to UV, gamma-radiation, H2O2 and desiccation. The 18S rDNA sequence analysis revealed a clear affiliation between this strain and members of the low G+C Firmicutes. High 16S rDNA sequence similarity values were found with members of the genus Bacillus and this was supported by fatty acid profiles. The 16S rDNA sequence similarity between strain FO-92T and Bacillus benzoevorans DSM 5391T was very high. However, molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in this genus, but DNA-DNA hybridization data support the proposal of FO-92T as Bacillus nealsonii sp. nov. (type strain is FO-92T =ATCC BAAM-519T =DSM 15077T). PMID: 12656168 [PubMed - indexed for MEDLINE] 130. Bacillus neizhouensis Int J Syst Evol Microbiol. 2009 Dec;59(Pt 12):3035-9. doi: 10.1099/ijs.0.009522-0. Epub 2009 Jul 30. Bacillus neizhouensis sp. nov., a halophilic marine bacterium isolated from a sea anemone. Chen YG(1), Zhang YQ, Wang YX, Liu ZX, Klenk HP, Xiao HD, Tang SK, Cui XL, Li WJ. Author information: (1)College of Biology and Environmental Sciences, College of Chemistry and Chemical Engineering, Jishou University, Jishou 416000, PR China. [email protected] A novel Gram-stain-positive, slightly halophilic, facultatively alkaliphilic, non-motile, catalase- and oxidase-positive, endospore-forming, rod-shaped, aerobic bacterium, strain JSM 071004(T), was isolated from a sea anemone collected from Neizhou Bay in the South China Sea. Growth occurred with 0.5-10 % (w/v) total salts (optimum 2-4 %) and at pH 6.5-10.0 (optimum pH 8.5) and 4-30 degrees C (optimum 25 degrees C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The predominant respiratory quinone was menaquinone 7 (MK-7) and the polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were anteiso-C(15 : 0) and iso-C(15 : 0). The genomic DNA G+C content was 39.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 071004(T) belongs to the genus Bacillus, being related most closely to the type strain of Bacillus agaradhaerens (sequence similarity 97.3 %), followed by the type strains of Bacillus cellulosilyticus (96.2 %), Bacillus clarkii (96.1 %) and Bacillus polygoni (96.0 %). The combination of phylogenetic analysis, DNA-DNA hybridization, phenotypic characteristics and chemotaxonomic data support the proposal that strain JSM 071004(T) represents a novel species of the genus Bacillus, for which the name Bacillus neizhouensis sp. nov. is proposed, with JSM 071004(T) (=CCTCC AB 207161(T) =DSM 19794(T) =KCTC 13187(T)) as the type strain. PMID: 19643899 [PubMed - indexed for MEDLINE] 131. Bacillus nematocida Syst Appl Microbiol. 2005 Jun;28(4):323-7. Bacillus nematocida sp. nov., a novel bacterial strain with nematotoxic activity isolated from soil in Yunnan, China. Huang XW(1), Niu QH, Zhou W, Zhang KQ. Author information: (1)Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan 650091, P.R. China. An endospore-forming bacterium, designated strain B-16T, was isolated from a forest soil sample in Yunnan, China. The isolate presented remarkable nematotoxic activity against nematode Panagrellus redivivus. The organism was strictly aerobic, motile, spore forming and rod shaped, catalase- and oxidase-positive. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The major cellular fatty acid profiles were anteiso-C15:0 (48.67%), iso-C15:0 (13.45%), C16:0 (9.06%) and anteiso-Cl7:0 (8.29%). The DNA G+C content was 46%. Phylogenetic analyses based on 16S rDNA sequence revealed that isolate belongs to the genus Bacillus. Strain B-16T exhibited high 16S rDNA similarity with its closest neighbors Bacillus vallismortis (99.79%), B. subtilis (99.43%), B. atrophaeus (99.43%), B. amyloliquefaciens (99.36%), B. licheniformis (98.0%) and less than 97.0% with all the other relative type strains in the genus Bacillus. The phenotypic and genotypic characteristics and DNA-DNA relatedness data indicate that strain B-16T should be distinguished from all the relative species of genus Bacillus. Therefore, on the basis of the polyphasic taxonomic data presented, a new species of the ge- 36 132. 133. 134. 135. nus Bacillus, B. nematocida, with the type strain B-16T ( = CGMCC 1128T) is proposed. The GenBank accession number for the sequence reported in this paper is AY820954. PMID: 15997705 [PubMed - indexed for MEDLINE] Bacillus niabensis Int J Syst Evol Microbiol. 2007 Aug;57(Pt 8):1909-13. Bacillus niabensis sp. nov., isolated from cotton-waste composts for mushroom cultivation. Kwon SW(1), Lee SY, Kim BY, Weon HY, Kim JB, Go SJ, Lee GB. Author information: (1)Korean Agricultural Culture Collection (KACC), Microbial Genetics Division, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Republic of Korea. A group of five bacilli, designated strains 4T12, 4T19(T), 5M45, 5M53 and 5T52, isolated from cotton-waste composts for mushroom cultivation, were examined. These strains were Gram-positive, aerobic, motile, spore-forming rods. 16S rRNA gene sequence analyses revealed that the isolates belonged to the genus Bacillus, showing the highest levels of similarity (approx. 96.6-96.9 %) with respect to Bacillus herbersteinensis DSM 16534(T). The values for DNA-DNA hybridization (approx. 85-96 %) among these five strains revealed that they belong to the same species. The major menaquinone present was MK-7 and the predominant cellular fatty acids were anteiso-C(15 : 0) (approx. 24.5-33.9 %) and C(16 : 0) (approx. 15.1-34.1 %). The DNA G+C contents were 37.7-40.9 mol%. On the basis of physiological, biochemical, chemotaxonomic and comparative genomic analyses, the five isolates represent a novel species of the genus Bacillus, for which the name Bacillus niabensis sp. nov. is proposed. The type strain is 4T19(T) (=KACC 11279(T) =DSM 17723(T)). PMID: 17684280 [PubMed - indexed for MEDLINE] Bacillus novalis Int J Syst Evol Microbiol. 2004 Jan;54(Pt 1):47-57. Bacillus novalis sp. nov., Bacillus vireti sp. nov., Bacillus soli sp. nov., Bacillus bataviensis sp. nov. and Bacillus drentensis sp. nov., from the Drentse A grasslands. Heyrman J(1), Vanparys B, Logan NA, Balcaen A, Rodríguez-Díaz M, Felske A, De Vos P. Author information: (1)Ghent University, Department BFM (WE10V), Laboratory of Microbiology, K-L Ledeganckstraat 35, B-9000 Gent, Belgium. [email protected] A group of 42 isolates were isolated from the soil of several disused hay fields, in the Drentse A agricultural research area (The Netherlands), that were taken out of production at different times. The group represents hitherto-uncultured Bacillus lineages that have previously been found, by a non-cultural method, to be predominant in soil. The strains were subjected to a polyphasic taxonomic study, including (GTG)5-PCR, 16S rDNA sequence analysis, DNA-DNA hybridizations, DNA base-ratio determination, fatty acid analysis and morphological and biochemical characterization. By comparing the groupings obtained by (GTG)5-PCR and 16S rDNA sequence analysis, six clusters of similar strains could be recognized. A DNA-DNA relatedness study showed that these clusters represented five novel genospecies. Further analysis supported the proposal of five novel species in the genus Bacillus, namely Bacillus novalis sp. nov. (type strain IDA3307T=R-15439T=LMG 21837T=DSM 15603T), Bacillus vireti sp. nov. (type strain IDA3632T=R-15447T=LMG 21834T=DSM 15602T), Bacillus soli sp. nov. (type strain IDA0086T=R-16300T=LMG 21838T=DSM 15604T), Bacillus bataviensis sp. nov. (type strain IDA1115T=R-16315T=LMG 21833T=DSM 15601T) and Bacillus drentensis sp. nov. (type strain IDA1967T=R-16337T=LMG 21831T=DSM 15600T). PMID: 14742458 [PubMed - indexed for MEDLINE] Bacillus oceani Antonie Van Leeuwenhoek. 2013 Nov;104(5):829-36. doi: 10.1007/s10482-013-9995-0. Epub 2013 Aug 11. Bacillus oceani sp. nov., a new slightly halophilic bacterium, isolated from a deep sea sediment environment. Liu YJ(1), Long LJ, Huang XF, You ZQ, Wang FZ, Li J, Kim CJ, Tian XP, Zhang S. Author information: (1)CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, CAS, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China. A strictly aerobic, Gram-stain positive, slightly halophilic strain, designated SCSIO 04524(T), was isolated from a deep sea sediment sample collected from the northern South China Sea at a depth of 3415 m. The isolate slightly embedded into the medium after 72 h incubation at 30 °C. Growth was found to occur on media with 0-10 % NaCl but extremely weak growth occurred without supplying NaCl. The predominant menaquinone was determined to be MK-7. The major cellular fatty acid identified was iso-C15:0. The diagnostic polar lipids were determined to be diphosphatidylglycerol, phosphatidyl methylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA G+C content was determined to be 38 mol%. 16S rRNA gene sequences analysis showed that this strain had the highest similarities with Bacillus carboniphilus JCM 9731(T) (94.7 %) and Bacillus endophyticus 2DT(T) (94.3 %). Phylogenetic analysis revealed that strain SCSIO 04524(T) formed a distinct lineage with Bacillus chungangensis CAU 348(T) and B. carboniphilus JCM 9731(T). Physiological characteristics including utilization of sole nitrogen and carbon sources, and chemotaxonomic properties of cellular fatty acids and polar lipids could readily distinguish strain SCSIO 04524(T) from its most closely related species. Based on this polyphasic taxonomic data, a new species, Bacillus oceani sp. nov., is proposed, with the type strain SCSIO 04524(T) (=DSM 26213(T) = KCTC 33077(T)). PMID: 23934481 [PubMed - indexed for MEDLINE]$$ Bacillus oceanisediminis Int J Syst Evol Microbiol. 2010 Dec;60(Pt 12):2924-9. doi: 10.1099/ijs.0.019851-0. Epub 2010 Jan 29. Bacillus oceanisediminis sp. nov., isolated from marine sediment. Zhang J(1), Wang J, Fang C, Song F, Xin Y, Qu L, Ding K. Author information: (1)School of Life Science and Technology, Beijing Institute of Technology, Beijing 100081, PR China. [email protected] A Gram-stain-positive, spore-forming, rod-shaped and aerobic bacterium was isolated from a sediment sample from the South Sea in China. The isolate, designated H2(T), grew at 4-45 °C (optimum 37 °C) and pH 6-10 (optimum pH 7.0). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major isoprenoid quinone was MK-7 and the polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown aminophospholipid. The major fatty acid 37 136. 137. 138. 139. was iso-C(15 : 0). The genomic DNA G+C content of strain H2(T) was 44.8mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a monophyletic clade with Bacillus firmus IAM 12464(T). DNA-DNA relatedness between the isolate and B. firmus ATCC 14575(T) was low (27.5 %). Strain H2(T) also had a phenotypic profile that readily distinguished it from its closest phylogenetic neighbours. It is evident from the combination of genotypic and phenotypic data that the organism should be classified in a novel species of the genus Bacillus, for which the name Bacillus oceanisediminis sp. nov. is proposed. The type strain is H2(T) (=CGMCC 1.10115(T) =JCM 16506(T)). PMID: 20118297 [PubMed - in process] Bacillus odysseyi Int J Syst Evol Microbiol. 2004 Jan;54(Pt 1):195-201. Bacillus odysseyi sp. nov., a round-spore-forming bacillus isolated from the Mars Odyssey spacecraft. La Duc MT(1), Satomi M, Venkateswaran K. Collaborators: Venkateswaran K(2). Author information: (1)Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA. [email protected] (2)NASA JPL A round-spore-forming Bacillus species that produces an exosporium was isolated from the surface of the Mars Odyssey spacecraft. This novel species has been characterized on the basis of phenotypic traits, 16S rDNA sequence analysis and DNA-DNA hybridization. According to the results of these analyses, this strain belongs to the genus Bacillus and is a Gram-positive, aerobic, rod-shaped, endospore-forming eubacterium. Ultrathin sections of the spores showed the presence of an exosporium, spore coat, cortex and core. 16S rDNA sequence similarities between this strain, Bacillus fusiformis and Bacillus silvestris were approximately 96% and DNA-DNA reassociation values with these two bacilli were 23 and 17%, respectively. Spores of the novel species were resistant to desiccation, H2O2 and UV and gamma radiation. Of all strains tested, the spores of this strain were the most consistently resistant and survived all of the challenges posed, i.e. exposure to conditions of desiccation (100% survival), H2O2 (26% survival), UV radiation (10% survival at 660 J m(-2)) and gamma radiation (0.4% survival). The name proposed for this novel bacterium is Bacillus odysseyi sp. nov.; the type strain is 34hs-1T (=ATCC PTA-4993T=NRRL B-30641T=NBRC 100172T). PMID: 14742480 [PubMed - indexed for MEDLINE] Bacillus okhensis Int J Syst Evol Microbiol. 2006 May;56(Pt 5):1073-7. Bacillus okhensis sp. nov., a halotolerant and alkalitolerant bacterium from an Indian saltpan. Nowlan B(1), Dodia MS, Singh SP, Patel BK. Author information: (1)Microbial Gene Research and Resources Facility, School of Biomolecular and Biomedical Sciences, Griffith University, Brisbane, Australia 4111. A strictly aerobic, rod-shaped bacterium (0.6-0.8 x2-3 microm), designated strain Kh10-101T, was isolated from a saltpan (22 degrees 15' N, 69 degrees 1' E) in the vicinity of Port Okha, India. The creamish pigmented colonies of strain Kh10-101T were round, flat and translucent with irregular margins and a smooth surface. The strain possessed up to three subpolar flagella, and was motile by a corkscrew motion. The strain grew optimally at 37 degrees C (temperature growth range 25-40 degrees C) in a complex glucose-containing medium with 5 % NaCl (NaCl growth range 0-10 %) at pH 9 (pH growth range pH 7-10), indicating that it was a mesophilic halotolerant alkaliphile. The strain was sensitive to lincomycin, meticillin, cefuroxime and cephalexin, but resistant to gentamicin, tetracycline and cotrimazine. Spores were not detected and cells were heat sensitive. The isolate metabolized a range of carbohydrates and hydrolysed casein, gelatin and starch. Growth was not observed on aromatic compounds, Tween 40 or Tween 80. Nitrate was not reduced and catalase was produced. Electron microscopic examination of thin sections revealed a single thick Gram-positive cell wall. The DNA G+C content was 41+/-1 mol%. Phylogenetic analyses of the 16S rRNA gene sequence revealed that strain Kh10-101T was a member of the sixth rRNA group of the genus Bacillus, which includes alkalitolerant, alkaliphilic and halotolerant species. The halotolerant obligate alkaliphile Bacillus krulwichiae is the closest relative of strain Kh10-101T (96 % similarity) but a number of phenotypic differences suggest that strain Kh10-101T (=JCM 13040T=ATCC BAA-1137T) should be designated the type strain of a new species, for which the name Bacillus okhensis sp. nov. is proposed. PMID: 16627657 [PubMed - indexed for MEDLINE] Bacillus okuhidensis Int J Syst Evol Microbiol. 2002 Jul;52(Pt 4):1205-9. Bacillus okuhidensis sp. nov., isolated from the Okuhida spa area of Japan. Li Z(1), Kawamura Y, Shida O, Yamagata S, Deguchi T, Ezaki T. Author information: (1)Department of Urology, Gifu University School of Medicine, Japan. [email protected] Two Gram-positive, endospore-forming, alkaliphilic bacteria were isolated from water samples obtained from the Okuhida hot spa area of Japan. The unknown bacteria were characterized using phenotypic and molecular taxonomic methods. On the basis of phylogenetic evidence and phenotypic distinctiveness, a new species, Bacillus okuhidensis sp. nov., is proposed. The type strain of Bacillus okuhidensis is GTC 854T (= JCM 10945T = DSM 13666T). PMID: 12148629 [PubMed - indexed for MEDLINE] Bacillus oryzaecorticis Hong SW(1), Kwon SW(2), Kim SJ(2), Kim SY(3), Kim JJ(3), Lee JS(3), Oh MH(1), Kim AJ(4), Chung KS(5). Bacillus oryzaecorticis sp. nov., a moderately halophilic bacterium isolated from the rice-husk. Int J Syst Evol Microbiol. 2014 May 23. pii: ijs.0.058768-0. doi: 10.1099/ijs.0.058768-0. [Epub ahead of print] Author information: (1)Rural Development Administration; (2)Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, RDA; (3)Bio Center, Chungbuk Techno Park; (4)Kyonggi University; (5)Yonsei University [email protected]. A Gram-positive, aerobic, endospore forming, and moderately halophilic rod, designated strain R1T, was isolated from the rice husks and was subjected to a polyphasic taxonomic study. Strain R1T produced spherical or ellipsoidal endospores at a subterminal position in swollen sporangia, and was catalase and oxidase positive. The isolate grew optimally at 37 °C and pH 6.0-7.0, and could grow with up to 9% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R1T belongs to the genus Bacillus. The species most closely related to strain R1T were Bacillus subtilis subsp. subtilis NCIB3610T, Bacillus aquimaris TF12T, and Bacillus marisflavi TF11T, with 16S rRNA 38 140. 141. 142. 143. similarities of 96.0%, 98.4%, and 98.7%, respectively. DNA-DNA relatedness values between the isolate and the reference strains were ≤ 42±3%. The predominant menaquinones were MK-5 (50%) and MK-7 (50%). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethanolamine. The major cellular fatty acids were iso-C15:0 (48.6%) and anteiso-C15:0 (20.6%), and the cell-wall diamino acid was meso-diaminopimelic acid. On the basis of the 16S rRNA gene sequence and the chemotaxonomic and phenotypic characteristics, it is concluded that strain R1T represents a novel species of the genus Bacillus, for which we propose the name Bacillus oryzaecorticis sp. nov. The type strain is R1T (=KACC 17217T =KCCM 90231T=JCM 19602T). Copyright © 2014, the Society for General Microbiology. PMID: 24860111 [PubMed - as supplied by publisher] Bacillus oshimensis Int J Syst Evol Microbiol. 2005 Mar;55(Pt 2):907-11. Bacillus oshimensis sp. nov., a moderately halophilic, non-motile alkaliphile. Yumoto I(1), Hirota K, Goto T, Nodasaka Y, Nakajima K. Author information: (1)Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan. A halophilic and halotolerant, facultatively alkaliphilic strain, K11(T), was isolated from soil obtained from Oshyamanbe, Oshima, Hokkaido, Japan. The isolate grew at pH 7-10. It was non-motile, Gram-positive and aerobic. Cells comprised straight rods and produced ellipsoidal spores. The isolate grew in 0-20 % NaCl, with optimum growth at 7 % NaCl, and hydrolysed casein, gelatin, starch, DNA and Tweens 20, 40, 60 and 80. The major isoprenoid quinone was menaquinone-7, and the cellular fatty acid profile consisted of significant amounts of C(15) branched-chain acids, iso C(15 : 0) and anteiso C(15 : 0). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain K11(T) was a member of group 6 [Nielsen et al., FEMS Microbiol Lett 117 (1994), 61-66] (alkaliphiles) of the genus Bacillus. DNA-DNA hybridization revealed a low relatedness (14 %) of the isolate to its closest phylogenetic neighbour, Bacillus clausii. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic data and DNA-DNA relatedness data, it was concluded that K11(T) (=JCM 12663(T)=NCIMB 14023(T)) merits classification as the type strain of a novel species, for which the name Bacillus oshimensis sp. nov. is proposed. PMID: 15774684 [PubMed - indexed for MEDLINE] Bacillus pakistanensis Antonie Van Leeuwenhoek. 2014 Jun;105(6):1163-72. doi: 10.1007/s 10482- 014-0177-5. Epub 2014 Apr 29. Bacillus pakistanensis sp. nov., a halotolerant bacterium isolated from salt mines of the Karak Area in Pakistan. Roohi A(1), Ahmed I, Paek J, Sin Y, Abbas S, Jamil M, Chang YH. Author information: (1)National Culture Collection of Pakistan (NCCP), National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Park Road, Islamabad, 45500, Pakistan. A rod shaped, non-motile, endospore forming, Gram-stain positive and moderately halotolerant strain, designated as NCCP-168(T), was isolated from salt mines sampled in the Karak district of Khyber Pakhtunkhwa Province in Pakistan. To delineate its taxonomic position, the strain was subjected to polyphasic characterization. Cells of strain NCCP-168(T) can grow at 10-40 (○)C (optimum at 30-35 (○)C), in a pH range of 5.0-9.0 (optimum at pH 8.0) and in 0-17 % (w/v) NaCl on agar medium. The phylogenetic analysis based on the 16S rRNA gene sequence showed that strain NCCP-168(T) belongs to the genus Bacillus with the highest similarity to Bacillus seohaeanensis BH724(T) (97.1 %), and less than 97 % similarity with other closely related taxa (95.6 % with B. subtilis subsp. subtilis NCIB3610(T)). DNA-DNA relatedness between strain NCCP-168(T) and the type strains of closely related species was lower than 30 %. Chemotaxonomic data (major menaquinone, MK-7; cell wall peptidoglycan type, A1γ [meso-diaminopimelic acid]; major fatty acids, iso-C15:0 29.9 %, anteiso-C15:0 29.3 %, iso-C16:0 11.4 %, iso-C14:0 8.9 % and anteiso-C17:0 7.0 %; major polar lipids, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine) support the affiliation of strain NCCP-168(T) with genus Bacillus. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain NCCP-168(T) can be distinguished from the closely related taxa and thus represents a novel species in the genus Bacillus, for which the name Bacillus pakistanensis sp. nov. is proposed, with the type strain NCCP-168(T) (= KCTC 13786(T) = DSM 24834(T) = JCM 18975(T)). PMID: 24777297 [PubMed - in process]$$ Bacillus pallidus Int J Syst Evol Microbiol. 2008 Dec;58(Pt 12):2850-4. doi: 10.1099/ijs.0.2008/000075-0. Bacillus pallidus sp. nov., isolated from forest soil. Zhou Y(1), Wei W, Che Q, Xu Y, Wang X, Huang X, Lai R. Author information: (1)Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, Jiangsu, PR China. A Gram-positive bacterium, designated strain CW 7(T), was isolated from forest soil in Anhui Province, south-east China. Cells were strictly aerobic, motile with peritrichous flagella and rod-shaped. The strain grew optimally at 30-37 degrees C and pH 7.0-8.0. The major fatty acids of strain CW 7(T) were anteiso-C(15 : 0), iso-C(15 : 0) and anteiso-C(17 : 0). The predominant menaquinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The G+C content of the genomic DNA was 42.3 mol%. Phylogenetic analysis indicated that strain CW 7(T) belonged to a monophyletic cluster within the genus Bacillus and showed 16S rRNA gene sequence similarities of less than 96.5 % to recognized species of the genus Bacillus. The results of the polyphasic taxonomic study, including phenotypic, chemotaxonomic and phylogenetic analyses, showed that strain CW 7(T) represents a novel species of the genus Bacillus, for which the name Bacillus pallidus sp. nov. is proposed. The type strain is CW 7(T) (=KCTC 13200(T)=CCTCC AB 207188(T)=LMG 24451(T)). PMID: 19060070 [PubMed - indexed for MEDLINE] Bacillus panacisoli Int J Syst Evol Microbiol. 2014 Mar;64(Pt 3):901-6. doi: 10.1099/ijs.0.054320-0. Epub 2013 Nov 25. Bacillus panacisoli sp. nov., isolated from ginseng soil. Choi JH(1), Cha CJ. Author information: (1)Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea. A Gram-staining-positive, motile, facultatively anaerobic, endo- 39 spore-forming and rod-shaped bacterium, designated strain CJ32(T), was isolated from ginseng soil at Geumsan in Korea. The isolate grew optimally at 30 °C, 2% (w/v) NaCl and pH 7.0. Colonies of strain CJ32(T) were beige and circular with an entire margin on LB agar plates. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CJ32(T) was associated with the genus Bacillus and was most closely related to Bacillus graminis YC6957(T) (97.3% similarity) and Bacillus lentus IAM 12466(T) (97.1%). DNA-DNA hybridization with closely related strains was below 31.3%. The major respiratory isoprenoid quinone was MK-7. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The polar lipid profile of strain CJ32(T) consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified lipids, including phospholipids, aminolipids and aminophospholipids. The predominant fatty acids of strain CJ32(T) were iso-C15:0 and anteiso-C15:0. The G+C content of the genomic DNA was 35.1 mol%. Based on phenotypic, genotypic and phylogenetic data, strain CJ32(T) should be classified within a novel species of the genus Bacillus, for which the name Bacillus panacisoli sp. nov. is proposed. The type strain is strain CJ32(T) ( = KACC 17503(T) = JCM 19226(T)). PMID: 24277860 [PubMed - indexed for MEDLINE]$$ 144. Bacillus panaciterrae Int J Syst Evol Microbiol. 2006 Dec;56(Pt 12):2861-6. Bacillus panaciterrae sp. nov., isolated from soil of a ginseng field. Ten LN(1), Baek SH, Im WT, Liu QM, Aslam Z, Lee ST. Author information: (1)Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea. A Gram-positive, non-motile, endospore-forming bacterium, designated Gsoil 1517(T), was isolated from soil of a ginseng field in Pocheon Province (South Korea) and was characterized in order to determine its taxonomic position, using a polyphasic approach. It was found to rod-shaped and aerobic or facultatively anaerobic. It grew optimally at 30 degrees C and at pH 6.5-7.0. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 1517(T) forms a distinct phylogenetic lineage within the genus Bacillus, being related to Bacillus funiculus JCM 11201(T) (96.8 %). The strain showed less than 94.3 % sequence similarity with other Bacillus species. The G+C content of the genomic DNA was found to be 47.8 mol% and the predominant respiratory quinone was MK-7. The major fatty acids were iso-C(15 : 0) (42.4 %), anteiso-C(15 : 0) (17.4 %), iso-C(14 : 0) (9.7 %) and C(16 : 0) (6.0 %). On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 1517(T) represents a novel species of the genus Bacillus, for which the name Bacillus panaciterrae sp. nov. is proposed. The type strain is Gsoil 1517(T) (=KCTC 13929(T)=CCUG 52470(T)=LMG 23408(T)). PMID: 17158988 [PubMed - indexed for MEDLINE] 145. Bacillus paraflexus Int J Syst Evol Microbiol. 2013 Dec;63(Pt 12):4735-43. doi: 10.1099/ijs. 0.048223-0. Epub 2013 Aug 29. Bacillus paraflexus sp. nov., isolated from compost. Chandna P(1), Mayilraj S, Kuhad RC. Author information: (1)Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South Campus, New Delhi 110 021, India. A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium capable of growing at 15-42 °C (optimum 30 °C) and at pH 5-11 (optimum pH 7) was isolated from compost. Its taxonomic position was deduced using a polyphasic approach and the strain was designated RC2(T). 16S rRNA gene sequence analysis showed that the isolate belongs to the division Firmicutes, forming a clade within the cluster containing Bacillus flexus IFO 15715(T), and showed highest similarity to B. flexus IFO 15715(T) (98.1 %). The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The major cellular fatty acids of the novel strain were iso-C15:0 (36.83 %), anteiso-C15:0 (49.19 %) and C16:0 (5.19 %). DNA-DNA hybridization between strain RC2(T) and B. flexus DSM 1320(T) showed a level of relatedness of 54.5 %. The polar lipid profile of strain RC2(T) showed the presence of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The predominant isoprenoid quinone was MK-7 and the G+C content of strain RC2(T) was 37.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and the results of biochemical and physiological tests, strain RC2(T) was clearly distinguished from closely related members of the genus, and the strain is assigned to a novel species, for which the name Bacillus paraflexus sp. nov. is proposed. The type strain is RC2(T) ( = MTCC 9831(T) = MCC 2100(T) = KCTC 13724(T) = CCM 7754(T)). PMID: 23990650 [PubMed - indexed for MEDLINE]$$ 146. Bacillus patagoniensis Int J Syst Evol Microbiol. 2005 Jan;55(Pt 1):443-7. Bacillus patagoniensis sp. nov., a novel alkalitolerant bacterium from the rhizosphere of Atriplex lampa in Patagonia, Argentina. Olivera N(1), Siñeriz F, Breccia JD. Author information: (1)PROIMI Planta Piloto de Procesos Industriales Microbiológicos, Av. Belgrano y Pasaje Caseros, 4000 San Miguel de Tucumán, Tucumán, Argentina. [email protected] A Gram-positive, rod-shaped, spore-forming bacterium (PAT 05T) was isolated from the rhizosphere of the perennial shrub Atriplex lampa in north-eastern Patagonia, Argentina. Its overall biochemical and physiological characteristics indicated that this strain should be placed in the alkaliphilic Bacillus group. Strain PAT 05T grew at pH 7-10 (optimum pH 8), but not at pH 6. Its DNA G+C content was 39.7 mol%. Sequence analysis of the 16S rRNA gene of PAT 05T revealed the closest match (99.6 % similarity) with Bacillus sp. DSM 8714. The highest level of DNA-DNA relatedness (88.6 %) was also found with this strain. On the basis of 16S rRNA gene sequence similarity and phylogenetic analysis, G+C content and DNA-DNA hybridization data, strain PAT 05T is related at the species level to Bacillus sp. DSM 8714, a member of a group referred as phenon 4a by Nielsen et al. [Nielsen, P., Fritze, D. & Priest, F. G. (1995). Microbiology 141, 1745-1761], which still lacks taxonomic standing. These results support the proposal of strain PAT 05T (=DSM 16117T=ATCC BAA-965T) as the type strain of Bacillus patagoniensis sp. nov. PMID: 15653916 [PubMed - indexed for MEDLINE] 147. Bacillus persepolensis Int J Syst Evol Microbiol. 2009 Sep;59(Pt 9):2352-8. doi: 10.1099/ijs.0.010090-0. Epub 2009 Jul 20. Bacillus persepolensis sp. nov., a moderately halophilic bacterium from a hypersaline lake. Amoozegar MA(1), Sánchez-Porro C, Rohban R, 40 Hajighasemi M, Ventosa A. Author information: (1)Extremophiles Laboratory, Department of Microbiology, Faculty of Biology, College of Science, University of Tehran, Tehran, Iran. A Gram-positive, moderately halophilic, endospore-forming bacterium, designated strain HS136T, was isolated from the hypersaline lake Howz-Soltan in Iran. Cells were motile rods, producing ellipsoidal endospores at a central-subterminal position in non-swollen sporangia. Strain HS136T, a strictly aerobic bacterium, grew between pH 7.0 and 10.0 (optimal growth at pH 8.0-8.5), between 25 and 45 degrees C (optimal growth at 40 degrees C) and at salinities of 5-20% (w/v) NaCl, growing optimally at 10% (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain HS136T was shown to belong to the genus Bacillus within the phylum Firmicutes and showed closest phylogenetic similarity to Bacillus salarius BH169T (95.2%) and Bacillus qingdaonensis CM1T (94.5%). The DNA G+C content of this new isolate was 37.1 mol%. The major cellular fatty acids of strain HS136T were iso-C15:0, anteiso-C15:0 and anteiso-C17:0, and its polar lipid pattern consisted of phosphatidylglycerol and diphosphatidylglycerol. The isoprenoid quinone was MK-7. The peptidoglycan type is A1gamma, with meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of polyphasic evidence from this study, Bacillus persepolensis sp. nov. is proposed, with strain HS136T (=CCM 7595T=DSM 21632T=JCM 15720T=LMG 25222T) as the type strain. PMID: 19620367 [PubMed - indexed for MEDLINE] 148. Bacillus persicus Int J Syst Evol Microbiol. 2013 Apr;63(Pt 4):1229-34. doi: 10.1099/ijs.0.042689-0. Epub 2012 Jul 6. Bacillus persicus sp. nov., a halophilic bacterium from a hypersaline lake. Didari M(1), Amoozegar MA, Bagheri M, Mehrshad M, Schumann P, Spröer C, Sánchez-Porro C, Ventosa A. Author information: (1)Extremophiles Lab., Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran. A novel gram-positive, slightly halophilic bacterium, designated strain B48(T), was isolated from soil around the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using a polyphasic approach. Cells of strain B48(T) were non-motile rods and produced ellipsoidal endospores at a central or subterminal position in swollen sporangia. Strain B48(T) was a strictly aerobic bacterium, catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5-10.0 % (w/v), with optimum growth occurring at 2.5 % (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.5-8.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain B48(T) was shown to belong to the genus Bacillus within the phylum Firmicutes and showed the closest phylogenetic similarity to the species Bacillus foraminis CV53(T) (97.4 %) and Bacillus purgationiresistens DS22(T) (96.9 %). The DNA G+C content of this new isolate was 40.1 mol%. The major cellular fatty acids of strain B48(T) were iso-C15 : 0 and anteiso-C15 : 0, and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an aminophospholipid and two unknown phospholipids. The only quinone present was menaquinone 7 (MK-7). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All these features confirm the placement of isolate B48(T) within the genus Bacillus. DNA-DNA hybridization experiments revealed a low level of relatedness between strain B48(T) and Bacillus foraminis IBRC-M 10625(T) (8.1 %). On the basis of polyphasic evidence from this study, a new species of the genus Bacillus, Bacillus persicus sp. nov., is proposed, with strain B48(T) ( = IBRC-M 10115(T) = DSM 25386(T) = CECT 8001(T)) as the type strain. PMID: 22771682 [PubMed - indexed for MEDLINE] 149. Bacillus pervagus Curr Microbiol. 2014 Jan;68(1):88-95. doi: 10.1007/s00284-013-0443-1. Epub 2013 Aug 31. Bacillus thaonhiensis sp. nov., a new species, was isolated from the forest soil of Kyonggi University by using a modified culture method. Van Pham HT(1), Kim J. Author information: (1)Department of Life Science, Graduate School of Kyonggi University, Suwon, Gyeonggi-Do, 443-760, South Korea. Erratum in$$ 150. Bacillus pervagus Int J Syst Evol Microbiol. 2014 Jan;64(Pt 1):88-94. doi: 10.1099/ijs.0.054833-0. Epub 2013 Sep 10. Bacillus pervagus sp. nov. and Bacillus andreesenii sp. nov., isolated from a composting reactor. Kosowski K(1), Schmidt M, Pukall R, Hause G, Kämpfer P, Lechner U. Author information: (1)Institut für Biologie/Mikrobiologie, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle, Germany. Two strains, 8-4-E12(T) and 8-4-E13(T), were isolated from a biowaste composting reactor. Based on 16S rRNA gene sequences, both strains belong to the genus Bacillus. Strain 8-4-E12(T) was most closely related to the type strains of Bacillus shackletonii, B. acidicola, B. sporothermodurans and B. oleronius (96.4, 96.3, 96.0 and 95.6 % 16S rRNA gene similarity, respectively), whereas strain 8-4-E13(T) was most closely related to the type strain of Bacillus humi (96.5 % sequence similarity). Strains 8-4-E12(T) and 8-4-E13(T) shared 94 % 16S rRNA gene sequence similarity. The fatty acid profile of strain 8-4-E12(T) was dominated by saturated iso- and anteiso-branched fatty acids (iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0), and also contained considerable amounts of C16 : 0. The fatty acid profile of strain 8-4-E13(T) showed a predominance of iso-C15 : 0 (65 %), with smaller amounts of other saturated branched-chain fatty acids along with an unsaturated alcohol. Both strains contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major polar lipids. Additionally, strain 8-4-E12(T) contained an unknown lipid and strain 8-4-E13(T) two unknown (amino-)phospholipids. The diagnostic diamino acid found in the cell-wall peptidoglycan of 8-4-E12(T) and 8-4-E13(T) was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The results of physiological and biochemical tests also allowed phenotypic differentiation of the two strains from each other and from related Bacillus species. On the basis of their phylogenetic, phenotypic and chemotaxonomic properties, strains 8-4-E12(T) and 8-4-E13(T) represent novel species of the genus Bacillus, for which the names Bacillus pervagus sp. nov. (type strain 8-4-E12(T) = DSM 23947(T) = LMG 27601(T)) 41 151. 152. 153. 154. and Bacillus andreesenii sp. nov. (type strain 8-4-E13(T) = DSM 23948(T) = LMG 27602(T)) are proposed. PMID: 24021730 [PubMed - indexed for MEDLINE]$$ Bacillus plakortidis Int J Syst Evol Microbiol. 2007 Dec;57(Pt 12):2888-93. Bacillus plakortidis sp. nov. and Bacillus murimartini sp. nov., novel alkalitolerant members of rRNA group 6. Borchert MS(1), Nielsen P, Graeber I, Kaesler I, Szewzyk U, Pape T, Antranikian G, Schäfer T. Author information: (1)Hamburg University of Technology, Technical Microbiology, Kasernenstrasse 12, D-21073 Hamburg, Germany. [email protected] The Gram-positive, alkali- and salt-tolerant marine bacterium strain P203(T) is described together with its closest phylogenetic neighbour, terrestrial isolate LMG 21005(T). Strain P203(T) was isolated from material from the sponge Plakortis simplex that was obtained from the Sula-Ridge, Norwegian Sea. Strain LMG 21005(T) was an undescribed strain that was isolated from a church wall mural in Germany. Strains P203(T) and LMG 21005(T) were identified as novel alkalitolerant members of the Bacillus rRNA group 6 with a 16S rRNA gene sequence similarity of 99.5 %. The closest described neighbour, Bacillus gibsonii DSM 8722(T), showed 99.0 % gene sequence similarity with P203(T) and 98.8 % similarity with strain LMG 21005(T). Despite the high 16S rRNA gene sequence similarity, DNA-DNA cross-hybridization revealed only 25.8-34.1 % similarity amongst the three strains. The DNA G+C contents were 41.1 mol% for strain P203(T) and 39.6 mol% for strain LMG 21005(T). Both strains grew well between pH 7 and pH 11. Strain P203(T) showed growth at moderate temperatures (from 4 to 30 degrees C) and in the presence of up to 12 % (w/v) NaCl at pH 9.7, whereas strain LMG 21005(T) was not salt tolerant (up to 4 % NaCl) and no growth was observed at 4 degrees C. The major fatty acids of strains P203(T), LMG 21005(T) and the type strain of B. gibsonii were the saturated terminally methyl-branched compounds iso-C(15 : 0) (19.8, 15.6 and 28.0 %, respectively) and anteiso-C(15 : 0) (57.1, 48.6 and 45.2 %, respectively). Physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains P203(T) and LMG 21005(T) from the six related Bacillus species with validly published names and supported the proposal of two novel species, Bacillus plakortidis [type strain P203(T) (=DSM 19153(T)=NCIMB 14288(T))] and Bacillus murimartini [type strain LMG 21005(T) (=NCIMB 14102(T))]. PMID: 18048744 [PubMed - indexed for MEDLINE] Bacillus pocheonensis Int J Syst Evol Microbiol. 2007 Nov;57(Pt 11):2532-7. Bacillus pocheonensis sp. nov., a moderately halotolerant, aerobic bacterium isolated from soil of a ginseng field. Ten LN(1), Baek SH, Im WT, Larina LL, Lee JS, Oh HM, Lee ST. Author information: (1)Department of Biology and Medicinal Science, Pai Chai University, 14 Yeonja-1-Gil, Seo-Gu, Daejeon 302-735, Republic of Korea. A Gram-positive, non-motile, endospore-forming bacterial strain, designated Gsoil 420T, was isolated from soil of a ginseng field in Pocheon Province, South Korea, and was characterized, using a polyphasic approach, in order to determine its taxonomic position. The novel isolate consisted of strictly aerobic, rod-shaped cells and was able to grow in medium supplemented with up to 12% NaCl at 25 degrees C and pH 6.5-7.0. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 420T fell within the radiation of the cluster comprising Bacillus species and formed a coherent cluster with Bacillus niacini (16S rRNA gene sequence similarity, 98.6%), Bacillus bataviensis (98.6%), Bacillus soli (98.3%), Bacillus drentensis (98.0%), Bacillus novalis (98.0%), Bacillus vireti (97.9%), Bacillus foraminis (97.6%), Bacillus fumarioli (97.4%) and Bacillus jeotgali (97.0%). The levels of 16S rRNA gene sequence similarity with respect to other Bacillus species with validly published names were less than 96.8%. Strain Gsoil 420T had a genomic DNA G+C content of 44.9 mol% and the predominant respiratory quinone was MK-7. The major fatty acids were anteiso-C15:0 (33.9%), iso-C15:0 (24.5%) and iso-C14:0 (19.9%). These chemotaxonomic results supported the affiliation of strain Gsoil 420T to the genus Bacillus. However, low DNA-DNA relatedness values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain Gsoil 420T from recognized Bacillus species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 420T represents a novel species of the genus Bacillus, for which the name Bacillus pocheonensis sp. nov. is proposed. The type strain is Gsoil 420T (=KCTC 13943T=DSM 18135T). PMID: 17978214 [PubMed - indexed for MEDLINE] Bacillus polygoni Int J Syst Evol Microbiol. 2008 Jan;58(Pt 1):120-4. doi: 10.1099/ijs.0.65193-0. Bacillus polygoni sp. nov., a moderately halophilic, non-motile obligate alkaliphile isolated from indigo balls. Aino K(1), Hirota K, Matsuno T, Morita N, Nodasaka Y, Fujiwara T, Matsuyama H, Yoshimune K, Yumoto I. Author information: (1)Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology, Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan. A moderately halophilic, obligate alkaliphile (growth range pH 8-12), designated strain YN-1(T), was isolated from indigo balls obtained from Ibaraki, Japan. The cells of the isolate stained Gram-positive, and were aerobic, non-motile, sporulating rods which grew optimally at pH 9. The strain grew in 3-14% NaCl with optimum growth in 5% NaCl. It hydrolysed casein and Tweens 20, 40 and 60, but not gelatin, starch, DNA or pullulan. Its major isoprenoid quinone was MK-7 and its cellular fatty acid profile mainly consisted of anteiso-C(15:0), anteiso-C(17:0) and anteiso-C(17:1). 16S rRNA phylogeny suggested that strain YN-1(T) was a member of group 7 (alkaliphiles) of the genus Bacillus, with the closest relative being Bacillus clarkii DSM 8720(T) (similarity 99.5%). However, DNA-DNA hybridization showed a low DNA-DNA relatedness (7%) of strain YN-1(T) with B. clarkii DSM 8720(T). Owing to the significant differences in phenotypic and chemotaxonomic characteristics, and phylogenetic and DNA-DNA relatedness data, the isolate merits classification as a new species, for which the name Bacillus polygoni is proposed. The type strain of this species is YN-1(T) (=JCM 14604(T)=NCIMB 14282(T)). PMID: 18175695 [PubMed - indexed for MEDLINE] Bacillus pseudomycoides Int J Syst Bacteriol. 1998 Jul;48 Pt 3:1031-5. Bacillus pseudomycoides sp. nov. Nakamura LK. Author 42 155. 156. 157. 158. information: National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA. [email protected] Previous DNA relatedness studies showed that strains identified as Bacillus mycoides segregated into two genetically distinct yet phenotypically similar groups, one being B. mycoides sensu stricto and the other, an unclassified taxon. In the present study, the taxonomic position of this second group was assessed by measuring DNA relatedness and determining phenotypic characteristics of an increased number of B. mycoides strains. Also determined was the second group's 16S RNA gene sequence. The 36 B. mycoides strains studied segregated into two genetically distinct groups showing DNA relatedness of about 30%; 18 strains represented the species proper and 18 the second group with intragroup DNA relatedness for both groups ranging from 70 to 100%. DNA relatedness to the type strains of presently recognized species with G+C contents of approximately 35 mol% (Bacillus alcalophilus, Bacillus cereus, Bacillus circulans, Bacillus lentus, Bacillus megaterium and Bacillus sphaericus) ranged from 22 to 37%. Although shown to be genetically distinct taxa, the two B. mycoides groups exhibited highly similar (98%) 16S RNA sequences. Phylogenetic analyses showed that both B. mycoides and the second group clustered closely with B. cereus. Although not distinguishable by physiological and morphological characteristics, the two B. mycoides groups and B. cereus were clearly separable based on fatty acid composition. The data established that the second B. mycoides group merits recognition as a new species for which the name Bacillus pseudomycoides is proposed. The type stain is NRRL B-617(T). PMID: 9734060 [PubMed - indexed for MEDLINE] Bacillus psychrotolerans Int J Syst Evol Microbiol. 2002 Nov;52(Pt 6):2127-33. Two novel psychrotolerant species, Bacillus psychrotolerans sp. nov. and Bacillus psychrodurans sp. nov., which contain ornithine in their cell walls. Abd El-Rahman HA(1), Fritze D, Spröer C, Claus D. Author information: (1)DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany. Eleven psychrotolerant Bacillus strains with ornithine as diamino acid in position 3 of the peptide side chain of the cell wall and a G+C range of 35.7-38.4 mol% were characterized taxonomically. DNA-DNA hybridization studies confirmed previously physiologically established groups. High DNA-binding values (> 70%) were found within groups I A (consisting of the type strain of Bacillus insolitus DSM 5(T) and Bacillus insolitus DSM 2272), I B (consisting of isolates 3H1(T0, 71H1, 84E1, 87H2 and 4H2) and I C (consisting of isolates 68E39T), 61E1, 4E3 and 67E1). Low DNA-binding values (< 60%) were revealed between the three groups. Consequently, strains of groups I B and I C were considered as being representatives of new psychrotolerant species. For group I B strains the name Bacillus psychrotolerans sp. nov. is proposed with the type strain 3H1(T) (= DSM 11706(T) = NCIMB 13838(T)) and for group I C strains the name Bacillus psychrodurans sp. nov. is proposed with the type strain 68E3(T) (= DSM 11713(T) = NCIMB 13837(T)). PMID: 12508879 [PubMed - indexed for MEDLINE] Bacillus purgationiresistans Int J Syst Evol Microbiol. 2012 Jan;62(Pt 1):71-7. doi: 10.1099/ijs.0.028605-0. Epub 2011 Feb 18. Bacillus purgationiresistans sp. nov., isolated from a drinking-water treatment plant. Vaz-Moreira I(1), Figueira V, Lopes AR, Lobo-da-Cunha A, Spröer C, Schumann P, Nunes OC, Manaia CM. Author information: (1)CBQF-Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal. A Gram-positive, aerobic, non-motile, endospore-forming rod, designated DS22(T), was isolated from a drinking-water treatment plant. Cells were catalase- and oxidase-positive. Growth occurred at 15-37 °C, at pH 7-10 and with <8% (w/v) NaCl (optimum growth: 30 °C, pH 7-8 and 1-3% NaCl). The major respiratory quinone was menaquinone 7, the G+C content of the genomic DNA was 36.5 mol% and the cell wall contained meso-diaminopimelic acid. On the basis of 16S rRNA gene sequence analysis, strain DS22(T) was a member of the genus Bacillus. Its closest phylogenetic neighbours were Bacillus horneckiae NRRL B-59162(T) (98.5% 16S rRNA gene sequence similarity), Bacillus oceanisediminis H2(T) (97.9%), Bacillus infantis SMC 4352-1(T) (97.4%), Bacillus firmus IAM 12464(T) (96.8%) and Bacillus muralis LMG 20238(T) (96.8%). DNA-DNA hybridization, and biochemical and physiological characterization allowed the differentiation of strain DS22(T) from its closest phylogenetic neighbours. The data supports the proposal of a novel species, Bacillus purgationiresistans sp. nov.; the type strain is DS22(T) (=DSM 23494(T)=NRRL B-59432(T)=LMG 25783(T)). PMID: 21335493 [PubMed - indexed for MEDLINE] Bacillus pycnus Int J Syst Evol Microbiol. 2002 Mar;52(Pt 2):501-5. Bacillus pycnus sp. nov. and Bacillus neidei sp. nov., round-spored bacteria from soil. Nakamura LK(1), Shida O, Takagi H, Komagata K. Author information: (1)Microbial Properties Research Unit, National Center for Agricultural Utilization Research, Peoria, IL 61604, USA. [email protected] Bacillus sphaericus sensu lato currently consists of seven or more groups of unrelated taxa, one of which is B. sphaericus sensu stricto and another of which is Bacillus fusiformis. Members of two groups (groups 6 and 7), in common with all other B. sphaericus-like organisms, are unable to grow anaerobically or to use common hexoses, pentoses and hexitols as sources of carbon, have G+C contents of 34-36 mol % and form round spores. Groups 6 and 7 can be differentiated from other B. sphaericus-like organisms by low DNA relatedness and by variations in whole-cell fatty acid composition. Unique characteristics of group 6 include the ability to oxidize beta-hydroxybutyrate, the non-requirement for biotin and thiamin and failure to grow in 5% NaCl. Distinctive traits of group 7 include the inability to oxidize pyruvate and a requirement for biotin, thiamin and cystine for growth. These data show that groups 6 and 7 represent two novel species, for which the names Bacillus pycnus sp. nov. and Bacillus neidei sp. nov., respectively, are proposed; the corresponding type strains are NRRL NRS-1691T (= JCM 11075T) and NRRL BD-87T (= JCM 11077T). PMID: 11931162 [PubMed indexed for MEDLINE] Bacillus qingdaonensis Int J Syst Evol Microbiol. 2007 May;57(Pt 5):1143-7. Bacillus qingdaonensis sp. nov., a moderately haloal- 43 kaliphilic bacterium isolated from a crude sea-salt sample collected near Qingdao in eastern China. Wang QF(1), Li W, Liu YL, Cao HH, Li Z, Guo GQ. Author information: (1)Institute of Cell Biology, School of Life Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China. A moderately haloalkaliphilic, Gram-positive bacterium, designated as strain CM1(T), was isolated from a crude sea-salt sample collected near Qingdao in eastern China. Strain CM1(T) was found to grow optimally at 37 degrees C and pH 9.0. It was shown to be aerobic, rod-shaped and capable of growth at salinities of 2.5-20 % (w/v) NaCl (optimum, 12 %). The genomic DNA G+C content was about 48 mol%. The major cellular fatty acids were anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(16 : 0) and the major isoprenoid quinones were MK-7(H(2)) and MK-6(H(2)). Phylogenetic analyses based on 16S rRNA gene sequences revealed that CM1(T) is a member of the genus Bacillus and has less than 95.2 % gene sequence similarity to the most closely related strain, Bacillus salarius BH169(T). Its DNA-DNA reassociation value with respect to B. salarius BH169(T) was 35.4 %. On the basis of phenotypic and molecular properties, strain CM1(T) represents a novel Bacillus species, for which the name Bacillus qingdaonensis sp. nov. is proposed. The type strain is CM1(T) (=CGMCC 1.6134(T)=JCM 14087(T)). PMID: 17473273 [PubMed - indexed for MEDLINE] 159. Bacillus qingshengii Int J Syst Evol Microbiol. 2014 Jul;64(Pt 7):2473-9. doi: 10.1099/ijs.0.061929-0. Epub 2014 May 6. Bacillus qingshengii sp. nov., a rock-weathering bacterium isolated from weathered rock surface. Xi J(1), He LY(1), Huang Z(1), Sheng XF(2). Author information: (1)Key Laboratory of Agricultural Environment Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China. (2)Key Laboratory of Agricultural Environment Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China [email protected]. A novel type of rock-weathering bacterium was isolated from weathered rock (tuff) surface collected from Dongxiang (Jiangxi, eastern China). Cells of strain G19(T) were Gram-reaction-positive, rod-shaped, endospore-forming and non-motile. The strain was aerobic, catalase- and oxidase-positive, and grew optimally at 30 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain G19(T) was shown to belong to the genus Bacillus and the closest phylogenetic relatives were Bacillus aryabhattai B8W22(T) (97.4 %) and Bacillus megaterium IAM 13418(T) (97.1 %). The DNA G+C content was 36.7 mol% and the predominant respiratory quinone was MK-7. The major fatty acids were iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0. The polar lipid profile of strain G19(T) contained phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and an unidentified lipid. Based on the low level of DNA-DNA relatedness (ranging from 49.4 % to 55.0 %) to these type strains of species of the genus Bacillus and unique phenotypic characteristics, strain G19(T) represents a novel species of the genus Bacillus, for which the name Bacillus qingshengii sp. nov. is proposed. The type strain is G19(T) ( = CCTCC AB 2013273(T) = JCM 19454(T)). © 2014 IUMS. PMID: 24801156 [PubMed - in process]$$ 160. Bacillus rhizosphaerae Antonie Van Leeuwenhoek. 2011 Oct;100(3):437-44. doi: 10.1007/s10482-011-9600-3. Epub 2011 Jun 14. Bacillus rhizosphaerae sp. nov., an novel diazotrophic bacterium isolated from sugarcane rhizosphere soil. Madhaiyan M(1), Poonguzhali S, Lee JS, Lee KC, Hari K. Author information: (1)Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India. [email protected] A Gram-positive, non-pigmented, rod-shaped, diazotrophic bacterial strain, designated SC-N012(T), was isolated from rhizosphere soil of sugarcane and was subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genus Bacillus. Sequence analysis of the 16S rRNA gene of SC-N012(T) revealed the closest match (98.9% pair wise similarity) with Bacillus clausii DSM 8716(T). However, DNA-DNA hybridization experiments indicated low levels of genomic relatedness (32%) with this strain. The major components of the fatty acid profile are iso-C(15:0), anteiso-C(15:0), iso-C(17:0) and anteiso-C(17:0). The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. The G+C content of the genomic DNA is 43.0 mol%. The lipids present in strain SC-N012(T) are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and two unknown phospholipids. Their predominant respiratory quinone was MK-7. Studies of DNA-DNA relatedness, morphological, physiological and chemotaxonomic analyses and phylogenetic data based on 16S rRNA gene sequencing allowed strain SC-N012(T) to be described as members of novel species of the genus Bacillus, for which the name Bacillus rhizosphaerae sp. nov. is proposed. The type strain is SC-N012(T) (=DSM 21911(T) = NCCB 100267(T)). PMID: 21671194 [PubMed - indexed for MEDLINE] 161. Bacillus rigui Int J Syst Evol Microbiol. 2010 Sep;60(Pt 9):2204-9. doi: 10.1099/ijs.0.018184-0. Epub 2009 Nov 6. Bacillus rigui sp. nov., isolated from wetland fresh water. Baik KS(1), Lim CH, Park SC, Kim EM, Rhee MS, Seong CN. Author information: (1)Department of Biology, Sunchon National University, Suncheon 540-742, Republic of Korea. Two Gram-stain-positive strains, WPCB074(T) and WPCB165, were isolated from fresh water collected from the Woopo wetland (Republic of Korea). Both strains were strictly aerobic, motile, endospore-forming rods. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WPCB074(T) and WPCB165 belonged to the genus Bacillus and that strain WPCB074(T) was most closely related to Bacillus solisalsi YC1(T) (98.4 % sequence similarity), B. barbaricus V2-BIII-A2(T) (97.7 %), B. macauensis ZFHKF-1(T) (96.9 %), B. arsenicus Con a/3(T) (96.4 %) and B. gelatini LMG 21880(T) (95.1 %). The 16S rRNA gene sequences of strains WPCB074(T) and WPCB165 differed at one position (99.9 % similarity), suggesting that these two strains constitute a single species. DNA-DNA relatedness between strain WPCB074(T) and the type strains of B. solisalsi, B. barbaricus, B. macauensis, B. arsenicus and B. gelatini were 26, 17, 20, 14 and 7 %, respectively. Strain WPCB074(T) was characterized by having cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as the predominant menaquinone and iso-C(15 : 0) and anteiso-C(15 : 0) as the major fatty acids. The 44 162. 163. 164. 165. 166. DNA G+C content of strain WPCB074(T) was 41.9 mol%. On the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain WPCB074(T) represents a novel species of the genus Bacillus for which the name Bacillus rigui sp. nov. is proposed. The type strain is WPCB074(T) (=KCTC 13278(T) =JCM 16348(T)). PMID: 19897614 [PubMed - indexed for MEDLINE] Bacillus ruris Int J Syst Evol Microbiol. 2005 Nov;55(Pt 6):2551-4. Bacillus ruris sp. nov., from dairy farms. Heyndrickx M(1), Scheldeman P, Forsyth G, Lebbe L, Rodríguez-Díaz M, Logan NA, De Vos P. Author information: (1)Department of Animal Product Quality, Centre for Agricultural Research-Ghent, Brusselsesteenweg 370, B-9090 Melle, Belgium. [email protected] Four novel ellipsoidal spore-forming Bacillus isolates with swollen sporangia, isolated from raw milk and feed concentrate, showed a high level of similarity in SDS-PAGE, fatty acid methyl esters and routine phenotypic tests. However, 16S rRNA gene sequence comparisons showed that this taxon was different from other related Bacillus species, and only a low level of DNA relatedness was found with the closest phylogenetic and phenotypic relative, Bacillus galactosidilyticus. This taxon could be differentiated from B. galactosidilyticus on the basis of morphological differences, stronger acid reactions with a wide range of substrates after 48 h incubation, and qualitative and quantitative differences in fatty acid content. On the basis of these data, a novel species, Bacillus ruris sp. nov., is proposed, with LMG 22866T (=DSM 17057T) as the type strain. PMID: 16280525 [PubMed - indexed for MEDLINE] Bacillus safensis Int J Syst Evol Microbiol. 2006 Aug;56(Pt 8):1735-40. Bacillus safensis sp. nov., isolated from spacecraft and assembly-facility surfaces. Satomi M(1), La Duc MT, Venkateswaran K. Author information: (1)National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, 236-8648, Japan. Thirteen strains of a novel spore-forming, Gram-positive, mesophilic heterotrophic bacterium were isolated from spacecraft surfaces (Mars Odyssey Orbiter) and assembly-facility surfaces at the Jet Propulsion Laboratory in California and the Kennedy Space Center in Florida. Phylogenetic analysis of 16S rRNA gene sequences has placed these novel isolates within the genus Bacillus, the greatest sequence similarity (99.9 %) being found with Bacillus pumilus. However, these isolates share a mere 91.2 % gyrB sequence similarity with Bacillus pumilus, rendering their 16S rRNA gene-derived relatedness suspect. Furthermore, DNA-DNA hybridization showed only 54-66 % DNA relatedness between the novel isolates and strains of B. pumilus. rep-PCR fingerprinting and previously reported matrix-assisted laser desorption/ionization time-of-flight mass spectrometry protein profiling clearly distinguished these isolates from B. pumilus. Phenotypic analyses also showed some differentiation between the two genotypic groups, although the fatty acid compositions were almost identical. The polyphasic taxonomic studies revealed distinct clustering of the tested strains into two distinct species. On the basis of phenotypic characteristics and the results of phylogenetic analyses of 16S rRNA and gyrB gene sequences, repetitive element primer-PCR fingerprinting and DNA-DNA hybridization, the 13 isolates represent a novel species of the genus Bacillus, for which the name Bacillus safensis sp. nov. is proposed. The type strain is FO-36b(T) (=ATCC BAA-1126(T)=NBRC 100820(T)). PMID: 16902000 [PubMed indexed for MEDLINE] Bacillus salarius Int J Syst Evol Microbiol. 2006 Feb;56(Pt 2):373-7. Bacillus salarius sp. nov., a halophilic, spore-forming bacterium isolated from a salt lake in China. Lim JM(1), Jeon CO, Lee SM, Lee JC, Xu LH, Jiang CL, Kim CJ. Author information: (1)Korea Research Institute of Bioscience and Biotechnology, 52 Oeundong, Yusong, Daejeon 305-333, Republic of Korea. A moderately halophilic bacterium, strain BH169T, capable of growing at salinities of 3-20% (w/v) NaCl was isolated from a saline lake in China. Strain BH169T was strictly aerobic, short-rod-shaped and non-motile (non-flagellated). Its major cellular fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C15:0 and iso-C16:0. The genomic DNA G+C content was about 43 mol% and the predominant quinone was MK-7. The cell-wall peptidoglycan was of the A1gamma type, containing meso-diaminopimelic acid as the diagnostic diamino acid. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a distinct phylogenetic line within the spore-forming rods of the genus Bacillus. The levels of 16S rRNA gene sequence similarity to the type strains of Bacillus species were below 93%. On the basis of phenotypic and molecular properties, strain BH169T (=KCTC 3912T=DSM 16461T) represents the type strain of a novel species within the genus Bacillus, for which the name Bacillus salarius sp. nov. is proposed. PMID: 16449443 [PubMed - indexed for MEDLINE] Bacillus salexigens Int J Syst Bacteriol. 1997 Jul;47(3):735-41. Bacillus salexigens sp. nov., a new moderately halophilic Bacillus species. Garabito MJ(1), Arahal DR, Mellado E, Márquez MC, Ventosa A. Author information: (1)Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Spain. Bacillus salexigens sp. nov. is proposed based on the characteristics of six moderately halophilic, grampositive, rod-shaped strains isolated from salterns and hypersaline soils located in different geographical areas of Spain. These strains were motile, formed endospores, were strictly aerobic, were catalase and oxidase positive, and contained peptidoglycan of the meso-diamlnopimelic acid type in their vegetative cell walls. The DNA base compositions of these strains ranged from 36.3 to 39.5 mol%, and these organisms constitute a homology group with levels of DNA-DNA homology ranging from 73 to 100%. The 16S rRNA sequence of strain C-20MoT, which was used as the representative strain of these isolates, groups with the 16S rRNA sequences of members of the genus Bacillus, and the highest level of similarity is 95.4%. The type strain is strain C-20Mo (= ATCC 700290 = DSM 11483 = CCM 4646). PMID: 9226905 [PubMed - indexed for MEDLINE] Bacillus saliphilus Int J Syst Evol Microbiol. 2005 Jan;55(Pt 1):159-63. Bacillus saliphilus sp. nov., isolated from a mineral pool in Campania, Italy. Romano I(1), Lama L, Nicolaus B, Gambacorta A, Giordano A. Author information: (1)Istituto di Chimica Biomolecolare, Comprensorio ex Olivetti, via Campi Flegrei 34, 80078 Pozzuoli, Na, Italy. A haloalkaliphilic Gram-positive bacterium, strain 45 6AGT, that grew aerobically at an optimum temperature of 37 degrees C and at pH 7-10 (optimum 9.0), was isolated from algal mat from a mineral pool located in Malvizza in the Campania region (southern Italy). The isolate tolerated high concentrations of NaCl, up to 25 %. On the basis of 16S rRNA gene sequence similarity, the strain was shown to belong to the genus Bacillus. Analysis of the 16S rRNA gene sequence revealed high similarity between strain 6AGT and an unidentified isolate from Hailaer soda lake (China) (99.9 % identity) and two Kenyan isolates, 3E1 and WE4 (98.3 and 97.8 % identity, respectively). The G+C content of the DNA was 48.4 mol%. The predominant respiratory quinones were MK-7(H2), MK-7(H4) and DMK-7(H2); phosphatidylglycerol and diphosphatidylglycerol were the predominant polar lipids. iC15 : 0 and aiC15 : 0 were the major fatty acids. Strain 6AGT accumulated osmolytes. The phylogenetic distance of strain 6AGT (=DSM 15402T=ATCC BAA-957T) from any recognized species within the genus Bacillus allowed it to be classified as the type strain of Bacillus saliphilus sp. nov. PMID: 15653870 [PubMed - indexed for MEDLINE] 167. Bacillus salsus Int J Syst Evol Microbiol. 2013 Sep;63(Pt 9):3324-9. doi: 10.1099/ijs.0.050120-0. Epub 2013 Mar 15. Bacillus salsus sp. nov., a halophilic bacterium from a hypersaline lake. Amoozegar MA(1), Didari M, Bagheri M, Fazeli SA, Schumann P, Spröer C, Sánchez-Porro C, Ventosa A. Author information: (1)Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran. [email protected] A Gram-staining-positive, endospore-forming, rod-shaped, strictly aerobic, slightly halophilic bacterium, designated strain A24(T), was isolated from the hypersaline lake Aran-Bidgol in Iran. Cells of strain A24(T) were motile rods and produced oval endospores at a terminal position in swollen sporangia. Strain A24(T) was catalase and oxidase positive. Growth occurred with between 0.5 and 7.5% (w/v) NaCl and the isolate grew optimally at 3% (v/w) NaCl. The optimum temperature and pH for growth were 35 °C and pH 8.0, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain A24(T) belonged to the genus Bacillus within the phylum Firmicutes and showed the closest phylogenetic similarity with the species Bacillus alkalitelluris BA288(T) (97.2%), Bacillus herbersteinensis D-1,5a(T) (96.0%) and Bacillus litoralis SW-211(T) (95.6%). The G+C content of the genomic DNA of this strain was 35.9 mol%. The polar lipid pattern of strain A24(T) consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and two unknown phospholipids. The major cellular fatty acids of strain A24(T) were anteiso-C(15:0) and iso-C(15:0). The respiratory quinones were MK-7 (94%) and MK-6 (4%). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All these features confirm the placement of isolate A24(T) within the genus Bacillus. DNA-DNA hybridization experiments revealed a relatedness of 8% between strain A24(T) and Bacillus alkalitelluris IBRC-M 10596(T), supporting its placement as a novel species. Phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data suggest that this strain represents a novel species of the genus Bacillus, for which the name Bacillus salsus sp. nov. is proposed. The type strain is strain A24(T) ( = IBRC-M 10078 (T) = KCTC 13816(T)). PMID: 23504967 [PubMed - indexed for MEDLINE]$$ 168. Bacillus sediminis Antonie Van Leeuwenhoek. 2013 Dec;104(6):1109-16. doi: 10.1007/s10482- 013-0032-0. Epub 2013 Sep 14. Bacillus sediminis sp. nov., isolated from an electroactive biofilm. Yu Z(1), Wang Y, Qin D, Yang G, Zhou S. Author information: (1)Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou, 510650, People's Republic of China. A Gram-stain positive, facultative anaerobic, motile, spore-forming rod-shaped bacterium with peritrichous flagella, designated DX-5(T), was isolated from an electroactive biofilm. Growth was observed to occur at 35-60 °C, at pH 7.0-10.0 and with 0.5-10 % (w/v) NaCl (optimum growth: 50 °C, pH 8.0 and 0.5-3 % NaCl). Cells were determined to be catalase- and oxidase-positive. The predominant respiratory quinone was identified as MK-7; the major polar lipids were determined to be diphosphatidylglycerol, phosphatidylglycerol, glycolipid, aminoglycolipid and an unidentified phospholipid; the DNA G+C content was determined to be 46.6 mol%; and the major fatty acids (>5 %) were identified as anteiso-C15:0 (33.6 %), iso-C15:0 (24.1 %) and anteiso-C17:0 (13.4 %). The phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain DX-5(T) should be assigned to the genus Bacillus, and was related most closely to the type strains of B. fortis DSM 16012(T) (96.3 %), B. composti KACC 16872(T) (96.3 %) and B. fordii DSM 16014(T) (95.8 %). Results of phenotypic, chemotaxonomic and genotypic analysis indicated that strain DX-5(T) represents a novel species, for which the name B. sediminis sp. nov. is proposed. The type strain is DX-5(T) (=CGMCC 1.12412(T) = KCTC 33102(T)). PMID: 24037481 [PubMed - indexed for MEDLINE]$$ 169. Bacillus selenatarsenatis Int J Syst Evol Microbiol. 2007 May;57(Pt 5):1060-4. Bacillus selenatarsenatis sp. nov., a selenate- and arsenate-reducing bacterium isolated from the effluent drain of a glass-manufacturing plant. Yamamura S(1), Yamashita M, Fujimoto N, Kuroda M, Kashiwa M, Sei K, Fujita M, Ike M. Author information: (1)Water and Soil Environment Division, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan. [email protected] A facultatively anaerobic, selenateand arsenate-reducing bacterium, designated strain SF-1(T), was isolated from a selenium-contaminated sediment obtained from an effluent drain of a glass-manufacturing plant in Japan. The bacterium stained Gram-positive and was a motile, spore-forming rod capable of respiring with selenate, arsenate and nitrate as terminal electron acceptors. The major cellular fatty acids of the strain were iso-C(15 : 0), iso-C(17 : 1)omega10c and C(16 : 1)omega7c alcohol. The G+C content of the genomic DNA was 42.8 mol%. Though the nearest phylogenetic neighbour was Bacillus jeotgali JCM 10885(T), with a 16S rRNA gene sequence similarity of 99.6 %, DNA-DNA hybridization studies showed only 14 % relatedness between these strains, a level that is clearly below the value recommended to delimit different species. This, together with the phenotypic differences (utilization of electron acceptors, NaCl tolerance), suggests that strain SF-1(T) represents a novel species of the genus Bacillus, for which the name Bacillus selenatarsenatis sp. nov. 46 170. 171. 172. 173. is proposed. The type strain is SF-1(T) (=JCM 14380(T)=DSM 18680(T)). PMID: 17473259 [PubMed - indexed for MEDLINE] Bacillus seohaeanensis Int J Syst Evol Microbiol. 2006 Aug;56(Pt 8):1893-8. Bacillus seohaeanensis sp. nov., a halotolerant bacterium that contains L-lysine in its cell wall. Lee JC(1), Lim JM, Park DJ, Jeon CO, Li WJ, Kim CJ. Author information: (1)Korea Research Institute of Bioscience and Biotechnology, 52 Oeundong, Yusong, Daejeon 305-333, Republic of Korea. A halotolerant, round-endospore-forming, aerobic, Gram-positive bacterium, designated BH724(T), was isolated from a solar saltern at Taean in Korea. Cells of this strain were rod-shaped and found to be non-motile. Strain BH724(T) grew at salinities of 0-10 % (w/v) NaCl with an optimum of 3 % (w/v) NaCl and at temperatures of 15-50 degrees C with an optimum of 40 degrees C. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BH724(T) belonged to the genus Bacillus and that Bacillus aquimaris TF-12(T), Bacillus marisflavi TF-11(T) and Bacillus vietnamensis JCM 11124(T) were its closest neighbours, sharing 97.3, 97.2 and 97.0 % 16S rRNA gene sequence similarity, respectively. The genomic DNA G+C content was 39 mol% and the predominant menaquinone was MK-7. Its major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0), iso-C(16 : 0) and iso-C(14 : 0). The peptidoglycan type was A1alpha, linked directly through l-lysine. On the basis of morphological, chemotaxonomic, physiological and phylogenetic properties, strain BH724(T) represents a novel species of the genus Bacillus, for which the name Bacillus seohaeanensis sp. nov. is proposed. The type strain is BH724(T) (=KCTC 3913(T)=DSM 16464(T)). PMID: 16902027 [PubMed - indexed for MEDLINE] Bacillus shacheensis J Gen Appl Microbiol. 2014;60(3):101-5. Lei Z(1), Qiu P, Ye R, Tian J, Liu Y, Wang L, Tang SK, Li WJ, Tian Y. Bacillus shacheensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil. Author information: (1)Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile & Food Engineering, Sichuan University. A moderately halophilic bacterium, strain HNA-14(T), was isolated from a saline-alkali soil sample collected in Shache County, Xinjiang Province. On the basis of the polyphasic taxonomic data, the isolate was considered to be a member of the genus Bacillus. The organism grew optimally at 30°C and pH 8.0. It was moderately halophilic and its optimum growth occurred at 5-10% NaCl. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid and the predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15:0 and iso-C15:0 and the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol manno- sides and two unknown phospholipids. The G+C content of the genomic DNA was 48.6 mol%. Strain HNA-14(T) exhibited a low 16S rRNA gene sequence similarity of 96% with its nearest neighbors [Bacillus clausii KSM-K16 (96.5%), Bacillus xiaoxiensis DSM 21943(T)(96.2%), Bacillus clausii DSM 8716(T) (96.1%), Bacillus patagoniensis PAT05(T) (96.1%), Bacillus lehensis MLB-2(T) (96.0%), Bacillus oshimensis K11(T) (95.9%) and Bacillus hunanensis DSM 23008(T) (95.8%)] and the phenotypic characteristics indicate that strain HNA-14(T) can be distinguished from them. Therefore, a novel species of the genus Bacillus, Bacillus shacheensis sp. nov. (type strain, HNA-14(T)=KCTC 33145=DSM 26902) is proposed. PMID: 25008165 [PubMed - in process] Bacillus shackletonii Int J Syst Evol Microbiol. 2004 Mar;54(Pt 2):373-6. Bacillus shackletonii sp. nov., from volcanic soil on Candlemas Island, South Sandwich archipelago. Logan NA(1), Lebbe L, Verhelst A, Goris J, Forsyth G, Rodríguez-Díaz M, Heyndrickx M, De Vos P. Author information: (1)School of Biological and Biomedical Sciences, Glasgow Caledonian University, Cowcaddens Road, Glasgow G4 0BA, UK. [email protected] A sample of mossy soil taken from the eastern lava flow of northern Candlemas Island, South Sandwich archipelago, yielded six isolates of aerobic, endospore-forming bacteria. Miniaturized routine phenotypic tests and other observations, amplified rDNA restriction analysis and SDS-PAGE analysis suggested that the strains represent a novel taxon. 16S rDNA sequence comparisons support the proposal of a novel species, Bacillus shackletonii sp. nov., the type strain of which is LMG 18435(T) (=CIP 107762(T)). PMID: 15023945 [PubMed - indexed for MEDLINE] Bacillus siamensis Int J Syst Evol Microbiol. 2010 Oct;60(Pt 10):2364-70. doi: 10.1099/ijs. 0.018879-0. Epub 2009 Nov 20. Bacillus siamensis sp. nov., isolated from salted crab (poo-khem) in Thailand. Sumpavapol P(1), Tongyonk L, Tanasupawat S, Chokesajjawatee N, Luxananil P, Visessanguan W. Author information: (1)Department of Food and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand. A Gram-positive, endospore-forming, rod-shaped bacterium, strain PD-A10(T), was isolated from salted crab (poo-khem) in Thailand and subjected to a taxonomic study. Phenotypic and chemotaxonomic characteristics, including phylogenetic analyses, showed that the novel strain was a member of the genus Bacillus. The novel strain grew in medium with 0-14 % (w/v) NaCl, at 4-55°C and at pH4.5-9. The predominant quinone was a menaquinone with seven isoprene units (MK-7). The major fatty acids were anteiso-C₁₅:₀ and anteiso-C₁₇:₀. Polar lipid analysis revealed the presence of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, lysylphosphatidylglycerol, glycolipid and unknown lipids. The DNA G+C content was 41.4 mol%. The 16S rRNA gene sequence similarities between strain PD-A10(T) and Bacillus amyloliquefaciens NBRC 15535(T), Bacillus subtilis DSM 10(T), Bacillus vallismortis DSM 11031(T) and Bacillus mojavensis IFO 15718(T) were 99.5, 99.4, 99.4 and 99.2 %, respectively. Strain PD-A10(T) showed a low degree similarity of rep-PCR fingerprints and low DNA-DNA relatedness with the above-mentioned species. On the basis of the data gathered in this study, strain PD-A10(T) should be classified as representing a novel species of the genus Bacillus, for which the name Bacillus siamensis sp. nov. is proposed. The type strain is PD-A10(T) (=BCC 22614(T)=KCTC 13613(T)). PMID: 19933584 [PubMed - indexed for MEDLINE] 174. Bacillus silvestris Int J Syst Bacteriol. 1999 Apr;49 Pt 2:795-802. Bacillus silvestris sp. nov., a new member of the genus Bacillus that contains lysine in its cell wall. Rheims H(1), Frühling A, Schumann P, Rohde M, Stackebrandt E. Author information: 47 (1)DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany. A Gram-positive, aerobic, rod-shaped, peritrichously flagellated, round-endospore-forming bacterium was isolated from a forest soil near Braunschweig, Lower Saxony, Germany, and designated strain HR3-23T (T = type strain). Morphologically, strain HR3-23T shows the characteristics of a member of the genus Bacillus. The spore position is terminal in a swollen sporangium. Comparative analysis of the 16S rDNA sequence shows strain HR3-23T to be most closely related to Caryophanon tenue (95.8% 16S rRNA similarity) and to Bacillus sphaericus (95.4% 16S rRNA similarity). Phylogenetically, the isolate clusters among species of Bacillus RNA group 2. The DNA G + C content of isolate HR3-23T is 39.3 mol%, the peptidoglycan type is A4 alpha (L-Lys-D-Glu), the major respiratory lipoquinone is menaquinone MK-7 and the predominant fatty acid is of the iso-C15:0 type. Based on the morphological, chemotaxonomic, physiological and phylogenetic properties, a new species, Bacillus silvestris, is proposed; strain HR3-23T is the type strain (= DSM 12223T). PMID: 10319505 [PubMed - indexed for MEDLINE] 175. Bacillus siralis Int J Syst Evol Microbiol. 2000 Nov;50 Pt 6:2181-7. Bacillus siralis sp. nov., a novel species from silage with a higher order structural attribute in the 16S rRNA genes. Pettersson B(1), de Silva SK, Uhlén M, Priest FG. Author information: (1)Department of Biotechnology, Royal Institute of Technology, Stockholm, Sweden. A novel bacterial strain (171544T) was recently isolated from silage and was classified in the genus Bacillus by 16S rDNA sequence analysis. Additional silage samples have been investigated in the present study and four organisms resembling strain 171544T were isolated. Phenotypic and genotypic characterization of these bacteria showed that they constitute a new species of the genus Bacillus. This taxon was positioned in the family Bacillaceae on the basis of evolutionary distance trees using 16S rDNA sequences. Bacillus circulans, Bacillus firmus and Bacillus benzoevorans were the most closely related species with 165 rDNA similarities of 97.2, 96.3 and 95.9%, respectively. All five silage isolates shared a higher order structural feature in the 3' region of the 16S rRNA gene comprising an extension to helix 49 of 24 bp and highly similar random amplified polymorphic DNA patterns that distinguished them from the type strains of B. circulans and B. firmus. Moreover, they possessed a unique pattern of phenotypic features including subterminally or terminally located endospores which distinctly swelled the sporangium, strictly aerobic metabolism but with the ability to utilize nitrate as a terminal electron acceptor under anaerobic conditions, and hydrolysis of casein but not starch. The name Bacillus siralis is therefore proposed for this new taxon. The type strain of B. siralis is strain 171544T (= NCIMB 13601T = CIP 106295T). PMID: 11155995 [PubMed - indexed for MEDLINE] 176. Bacillus solimangrovi Int J Syst Evol Microbiol. 2014 May;64(Pt 5):1622-8. doi: 10.1099/ijs. 0.058230-0. Epub 2014 Jan 31. Bacillus solimangrovi sp. nov., isolated from mangrove soil. Lee GH(1), Rhee MS, Chang DH, Kwon KK, Bae KS, Yang SH, Kim BC. Author information: (1)Korean Collection for Type Cultures (KCTC), Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-gu, Daejeon 305-806, Republic of Korea. Two novel bacterial strains, GH2-4T and GH2-5, were isolated from mangrove soil near the seashore of Weno island in Chuuk state, Micronesia, and were characterized by a polyphasic approach. The two strains were strictly aerobic, Gram-staining-positive, motile, endospore-forming rods that were catalase- and oxidase-positive. Colonies were circular, convex, stringy and transparent yellowish (GH2-4T) or opaque whitish (GH2-5). The 16S rRNA gene sequences of the two isolates were identical. The most closely related strains in terms of 16S rRNA gene sequence similarity were Bacillus kochii WCC 4582T, B. horneckiae DSM 23495T, B. azotoformans LMG 9581T, B. cohnii DSM 6307T and B. halmapalus DSM 8723T (95.6, 95.4, 95.4, 95.2 and 95.2% similarity, respectively). The partial groEL sequence of strain GH2-4T was identical to that of strain GH2-5 and showed <85% similarity to those of the most closely related strains. The isolates grew at pH 5-12 (optimal growth at pH 9), at 10-40 °C (optimum 30-35 °C) and at 0-9% (w/v) NaCl (optimum 1-3% NaCl). The cell-wall peptidoglycan of strains GH2-4T and GH2-5 contained meso-diaminopimelic acid and cell-wall hydrolysates contained ribose as a major sugar. The DNA G+C content was 36 mol%, and DNA-DNA relatedness between the isolates and five related reference strains was 20-24%. Strain GH2-4T exhibited 81% DNA-DNA relatedness with strain GH2-5. The major cellular fatty acids of both strains were iso-C15:0, iso-C16:0, iso-C14:0 and anteiso-C15:0 and the predominant menaquinone was MK-7. On the basis of the evidence from this polyphasic study, strains GH2-4T and GH2-5 (=KCTC 33143=JCM 18995=DSM 27084) represent a novel species of the genus Bacillus, for which the name Bacillus solimangrovi sp. nov. is proposed; the type strain is GH2-4T (=KCTC 33142T=JCM 18994T=DSM 27083T). PMID: 24488932 [PubMed - indexed for MEDLINE]$$ 177. Bacillus solisalsi Int J Syst Evol Microbiol. 2009 Jun;59(Pt 6):1460-4. doi: 10.1099/ijs.0.000653-0. Bacillus solisalsi sp. nov., a halotolerant, alkaliphilic bacterium isolated from soil around a salt lake. Liu H(1), Zhou Y, Liu R, Zhang KY, Lai R. Author information: (1)Biotoxin Units of Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, PR China. A novel Gram-positive, motile, rod-shaped bacterium isolated from a saline soil in China was characterized by a polyphasic taxonomic approach. The strain, designated YC1(T), was halotolerant [tolerating up to 15 % (w/v) NaCl] and alkaliphilic (growing at a broad pH range of 5-13). 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Bacillus, showing highest similarity to Bacillus macauensis JCM 13285(T) (98.0 %). However, DNA-DNA hybridization indicated low levels of genomic relatedness with B. macauensis JCM 13285(T) (8.5 %). The major isoprenoid quinone was MK-7 and the cellular fatty acid profile consisted of significant amounts of iso-C(15 : 0) (38.6 %) and anteiso-C(15 : 0) (35.9 %). The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C 48 content of the genomic DNA was 41.8 mol%. On the basis of the polyphasic evidence from this study, strain YC1(T) (=KCTC 13181(T)=CGMCC 1.6854(T)) should be classified as the type strain of a novel species of the genus Bacillus, for which the name Bacillus solisalsi sp. nov. is proposed. PMID: 19502335 [PubMed - indexed for MEDLINE] 178. Bacillus songklensis Int J Syst Evol Microbiol. 2013 Nov;63(Pt 11):4189-95. doi: 10.1099/ijs.0.050682-0. Epub 2013 Jun 14. Bacillus songklensis sp. nov., isolated from soil. Kang H(1), Weerawongwiwat V, Kim JH, Sukhoom A, Kim W. Author information: (1)Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea. A Gram-stain-positive, spore-forming, rod-shaped, motile, strictly aerobic bacterial strain, designated CAU 1033(T), was isolated from soil and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1033(T) formed a distinct lineage within the genus Bacillus and was most closely related to Bacillus drentensis KCTC 13025(T) (similarity 95.9 %). CAU 1033(T) contained MK-7 as the only isoprenoid quinone and iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. The cell wall peptidoglycan of strain CAU 1033(T) contained meso-diaminopimelic acid and the major whole-cell sugars were arabinose, sucrose and ribose. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, four unidentified aminophospholipids, an unidentified aminolipid, two unidentified glycolipids and another unidentified polar lipid. The DNA G+C content was 41.4 mol%. On the basis of phenotypic data and phylogenetic inference, strain CAU 1033(T) was classified as a representative of a novel species in the genus Bacillus for which the name Bacillus songklensis sp. nov. is proposed. The type strain is CAU 1033(T) ( = KCTC 13881(T) = CCUG 61889(T)). PMID: 23771626 [PubMed - indexed for MEDLINE]$$ 179. Bacillus sonorensis Int J Syst Evol Microbiol. 2001 Sep;51(Pt 5):1671-9. Bacillus sonorensis sp. nov., a close relative of Bacillus licheniformis, isolated from soil in the Sonoran Desert, Arizona. Palmisano MM(1), Nakamura LK, Duncan KE, Istock CA, Cohan FM. Author information: (1)Department of Biology, Wesleyan University, Middletown, CT 06459-0170, USA. Eight Bacillus strains isolated from Sonoran Desert soil were shown to belong to a previously unidentified species, for which the name Bacillus sonorensis sp. nov. is proposed. The type strain is strain L87-10T (= NRRL B-23154T). On the basis of phenotypic and genetic data, B. sonorensis is most closely related to Bacillus licheniformis. B. sonorensis can be distinguished from B. licheniformis by salt tolerance, pigmentation, multilocus enzyme electrophoresis, reassociation of genomic DNA and sequence differences in protein-coding genes and 16S rRNA. PMID: 11594594 [PubMed - indexed for MEDLINE] 180. Bacillus subterraneus Int J Syst Evol Microbiol. 2002 May;52(Pt 3):869-74. Bacillus subterraneus sp. nov., an iron- and manganese-reducing bacterium from a deep subsurface Australian thermal aquifer. Kanso S(1), Greene AC, Patel BK. Author information: (1)Microbial Research Discovery Unit, School of Biomolecular and Biomedical Sciences, Faculty of Science, Griffith University, Brisbane, Queensland, Australia. A facultatively anaerobic bacterium, designated strain COOI3B(T) (= ATCC BAA 136T = DSM 13966T), was isolated from the waters emitted by a bore well tapping the deep subterranean thermal waters of the Great Artesian Basin of Australia. The cells were straight to slightly curved rods (0.5-0.8 x 2-25 microm) that occurred singly and rarely in pairs or in chains. Strain COOI3B(T) was motile by peritrichous flagella. It stained gram-negative, but electron micrographs showed a gram-positive-type cell wall. Spores were never observed and cells were heat-sensitive. Yeast extract at 0.02% (w/v) was required for growth and could also be used as a sole carbon and energy source at concentrations higher than 0.1% (w/v). The strain utilized amorphous iron(III), manganese(IV), nitrate, nitrite and fumarate as electron acceptors in the presence of yeast extract, glucose, sucrose, fructose, maltose, xylose, starch, glycerol, ethanol or lactate. Electron acceptors were not obligately required and growth was better in the presence of nitrate than in its absence. Acid was not produced from growth on carbohydrates. Tryptophan deaminase, H2S, arginine dihydrolase, lysine decarboxylase, beta-galactosidase, arabinosidase, glucuronidase, glucosaminidase, nitroanilidase, xylosidase and ornithine decarboxylase were not produced. Starch and gelatin, but not casein, were hydrolysed. Aesculin and catalase, but not oxidase and urease, were produced. Strain COOI3B(T) grew optimally at temperatures between 37 and 40 degrees C (the temperature growth range was 25-45 degrees C) and at pH 7.0-9.0 (the pH growth range was 6.0 to 9.5) with 5% (w/v) NaCl (the NaCl concentration growth range was 0.9%, w/v). The DNA base composition was 43 +/- 1 mol % G+C. Phylogenetic analysis indicated that it was a member of the family Bacillaceae, Bacillus infernus and Bacillus firmus being the closest phylogenetic neighbours (having a mean similarity value of 96%); hence, strain COOI3B(T) is designated as a novel species, Bacillus subterraneus sp. nov. PMID: 12054251 [PubMed - indexed for MEDLINE] 181. Bacillus taeanensis Int J Syst Evol Microbiol. 2006 Dec;56(Pt 12):2903-8. Bacillus taeanensis sp. nov., a halophilic Gram-positive bacterium from a solar saltern in Korea. Lim JM(1), Jeon CO, Kim CJ. Author information: (1)Korea Research Institute of Bioscience and Biotechnology, 52 Oeundong, Yusong, Daejeon 305-333, Republic of Korea. A halophilic bacterium, strain BH030017(T), showing optimum growth at 2-5 % (w/v) NaCl was isolated from solar-saltern sediment from the Tae-An area of Korea and was characterized taxonomically. The cells of strain BH030017(T) were Gram-positive, motile, short rods containing cell-wall peptidoglycan based on meso-diaminopimelic acid. The major cellular fatty acids were anteiso-C(15 : 0) and iso-C(15 : 0). The DNA G+C content was 36 mol% and the predominant lipoquinone was MK-7. The major cellular phospholipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BH030017(T) formed a cluster with Bacillus clarkii DSM 8720(T) and Bacillus agaradhaerens DSM 8721(T) within the family Bacillaceae. 16S rRNA 49 182. 183. 184. 185. gene sequence similarities with respect to closely related type strains were less than 95.1 %. On the basis of its phylogenetic, phenotypic and chemotaxonomic properties, strain BH030017(T) represents a novel species within the genus Bacillus, for which the name Bacillus taeanensis sp. nov. is proposed. The type strain is BH030017(T) (=KCTC 3918(T)=DSM 16466(T)). PMID: 17158996 [PubMed - indexed for MEDLINE] Bacillus tequilensis Int J Syst Evol Microbiol. 2006 Jul;56(Pt 7):1475-84. Bacillus tequilensis sp. nov., isolated from a 2000-year-old Mexican shaft-tomb, is closely related to Bacillus subtilis. Gatson JW(1), Benz BF, Chandrasekaran C, Satomi M, Venkateswaran K, Hart ME. Author information: (1)Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, TX 76107, USA. A Gram-positive, spore-forming bacillus was isolated from a sample taken from an approximately 2000-year-old shaft-tomb located in the Mexican state of Jalisco, near the city of Tequila. Tentative identification using conventional biochemical analysis consistently identified the isolate as Bacillus subtilis. DNA isolated from the tomb isolate, strain 10b(T), and closely related species was used to amplify a Bacillus-specific portion of the highly conserved 16S rRNA gene and an internal region of the superoxide dismutase gene (sodA(int)). Trees derived from maximum-likelihood methods applied to the sodA(int) sequences yielded non-zero branch lengths between strain 10b(T) and its closest relative, whereas a comparison of a Bacillus-specific 546 bp amplicon of the 16S rRNA gene demonstrated 99 % similarity with B. subtilis. Although the 16S rRNA gene sequences of strain 10b(T) and B. subtilis were 99 % similar, PFGE of NotI-digested DNA of strain 10b(T) revealed a restriction profile that was considerably different from those of B. subtilis and other closely related species. Whereas qualitative differences in whole-cell fatty acids were not observed, significant quantitative differences were found to exist between strain 10b(T) and each of the other closely related Bacillus species examined. In addition, DNA-DNA hybridization studies demonstrated that strain 10b(T) had a relatedness value of less than 70 % with B. subtilis and other closely related species. Evidence from the sodA(int) sequences, whole-cell fatty acid profiles and PFGE analysis, together with results from DNA-DNA hybridization studies, justify the classification of strain 10b(T) as representing a distinct species, for which the name Bacillus tequilensis sp. nov. is proposed. The type strain is 10b(T) (=ATCC BAA-819(T)=NCTC 13306(T)). PMID: 16825615 [PubMed - indexed for MEDLINE] Bacillus thaonhiensis Curr Microbiol. 2014 Aug;69(2):225. Using a new culture method for unculturable soil bacteria, we discovered a novel species, NHI-38(T), from the forest soil of Kyonggi University campus, South Korea. It was a Gram-positive, rod-shaped, and endospore-forming bacterial strain. It grew over a wide pH range (6.5-9.5), with an optimum range of pH 7-9, and in a wide range of temperatures (15-60 °C), with an optimum range of 35-45 °C. Growth was possible at 0-2 % NaCl concentration, and the optimal range was between 0.5 and 1.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that this new species clustered within the genus Bacillus; it was closely related to "Bacillus abyssalis" SCSIO 15042(T) (98.86 %), B. methanolicus NCIMB 13113(T) (95.97 %), B. vietnamensis 15-1(T) (95.8 %), B. seohaeanensis BH724(T) (95.5 %), B. timonensis MM10403188(T) (95.33 %), and B. subtilis subsp. subtilis NCIB 3610(T) (94.87 %). The main fatty acid components of this bacterium were iso-C15:0 (35.92 %), summed feature 3 (C16:1ω7c/C16:1ω6c; 16.92 %), and anteiso-C15:0 (14.19 %). The predominant quinone in this bacterial strain was MK-7. The polar lipid profile primarily comprised phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The genomic DNA G+C composition of the isolate was 40.7 mol%. The DNA-DNA hybridization results indicated that this strain was distinct from other Bacillus species, the degree of similarity being 50 % with "B. abyssalis", 56 % with B. methanolicus, 47 % with B. vietnamensis, 43 % with B. seohaeanensis, 46 % with B. timonensis, and 32 % with B. subtilis. Based on our results, we regard strain NHI-38(T) as a novel member of the Bacillus genus, and we propose the name Bacillus thaonhiensis (=KACC 17216(T) = KEMB 9005-019(T) = JCM 18863(T)). PMID: 23995763 [PubMed - in process]$$ Bacillus thermoamylovorans Int J Syst Bacteriol. 1995 Jan;45(1):9-16. Bacillus thermoamylovorans sp. nov., a moderately thermophilic and amylolytic bacterium. Combet-Blanc Y(1), Ollivier B, Streicher C, Patel BK, Dwivedi PP, Pot B, Prensier G, Garcia JL. Author information: (1)Laboratoire de Microbiologie ORSTOM, Université de Provence, Marseille, France. A moderately thermophilic, facultatively anaerobic, amylolytic bacterium was isolated from palm wine, a tropical alcoholic beverage that was sampled in Senegal. The cells were gram positive, catalase positive, non-spore forming, rod shaped, and slightly motile with peritrichous flagella. The strain which we examined did not possess cytochrome and produced L-(+)-lactate, acetate, ethanol, and formate but not hydrogen during carbohydrate fermentation. Growth occurred at pH values ranging from 5.4 to 8.5, and optimum growth occurred at around pH 7.0. The optimum temperature for growth was around 50 degrees C, and the upper temperature limit for growth was 58 degrees C. The guanine-plus-cytosine content of the DNA was 38.8 +/- 0.2 mol%. A sequence analysis of the 16S rRNA gene revealed that the new organism is closely related phylogenetically to members of genus Bacillus. Despite the lack of spores, we propose that on the basis of phylogenetic characteristics, the new isolate should be classified as a new Bacillus species, Bacillus thermoamylovorans. The type strain is strain DKP (= Collection of Institut Pasteur CNCM I-1378). PMID: 7857812 [PubMed - indexed for MEDLINE] Bacillus thermocatenulatus Mikrobiologiia. 1975 Mar-Apr;44(2):265-8. [New species of thermophilic bacilli--Bacillus thermocatenulatus nov. sp]. [Article in Russian] Golovacheva RS, Loginova LG, Salikhov TA, Kolesnikov AA, Zaĭtseva GN. Detailed study of the obligate-thermophilic aerobic spore-forming bacterium, indentified earlier as Bacillus megaterium, allowed to describe it as a new species--Bacillus thermocatenulatus nov. sp. This organism is characterized by a high content of GC in DNA (69 mole percent). PMID: 1226140 [PubMed - indexed for MEDLINE]。 50 186. Bacillus thermocopriae Int J Syst Evol Microbiol. 2013 Aug;63(Pt 8):3024-9. doi: 10.1099/ijs.0.046953-0. Epub 2013 Feb 8. Bacillus thermocopriae sp. nov., isolated from a compost. Han L(1), Yang G, Zhou X, Yang D, Hu P, Lu Q, Zhou S. Author information: (1)Guangdong Institute of Eco-Environmental and Soil Science, Guangzhou 510650, PR China. A Gram-reaction-positive, facultatively anaerobic, motile, endospore-forming, rod-shaped strain, designated SgZ-7(T), was isolated from a windrow compost pile and was characterized by means of a polyphasic approach. Growth occurred with 0-3 % (w/v) NaCl (optimum 1 %), at pH 6.0-10.0 (optimum pH 7.2) and at 40-60 °C (optimum 50 °C). The main respiratory quinone was MK-7. The predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content was 46.6 mol%. The phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain SgZ-7(T) should be assigned to the genus Bacillus and was related most closely to Bacillus drentensis LMG 21831(T) (sequence similarity 97.2 %). The result of the DNA-DNA hybridization experiment revealed a low relatedness (27.2 %) between the isolate and B. drentensis LMG 21831(T). The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated that strain SgZ-7(T) represents a novel species, for which the name Bacillus thermocopriae sp. nov. is proposed. The type strain is SgZ-7(T) (= CCTCC AB 2012030(T) = KACC 16700(T)). PMID: 23396718 [PubMed - indexed for MEDLINE] 187. Bacillus thermodenitrificans Int J Syst Evol Microbiol. 2000 May;50 Pt 3:1331-7. Bacillus thermodenitrificans sp. nov., nom. rev. Manachini PL(1), Mora D, Nicastro G, Parini C, Stackebrandt E, Pukall R, Fortina MG. Author information: (1)Department of Food Science and Microbiology, University of Milan, Italy. A polyphasic study was performed on 10 soil isolates of thermophilic denitrifying Bacillus strains from different geographical areas. The presence of two main characteristic bands following amplification of the internal transcribed spacer (ITS) region of rrn operons suggests a close relatedness to 'Bacillus thermodenitrificans'. The isolates cluster around two strains of 'B. thermodenitrificans' in riboprint and fatty acid analyses, though differences occur at the strain level. Subsequent DNA-DNA reassociation studies including the 10 isolates, 'B. thermodenitrificans' DSM 465T and DSM 466, and Bacillus stearothermophilus ATCC 12980T and Bacillus thermoleovorans ATCC 43513T revealed such a high level of genomic relatedness between the isolates and the DSM strains (> 73% similarity) that they must be considered strains of the same taxon. The degree of DNA-DNA similarity between the 12 strains of 'B. thermodenitrificans' and the type strains of the other two phylogenetically neighbouring Bacillus species was significantly lower (21-43% similarity). Based upon phylogenetic, chemotaxonomic and phenotypic evidence, the designation of B. thermodenitrificans sp. nov., nom. rev. is proposed. The type strain of B. thermodenitrificans is DSM 465T. PMID: 10843079 [PubMed - indexed for MEDLINE] 188. Bacillus thermoglucosidasius Syst Appl Microbiol. 1983;4(4):487-95. doi: 10.1016/S0723-2020(83)80006-X. Bacillus thermoglucosidasius sp. nov., a New Species of Obligately Thermophilic Bacilli. Suzuki Y(1), Kishigami T, Inoue K, Mizoguchi Y, Eto N, Takagi M, Abe S. Author information: (1)Department of Agricultural Chemistry, Kyoto Prefectural University, Shimogamo, Sakyo-ku, Kyoto 606, Japan. A group of 6 strains of obligately thermophilic spore-formers is described as a novel species named Bacillus thermoglucosidasius. The strains are strictly aerobic, neutrophilic, amylolytic, Gram-positive, azide sensitive, produce terminally swollen sporangia and exo-oligo-1,6-glucosidase in large amounts. Strain KP 1006 (DSM 2542) is designated as the type strain. Growth occurs at temperatures from 42°C to 69°C with an optimum at 61-63°C, and at an initial pH of 6.5-8.5. The guanine + cytosine content of DNA, estimated by thermal DNA denaturation, is 45-46 mol%. Copyright Â© 1983 Gustav Fischer Verlag, Stuttgart/New York. Published by Elsevier GmbH.. All rights reserved. PMID: 23194806 [PubMed] 189. Bacillus thermolactis Int J Syst Evol Microbiol. 2011 Aug;61(Pt 8):1954-61. doi: 10.1099/ijs.0.024240-0. Epub 2010 Sep 10. Bacillus thermolactis sp. nov., isolated from dairy farms, and emended description of Bacillus thermoamylovorans. Coorevits A(1), Logan NA, Dinsdale AE, Halket G, Scheldeman P, Heyndrickx M, Schumann P, Van Landschoot A, De Vos P. Author information: (1)Laboratory of Biochemistry and Brewing, Faculty of Applied Engineering Sciences, University College Ghent, Schoonmeerstraat 52, 9000 Ghent, Belgium. [email protected] A polyphasic taxonomic study was performed on 22 thermotolerant, aerobic, endospore-forming bacteria from dairy environments. Seventeen isolates were retrieved from raw milk, one from a filter cloth and four from grass, straw or milking equipment. These latter four isolates (R-6546, R-7499, R-7764 and R-7440) were identified as Bacillus thermoamylovorans based on DNA-DNA hybridizations (values above 70 % with Bacillus thermoamylovorans LMG 18084(T)) but showed discrepancies in characteristics with the original species description, so an emended description of this species is given. According to 16S rRNA gene sequence analysis and DNA-DNA hybridization experiments, the remaining 18 isolates (R-6488(T), R-28193, R-6491, R-6492, R-7336, R-33367, R-6486, R-6770, R-31288, R-28160, R-26358, R-7632, R-26955, R-26950, R-33520, R-6484, R-26954 and R-7165) represented one single species, most closely related to Bacillus thermoamylovorans (93.9 % 16S rRNA gene sequence similarity), for which the name Bacillus thermolactis is proposed. Cells were Gram-stain-positive, facultatively anaerobic, endospore-forming rods that grew optimally at 40-50 °C. The cell wall peptidoglycan type of strain R-6488(T), the proposed type strain, was A1γ based on meso-diaminopimelic acid. Major fatty acids of the strains were C(16 : 0) (28.0 %), iso-C(16 : 0) (12.1 %) and iso-C(15 : 0) (12.0 %). MK-7 was the predominant menaquinone, and major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and some unidentified phospholipids. DNA G+C content was 35.0 mol%. Phenotypic properties allowed discrimination from other thermotolerant species of the genus Bacillus and supported the description of the novel species Bacillus thermolactis, with strain R-6488(T) ( = LMG 25569(T) = DSM 23332(T)) as the proposed type strain. PMID: 20833876 [PubMed - indexed for MEDLINE] 51 190. Bacillus thermoleovorans Extremophiles. 2000 Dec;4(6):365-71. Isolation and characterization of lipid-degrading Bacillus thermoleovorans IHI-91 from an icelandic hot spring. Markossian S(1), Becker P, Märkl H, Antranikian G. Author information: (1)Institute of Technical Microbiology, Technical University Hamburg-Harburg, Hamburg, Germany. An efficient lipid-degrading thermophilic aerobic bacterium was isolated from an icelandic hot spring and classified as Bacillus thermoleovorans IHI-91. The aerobic bacterium grows optimally at 65 degrees C and pH 6.0 and secretes a high level of lipase (300 Ul(-1)). The newly isolated strain utilizes several lipids such as palmitic acid, stearic acid, lanolin, olive oil, sunflower seed oil, soya oil, and fish oil as sole carbon and energy source without an additional supply of growth factors. The degradation of about 93% of triolein, which is present in olive oil, was observed after only 7h of fermentation at a maximal growth rate of 1.0 h(-1). During growth at optimal conditions on yeast extract, the doubling time was only 15 min. Based on 16S rDNA studies, DNA-DNA hybridization and morphological and physiological properties, the isolate IHI-91 was identified as Bacillus thermoleovorans IHI-91 sp. nov. Because of its production of high concentrations of thermoactive lipases and esterases and the capability of degrading a wide range of lipids at high temperatures, the isolated strain is an ideal candidate for application in various biotechnological processes such as wastewater treatment. PMID: 11139079 [PubMed - indexed for MEDLINE] 191. Bacillus thermophilum Tang J(1), Yang G, Wen J, Yu Z, Zhou S, Liu Z. Bacillus thermophilum sp. nov., isolated from a microbial fuel cell. Arch Microbiol. 2014 Jun 8. [Epub ahead of print] Author information: (1)Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou, 510650, People's Republic of China. A novel thermophilic, Gram-staining positive bacterium, designated DX-2(T), was isolated from the anode biofilm of a microbial fuel cell. Cells of the strain were oxidase positive, catalase positive, facultative anaerobic, motile rods. The isolate grew at 30-60 °C (optimum 50 °C) and pH 5-9 (optimum pH 8-8.5). The pairwise 16S rRNA gene sequence similarities showed that strain DX-2(T) was most closely related to Bacillus fumarioli LMG 17489(T) (96.2 %), B. firmus JCM 2512(T) (96.0 %) and B. foraminis DSM 19613(T) (95.7 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DX-2(T) formed a cluster with B. smithii (95.5 %) and B. infernus (94.9 %). The genomic G+C content of DX-2(T) was 43.7 mol%. The predominant respiratory quinone was MK-7. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unknown phospholipids. The major cellular fatty acid was iso-C16:0. Based on its phenotypic characteristics, chemotaxonomic features, and results of phylogenetic analysis, the strain was identified to represent a distinct novel species in the genus Bacillus, and the name proposed is B. thermophilum sp. nov. The type strain is DX-2(T) (=CCTCC AB2012194(T) = KCTC 33128(T)). PMID: 24908072 [PubMed - as supplied by publisher] 192. Bacillus thermotolerans Int J Syst Evol Microbiol. 2013 Oct;63(Pt 10):3672-8. doi: 10.1099/ijs.0.048942-0. Epub 2013 Apr 26. Bacillus thermotolerans sp. nov., a thermophilic bacterium capable of reducing humus. Yang G(1), Zhou X, Zhou S, Yang D, Wang Y, Wang D. Author information: (1)Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China. A novel thermotolerant bacterium, designated SgZ-8(T), was isolated from a compost sample. Cells were non-motile, endospore-forming, Gram-staining positive, oxidase-negative and catalase-positive. The isolate was able to grow at 20-65 °C (optimum 50 °C) and pH 6.0-9.0 (optimum 6.5-7.0), and tolerate up to 9.0 % NaCl (w/v) under aerobic conditions. Anaerobic growth occurred with anthraquinone-2,6- disulphonate (AQDS), fumarate and NO3(-) as electron acceptors. Phylogenetic analysis based on the16S rRNA and gyrB genes grouped strain SgZ-8(T) into the genus Bacillus, with the highest similarity to Bacillus badius JCM 12228(T) (96.2 % for 16S rRNA gene sequence and 83.5 % for gyrB gene sequence) among all recognized species in the genus Bacillus. The G+C content of the genomic DNA was 49.3 mol%. The major isoprenoid quinone was menaquinone 7 (MK-7) and the polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The major cellular fatty acid was iso-C16 : 0. On the basis of its phenotypic and phylogenetic properties, chemotaxonomic analysis and the results of physiological and biochemical tests, strain SgZ-8(T) ( = CCTCC AB 2012108(T) = KACC 16706(T)) was designated the type strain of a novel species of the genus Bacillus, for which the name Bacillus thermotolerans sp. nov. is proposed. PMID: 23625259 [PubMed - indexed for MEDLINE]$$ 193. Bacillus thiaminolyticus Int J Syst Bacteriol. 1990 Jul;40(3):242-6. Bacillus thiaminolyticus sp. nov., nom. rev. Nakamura LK. Author information: Northern Regional Research Center, U.S. Department of Agriculture, Peoria, Illinois 61604. The name "Bacillus thiaminolyticus" Kuno 1951 was not included on the Approved Lists of Bacterial Names and has lost standing in bacteriological nomenclature. The genetic homogeneity of "Bacillus thiaminolyticus" was assessed by determining guanine-plus-cytosine contents by the buoyant density method and by measuring DNA relatedness by using spectrophotometric reassociation procedures. Of the 26 strains which I studied, 24 had guanine-plus-cytosine contents in the range from 52 to 54 mol%. The consistently high DNA relatedness values of 60 to 100% of these 24 strains to the type strain indicated that the "B. thiaminolyticus" group is genetically homogeneous. Low DNA relatedness values of 20 to 31% showed that "B. thiaminolyticus" is genetically unrelated to Bacillus alvei, "Bacillus aneurinolyticus," "Bacillus apiarius," Bacillus larvae, Bacillus laterosporus, Bacillus macerans, and Bacillus stearothermophilus. In general, the "B. thiaminolyticus" group was highly homogeneous for 49 phenotypic characteristics and clearly distinguishable from B. alvei, with which it was allegedly synonymous. On the basis of these findings, revival of the name Bacillus thiaminolyticus is proposed. PMID: 2397192 [PubMed - indexed for MEDLINE] 194. Bacillus thioparus FEMS Microbiol Lett. 2007 Jun;271(2):289-96. Epub 2007 Apr 20. Isolation and characterization of Bacillus thi- 52 oparus sp. nov., chemolithoautotrophic, thiosulfate-oxidizing bacterium. Pérez-Ibarra BM(1), Flores ME, García-Varela M. Author information: (1)Doctorado en Ciencias Biológicas de la Universidad Autónoma Metropolitana, México. [email protected] A novel bacterium, strain BMP-1(T), was isolated from a continuous wastewater treatment culture system operating with a bacterial consortium. Cells of the isolate were Gram-variable, aerobic, moderately halotolerant, motile and endospore-forming rods. Strain BMP-1(T) grew chemolithoautotrophically by oxidation of thiosulfate to sulfate with a growth yield of 1.07 g protein mol(-1) of thiosulfate consumed. DNA G+C content was 43.8 mol%. Its cell wall had peptidoglycan based on m-diaminopimelic acid, and the major component of fatty acid was C(15 : 0). The 16S rRNA gene analysis showed that strain belongs to the genus Bacillus, sharing a 99.5% of sequence similarity with Bacillus jeotgali CCM 7133(T). DNA-DNA hybridization between the isolate of this study and this strain was 44%. Thus, the inclusion of strain BMP-1(T) in the genus Bacillus is suggested as a novel species and the name Bacillus thioparus sp. nov. (Type strain BMP-1(T)=BM-B-436(T)=CECT 7196(T)) is proposed. The sequence of the 16S rRNA gene has been deposited in GenBank with accession number DQ371431. PMID: 17451444 [PubMed - indexed for MEDLINE] 195. Bacillus tianmuensis FEMS Microbiol Lett. 2009 Jul;296(1):26-30. doi: 10.1111/j.1574- 6968.2009. 01610.x. Epub 2009 May 1. Bacillus tianmuensis sp. nov., isolated from soil in Tianmu Mountain national natural reserve, Hangzhou, China. Wen YP(1), Wu XC, Qian CD, Zhao YH, Fang HH, Li O. Author information: (1)Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China. In a project aiming to isolate strains with the ability to produce nonribosomal peptides, a gram-negative, endospore-forming, rod-shaped strain, designated B5(T), was isolated from a soil sample collected from Tianmu Mountain national natural reserve in Hangzhou, China. Strain B5(T) contained meso-diaminopimelic acid in the cell wall peptidoglycan. The major cellular fatty acids were anteiso-C(15:0) and iso-C(15:0). The DNA G+C content was 42.5 mol%. The phylogenetic analysis based on 16S rRNA gene sequence indicated that strain B5(T) fell within the genus Bacillus, with highest sequence similarity values to Bacillus barbaricus DSM 14730(T) (96.4%) and Bacillus macauensis JCM 13285(T) (95.5%). The isolate, however, could be distinguished from Bacillus strains with validly published names by low 16S rRNA gene sequence similarity values, distinct phenotypic and chemotaxonomic characteristics. On the basis of these polyphasic evidences, it is demonstrated that the isolate B5(T) represents a novel species of the genus Bacillus, for which the name Bacillus tianmuensis sp. nov. is proposed. The type strain is B5(T) (=DSM 22111(T)=CGMCC 1.8879(T)). PMID: 19459975 [PubMed - indexed for MEDLINE] 196. Bacillus tianshenii Int J Syst Evol Microbiol. 2014 Jun;64(Pt 6):1998-2002. doi: 10.1099/ijs.0.062224-0. Epub 2014 Mar 10. Bacillus tianshenii sp. nov., isolated from a marine sediment sample. Jiang Z(1), Zhang DF(1), Khieu TN(2), Son CK(3), Zhang XM(1), Cheng J(1), Tian XP(4), Zhang S(5), Li WJ(6). Author information: (1)Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China. (2)Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Vietnam. (3)School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Vietnam. (4)Key laboratory of Tropical Marine Bio-resources and Ecology, Chinese Academy of Sciences (CAS); RNAM Center for Marine Microbiology, CAS; Guangdong Key laboratory of Marine Materia Medica; South China Sea Institute of Oceanology, CAS, Guangzhou, 510301, PR China. (5)Key laboratory of Tropical Marine Bio-resources and Ecology, Chinese Academy of Sciences (CAS); RNAM Center for Marine Microbiology, CAS; Guangdong Key laboratory of Marine Materia Medica; South China Sea Institute of Oceanology, CAS, Guangzhou, 510301, PR China [email protected] [email protected]. (6)Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China [email protected] [email protected]. A novel Gram-stain-positive, motile, catalase- and oxidase-positive, aerobic, endospore-forming, peritrichous, rod-shaped bacterium, designated YIM M13235(T), was isolated from a marine sediment sample collected from the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM M13235(T) belonged to the genus Bacillus. The strain grew optimally at 30 °C, pH 7.0 and in the presence of 2-4% (w/v) NaCl. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. Strain YIM M13235(T) exhibited a menaquinone system with MK-7, and the major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unknown phospholipids and one unknown glycolipid. The major fatty acids (>5%) were iso-C(15 : 0), anteiso-C(15 : 0), anteiso-C(17 : 0), iso-C(17 : 1)ω10c and summed feature 4 (anteiso-C(17 : 1) and/or iso-C(17 : 1)). The genomic DNA G+C content was 42.1 mol%. The DNA-DNA relatedness values between strain YIM M13235(T) and its close relatives (16S rRNA gene sequence similarities >97%) including Bacillus halmapalus DSM 8723(T), Bacillus horikoshii DSM 8719(T) and Bacillus zhanjiangensis JSM 099021(T) were 41%, 44% and 44%, respectively. On the basis of genotypic, phenotypic and DNA-DNA relatedness data, it is apparent that strain YIM M13235(T) represents a novel species of the genus Bacillus, for which the name Bacillus tianshenii sp. nov. is proposed. The type strain is YIM M13235(T) ( = DSM 25879(T) = KCTC 33044(T)). © 2014 IUMS. PMID: 24614848 [PubMed - indexed for MEDLINE]$$ 197. Bacillus timonensis Stand Genomic Sci. 2012 Jul 30;6(3):346-55. doi: 10.4056/sigs.2776064. Epub 2012 Jul 20. Non contiguous-finished genome sequence and description of Bacillus timonensis sp. nov. Kokcha S(1), Mishra AK, Lagier JC, Million M, Leroy Q, Raoult D, Fournier PE. Author information: (1)Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR 53 198. 199. 200. 201. CNRS 6236 - IRD 198, Faculté de médecine, Aix-Marseille Université Bacillus timonensis strain MM10403188(T) sp. nov. is the type strain of a proposed new species within the genus Bacillus. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. B. timonensis is an aerobic Gram-negative rod shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,632,049 bp long genome (1 chromosome but no plasmid) contains 4,610 protein-coding and 74 RNA genes, including 5 rRNA genes. PMCID: PMC3558959 PMID: 23408487 [PubMed] Bacillus toyonensis Syst Appl Microbiol. 2013 Sep;36(6):383-91. doi: 10.1016/j.syapm.2013.04.008. Epub 2013 Jun 19. Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations. Jiménez G(1), Urdiain M, Cifuentes A, López-López A, Blanch AR, Tamames J, Kämpfer P, Kolstø AB, Ramón D, Martínez JF, Codoñer FM, Rosselló-Móra R. Author information: (1)Rubinum SA, Avda de La Llana 123, 08191 Rubí, Catalonia, Spain. [email protected] Strain BCT-7112(T) was isolated in 1966 in Japan from a survey designed to obtain naturally occurring microorganisms as pure cultures in the laboratory for use as probiotics in animal nutrition. This strain, which was primarily identified as Bacillus cereus var toyoi, has been in use for more than 30 years as the active ingredient of the preparation TOYOCERIN(®), an additive for use in animal nutrition (e.g. swine, poultry, cattle, rabbits and aquaculture). Despite the fact that the strain was initially classified as B. cereus, it showed significant genomic differences from the type strains of the B. cereus group that were large enough (ANI values below 92%) to allow it to be considered as a different species within the group. The polyphasic taxonomic study presented here provides sufficient discriminative parameters to classify BCT-7112(T) as a new species for which the name Bacillus toyonensis sp. nov. is proposed, with BCT-7112(T) (=CECT 876(T); =NCIMB 14858(T)) being designated as the type strain. In addition, a pairwise comparison between the available genomes of the whole B. cereus group by means of average nucleotide identity (ANI) calculations indicated that besides the eight classified species (including B. toyonensis), additional genomospecies could be detected, and most of them also had ANI values below 94%. ANI values were on the borderline of a species definition only in the cases of representatives of B. cereus versus B. thuringiensis, and B. mycoides and B. weihenstephanensis. Copyright © 2013 Elsevier GmbH. All rights reserved. PMID: 23791203 [PubMed - indexed for MEDLINE]$$ Bacillus trypoxylicola Int J Syst Evol Microbiol. 2010 Jan;60(Pt 1):61-6. doi: 10.1099/ijs.0.005843-0. Epub 2009 Jul 31. Bacillus trypoxylicola sp. nov., xylanase-producing alkaliphilic bacteria isolated from the guts of Japanese horned beetle larvae (Trypoxylus dichotomus septentrionalis). Aizawa T(1), Urai M, Iwabuchi N, Nakajima M, Sunairi M. Author information: (1)Department of Applied Biological Sciences, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-8510, Japan. Three xylanase-producing alkaliphilic strains, SU1(T), 36AC4 and 36AC6, were isolated from the guts of larvae of the Japanese horned beetle (Trypoxylus dichotomus septentrionalis). The isolates stained Gram-positive and were aerobic, spore-forming, non-motile and rod-shaped and grew optimally at 30 degrees C and pH 9. They contained MK-7 as the major isoprenoid quinone and iso-C(15 : 0), anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(17 : 0) as the major fatty acids. The DNA G+C contents of the strains were 37.4-37.7 mol%. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the genus Bacillus. Although their 16S rRNA gene sequence similarity to the type strains of the alkaliphilic species Bacillus pseudalcaliphilus and B. alcalophilus was 97 %, the novel isolates formed a distinct group in the phylogenetic trees and DNA-DNA relatedness values to the type strains of these species were less than 30 %. Results of physiological and biochemical tests, including salt preference, enabled these strains to be differentiated phenotypically from described Bacillus species. Therefore, strains SU1(T), 36AC4 and 36AC6 represent a novel species for which the name Bacillus trypoxylicola sp. nov. is proposed; the type strain is SU1(T) (=NBRC 102646(T) =KCTC 13244(T)). PMID: 19648346 [PubMed - indexed for MEDLINE] Bacillus vallismortis Int J Syst Bacteriol. 1996 Apr;46(2):470-5. Bacillus vallismortis sp. nov., a close relative of Bacillus subtilis, isolated from soil in Death Valley, California. Roberts MS(1), Nakamura LK, Cohan FM. Author information: (1)Center for Microbial Ecology, Michigan State University, East Lansing 48824-1101, USA. Five Bacillus strains isolated from Death Valley soil were shown to belong to a previously unidentified species, for which we propose the name Bacillus vallismortis. The type strain is strain DV1-F-3 (= NRRL B-14890). On the basis of previously published restriction digestion data, B. vallismortis is most closely related to Bacillus subtilis. At this time B. vallismortis can be distinguished from B. subtilis only by differences in whole-cell fatty acid compositions, DNA sequences, and levels of reassociation of genomic DNA. PMID: 8934905 [PubMed - indexed for MEDLINE] Bacillus velezensis Int J Syst Evol Microbiol. 2005 Jan;55(Pt 1):191-5. Bacillus velezensis sp. nov., a surfactant-producing bacterium isolated from the river Vélez in Málaga, southern Spain. Ruiz-García C(1), Béjar V, Martínez-Checa F, Llamas I, Quesada E. Author information: (1)Department of Microbiology, Faculty of Pharmacy, Campus Universitario de Cartuja, University of Granada, 18071 Granada, Spain. Two Gram-positive, endospore-forming bacterial strains, CR-502T and CR-14b, which produce surfactant molecules are described. Phenotypic tests and phylogenetic analyses showed these strains to be members of the genus Bacillus and related to the species Bacillus atrophaeus, Bacillus mojavensis, Bacillus subtilis, Bacillus vallismortis and Bacillus amyloliquefaciens, although they differ from these species in a number of phenotypic characteristics. DNA-DNA hybridization confirmed that they show less than 20 % hybridization with the above-mentioned species and therefore represent a novel species of Bacillus. The DNA G+C content is 46.4 mol% in strain CR-502T and 46.1 mol% in strain CR-14b. The main fatty acids in strain CR-502T are 15 : 0 anteiso (32.70 %), 15 : 0 iso (29.86 %) and 16 : 0 (13.41 %). The main quinone in strain CR-502T is MK-7 (96.6 %). In the light of the poly- 54 202. 203. 204. 205. 206. phasic evidence gathered in this study, it is proposed that these strains be classified as a novel species of the genus Bacillus, with the name Bacillus velezensis sp. nov. The type strain (CR-502T=CECT 5686T=LMG 22478T) was isolated from a brackish water sample taken from the river Vélez at Torredelmar in Málaga, southern Spain. PMID: 15653875 [PubMed - indexed for MEDLINE] Bacillus vietnamensis Int J Syst Evol Microbiol. 2004 Nov;54(Pt 6):2117-20. Bacillus vietnamensis sp. nov., a moderately halotolerant, aerobic, endospore-forming bacterium isolated from Vietnamese fish sauce. Noguchi H(1), Uchino M, Shida O, Takano K, Nakamura LK, Komagata K. Author information: (1)Department of Applied Biology and Chemistry, Faculty of Applied Bioscience, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya-ku, Tokyo 156-8502, Japan. Erratum in Int J Syst Evol Microbiol. 2005 Jan;55(Pt 1):545. Five strains of Gram-positive, endospore-forming, moderately halotolerant bacteria were studied taxonomically. Four were isolated from Vietnamese fish sauce and one from the Gulf of Mexico. Phylogenetic analysis based on 16S rRNA gene sequences showed that these strains clustered within the radiation of the genus Bacillus but separately from recognized Bacillus species. DNA G+C composition of the isolates ranged from 43 to 44 mol%. Strains 15-1(T) and NRRL B-14850 showed high levels of DNA-DNA relatedness (82-100 %) to each other and to the other strains isolated here; they displayed low levels of DNA-DNA relatedness (<29 %) to the type strains of selected recognized Bacillus species. They grew in 15 % NaCl and optimally in 1 % NaCl, which is characteristic of moderately halotolerant bacteria. The isolates grew at pH 6.5 to 10.0 but not at pH 6.0. Their cell walls contained meso-diaminopimelic acid. The major isoprenoid quinone was MK-7 and the principal cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0) and anteiso-C(17 : 0). Based on these results, the strains tested were regarded as members of a novel Bacillus species for which the name Bacillus vietnamensis sp. nov. is proposed. The type strain is 15-1(T) (=JCM 11124(T)=NRIC 0531(T)=NRRL 23890(T)). PMID: 15545444 [PubMed - indexed for MEDLINE] Bacillus vulcani Int J Syst Evol Microbiol. 2000 Nov;50 Pt 6:2009-12. Bacillus vulcani sp. nov., a novel thermophilic species isolated from a shallow marine hydrothermal vent. Caccamo D(1), Gugliandolo C, Stackebrandt E, Maugeri TL. Author information: (1)Dipartimento di Biologia Animale ed Ecologia Marina, Università Messina, Italy. A thermophilic spore-forming bacterium was isolated from sediment of a shallow hydrothermal vent at Vulcano Island (Italy). After phenotypic and molecular analyses, it was identified as a novel Bacillus species, for which the name Bacillus vulcani is proposed. The type strain is strain 3s-1T (= DSM 13174T = CIP 106305T). PMID: 11155974 [PubMed - indexed for MEDLINE] Bacillus wakoensis Int J Syst Evol Microbiol. 2005 Nov;55(Pt 6):2309-15. Characterization of alkaliphilic Bacillus strains used in industry: proposal of five novel species. Nogi Y(1), Takami H, Horikoshi K. Author information: (1)Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan. [email protected] Twenty alkaliphilic bacterial strains from industrial applications or enzyme studies were subjected to a polyphasic taxonomic investigation, including 16S rRNA gene sequencing, determination of genomic DNA G+C content, DNA-DNA hybridization, fatty acid analysis and standard bacteriological characterization. By comparing the groupings obtained based on the genomic DNA G+C content and the construction of a phylogenetic tree based on the 16S rRNA gene sequence, 12 clusters of similar strains were recognized. DNA-DNA hybridization revealed that these clusters represented five novel genospecies. Further analysis supported the proposal of five novel species in the genus Bacillus: Bacillus wakoensis sp. nov. (type strain N-1T=JCM 9140T=DSM 2521T), Bacillus hemicellulosilyticus sp. nov. (type strain C-11T=JCM 9152T=DSM 16731T), Bacillus cellulosilyticus sp. nov. (type strain N-4T=JCM 9156T=DSM 2522T), Bacillus akibai sp. nov. (type strain 1139T=JCM 9157T=ATCC 43226T) and Bacillus mannanilyticus sp. nov. (type strain AM-001T=JCM 10596T=DSM 16130T). PMID: 16280488 [PubMed - indexed for MEDLINE] Bacillus weihenstephanensis Int J Syst Bacteriol. 1998 Oct;48 Pt 4:1373-82. Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group. Lechner S(1), Mayr R, Francis KP, Prüss BM, Kaplan T, Wiessner-Gunkel E, Stewart GS, Scherer S. Author information: (1)Institut für Mikrobiologie, Technische Universität München, Germany. The Bacillus cereus group comprises the four valid species Bacillus cereus, Bacillus mycoides, Bacillus thuringiensis and bacillus anthracis. Some isolates of B. cereus are known to be psychrotolerant (growth at 7 degrees C or below). Here, specific sequence differences are described between the 16S rDNA, the 23S rDNA, the 16S-23S rDNA spacer region and the genes of the major cold-shock protein homologue cspA in a variety of psychrotolerant and mesophilic B. cereus and B. mycoides strains. Randomly amplified polymorphic DNA analysis using three different primers clearly separated psychrotolerant strains of both species from the rest of the B. cereus group, as did inverse PCR patterns of the rDNA operons. These data strongly support a hitherto unrecognized fifth sub-group within the B. cereus species group comprising psychrotolerant, but not mesophilic, B. cereus strains. Despite the latter finding, the DNA sequences investigated exhibited a high degree of sequence similarity indicating a close relationship between the species of the B. cereus group. Considering the unusual importance of B. cereus in both food poisoning and food spoilage and to avoid merging all species of the group, a new species, Bacillus weihenstephanensis sp. nov., comprising psychrotolerant 'cereus' strains, is proposed. Isolates of the new species grow at 4-7 degrees C but not at 43 degrees C and can be identified rapidly using rDNA or cspA targeted PCR. The type strain is B. weihenstephanensis WSBC 10204T (= DSM 11821T). PMID: 9828439 [PubMed - indexed for MEDLINE] Bacillus xiamenensis Antonie Van Leeuwenhoek. 2014 Jan;105(1):99-107. doi: 10.1007/s 10482- 013-0057-4. Epub 2013 Oct 25. Bacillus xiamenensis sp. nov., isolated from intestinal tract contents of a flathead mullet (Mugil cephalus). Lai Q(1), Liu Y, Shao Z. Author information: (1)State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Re- 55 sources, Third Institute of Oceanography, SOA, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, China. A taxonomic study was carried out on strain HYC-10(T), which was isolated from the intestinal tract contents of a flathead mullet, Mugil cephalus, captured from the sea off Xiamen Island, China. The bacterium was observed to be Gram positive, oxidase and catalase positive, rod shaped, and motile by subpolar flagella. The bacterium was found to grow at salinities of 0-12 % and at temperatures of 8-45 °C. The isolate was found to hydrolyze aesculin and gelatin, but was unable to reduce nitrate to nitrite. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HYC-10(T) belongs to the genus Bacillus, with highest sequence similarity (99.3 %) to Bacillus aerophilus 28K(T), Bacillus stratosphericus 41KF2a(T) and Bacillus altitudinis DSM 21631(T), followed by Bacillus safensis DSM 19292(T) (99.5 %) and Bacillus pumilus DSM 27(T) (99.5 %), while the sequence similarities to others were all below 97.6 %. The genomic ANIm values between strain HYC-10(T) and three type strains (B. altitudinis DSM 21631(T), B. safensis DSM 19292(T) and B. pumilus DSM 27(T)) were determined to range from 89.11 to 91.53 %. The DNA-DNA hybridization estimate values between strain HYC-10(T) and the three type strains were from 36.60 to 44.00 %. The principal fatty acids identified were iso-C15:0 (39.1 %), anteiso-C15:0 (22.7 %), iso-C17:0 (13.1 %), C16:0 (6.1 %), anteiso-C17:0 (5.8 %) and iso-C16:0 (5.1 %). The G+C content of the chromosomal DNA was determined from the draft genome sequence to be 41.3 mol%. The respiratory quinone was determined to be MK-7 (100 %). Phosphatidylglycerol, diphosphatidylglycerol, aminoglycolipid, two glycolipids and two unknown phospholipids were found to be present. The combined genotypic and phenotypic data show that strain HYC-10(T) represents a novel species of the genus Bacillus, for which the name Bacillus xiamenensis sp. nov. is proposed, with the type strain HYC-10(T) (=CGMCC NO.1.12326(T) = LMG 27143(T) = MCCC 1A00008(T)). PMID: 24158533 [PubMed - in process]$$ 207. Bacillus xiaoxiensis Int J Syst Evol Microbiol. 2011 Sep;61(Pt 9):2095-100. doi: 10.1099/ijs.0.026286-0. Epub 2010 Sep 24. Bacillus xiaoxiensis sp. nov., a slightly halophilic bacterium isolated from non-saline forest soil. Chen YG(1), Zhang YQ, Chen QH, Klenk HP, He JW, Tang SK, Cui XL, Li WJ. Author information: (1)Key Laboratory of Ecotourism's Application Technology of Hunan Province, College of Biology and Environmental Sciences, Jishou University, Jishou 416000, PR China. [email protected] A novel Gram-stain-positive, slightly halophilic, catalase-positive, oxidase-negative, endospore-forming, motile, facultatively anaerobic, rod-shaped bacterium, designated strain JSM 081004(T), was isolated from non-saline forest soil in Xiaoxi National Natural Reserve, China. Growth occurred with 0.5-20 % (w/v) NaCl (optimum 2-4 %), at pH 6.0-10.5 (optimum pH 8.0) and at 5-40 °C (optimum 25-30 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were iso-C₁₅:₀ and anteiso-C₁₅:₀. Strain JSM 081004(T) contained MK-7 as the predominant respiratory quinone, and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genomic DNA G+C content of strain JSM 081004(T) was 40.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 081004(T) should be assigned to the genus Bacillus and was most closely related to the type strains of Bacillus lehensis (sequence similarity 97.8 %), Bacillus oshimensis (97.8 %) and Bacillus patagoniensis (97.3 %). Phylogenetic analysis, DNA-DNA relatedness values, phenotypic characteristics and chemotaxonomic data all support the proposal of strain JSM 081004(T) as a representative of a novel species of the genus Bacillus, for which the name Bacillus xiaoxiensis sp. nov. is proposed; the type strain is JSM 081004(T) ( = CCTCC AA 208057(T) = DSM 21943(T)). PMID: 20870888 [PubMed - indexed for MEDLINE] 208. Bacillus zhanjiangensis Antonie Van Leeuwenhoek. 2011 Mar;99(3):473-80. doi: 10.1007/s10482-010-9510-9. Epub 2010 Sep 24. Bacillus zhanjiangensis sp. nov., isolated from an oyster in South China Sea. Chen YG(1), Hu SP, Tang SK, He JW, Xiao JQ, Zhu HY, Li WJ. Author information: (1)Key Laboratory of Ecotourism's Application Technology of Hunan Province, College of Biology and Environmental Sciences, Jishou University, Jishou 416000, People's Republic of China. A novel Gram-stain-positive, motile, catalaseand oxidase-positive, endospore-forming, aerobic, rod-shaped bacterium, designated strain JSM 099021(T), was isolated from an oyster collected from Naozhou Island in the South China Sea. Growth occurred with 0-15% (w/v) NaCl (optimum 2-4%) and at pH 6.0-10.0 (optimum pH 7.5) and at 10-45°C (optimum 30-35°C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The predominant respiratory quinone was menaquinone 7 (MK-7) and the major polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major cellular fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C15:0 and iso-C16:0. The genomic DNA G + C content was 39.5 mol%. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 099021(T) belongs to the genus Bacillus, and was most closely related to the type strains of Bacillus halmapalus (sequence similarity 99.0%), Bacillus horikoshii (98.4%) and Bacillus cohnii (98.0%). The combination of phylogenetic analysis, DNA-DNA hybridization, phenotypic characteristics and chemotaxonomic data supported the proposal that strain JSM 099021(T) represents a new species of the genus Bacillus, for which the name Bacillus zhanjiangensis sp. nov. is proposed. The type strain was JSM 099021(T) (=DSM 23010(T) = KCTC 13713(T)). PMID: 20865333 [PubMed - indexed for MEDLINE] 56 第六节 Brevibacillus 209. Brevibacillus invocatus Int J Syst Evol Microbiol. 2002 May;52(Pt 3):953-66. Polyphasic identification of Bacillus and Brevibacillus strains from clinical, dairy and industrial specimens and proposal of Brevibacillus invocatus sp. nov.. Logan NA(1), Forsyth G, Lebbe L, Goris J, Heyndrickx M, Balcaen A, Verhelst A, Falsen E, Ljungh A, Hansson HB, De Vos P. Author information: (1)School of Biological and Biomedical Sciences, Glasgow Caledonian University, UK. [email protected] Thirty-three clinical, dairy and industrial isolates of aerobic endospore-forming bacteria which were unreactive in routine identification tests were characterized genotypically by using amplified rDNA restriction analysis (ARDRA), 16S rDNA sequencing and DNA-DNA reassociation, and phenotypically by using fatty acid methyl ester (FAME) analysis, SDS-PAGE of whole-cell proteins, API Biotype 100 assimilation tests and 16 other routine phenotypic tests. Three isolates were identified as strains of Bacillus badius, 12 as Brevibacillus agri, including 3 strains associated with an outbreak of waterborne illness, 4 as Brevibacillus centrosporus and 2 as Brevibacillus parabrevis; 12 strains contaminating an antibiotic production plant were recognized as members of a new species, for which the name Brevibacillus invocatus is proposed, with the type strain LMG 18962T (= B2156T = CIP 106911T = NCIMB 13772T). PMID: 12054263 [PubMed - indexed for MEDLINE] 第七节 Caldalkalibacillus 210. Caldalkalibacillus thermarum Int J Syst Evol Microbiol. 2006 Jun;56(Pt 6):1217-21. Caldalkalibacillus thermarum gen. nov., sp. nov., a novel alkalithermophilic bacterium from a hot spring in China. Xue Y(1), Zhang X, Zhou C, Zhao Y, Cowan DA, Heaphy S, Grant WD, Jones BE, Ventosa A, Ma Y. Author information: (1)State Key laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China. A thermophilic, alkaliphilic and catalase-positive bacterium, designated strain HA6(T), was isolated from a hot spring in China. The strain was aerobic and chemo-organotrophic and grew optimally at 60 degrees C, pH 8.5 and 1.5 % (w/v) NaCl. The cells were Gram-positive rods, forming single terminal endospores. The predominant cellular fatty acids were iso-C(15 : 0) and iso-C(17 : 0). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The genomic DNA G+C content was 45.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain HA6(T) formed a distinct lineage within the family Bacillaceae and was most closely related to Bacillus horti K13(T) and Bacillus smithii DSM 4216(T), with sequence similarities of 91.8 and 93.1 %, respectively. On the basis of its physiological and molecular properties, strain HA6(T) should be placed in a novel genus and species, for which the name Caldalkalibacillus thermarum gen. nov., sp. nov. is proposed. The type strain of Caldalkalibacillus thermarum is strain HA6(T) (=CGMCC 1.4242(T)=JCM 13486(T)). PMID: 16738094 [PubMed - indexed for MEDLINE] 第八节 Caldibacillus 211. Caldibacillus debilis Int J Syst Evol Microbiol. 2012 Jul;62(Pt 7):1470-85. doi: 10.1099/ijs.0.030346-0. Epub 2011 Aug 19. Taxonomic revision of the genus Geobacillus: emendation of Geobacillus, G. stearothermophilus, G. jurassicus, G. toebii, G. thermodenitrificans and G. thermoglucosidans (nom. corrig., formerly 'thermoglucosidasius'); transfer of Bacillus thermantarcticus to the genus as G. thermantarcticus comb. nov.; proposal of Caldibacillus debilis gen. nov., comb. nov.; transfer of G. tepidamans to Anoxybacillus as A. tepidamans comb. nov.; and proposal of Anoxybacillus caldiproteolyticus sp. nov. Coorevits A(1), Dinsdale AE, Halket G, Lebbe L, De Vos P, Van Landschoot A, Logan NA. Author information: (1)Department of Applied Engineering Sciences, University College Ghent, Ghent, Belgium. [email protected] Sixty-two strains of thermophilic aerobic endospore-forming bacteria were subjected to polyphasic taxonomic study including 16S rRNA gene sequence analysis, polar lipid and fatty acid analysis, phenotypic characterization, and DNA-DNA hybridization experiments. Distinct clusters of the species Geobacillus stearothermophilus, Geobacillus thermodenitrificans, Geobacillus toebii and Geobacillus thermoglucosidasius were formed, allowing their descriptions to be emended, and the distinctiveness of the poorly represented species Geobacillus jurassicus, Geobacillus subterraneus and Geobacillus caldoxylosilyticus was confirmed. It is proposed that the name Geobacillus thermoglucosidasius be corrected to Geobacillus thermogluco- 57 sidans nom. corrig. Bacillus thermantarcticus clustered between Geobacillus species on the basis of 16S rRNA gene sequence analysis, and its transfer to the genus Geobacillus as Geobacillus thermantarcticus comb. nov. (type strain LMG 23032(T)=DSM 9572(T)=strain M1(T)=R-35644(T)) is proposed. The above-mentioned species, together with Geobacillus thermoleovorans and Geobacillus thermocatenulatus, form a monophyletic cluster representing the genus Geobacillus. The distinctiveness of 'Geobacillus caldoproteolyticus' was confirmed and it is proposed that it be accommodated, along with Geobacillus tepidamans, in the genus Anoxybacillus as Anoxybacillus caldiproteolyticus sp. nov. (type strain DSM 15730(T)=ATCC BAA-818(T)=LMG 26209(T)=R-35652(T)) and Anoxybacillus tepidamans comb. nov. (type strain LMG 26208(T)=ATCC BAA-942(T)=DSM 16325(T)=R-35643(T)), respectively. The type strain of Geobacillus debilis was not closely related to any members of the genera Anoxybacillus and Geobacillus, and it is proposed that this species be placed in the new genus Caldibacillus as Caldibacillus debilis gen. nov. comb. nov. The type strain of the type species, Caldibacillus debilis, is LMG 23386(T) (=DSM 16016(T)=NCIMB 13995(T)=Tf(T)=R-35653(T)). PMID: 21856988 [PubMed - indexed for MEDLINE] 第九节 Cerasibacillus 212. Cerasibacillus quisquiliarum Int J Syst Evol Microbiol. 2004 Jul;54(Pt 4):1063-9. Cerasibacillus quisquiliarum gen. nov., sp. nov., isolated from a semi-continuous decomposing system of kitchen refuse. Nakamura K(1), Haruta S, Ueno S, Ishii M, Yokota A, Igarashi Y. Author information: (1)Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan. [email protected] A moderately thermophilic and alkaliphilic bacillus, which had been reported and designated BLx (Haruta et al., 2002), was isolated from a semi-continuous decomposing system of kitchen refuse. Cells of strain BLxT were strictly aerobic, rod-shaped, motile and spore forming. The optimum temperature and pH for growth were approximately 50 degrees C and pH 8-9. Strain BLxT was able to grow at NaCl concentrations from 0.5 to 7.5%, with optimum growth at 0.5% NaCl. The predominant menaquinone was MK-7, and the major fatty acid was iso-C(15 : 0). Phylogenetic analysis showed that strain BLxT was positioned in an independent lineage within the cluster that includes the genera Virgibacillus and Lentibacillus in Bacillus rRNA group 1. Strain BLxT exhibited 16S rDNA similarity of 92.8-94.8% to Virgibacillus species and 92.3% to Lentibacillus salicampi. Phenotypic, chemotaxonomic and phylogenetic analyses supported the classification of strain BLxT in a novel genus and species. Cerasibacillus quisquiliarum gen. nov., sp. nov. is proposed on the basis of phenotypic, chemotaxonomic and phylogenetic data. The type strain is BLxT (DSM 15825T=IAM15044T=KCTC 3815T). PMID: 15280270 [PubMed - indexed for MEDLINE] 第十节 Domibacillus 213. Domibacillus robiginosus Int J Syst Evol Microbiol. 2013 Jun;63(Pt 6):2054-61. doi: 10.1099/ijs.0.044396-0. Epub 2012 Oct 12. Domibacillus robiginosus gen. nov., sp. nov., isolated from a pharmaceutical clean room. Seiler H(1), Wenning M, Scherer S. Author information: (1)Department of Microbiology (ZIEL), Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany. [email protected] A novel red-pigmented bacterial strain, designated WS 4628(T), was isolated from a pharmaceutical clean room of a vaccine-producing company and was investigated in a taxonomic study using a polyphasic approach. The strain was Gram-stain-positive, strictly aerobic, motile, catalase-positive and produced spherical to slightly ellipsoidal endospores in rods. The genomic DNA G+C content was 44.1 mol%. The major fatty acids were anteiso-C15:0, iso-C15:0 and anteiso-C17:0 and the predominant quinone was MK-6. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid and an unidentified phospholipid. meso-diaminopimelic acid (type A1γ) was present in the cell-wall peptidoglycan and the major whole-cell sugars were glucose and ribose. The closest phylogenetic neighbours were identified as Bacillus badius ATCC 14574(T) (95.8% 16S rRNA gene sequence similarity), Bacillus indicus Sd/3(T) (94.8%), Jeotgalibacillus alimentarius YKJ-13(T) (94.8%) and Bacillus cibi JG-30(T) (94.8%). Phylogenetic, physiological, biochemical and morphological differences between strain WS 4628(T) and its closest relatives in the families Bacillaceae and Planococcaceae suggest that this strain represents a novel species in a new genus in the family Bacillaceae for which the name Domibacillus robiginosus gen. nov., sp. nov. is proposed; the type strain of the type species is WS 4628(T) (=DSM 25058(T)=LMG 26645(T)). PMID: 23064349 [PubMed - indexed for MEDLINE] 58 第十一节 Edaphobacillus 214. Edaphobacillus lindanitolerans Basic Microbiol. 2013 Sep;53(9):758-65. doi: 10.1002/jobm.201200150. Epub 2013 Jan 15. Edaphobacillus lindanitolerans gen. nov., sp. nov., isolated from hexachlorocyclohexane (HCH) contaminated soil. Lal D(1), Khan F, Gupta SK, Schumann P, Lal R. Author information: (1)Department of Zoology, Molecular Biology Laboratory, University of Delhi, Delhi, India. A Gram-staining-positive, aerobic, cocco-bacilli-shaped, non-motile, non-spore forming, cream colored strain bacterium (strain MNA4(T) ) was isolated from hexachlorocyclohexane (HCH) contaminated soil. Strain MNA4(T) showed the highest 16S rRNA gene sequence similarity of 97.47% with type species of the newly defined genus Bhargavaea cecembensis. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MNA4(T) belonged to a clade represented by Bhargavaea cecembensis, Bacillus beijingensis and Bacillus ginsengi. DNA-DNA hybridization values of the strain MNA4(T) with close relatives were well below the 70% threshold value recommended for delineation of species. The major fatty acids were anteiso C15:0 , anteiso C17:0 , iso C16:0 and iso C15:0 . The strain was found to contain respiratory quinones MK-8, MK-9 and MK-7 in an approximate molar ratio of 85:7:5. Polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol and two unknown phospholipids. The DNA G + C content was 55.6 mol%. Peptidoglycan type was A4α (L-Lys - L-Ala - D-Asp). Phylogenetic analysis, fatty acids profile, phenotypic properties and chemotaxonomic data of strain MNA4(T) indicated that it represents a novel species of a novel genus for which the name Edaphobacillus lindanitolerans gen. nov., sp. nov., is proposed. The type strain is MNA4(T) (=CCM 7584(T) = DSM 22424(T) ). © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. PMID: 23322487 [PubMed - indexed for MEDLINE] 第十二节 Fictibacillus 215. Fictibacillus phosphorivorans Int J Syst Evol Microbiol. 2013 Aug;63(Pt 8):2934-44. doi: 10.1099/ijs.0.049171-0. Epub 2013 Jan 25. Fictibacillus phosphorivorans gen. nov., sp. nov. and proposal to reclassify Bacillus arsenicus, Bacillus barbaricus, Bacillus macauensis, Bacillus nanhaiensis, Bacillus rigui, Bacillus solisalsi and Bacillus gelatini in the genus Fictibacillus. Glaeser SP(1), Dott W, Busse HJ, Kämpfer P. Author information: (1)Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany. Erratum in Int J Syst Evol Microbiol. 2013 Oct;63(Pt 10):3930. A Gram-positive-staining, aerobic, endospore-forming bacterium (Ca7(T)) was isolated from a bioreactor showing extensive phosphorus removal. Based on 16S rRNA gene sequence similarity comparisons, strain Ca7(T) was grouped in the genus Bacillus, most closely related to Bacillus nanhaiensis JSM 082006(T) (100 %), Bacillus barbaricus V2-BIII-A2(T) (99.2 %) and Bacillus arsenicus Con a/3(T) (97.7 %). Moderate 16S rRNA gene sequence similarities were found to the type strains of the species Bacillus gelatini and Bacillus rigui (96.4 %), Bacillus macauensis (95.1 %) and Bacillus solisalsi (96.1 %). All these species were grouped into a monophyletic cluster and showed very low sequence similarities (<94 %) to the type species of the genus Bacillus, Bacillus subtilis. The quinone system of strain Ca7(T) consists predominantly of menaquinone MK-7. The polar lipid profile exhibited the major compounds diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. In addition, minor compounds of an unidentified phospholipid and an aminophospholipid were detected. No glycolipids were found in strain Ca7(T), which was consistent with the lipid profiles of B. nanhaiensis, B. barbaricus, B. arsenicus, B. rigui, B. solisalsi, B. macauensis and B. gelatini, but in contrast to B. subtilis. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid and the polyamine pattern contained predominantly spermidine and spermine. The major fatty acids, which were iso-C15 : 0, anteiso-C15 : 0 and C16 : 0, supported the grouping of strain Ca7(T) in the family Bacillaceae. The strain showed DNA-DNA similarities of 48 % (reciprocal 47 %) to B. nanhaiensis DSM 23009(T), 31 % (reciprocal 36 %) to B. barbaricus V2-BIII-A2(T) and 29 % (reciprocal 39 %) to B. arsenicus DSM 15822(T), respectively. These results clearly demonstrate that strain Ca7(T) is a representative of a novel species, which can be differentiated from its closest relatives by physiological and biochemical tests. Because of the low sequence similarity of strain Ca7(T) to B. subtilis, which was shared by B. nanhaiensis, B. barbaricus, B. arsenicus, B. gelatini, B. rigui, B. solisalsi and B. macauensis, and their unique lipid patterns, we propose that strain Ca7(T) represents a novel species in a novel genus for which the name Fictibacillus phosphorivorans gen. nov., sp. nov. is proposed. The type strain is Ca7(T) (= CCM 8426(T) = LMG 27063(T)). In addition we propose the reclassification of B. nanhaiensis, B. barbaricus, B. arsenicus, B. rigui, B. macauensis, B. solisalsi and B. gelatini as Fictibacillus nanhaiensis comb. nov., Fictibacillus barbaricus comb. nov., Fictibacillus arsenicus comb. nov., Fictibacillus rigui comb. nov., Fictibacillus macauensis comb. nov., Fictibacillus solisalsi comb. nov. and Fictibacillus gelatini comb. nov., respectively [type strains JSM 082006(T) (= DSM 23009(T) = KCTC 13712(T)), V2-BIII-A2(T) ( = CCM 4982(T) = DSM 14730(T)), Con a/3(T) ( = MTCC 4380(T) = DSM 15822(T) = JCM 12167(T)), WPCB074(T) 59 ( = KCTC 13278(T) = JCM 16348(T)), ZFHKF-1(T) ( = JCM 13285(T) = DSM 17262(T)), YC1(T) ( = KCTC 13181(T) = CGMCC 1.6854(T)) and LMG 21881(T) ( = DSM 15866(T)), respectively]. PMID: 23355698 [PubMed - indexed for MEDLINE] 第十三节 Filobacillus 216. Filobacillus milensis Int J Syst Evol Microbiol. 2001 Mar;51(Pt 2):425-31. Filobacillus milensis gen. nov., sp. nov., a new halophilic spore-forming bacterium with Orn-D-Glu-type peptidoglycan. Schlesner H(1), Lawson PA, Collins MD, Weiss N, Wehmeyer U, Völker H, Thomm M. Author information: (1)Institut für Allgemeine Mikrobiologie der Universität Kiel, Germany. [email protected] A spore-forming, halophilic bacterium was isolated from surface sediment located on the beach of Palaeochori Bay near to a shallow water hydrothermal vent area, Milos, Greece. The bacterium, designated SH 714T, consisted of motile, strictly aerobic rods which contained an Orn-D-Glu type murein and a G+C content of 35 mol%. Thin sections showed a cell wall typical for Gram-positive bacteria; the peptidoglycan layer, however, was very thin. The Gram-reaction of the organism was negative. Comparative 16S rRNA gene sequencing demonstrated that the isolate represents a new line of descent within the spore-forming rods branching at the periphery of the rRNA group 1 Bacillus (Bacillus sensu stricto). The nearest phylogenetic neighbours of the unknown bacterium were Bacillus haloalkaliphilus, Marinococcus albus and Halobacillus species. Based on phylogenetic and phenotypic evidence it is proposed that the unknown bacterium be classified as Filobacillus milensis gen. nov., sp. nov. The type strain is SH 714T (= DSM 13259T = ATCC 700960T). PMID: 11324591 [PubMed - indexed for MEDLINE] 第十四节 Geobacillus 217. Geobacillus debilis Int J Syst Evol Microbiol. 2004 Nov;54(Pt 6):2197-201. Geobacillus debilis sp. nov., a novel obligately thermophilic bacterium isolated from a cool soil environment, and reassignment of Bacillus pallidus to Geobacillus pallidus comb. nov. Banat IM(1), Marchant R, Rahman TJ. Author information: (1)School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry BT52 1SA, Northern Ireland, UK. [email protected] Several aerobic, motile, rod-shaped, thermophilic, spore-forming Geobacillus bacteria predominantly giving a Gram-positive staining reaction were isolated from a cool soil environment in Northern Ireland and taxonomically investigated. Two isolates, F10 and Tf(T), showed low 16S rRNA gene sequence similarity to recognized members of the genus Geobacillus. Phylogenetic tree investigation using neighbour-joining, maximum-likelihood and parsimony methods indicated that strains F10 and Tf(T) represent a single novel species, for which the name Geobacillus debilis sp. nov. is proposed, with type strain Tf(T) (=DSM 16016(T)=NCIMB 13995(T)) and which belongs to a subgroup of the genus Geobacillus comprising Geobacillus toebii and Geobacillus caldoxylosilyticus. However, G. debilis showed closest affinities to Bacillus pallidus, which we propose should become Geobacillus pallidus comb. nov. PMID: 15545458 [PubMed - indexed for MEDLINE] 218. Geobacillus gargensis Int J Syst Evol Microbiol. 2004 Nov;54(Pt 6):2019-24. Geobacillus gargensis sp. nov., a novel thermophile from a hot spring, and the reclassification of Bacillus vulcani as Geobacillus vulcani comb. nov. Nazina TN(1), Lebedeva EV, Poltaraus AB, Tourova TP, Grigoryan AA, Sokolova DSh, Lysenko AM, Osipov GA. Author information: (1)Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7/2, Moscow, 117312 Russia. [email protected] A novel thermophilic spore-forming strain, Ga(T), was isolated from the Garga hot spring located in the northern part of the Transbaikal region (Russia). Strain Ga(T) was found to be an aerobic, Gram-positive, rod-shaped, thermophilic (optimum growth temperature is 60-65 degrees C), chemo-organotrophic bacterium that grows on various sugars, carboxylic acids and hydrocarbons. The G+C content of its DNA is 52.9 mol%. The 16S rRNA gene sequence similarity data show that strain Ga(T) is closely related to members of the genus Geobacillus. Relevant chemotaxonomic data (in particular, the major fatty acid profile of strain Ga(T), which includes iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0 acids) support the assignment of this strain to the genus Geobacillus. The physiological, biochemical and DNA-DNA hybridization studies of strain Ga(T) showed that it differs both genotypically and phenotypically from the recognized Geobacillus species. Based on these data, strain Ga(T) belongs to a novel species, Geobacillus gargensis sp. nov. (type strain, Ga(T)=VKM B-2300(T)=DSM 15378(T)). The analysis of the phenotypic characteristics (additional to those given in the original description) of the type strain of Bacillus vulcani (DSM 13174(T)) showed that they are very similar to the major phenotypic characteristics of the genus Geobacillus. The low DNA-DNA reassociation values of strain DSM 13174(T) with various species of this genus (from 38 to 54 %) clearly demonstrate a sufficient genomic distinction of this strain and its taxonomic status as a species. The physi- 60 ological characteristics, phylogenetic position and DNA-DNA reassociation values of B. vulcani allow this species to be reclassified as Geobacillus vulcani comb. nov. The main properties that differentiate G. vulcani from the other species of the genus are its ability to produce acids from glycerol, lactose and ribose. PMID: 15545427 [PubMed - indexed for MEDLINE] 219. Geobacillus stearothermophilus Int J Syst Evol Microbiol. 2001 Mar;51(Pt 2):433-46. Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. th. Nazina TN(1), Tourova TP, Poltaraus AB, Novikova EV, Grigoryan AA, Ivanova AE, Lysenko AM, Petrunyaka VV, Osipov GA, Belyaev SS, Ivanov MV. Author information: (1)Department of Microbial Biogeochemistry and Biotechnology, Institute of Microbiology, Russian Academy of Sciences, Moscow. [email protected] Five hydrocarbon-oxidizing strains were isolated from formation waters of oilfields in Russia, Kazakhstan and China. These strains were moderately thermophilic, neutrophilic, motile, spore-forming rods, aerobic or facultatively anaerobic. The G+C content of their DNA ranged from 49.7 to 52.3 mol%. The major isoprenoid quinone was menaquinone-7; cellular fatty acid profiles consisted of significant amounts of iso-15:0, iso-16:0 and iso-17:0 fatty acids (61.7-86.8% of the total). Based on data from 16S rDNA analysis and DNA-DNA hybridization, the subsurface isolates could be divided into two groups, one of which consisted of strains UT and X and the other of which consisted of strains K, Sam and 34T. The new strains exhibited a close phylogenetic relationship to thermophilic bacilli of 'Group 5' of Ash et al. [Ash, C., Farrow, J. A. E., Wallbanks, S. & Collins, M. D. (1991). Lett Appl Microbiol 13, 202-206] and a set of corresponding signature positions of 16S rRNA. Comparative analysis of the 16S rDNA sequences and fatty acid compositions of the novel isolates and established species of thermophilic bacilli indicated that the subsurface strains represent two new species within a new genus, for which the names Geobacillus subterraneus gen. nov., sp. nov., and Geobacillus uzenensis sp. nov. are proposed. It is also proposed that Bacillus stearothermophilus, Bacillus thermoleovorans, Bacillus thermocatenulatus, Bacillus kaustophilus, Bacillus thermoglucosidasius and Bacillus thermodenitrificans be transferred to this new genus, with Geobacillus stearothermophilus (formerly Bacillus stearothermophilus) as the type species. PMID: 11321089 [PubMed - indexed for MEDLINE] 220. Geobacillus tepidamans Int J Syst Evol Microbiol. 2004 Nov;54(Pt 6):2361-8. Classification of isolates from locations in Austria and Yellowstone National Park as Geobacillus tepidamans sp. nov. Schäffer C(1), Franck WL, Scheberl A, Kosma P, McDermott TR, Messner P. Author information: (1)Center for NanoBiotechnology, University of Applied Life Sciences and Natural Resources, A-1180 Wien, Austria. Two moderately thermophilic, Gram-positive, spore-forming bacteria were isolated from different geographical locations and sources; strain GS5-97(T) from a beet sugar factory in Leopoldsdorf, Lower Austria, and strain YNP10 from a geothermally heated soil, Yellowstone National Park, USA. The sequences of their 16S rRNA genes were found to be 99.8% identical, and DNA-DNA hybridization experiments revealed that strains GS5-97(T) and YNP10 share 89.9 mol% similarity to each other, but only 34.3 and 39.2 mol% similarity, respectively, to Geobacillus caldoxylosilyticus DSM 12041(T), which is their closest related type strain. A polyphasic analysis showed that these two isolates were more similar to each other than to other characterized geobacilli. Their DNA G+C content was 43.2 and 42.4 mol%, respectively, and they were identical with respect to many phenotypic features (e.g. T(opt) 55 degrees C; pH(opt) 7.0). Both strains clearly displayed best growth when cultured aerobically. They differed slightly in their cellular fatty acid profiles and polar lipid pattern, and genotypically they could also be distinguished based on randomly amplified polymorphic DNA fingerprints and internal transcribed spacer analysis. Freeze-etching experiments revealed oblique surface layer (S-layer) lattices in both strains, and biochemical analyses of the purified S-layer proteins indicated the occurrence of glycosylation. Based on the properties of these organisms relative to those currently documented for the genus Geobacillus and for the various sister genera in the Bacillus radiation, a novel species is proposed, Geobacillus tepidamans sp. nov., with GS5-97(T) (=ATCC BAA-942(T)=DSM 16325(T)) as the type strain. Strain YNP10 has been deposited in the American Type Culture Collection as ATCC BAA-943. PMID: 15545484 [PubMed - indexed for MEDLINE] 221. Geobacillus zalihae BMC Microbiol. 2007 Aug 10;7:77. Geobacillus zalihae sp. nov., a thermophilic lipolytic bacterium isolated from palm oil mill effluent in Malaysia. Abd Rahman RN(1), Leow TC, Salleh AB, Basri M. Author information: (1)Enzyme and Microbial Technology Research Group, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia. [email protected] BACKGROUND: Thermophilic Bacillus strains of phylogenetic Bacillus rRNA group 5 were described as a new genus Geobacillus. Their geographical distribution included oilfields, hay compost, hydrothermal vent or soils. The members from the genus Geobacillus have a growth temperatures ranging from 35 to 78 degrees C and contained iso-branched saturated fatty acids (iso-15:0, iso-16:0 and iso-17:0) as the major fatty acids. The members of Geobacillus have similarity in their 16S rRNA gene sequences (96.5-99.2%). Thermophiles harboring intrinsically stable enzymes are suitable for industrial applications. The quest for intrinsically thermostable lipases from thermophiles is a prominent task due to the laborious processes via genetic modification. RESULTS: Twenty-nine putative lipase producers were screened and isolated from palm oil mill effluent in Malaysia. Of these, isolate T1T was chosen for further study as relatively higher lipase activity was detected quantitatively. The crude T1 lipase showed high optimum temperature of 70 degrees C and was also stable up to 60 degrees C without significant loss of crude enzyme activity. Strain T1T was a Gram-positive, rod-shaped, endospore forming bacterium. On the basic of 16S rDNA analysis, 61 strain T1T was shown to belong to the Bacillus rRNA group 5 related to Geobacillus thermoleovorans (DSM 5366T) and Geobacillus kaustophilus (DSM 7263T). Chemotaxonomic data of cellular fatty acids supported the affiliation of strain T1T to the genus Geobacillus. The results of physiological and biochemical tests, DNA/DNA hybridization, RiboPrint analysis, the length of lipase gene and protein pattern allowed genotypic and phenotypic differentiation of strain T1T from its validly published closest phylogenetic neighbors. Strain T1T therefore represents a novel species, for which the name Geobacillus zalihae sp. nov. is proposed, with the type strain T1T (=DSM 18318T; NBRC 101842T). CONCLUSION: Strain T1T was able to secrete extracellular thermostable lipase into culture medium. The strain T1T was identified as Geobacillus zalihae T1T as it differs from its type strains Geobacillus kaustophilus (DSM 7263T) and Geobacillus thermoleovorans (DSM 5366T) on some physiological studies, cellular fatty acids composition, RiboPrint analysis, length of lipase gene and protein profile. PMCID: PMC2000885 PMID: 17692114 [PubMed - indexed for MEDLINE] 第十五节 Gracilibacillus 222. Gracilibacillus halotolerans Int J Syst Bacteriol. 1999 Apr;49 Pt 2:821-31. Gracilibacillus gen. nov., with description of Gracilibacillus halotolerans gen. nov., sp. nov.; transfer of Bacillus dipsosauri to Gracilibacillus dipsosauri comb. nov., and Bacillus salexigens to the genus Salibacillus gen. nov., as Salibacillus salexigens comb. nov. Wainø M(1), Tindall BJ, Schumann P, Ingvorsen K. Author information: (1)Department of Microbial Ecology, University of Arhus, Denmark. A Gram-positive, extremely halotolerant bacterium was isolated from the Great Salt Lake, Utah, USA. The strain, designated NNT (= DSM 11805T), was strictly aerobic, rod-shaped, motile by peritrichous flagella and spore-forming. Strain NNT grew at salinities of 0-20% (w/v) NaCl. A distinctive feature of strain NNT was its optimal growth in salt-free medium. The polar lipid pattern of strain NNT consisted of phosphatidyl glycerol, diphosphatidyl glycerol and two phospholipids of unknown structure. The G + C content of its DNA was 38 mol%. The morphological, physiological and, particularly, the 16S rDNA sequence data, showed that strain NNT was associated with 'Bacillus group 1'. However, the organisms showing the greatest degree of sequence similarity to strain NNT were members of the genus Halobacillus and the species Marinococcus albus, Virgibacillus pantothenticus, Bacillus salexigens and Bacillus dipsosauri. On the basis of chemotaxonomic data, strain NNT was shown to be chemically most similar to B. salexigens and B. dipsosauri, with the greatest degree of similarity being shown to the latter organism. This was consistent with the 16S rDNA sequence data. Members of the genus Halobacillus comprise a chemically distinct group and can easily be distinguished from all other organisms of 'Bacillus group 1'. On the basis of the 16S rDNA data, chemotaxonomy and the physiology of strain NNT, it is proposed that this organism is a member of a new species, within a new genus, for which the name Gracilibacillus halotolerans is proposed. It is also proposed that B. dipsosauri be transferred to this genus as Gracilibacillus dipsosauri comb. nov. and that B. salexigens be transferred to the genus Salibacillus gen. nov., as Salibacillus salexigens comb. nov. Finally, additional data is provided to support the transfer of Bacillus pantothenticus to the genus Virgibacillus, as Virgibacillus pantothenticus Heyndrickx et al. (1998). PMID: 10319508 [PubMed - indexed for MEDLINE] 第十六节 Halobacillus 223. Halobacillus karajensis Int J Syst Evol Microbiol. 2003 Jul;53(Pt 4):1059-63. Halobacillus karajensis sp. nov., a novel moderate halophile. Amoozegar MA(1), Malekzadeh F, Malik KA, Schumann P, Spröer C. Author information: (1)Department of Biology (Microbiology Unit), Faculty of Science, University of Tehran, Tehran, Iran. A moderately halophilic, gram-positive, spore-forming bacterium was isolated from surface saline soil of the Karaj region, Iran. The strain, designated MA-2T, was strictly aerobic with rod-shaped cells that occurred singly, in pairs or short chains. It contained L-Om-D-Asp-type peptidoglycan and the major respiratory lipoquinone was MK-7. It was non-motile and had an ellipsoidal endospore located centrally or subterminally. Growth occurred at 10-49 degrees C and in the pH range 6.0-9.6. Strain MA-2T grew at salinities of 1-24% (w/v) NaCl, showing optimal growth at 10% (w/v). The DNA G + C content was 41.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MA-2T was associated with Bacillus rRNA group 1. The micro-organisms showing the closest phylogenetic relationship to strain MA-2T were Halobacillus litoralis and Halobacillus trueperi. On the basis of phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence analysis and DNA-DNA similarity data, it is proposed that strain MA-2T (= DSM 14948T = LMG 21515T) should be placed in the genus Halobacillus as the type strain of a novel species, Halobacillus karajensis sp. nov. PMID: 12892126 [PubMed - indexed for MEDLINE] 224. Halobacillus thailandensis Syst Appl Microbiol. 1999 Sep;22(3):360-5. Polyphasic taxonomy of a novel Halobacillus, Halobacillus 62 thailandensis sp. nov. isolated from fish sauce. Chaiyanan S(1), Chaiyanan S, Maugel T, Huq A, Robb FT, Colwell RR. Author information: (1)Center of Marine Biotechnology, Columbus Center, University of Maryland, Baltimore. In order to speed up fish sauce production, a more complete understanding of the microorganisms associated with the fermentation was needed. This study was undertaken to meet that need. A bacterium was isolated from a fish sauce production line containing 25% NaCl. It is a Gram-positive, rod-shaped bacillus with pointed ends, occurring as single cells, pairs, or short chains. Endospores are produced on a low nutrient medium and, in old cultures, the cells round up, even when undergoing division. The cell wall is relatively amorphous and similar to that of Gram-positive bacteria in structure and composition. Cells grown in a medium containing 10-20% salt possess thicker cell walls than those grown in a medium with 3% salt. Based on 16S rRNA sequence and DNA/DNA hybridization data, we conclude that the bacterium is a species of Halobacillus. This bacterium shares 99.2% and 97.2% 16S rRNA similarity with Halobacillus litoralis and Halobacillus halophilus respectively and DNA/DNA homology was lower than 70%, considered indicative of species similarity. Three highly expressed extra-cellular proteolytic enzymes with M(r) of approximately 100 kDa, 42 kDa and 17 kDa, respectively, were detected by gelatin-polyacrylamide gel electrophoresis. Activity of the 100 kDa and 17 kDa proteases was inhibited by phenylmethanesulphonyl fluoride (PMSF), without being affected by L-trans epoxysuccinyl-leucylamide 4-guanidino-butane (E-64), pepstatin, EDTA, or 1, 10-phenanthroline, leading to the conclusion that these enzymes are serine proteases. The 42-kDa protease was inhibited by EDTA and 1,10-phenanthroline, but not by PMSF, thus, being classified a metalloprotease. The strain has been successfully employed to improve fermentation in industrial production of fish sauce in Thailand. PMID: 10553288 [PubMed - indexed for MEDLINE] 225. Halolactibacillus halophilus Int J Syst Evol Microbiol. 2005 Nov;55(Pt 6):2427-39. Halolactibacillus halophilus gen. nov., sp. nov. and Halolactibacillus miurensis sp. nov., halophilic and alkaliphilic marine lactic acid bacteria constituting a phylogenetic lineage in Bacillus rRNA group 1. Ishikawa M(1), Nakajima K, Itamiya Y, Furukawa S, Yamamoto Y, Yamasato K. Author information: (1)Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan. [email protected] Eleven novel strains of marine-inhabiting lactic acid bacteria that were isolated from living and decaying marine organisms collected from a temperate area of Japan are described. The isolates were motile with peritrichous flagella and non-sporulating. They lacked catalase, quinones and cytochromes. Fermentation products from glucose were lactate, formate, acetate and ethanol. Lactate yield as percentage conversion from glucose was affected by the pH of the fermentation medium: approximately 55 % at the optimal growth pH of 8.0, greater than approximately 70 % at pH 7.0 and less than approximately 30 % at pH 9.0. The molar ratio of the other three products was the same at each cultivation pH, approximately 2 : 1 : 1. Carbohydrates and related compounds were aerobically metabolized to acetate and pyruvate as well as lactate. The isolates were slightly halophilic, highly halotolerant and alkaliphilic. The optimum NaCl concentration for growth was 2.0-3.0 % (w/v), with a range of 0-25.5 %. The optimum pH for growth was 8.0-9.5, with a range of 6.0-10.0. The G+C content of the DNA was 38.5-40.7 mol%. The isolates constituted two genomic species (DNA-DNA relatedness of less than 41 %) each characterized by sugar fermentation profiles. The cell-wall peptidoglycan of both phenotypes contained meso-diaminopimelic acid. The major cellular fatty acids were C(16 : 0) and a-C(13 : 0). Comparative sequence analysis of the 16S rRNA genes revealed that these isolates represent novel species constituting a phylogenetic unit outside the radiation of typical lactic acid bacteria and an independent line of descent within the group composed of the halophilic/halotolerant/alkaliphilic and/or alkalitolerant species in Bacillus rRNA group 1, with 94.8-95.1 % similarity to the genus Paraliobacillus, 93.7-94.1 % to the genus Gracilibacillus and 93.8-94.2 % to Virgibacillus marismortui. On the basis of possession of physiological and biochemical characteristics common to typical lactic acid bacteria within Bacillus rRNA group 1, chemotaxonomic characteristics and phylogenetic independence, a new genus and two species, Halolactibacillus halophilus gen. nov., sp. nov. and Halolatibacillus miurensis sp. nov., are proposed. The type strains are Halolactibacillus halophilus M2-2T (=DSM 17073T=IAM 15242T=NBRC 100868T=NRIC 0628T) (G+C content 40.2 mol%) and Halolactibacillus miurensis M23-1T (=DSM 17074T=IAM 15247T=NBRC 100873T=NRIC 0633T) (G+C content 38.5 mol%). PMID: 16280507 [PubMed - indexed for MEDLINE] 第十七节 Jeotgalibacillus 226. Jeotgalibacillus alimentarius Int J Syst Evol Microbiol. 2001 Nov;51(Pt 6):2087-93. Jeotgalibacillus alimentarius gen. nov., sp. nov., a novel bacterium isolated from jeotgal with L-lysine in the cell wall, and reclassification of Bacillus marinus Rüger 1983 . as mMrinibacillus marinus gen nov., comb. nov. Yoon JH(1), Weiss N, Lee KC, Lee IS, Kang KH, Park YH. Author information: (1)Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yusong, Taejon. A moderately halophilic, round-endospore-forming bacterium (strain YKJ-13T) was isolated from jeotgal, a traditional Korean fermented seafood, and studied by a polyphasic taxonomic approach. This organism was related to the phylogenetic clade comprising members of Bacillus rRNA group 2 and formed a cluster with Bacillus marinus with a bootstrap fidelity value of 93.6%. The peptidoglycan type was A1alpha linked directly through L-Lys. Based on 63 cell morphology, peptidoglycan type and phylogeny, strain YKJ-13T, together with B. marinus, is considered to be a member of Bacillus rRNA group 2. Strain YKJ-13T was also characterized by having MK-7 and MK-8 as the predominant menaquinones and iso-C15:0 as the major fatty acid. The DNA G+C content was 44 mol%. Strain YKJ-13T exhibited a 16S rDNA similarity value of 95.7% with B. marinus DSM 1297T, its closest phylogenetic relative. Levels of 16S rDNA similarity between strain YKJ-13T and other Bacillus spp. were less than 94.2%. Therefore, on the basis of the data presented, the name Jeotgalibacillus alimentarius gen. nov., sp. nov. is proposed for strain YKJ-13T (= KCCM 80002T = JCM 10872T). It is also proposed that B. marinus be reclassified in Marinibacillus gen. nov. as Marinibacillus marinus comb. nov. PMID: 11760951 [PubMed - indexed for MEDLINE] 第十八节 Lentibacillus 227. Lentibacillus salicampi Int J Syst Evol Microbiol. 2002 Nov;52(Pt 6):2043-8. Lentibacillus salicampi gen. nov., sp. nov., a moderately halophilic bacterium isolated from a salt field in Korea. Yoon JH(1), Kang KH, Park YH. Author information: (1)Microbial Genomics Laboratory, Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea. A Gram-variable, aerobic, endospore-forming, rod-shaped bacterial strain, SF-20(T), which was isolated from a salt field in Korea, was subjected to a polyphasic taxonomic study. Cells of this organism were motile by means of single flagella. Strain SF-20(T) grew optimally in the presence of 4-8% NaCl. The cell wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone is MK-7. Strain SF-20(T) has a cellular fatty acid profile containing major amounts of branched fatty acids. The major fatty acids are anteiso-C15:0 and iso-C16:0. The cellular phospholipids are phosphatidylglycerol and diphosphatidylglycerol. The G+C content of the DNA is 44 mol%. Strain SF-20(T) is phylogenetically closely related to the genus Bacillus and some related genera and, particularly, formed a coherent cluster with the genera Salibacillus and Virgibacillus. The clustering fidelity between strain SF-20(T) and the cluster comprising these two genera was supported by bootstrap analysis at a confidence level of 67.2%. Strain SF-20(T) exhibited levels of 16S rDNA similarity of 93.0-94.7% to the genus Salibacillus and 94.0-94.1% to the genus Virgibacillus. On the basis of phenotypic and phylogenetic data, strain SF-20(T) should be classified in a novel genus and species, for which the name Lentibacillus salicampi gen. nov., sp. nov. is proposed. The type strain is strain SF-20(T) (= KCCM 41560(T) = JCM 11462(T)). PMID: 12508866 [PubMed - indexed for MEDLINE] 第十九节 Lysinibacillus 228. Lysinibacillus boronitolerans Int J Syst Evol Microbiol. 2007 May;57(Pt 5):1117-25. Proposal of Lysinibacillus boronitolerans gen. nov. sp. nov., and transfer of Bacillus fusiformis to Lysinibacillus fusiformis comb. nov. and Bacillus sphaericus to Lysinibacillus sphaericus comb. nov. Ahmed I(1), Yokota A, Yamazoe A, Fujiwara T. Author information: (1)Biotechnology Research Center, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan. [email protected] Three strains of a spore-forming, Gram-positive, motile, rod-shaped and boron-tolerant bacterium were isolated from soil. The strains, designated 10a(T), 11c and 12B, can tolerate 5 % (w/v) NaCl and up to 150 mM boron, but optimal growth was observed without addition of boron or NaCl in Luria-Bertani agar medium. The optimum temperature for growth was 37 degrees C (range 16-45 degrees C) and the optimum pH was 7.0-8.0 (range pH 5.5-9.5). A comparative analysis of the 16S rRNA gene sequence demonstrated that the isolated strains were closely related to Bacillus fusiformis DSM 2898(T) (97.2 % similarity) and Bacillus sphaericus DSM 28(T) (96.9 %). DNA-DNA relatedness was greater than 97 % among the isolated strains and 61.1 % with B. fusiformis DSM 2898(T) and 43.2 % with B. sphaericus IAM 13420(T). The phylogenetic and phenotypic analyses and DNA-DNA relatedness indicated that the three strains belong to the same species, that was characterized by a DNA G+C content of 36.5-37.9 mol%, MK-7 as the predominant menaquinone system and iso-C(15 : 0) (32 % of the total) as a major cellular fatty acid. In contrast to the type species of the genus Bacillus, the strains contained peptidoglycan with lysine, aspartic acid, alanine and glutamic acid. Based on the distinctive peptidoglycan composition, phylogenetic analyses and physiology, the strains are assigned to a novel species within a new genus, for which the name Lysinibacillus boronitolerans gen. nov., sp. nov. is proposed. The type strain of Lysinibacillus boronitolerans is strain 10a(T) (=DSM 17140(T)=IAM 15262(T)=ATCC BAA-1146(T)). It is also proposed that Bacillus fusiformis and Bacillus sphaericus be transferred to this genus as Lysinibacillus fusiformis comb. nov. and Lysinibacillus sphaericus comb. nov., respectively. PMID: 17473269 [PubMed indexed for MEDLINE] 64 229. Lysinibacillus macroides Int J Syst Evol Microbiol. 2012 May;62(Pt 5):1121-7. doi: 10.1099/ijs.0.027995-0. Epub 2011 Jul 1. Lysinibacillus macroides sp. nov., nom. rev. Coorevits A(1), Dinsdale AE, Heyrman J, Schumann P, Van Landschoot A, Logan NA, De Vos P. Author information: (1)Laboratory of Biochemistry and Brewing, Faculty of Applied Engineering Sciences, University College Ghent, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium. [email protected] 'Bacillus macroides' ATCC 12905(T) ( = DSM 54(T) = LMG 18474(T)), isolated in 1947 from cow dung, was not included in the Approved Lists of Bacterial Names and so it lost standing in bacteriological nomenclature. Reinvestigation of the strain, including DNA-DNA relatedness experiments, revealed that 'Bacillus macroides' is genomically distinct from its closest relatives Lysinibacillus xylanilyticus, Lysinibacillus boronitolerans and Lysinibacillus fusiformis (as determined by 16S rRNA gene sequence analysis, with pairwise similarity values of 99.2, 98.8 and 98.5 %, respectively, with the type strains of these species). Further analysis showed that 'Bacillus macroides' shares the A4α L-Lys-D-Asp peptidoglycan type with other members of the genus Lysinibacillus and can thus be attributed to this genus. These results, combined with additional phenotypic data, justify the description of strain LMG 18474(T) ( = DSM 54(T) = ATCC 12905(T)) as Lysinibacillus macroides sp. nov., nom. rev. PMID: 21724959 [PubMed - indexed for MEDLINE] 230. Lysinibacillus massiliensis Int J Syst Evol Microbiol. 2010 Dec;60(Pt 12):3003. Retraction. Proposal of Lysinibacillus sinduriensis sp. nov., and transfer of Bacillus massiliensis and Bacillus odysseyi to Lysinibacillus as Lysinibacillus massiliensis comb. nov. and Lysinibacillus odysseyi comb. nov. with emended descriptions of the genus. [No authors listed] PMID: 21148328 [PubMed - in process] 231. Lysinibacillus sinduriensis Int J Syst Evol Microbiol. 2012 Oct;62(Pt 10):2347-55. doi: 10.1099/ijs.0.033837-0. Epub 2011 Nov 18. Description of Lysinibacillus sinduriensis sp. nov., and transfer of Bacillus massiliensis and Bacillus odysseyi to the genus Lysinibacillus as Lysinibacillus massiliensis comb. nov. and Lysinibacillus odysseyi comb. nov. with emended description of the genus Lysinibacillus. Jung MY(1), Kim JS, Paek WK, Styrak I, Park IS, Sin Y, Paek J, Park KA, Kim H, Kim HL, Chang YH. Author information: (1)Korean Collection for Type Cultures, Biological Resource Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea. A Gram-positive, rod-shaped, endospore-forming bacterium, designated strain BLB-1(T), was isolated from samples of tidal flat sediment from the Yellow Sea. 16S rRNA gene sequence analysis demonstrated that the isolate belonged to the Bacillus rRNA group 2 and was closely related to Bacillus massiliensis CIP 108446(T) (97.4%), Bacillus odysseyi ATCC PTA-4993(T) (96.7%), Lysinibacillus fusiformis DSM 2898(T) (96.2%) and Lysinibacillus boronitolerans DSM 17140(T) (95.9%). Sequence similarities with related species in other genera, including Caryophanon, Sporosarcina and Solibacillus, were <96.1%. Chemotaxonomic data supported the affiliation of strain BLB-1(T) with the genus Lysinibacillus. The major menaquinone was MK-7, the cell-wall sugars were glucose and xylose, the cell-wall peptidoglycan type was A4α (L-Lys-D-Asp), the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown phospholipids, and the major fatty acids were anteiso-C(15:0) (35.6%), iso-C(15:0) (25.6%) and anteiso-C(17:0) (16.5%). The most closely related species, Bacillus massiliensis and Bacillus odysseyi, were also assigned to this genus based on phylogenetic analysis and phenotypic data. The results of DNA-DNA hybridizations and phenotypic tests supported the differentiation of all three taxa from species of the genus Lysinibacillus with validly published names. Thus, strain BLB-1(T) ( = KCTC 13296(T) = JCM 15800(T)) represents a novel species, for which the name Lysinibacillus sinduriensis sp. nov. is proposed. It is also proposed that Bacillus massiliensis CIP 108446(T) ( =4400831(T) = CCUG49529(T) =KCTC 13178(T)) and Bacillus odysseyi NBRC 100172(T) ( =34hs-1(T) =ATCC PTA-4993(T) =NRRL B-30641(T) =DSM 18869(T) =CIP 108263(T) =KCTC 3961(T)) be transferred to the genus Lysinibacillus as Lysinibacillus massiliensis comb. nov. and Lysinibacillus odysseyi comb. nov., respectively. PMID: 22140163 [PubMed - indexed for MEDLINE] 第二十节 Natronobacillus 232. Natronobacillus azotifigens Extremophiles. 2008 Nov;12(6):819-27. doi: 10.1007/s00792-008-0188-0. Epub 2008 Sep 4. Natronobacillus azotifigens gen. nov., sp. nov., an anaerobic diazotrophic haloalkaliphile from soda-rich habitats. Sorokin ID(1), Zadorina EV, Kravchenko IK, Boulygina ES, Tourova TP, Sorokin DY. Author information: (1)Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, 117312, Moscow, Russia. Gram-positive bacteria capable of nitrogen fixation were obtained in microoxic enrichments from soda soils in south-western Siberia, north-eastern Mongolia, and the Lybian desert (Egypt). The same organisms were obtained in anoxic enrichments with glucose from soda lake sediments in the Kulunda Steppe (Altai, Russia) using nitrogen-free alkaline medium of pH 10. The isolates were represented by thin motile rods forming terminal round endospores. They are strictly fermentative saccharolytic anaerobes but tolerate high oxygen concentrations, probably due to a high catalase activity. All of the strains are obligately alkaliphilic and highly salt-tolerant natronophiles (chloride-independent sodaphiles). Growth was possible within a pH range from 7.5 to 10.6, with an optimum at 9.5-10, and within a salt range from 0.2 to 4 M Na(+), 65 with an optimum at 0.5-1.5 M for the different strains. The nitrogenase activity in the whole cells also had an alkaline pH optimum but was much more sensitive to high salt concentrations compared to the growing cells. The isolates formed a compact genetic group with a high level of DNA similarity. Phylogenetic analysis based on 16S-rRNA gene sequences placed the isolates into Bacillus rRNA group 1 as a separate lineage with Amphibacillus tropicus as the nearest relative. In all isolates the key functional nitrogenase gene nifH was detected. A new genus and species, Natronobacillus azotifigens gen. nov., sp. nov., is proposed to accommodate the novel diazotrophic haloalkaliphiles. PMID: 18769867 [PubMed - indexed for MEDLINE] 第二十一节 Oceanobacillus 233. Oceanobacillus caeni Int J Syst Evol Microbiol. 2008 May;58(Pt 5):1109-13. doi: 10.1099/ijs.0.65335-0. Oceanobacillus caeni sp. nov., isolated from a Bacillus-dominated wastewater treatment system in Korea. Nam JH(1), Bae W, Lee DH. Author information: (1)Department of Microbiology, Chungbuk National University, 12, Gaeshin-dong, Heungduk-gu, Cheongju 361-763, Republic of Korea. A Gram-positive, rod-shaped, spore-forming bacterium, strain S-11T, was isolated from the activated sludge of a Bacillus-dominated wastewater treatment system in South Korea and was characterized using a polyphasic approach in order to determine its taxonomic position. Cells (0.5-0.6 x 2.0-2.2 microm) were motile by means of a single subpolar flagellum. They bore ellipsoidal endospores that lay in a central position in swollen sporangia. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S-11T was a member of the genus Oceanobacillus. 16S rRNA gene sequence similarity values and DNA-DNA relatedness of strain S-11T to the type strains of other Oceanobacillus species were less than 96.2 and 66.0 %, respectively. Strain S-11T showed distinct differences in the G+C content of the genomic DNA (33.6 mol%). The major cellular fatty acids were iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. The major isoprenoid quinone was MK-7. There were also some physiological differences in comparison with the type strains of Oceanobacillus species: tests for production of acetoin and acid production from dulcitol, erythritol, myo-inositol and sorbitol were positive. The results of DNA-DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain S-11T from the six Oceanobacillus species and subspecies with validly published names. Strain S-11T therefore represents a novel species, for which the name Oceanobacillus caeni sp. nov. is proposed, with the type strain S-11T (=KCTC 13061T =CCUG 53534T =CIP 109363T). PMID: 18450698 [PubMed - indexed for MEDLINE] 234. Oceanobacillus soja J Gen Appl Microbiol. 2009 Jun;55(3):225-32. Oceanobacillus soja sp. nov. isolated from soy sauce production equipment in Japan. Tominaga T(1), An SY, Oyaizu H, Yokota A. Author information: (1)Saitama Industrial Technology Center North Institute, Kumagaya, Japan. [email protected] A Gram-positive, spore-forming, motile rod-shaped bacterium, designated strain Y27T, was isolated from the bottom of a mold fermenter used in the process of soy sauce production. Phylogenetic analysis of the 16S rRNA gene sequence from this strain placed it within the genus Oceanobacillus, and further sequence analysis revealed that this strain has a sequence similarity of 95.0-98.7% to other known species of Oceanobacillus. The DNA-DNA relatedness between strain Y27T and related type strains of the genus Oceanobacillus is below 43%, indicating that it should be considered a separate species. Characterization of strain Y27T revealed that the major cellular fatty acid is anteiso-C(15:0), the cell wall contains meso-diaminopimelic acid-type peptidoglycans, the major menaquinone is MK-7, and the major polar lipids are diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content of the strain is 38.0 mol%. On the basis of these phylogenetic, physiological and chemotaxonomic data, we propose that this isolate represents a novel species of the genus Oceanobacillus, and propose the name Oceanobacillus soja sp. nov. The type strain is strain Y27T (= JCM 15792T = NRRL B-59181T = NBRC 105379T = NCIMB 14542T). PMID: 19590150 [PubMed - indexed for MEDLINE] 第二十二节 Ornithinibacillus 235. Ornithinibacillus bavariensis Int J Syst Evol Microbiol. 2006 Jun;56(Pt 6):1383-9. Ornithinibacillus gen. nov., with the species Ornithinibacillus bavariensis sp. nov. and Ornithinibacillus californiensis sp. nov. Mayr R(1), Busse HJ, Worliczek HL, Ehling-Schulz M, 66 Scherer S. Author information: (1)Lehrstuhl für Mikrobielle Okologie, Department für Grundlagen der Biowissenschaften, WZW, Technische Universität München, Freising, Germany. A Gram-positive, aerobic, rod-shaped, motile, endospore-forming bacterium was isolated from pasteurized milk from Bavaria, Germany. 16S rRNA gene sequence similarities indicated that strain WSBC 24001(T) was most closely related to Virgibacillus species (95.3-96.1 %), Oceanobacillus species (95.6-95.7 %), Bacillus firmus IAM 12464(T) (95.5 %) and Bacillus niacini IFO 15566(T) (95.2 %). However, strain WSBC 24001(T) showed the highest level of sequence similarity to an unnamed strain, MB-9(T) (97.6 %), which was isolated from coastal surface sediments in California. Hence, this strain was included in our study. The genomic DNA G + C contents of strains WSBC 24001(T) and MB-9(T) were 36.4 mol and 40.8 mol%, respectively. The major respiratory quinone of both strains was menaquinone MK-7 and the peptidoglycan type was A4beta (L-orn<--D-Asp). The polar lipid profiles of these strains contained a predominance of diphosphatidylglycerol and moderate to minor amounts of phosphatidylglycerol, an unknown phospholipid and an unknown aminophospholipid. However, strain WSBC 24001(T) could be distinguished from strain MB-9(T) by the presence of an unknown lipid. The fatty acid profiles of the two strains comprised mainly iso- and anteiso-branched acids, but showed some significant quantitative differences in the amounts of certain acids. The DNA-DNA relatedness value (15.5 %) clearly demonstrated that strains WSBC 24001(T) and MB-9(T) are representatives of two different species. On the basis of their phylogenetic position and morphological, physiological and chemotaxonomic properties, a novel genus is proposed, Ornithinibacillus gen. nov., with two novel species, the type species Ornithinibacillus bavariensis sp. nov. (type strain WSBC 24001(T) = DSM 15681(T) = CCM 7096(T)) and Ornithinibacillus californiensis sp. nov. (type strain MB-9(T) = DSM 16628(T) = CCM 7237(T)). PMID: 16738118 [PubMed - indexed for MEDLINE] 第二十三节 Paenibacillus 236. Paenibacillus agarexedens Int J Syst Evol Microbiol. 2003 Jul;53(Pt 4):1051-7. Paenibacillus agarexedens sp. nov., nom. rev., and Paenibacillus agaridevorans sp. nov. Uetanabaro AP(1), Wahrenburg C, Hunger W, Pukall R, Spröer C, Stackebrandt E, de Canhos VP, Claus D, Fritze D. Author information: (1)University of Campinas, 13084-510 Campinas, SP Brazil. Twenty-two agarolytic, aerobic, spore-forming strains were characterized taxonomically by DNA-DNA reassociation experiments, riboprint analyses, 16S rDNA sequencing and phenetic similarity analyses. Based on riboprint analyses, the strains formed eight ribogroups, six of which contained 2-6 strains and two encompassed single strains. Within the multi-strain ribogroups, similarities ranged from 91-99%. Phylogenetic analyses of representatives of the eight groups by 16S rDNA sequence analysis showed that the strains were affiliated to the genus Paenibacillus, but relatedness to described Paenibacillus species was only moderate (<97.8% sequence similarity). Published DNA-DNA similarity values for most of the agarolytic strains, supplemented with new data, supported the distinctiveness of the eight ribogroups. Intragroup DNA-DNA similarity values ranged from 80 to 104%, while intergroup DNA-DNA similarities were <35%. Based on genomic distinctiveness and supported by the presence of distinguishing phenotypic properties, multi-strain groups 1 and 2 are proposed as novel species, Paenibacillus agarexedens sp. nov., nom. rev. (type strain, DSM 1327T=CIP 107437T) and Paenibacillus agaridevorans sp. nov. (type strain, DSM 1355T=CIP 107436T). PMID: 12892125 [PubMed - indexed for MEDLINE] 237. Paenibacillus apiarius Int J Syst Bacteriol. 1996 Jul;46(3):688-93. Paenibacillus apiarius sp. nov. Nakamura LK. Author information: National Center for Agricultural Utilization Research, U.S. Department of Agriculture, Peoria, Illinois 61604, USA. The name "Bacillus apiarius" Katznelson 1955 was not included on the Approved Lists of Bacterial Names and thus lost standing in bacterial nomenclature. The genetic homogeneity of "B. apiarius" strains was assessed by determining their G+C contents by the buoyant density method and by measuring the levels of DNA relatedness by spectrophotometric reassociation procedures. The G+C contents of the 15 strains examined, ranged from 52 to 54 mol%. DNA reassociation revealed the presence of two clusters, each with high levels of intragroup relatedness (60 to 100%). One cluster consisted of six strains highly related to Bacillus thiaminolyticus, and the other consisted of nine strains related to the designated type strain of "B. apiarius." The strains in the second cluster were not closely related genetically to the type strains of organisms frequently associated with honey bees (namely, Paenibacillus alvei, Paenibacillus larvae, Bacillus laterosporus, and Paenibacillus pulvifaciens). The "B. apiarius" strains in the second cluster were also phenotypically homogeneous and distinguishable from the previously described species. Comparative analyses of the 16S rRNA gene DNA sequence showed that the proper phylogenetic position of the second cluster was in the genus Paenibacillus. These findings justify the proposal of a new species with the name Paenibacillus apiarius. The type strain is NRRL NRS-1438. PMID: 8782677 [PubMed - indexed for MEDLINE] 238. Paenibacillus azoreducens Int J Syst Evol Microbiol. 2001 Sep;51(Pt 5):1681-5. Paenibacillus azoreducens sp. nov., a synthetic azo dye decolorizing bacterium from industrial wastewater. Meehan C(1), Bjourson AJ, McMullan G. Author information: (1)School of Environmental Studies, University of Ulster, Coleraine, Northern Ireland, UK. An azo-dye-reducing, endospore-forming bacterium 67 239. 240. 241. 242. isolated from textile industry wastewater has been taxonomically studied. Particularly interesting was the ability of this organism to decolorize the azo dye Remazol Black B by 98% within 24 h. Levels of 16S rRNA similarity between the isolate and Paenibacillus species ranged from 92.1 to 95.0%. The DNA G+C content was 46.8 mol % and anteiso-branched C15:0 was the major fatty acid. Based upon the phenotypic properties and the phylogenetic inference, it is proposed that the bacterium should be designated Paenibacillus azoreducens sp. nov. The type strain of Paenibacillus azoreducens is CM1T (= DSM 13822T = NCIMB 13761T). PMID: 11594595 [PubMed - indexed for MEDLINE] Paenibacillus brasilensis Int J Syst Evol Microbiol. 2002 Nov;52(Pt 6):2147-53. Paenibacillus brasilensis sp. nov., a novel nitrogen-fixing species isolated from the maize rhizosphere in Brazil. von der Weid I(1), Duarte GF, van Elsas JD, Seldin L. Author information: (1)Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. Sixteen nitrogen-fixing strains isolated from the rhizosphere of maize planted in Cerrado soil, Brazil, which showed morphological and biochemical characteristics similar to the gas-forming Paenibacillus spp., were phenotypically and genetically characterized. Their identification as members of the genus Paenibacillus was confirmed by using specific primers based on the 16S rRNA gene. SDS-PAGE of whole-cell proteins, API 50CH, morphological and biochemical tests, amplified rDNA-restriction analysis (ARDRA), DNA-relatedness analyses, denaturing-gradient gel electrophoresis (DGGE) and 16S rRNA gene sequence determinations were performed to characterize the novel isolates and to compare them to strains of other nitrogen-fixing Paenibacillus spp. Phenotypic analyses showed that the 16 strains were very homogeneous and shared a high level of relatedness with Paenibacillus polymyxa and Paenibacillus peoriae. However, none of the novel isolates was able to ferment glycerol (positive test for P. polymyxa), L-arabinose or D-xylose (positive tests for P. polymyxa and P. peoriae) or utilize succinate (positive test for P. peoriae). Genetic approaches also indicated a high level of similarity among the novel isolates and P. polymyxa and P. peoriae, but the novel strains clearly could not be assigned to either of these two recognized species. On the basis of the features presented in this study, the 16 novel isolates were considered to represent members of a novel species within the genus Paenibacillus, for which the name Paenibacillus brasilensis is proposed. The type strain is PB1 72(T) (= ATCC BAA-413(T) = DSM 14914(T)). PMID: 12508882 [PubMed - indexed for MEDLINE] Paenibacillus campinasensis Int J Syst Bacteriol. 1998 Jul;48 Pt 3:833-7. Paenibacillus campinasensis sp. nov., a cyclodextrin-producing bacterium isolated in Brazil. Yoon JH(1), Yim DK, Lee JS, Shin KS, Sato HH, Lee ST, Park YK, Park YH. Author information: (1)Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yusong, Taejon, Korea. An alkaliphilic, endospore-forming bacterium isolated from Brazilian soil was taxonomically studied and is proposed as a new Paenibacillus species. This organism (strain 324T) was particularly distinguishable from other Paenibacillus species by its ability to grow optimally at pH 10 and 40 degrees C. The DNA G+C content was 5.0 mol%. The diamine acid of the cell-wall peptidoglycan was meso-diaminopimelic acid. MK-7 was the predominant menaquinone and anteiso-C15:0 was the major fatty acid. Levels of 16S rDNA similarity between strain 324T and other Paenibacillus species were 90.6-95.9%. Phylogenetically, strain 324T formed an evolutionary lineage distinct from other species within the evolutionary radiation encompassing the genus Paenibacillus. Based on phenotyic and chemotaxonomic properties, and phylogenetic inference, it is proposed that strain 324T should be placed in the genus Paenibacillus as a new species is strain 324T should be placed in the genus Paenibacilus as a new species, Paenibacillus campinasensis. This type strain of the new species is strain 325T (= KCTC 0364BP). PMID: 9734037 [PubMed - indexed for MEDLINE] Paenibacillus chinjuensis Int J Syst Evol Microbiol. 2002 Mar;52(Pt 2):415-21. Paenibacillus chinjuensis sp. nov., a novel exopolysaccharide-producing bacterium. Yoon JH(1), Seo WT, Shin YK, Kho YH, Kang KH, Park YH. Author information: (1)Korea Research Institute of Bioscience and Biotechnology, Yusong, Taejon. A novel exopolysaccharide-producing bacterium (WN9T) was isolated from Chinju, Korea, and was identified as a member of the genus Paenibacillus on the basis of phenotypic characteristics and phylogenetic inference based on 16S rDNA sequence. This organism is a facultatively anaerobic, endospore-forming rod. The diamino acid found in the peptidoglycan is meso-diaminopimelic acid. The predominant menaquinone is MK-7. The major cellular fatty acid is anteiso-C15:0. The G+C content is 53 mol%. The phylogenetic tree shows that strain WN9T falls within the radiation of a cluster comprising the Paenibacillus species. The levels of 16S rDNA similarity between strain WN9T and the type strains of validly described Paenibacillus species are 92.1-95.8%. Strain WN9T is clearly distinguishable from some phylogenetically related Paenibacillus species on the basis of DNA-DNA relatedness data and phenotypic characters. Therefore, on the basis of these data, a novel species of the genus Paenibacillus, Paenibacillus chinjuensis sp. nov., is proposed. The type strain is strain WN9T (= KCTC 8951PT = JCM 10939T). PMID: 11931150 [PubMed - indexed for MEDLINE] Paenibacillus daejeonensis Int J Syst Evol Microbiol. 2002 Nov;52(Pt 6):2107-11. Paenibacillus daejeonensis sp. nov., a novel alkaliphilic bacterium from soil. Lee JS(1), Lee KC, Chang YH, Hong SG, Oh HW, Pyun YR, Bae KS. Author information: (1)Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, #52 Oun-dong, Yusong-ku, Daejeon 305-333, Korea. The taxonomy of soil isolates AP-20(T) and AP-37 was examined. These alkaliphilic organisms grew over a wide pH range (pH 7.0-13.0). The growth rate was higher at pH 8.0-12.0 than at pH 7.0. The G+C composition of these strains averaged 53 mol%. These strains contained MK-7 as the main respiratory quinone and meso-diaminopimelic acid in the cell-wall peptidoglycan. The major cellular fatty acid of the isolates was 12-methyltetradecanoic acid. Levels of 16S rDNA similarity between strain AP-20(T), AP-37 and other Paenibacillus species were 94.2-90.2%. Phylogenetic analysis based on 16S rDNA sequence revealed that strains 68 243. 244. 245. 246. 247. AP-20(T) and AP-37 formed an evolutionary lineage distinct from other Paenibacillus species. Based on the evaluation of morphological, physiological and chemotaxonomic characteristics, and on 16S rDNA sequence comparison, the new species Paenibacillus daejeonensis sp. nov. is proposed; the type strain is AP-20(T) ( = KCTC 3745(T) = JCM 11236(T)). PMID: 12508876 [PubMed - indexed for MEDLINE] Paenibacillus glycanilyticus Int J Syst Evol Microbiol. 2002 Sep;52(Pt 5):1669-74. Paenibacillus glycanilyticus sp. nov., a novel species that degrades heteropolysaccharide produced by the cyanobacterium Nostoc commune. Dasman(1), Kajiyama S, Kawasaki H, Yagi M, Seki T, Fukusaki E, Kobayashi A. Author information: (1)Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan. A novel bacterial strain, DS-1T, was isolated that degrades heteropolysaccharide produced by the cyanobacterium Nostoc commune. The isolate was identified by a combination of phenotypic characterization, cellular fatty acid analysis, DNA base composition, DNA-DNA hybridization and 165 rRNA gene sequence analysis. Phylogenetic analysis placed strain DS-1T within the Paenibacillus cluster on a phylogenetic tree and the phenotypic characteristics of this strain appear to be similar to those of Paenibacillus curdlanolyticus IFO 15724T and Paenibacillus kobensis IFO 15729T. The strain was distinguished from P. curdlanolyticus IFO 15724T and P. kobensis IFO 15729T by its ability to degrade the polysaccharide of Nostoc commune, by assimilation of rhamnose, inositol and L-fucose and by its wide range of optimal growth temperature (28-37 degrees C). Like other Paenibacillus species, this strain contains anteiso-C15:0 as a major cellular fatty acid, and it has a DNA G+C content of 50.5 mol %. Based on these results, it is concluded that this isolate should be placed within a novel species of Paenibacillus, Paenibacillus glycanilyticus sp. nov., with the type strain DS-1T (= IFO 16618T = JCM 11221T = NRRL B-23455T). PMID: 12361272 [PubMed - indexed for MEDLINE] Paenibacillus graminis Int J Syst Evol Microbiol. 2002 Mar;52(Pt 2):607-16. Paenibacillus graminis sp. nov. and Paenibacillus odorifer sp. nov., isolated from plant roots, soil and food. Berge O(1), Guinebretière MH, Achouak W, Normand P, Heulin T. Author information: (1)CEA/Cadarache, DSV-DEVM, Laboratoire d'Ecologie Microbienne de la Rhizosphère, UMR 163 CNRS-CEA, Saint-Paul-Lez-Durance, France. [email protected] Sixteen gram-positive endospore-forming bacteria previously isolated from soil, plant rhizospheres, plant roots and pasteurized pureed vegetables were studied to determine their taxonomic positions. The isolates were formerly identified as Bacillus circulans based on their biochemical characters using API galleries. Two of these strains, RSA19T and TOD45T, were recently assigned to the genus Paenibacillus based on phylogenetic analysis of their 16S rRNA (rrs) gene sequence. In the present work, the sixteen isolates were assigned to two genomospecies using DNA-DNA hybridization, in agreement with rrs gene sequence analysis. These genomospecies can also be differentiated on the basis of their cultural and biochemical characters into two novel species, for which the names Paenibacillus graminis sp. nov. (type strain RSA19T = ATCC BAA-95T = LMG 19080T) and Paenibacillus odorifer sp. nov. (type strain TOD45T = ATCC BAA-93T = LMG 19079T) are proposed. PMID: 11931174 [PubMed - indexed for MEDLINE] Paenibacillus granivorans Syst Appl Microbiol. 2000 Oct;23(3):344-8. Paenibacillus granivorans sp. nov., a new Paenibacillus species which degrades native potato starch granules. van der Maarel MJ(1), Veen A, Wijbenga DJ. Author information: (1)Centre for Carbohydrate Bioengineering TNO-RUG, Haren, The Netherlands. [email protected] From a native potato starch-degrading enrichment culture, strain A30 had been isolated and had tentatively been identified as a member of the Bacillus firmus/lentus group (Wijbenga et al. Appl. Microbiol. Biotechnol. 35, 180-184, 1991). In this paper the isolate A30 is further characterized using phylogentic analysis of the 16S rDNA and determination of a number of additional phenotypic characteristics. These data are compared to those of Paenibacillus amylolyticus, P. chibensis, and P. thiaminolyticus. It is concluded that strain A30 is a new Paenibacillus species, for which the name Paenibacillus granivorans is suggested. PMID: 11108012 [PubMed - indexed for MEDLINE] Paenibacillus hodogayensis Int J Syst Evol Microbiol. 2005 Mar;55(Pt 2):737-41. Paenibacillus hodogayensis sp. nov., capable of degrading the polysaccharide produced by Sphaerotilus natans. Takeda M(1), Suzuki I, Koizumi J. Author information: (1)Division of Materials Science and Chemical Engineering, Faculty of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama 240-8501, Japan. [email protected] Sphaerotilus natans is a sheathed bacterium often found in activated sludge that has a bulking problem. A bacterial strain that is able to degrade the extracellular polysaccharide produced by S. natans was isolated. The isolate was a spore-forming, aerobic, rod-shaped bacterium. The Gram reaction was variable or negative. The optimum growth temperature was 30 degrees C and the optimum pH was 8. The G+C content of the DNA was 55 mol%. The major cellular fatty acid and respiratory quinone were anteiso-C(15 : 0) and MK-7, respectively. Phylogenetic analysis based on the 16S rRNA gene indicated that the isolate was a member of the genus Paenibacillus. The nearest relative, with a similarity of 94.2 %, was Paenibacillus koleovorans, a bacterium capable of degrading the sheath of S. natans. The phenotypic characteristics of the isolate were apparently different from those of related species in the genus Paenibacillus. It is proposed that the isolate be designated Paenibacillus hodogayensis sp. nov. The type strain is SG(T) (=JCM 12520(T)=KCTC 3919(T)). PMID: 15774654 [PubMed - indexed for MEDLINE] Paenibacillus hongkongensis Mol Pathol. 2003 Feb;56(1):29-35. Pseudobacteraemia in a patient with neutropenic fever caused by a novel paenibacillus species: Paenibacillus hongkongensis sp. nov. Teng JL(1), Woo PC, Leung KW, Lau SK, Wong MK, Yuen KY. Author information: (1)Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong. AIMS: To characterise a strain of Gram negative aerobic straight or slightly curved rods (HKU3) isolated from the blood 69 culture of a 9 year old Chinese boy with neutropenic fever and pseudobacteraemia. METHODS: The isolate was phenotypically investigated by standard biochemical methods using conventional biochemical tests, scanning electron microscopy, and transmission electron microscopy. Genotypically, the 16S rRNA gene of the bacterium was amplified by the polymerase chain reaction (PCR) and sequenced. The sequence of the PCR product was compared with known 16S rRNA gene sequences in the Genbank by multiple sequence alignment. The G + C content was determined by thermal denaturation. A phylogenetic tree was constructed by the PileUp method. RESULTS: The cells of the bacterial strain were aerobic, sporulating, Gram negative straight or slight curved rods. The bacterium grew on horse blood agar as non-haemolytic, grey colonies of 1 mm in diameter after 24 hours of incubation at 37 degrees C in ambient air. No enhancement of growth was seen in 5% CO(2). It grew at 50 degrees C as pinpoint colonies after 72 hours of incubation, but did not grow at 65 degrees C or on MacConkey agar. It was non-motile. It produced catalase (weakly positive) and cytochrome oxidase. It reduced nitrate, produced beta galactosidase, hydrolysed esculin, and utilised sodium acetate. A scanning electron micrograph of the bacterium showed straight or slightly curved rods. A transmission electron micrograph of the cell wall of the bacterium revealed multiple electron dense layers, including the outer membrane, middle murein layer, and inner cytoplasmic membrane, compatible with its Gram smear appearance. 16S rRNA gene sequencing showed that there were 7.7%, 8.0%, 8.2%, and 8.6% differences between the 16S rRNA gene sequence of the bacterium and those of Paenibacillus macerans, Paenibacillus borealis, Bacillus ehimensis, and Paenibacillus amylolyticus, respectively. The mean (SD) G + C content of the bacterium was 47.6 (2.1) mol%. Phylogenetically, it belongs to the genus paenibacillus (previously called group 3 bacillus). CONCLUSIONS: A bacterium that exhibited phenotypic and genotypic characteristics that are very different from closely related members of paenibacillus was the cause of pseudobacteraemia in a patient with neutropenic fever. A new species, Paenibacillus hongkongensis sp. nov. is proposed, for which HKU3 is the type strain. PMCID: PMC1187286 PMID: 12560460 [PubMed - indexed for MEDLINE] 248. Paenibacillus illinoisensis Int J Syst Bacteriol. 1997 Apr;47(2):299-306. Emended description of Paenibacillus amylolyticus and description of Paenibacillus illinoisensis sp. nov. and Paenibacillus chibensis sp. nov. Shida O(1), Takagi H, Kadowaki K, Nakamura LK, Komagata K. Author information: (1)Research Laboratory, Higeta Shoyu Co., Ltd, Chiba, Japan. [email protected] The taxonomic position of unidentified group 6 of Bacillus circulans as described by Nakamura and Swezey (L.K. Nakamura and J. Swezey, Int. J. Syst. Bacteriol. 33:46-52, 1983) was determined, and the taxonomy of Paenibacillus amylolyticus was reexamined. The results of PCR amplification of a 16S rRNA gene fragment with a specific primer and comparative analysis of 16S rRNA gene sequences warranted placing the two taxa in the genus Paenibacillus. The levels of DNA reassociation among the strains revealed four groups (designated groups I, II, III, and 6), each with a high level of intragroup relatedness (> 72%). Clustering based on phenotypic characteristics correlated well with DNA relatedness grouping. P. amylolyticus strains were scattered in groups I, II, and III. Strains labeled the type strain of P. amylolyticus from different culture collections appeared in groups I and III. Strains found in group I were identified as P. amylolyticus sensu stricto, and the one strain found in group III was identified as Paenibacillus lautus. Group 6 encompassed strains formerly assigned to B. circulans group 6, and group II contained other strains identified as P. amylolyticus. Groups 6 and II were phenotypically and genetically distinct taxa that were distinguishable from the previously described species. These findings showed that groups 6 and II were new species, for which we propose the names Paenibacillus illinoisensis and Paenibacillus chibensis, respectively. PMID: 9103613 [PubMed - indexed for MEDLINE] 249. Paenibacillus jamilae Int J Syst Evol Microbiol. 2001 Sep;51(Pt 5):1687-92. Paenibacillus jamilae sp. nov., an exopolysaccharide-producing bacterium able to grow in olive-mill wastewater. Aguilera M(1), Monteoliva-Sánchez M, Suárez A, Guerra V, Lizama C, Bennasar A, Ramos-Cormenzana A. Author information: (1)Department of Microbiology, Faculty of Pharmacy, University of Granada, Spain. Endospore-forming strains were isolated from corn-compost treated with olive-mill wastewater ('alpechin'). The strains were taxonomically studied and proposed as a novel Paenibacillus species. These organisms (strains B.3T, B.7 and B.9) were particularly distinguishable from other aerobic spore-forming species by their ability to grow optimally in 100% (v/v) olive-mill wastewater at 30 degrees C and pH 7.0 and concomitant production of an interesting exopolysaccharide. Chemotaxonomic analysis revealed that MK-7 was the predominant menaquinone, the major fatty acid was anteiso C15:0 and the cell wall contained meso-diaminopimelic acid. The DNA G+C content was 40.7 mol%. Comparative sequence analysis of 16S rDNA with different reference species from the genera Bacillus, Paenibacillus, Brevibacillus, Aneurinibacillus, Alicyclobacillus, Halobacillus, Virgibacillus, Amphibacillus, Coprobacillus and Gracilibacillus indicated that the isolated strains were highly related to the genus Paenibacillus. Strain B.3T formed an evolutionary lineage distinct from other species within the evolutionary radiation encompassing the genus Paenibacillus. Strain B.3T was a close relative of Paenibacillus polymyxa, but DNA-DNA relatedness data with this species was very low (relative binding ratio < 16%). Based on the morphological and physiological characteristics, as well as on the phylogenetic position determined by 16S rDNA analysis and DNA-DNA relatedness data, it is concluded that these strains should be designated a novel species, for which the name Paenibacillus jamilae sp. nov. is proposed. The type strain is B.3T (= CECT 5266T = DSM 13815T). PMID: 11594596 [PubMed - indexed for MEDLINE] 250. Paenibacillus koleovorans Int J Syst Evol Microbiol. 2002 Sep;52(Pt 5):1597-601. Paenibacillus koleovorans sp. nov., able to grow on the sheath of Sphaerotilus natans. Takeda M(1), Kamagata Y, Shinmaru S, Nishiyama T, Koizumi J. Author information: (1)Division of Materials Science and Chemical Engineering, Faculty of Engineering, Yokohama National University, Hodogaya, Japan. 70 [email protected] Two bacterial strains that are able to grow specifically on the sheath of a sheathed filamentous bacterium, Sphaerotilus natans, were isolated from soil samples. The sheath-degrading organisms, designated strains TB(T) and TK, are facultatively anaerobic and form endospores. The Gram reaction was negative at all stages of cultivation. The optimum growth temperature and pH were 30 degrees C and pH 7. The DNA G+C content was 54.0-55.8 mol%. MK-7 was the predominant menaquinone and anteiso-C15:0 was the major fatty acid. Phylogenetic analysis based on the 16S rDNA sequences revealed that the isolates were closely related to Paenibacillus chondroitinus, Paenibacillus alginolyticus, Paenibacillus koreensis, Paenibacillus validus, Paenibacillus larvae subsp. larvae and P. larvae subsp. pulvifaciens. The sequences were found to contain consensus sequences characteristic of all Paenibacillus species. The isolates were able to lyse and utilize the purified sheath of S. natans as the sole carbon and energy source. Acid was not produced from common carbon sources, allowing easy distinction from other members of Paenibacillus. It is concluded that the two strains represent a novel Paenibacillus species, for which the name Paenibacillus koleovorans sp. nov. is proposed. The type strain is strain TB(T) (= JCM 11186T = IAM 14926T = KCTC 13912T). PMID: 12361261 [PubMed - indexed for MEDLINE] 251. Paenibacillus kribbensis Int J Syst Evol Microbiol. 2003 Jan;53(Pt 1):295-301. Paenibacillus kribbensis sp. nov. and Paenibacillus terrae sp. nov., bioflocculants for efficient harvesting of algal cells. Yoon JH(1), Oh HM, Yoon BD, Kang KH, Park YH. Author information: (1)Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea. Two strains of Gram-variable, rod-shaped, endospore-forming, peritrichously flagellated, rod-shaped bacteria were isolated from a soil sample collected in Taejon City, Korea. The two strains (AM49T and AM141T) were found to be members of the genus Paenibacillus, on the basis of the results of phenotypic and phylogenetic analyses. Strains AM49T and AM141T were found to have a cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as their predominant menaquinone and anteiso-C15:0 as their major fatty acid. The DNA G + C contents of strains AM49T and AM141T were 48 and 47 mol%, respectively. The two strains formed distinct phylogenetic lineages within the radiation of the cluster comprising Paenibacillus spp. and a coherent cluster with Paenibacillus jamilae, Paenibacillus polymyxa, Paenibacillus azotofixans and Paenibacillus peoriae. The level of 16S rDNA similarity between strains AM49T and AM141T was 97.6%, and 16S rDNA similarity values between strains AM49T and AM141T and the type strains of other Paenibacillus spp. ranged from 90.3 to 98.7%. Levels of DNA-DNA similarity between the two strains and members of the genus Paenibacillus indicated that strains AM49T and AM141T were distinguishable from each other and from four phylogenetically related Paenibacillus spp. Therefore, on the basis of their phenotypic properties, phylogeny and genomic distinctiveness, it is proposed that strains AM49T and AM141T be placed in the genus Paenibacillus as two distinct novel species, Paenibacillus kribbensis (AM49T =KCTC 0766BPT =JCM 11465T) and Paenibacillus terrae (AM141T =KCCM 41557T =JCM 11466T). PMID: 12656187 [PubMed - indexed for MEDLINE] 252. Paenibacillus lactis Int J Syst Evol Microbiol. 2004 May;54(Pt 3):885-91. Paenibacillus lactis sp. nov., isolated from raw and heat-treated milk. Scheldeman P(1), Goossens K, Rodriguez-Diaz M, Pil A, Goris J, Herman L, De Vos P, Logan NA, Heyndrickx M. Author information: (1)Ministry of the Flemish Community, Centre for Agricultural Research, Department of Animal Product Quality, Brusselsesteenweg 370, 9090 Melle, Belgium. [email protected] Endospore-forming bacteria were recovered from individual packages from different processing lines in a dairy plant during a tenacious periodical contamination of their UHT-milk production. Two colony types were seen, one of which was identified as Bacillus sporothermodurans. Analysis of the 16S rRNA gene of the second colony type placed these isolates within the genus Paenibacillus, with Paenibacillus lautus as the closest known relative. Moreover, over 99 % similarity was observed to the 16S rDNA sequence of MB 2035, a strain isolated previously from raw milk during a survey at dairy farms for very heat-resistant spore-forming bacteria. Nine other potentially closely related strains among the dairy farm isolates were found using rep-PCR typing. The taxonomic positions of these 19 isolates were further investigated using 16S rRNA gene sequencing and DNA-DNA hybridizations of representative strains. All 19 isolates shared a high degree of phenotypic similarity and were easily distinguished from closely related members of the genus. Anteiso-C(15 : 0), C(16 : 0) and iso-C(15 : 0) were among the major fatty acids and the genomic DNA G+C content was 51.6-51.7 mol%. Therefore, based on their phenotypic, phylogenetic and genomic distinctiveness, these 19 strains, isolated from both raw and heat-treated milk, are placed in the genus Paenibacillus as Paenibacillus lactis sp. nov. The type strain is MB 1871(T) (=LMG 21940(T)=DSM 15596(T)). PMID: 15143040 [PubMed - indexed for MEDLINE] 253. Paenibacillus phyllosphaerae Int J Syst Evol Microbiol. 2005 Mar;55(Pt 2):743-6. Paenibacillus phyllosphaerae sp. nov., a xylanolytic bacterium isolated from the phyllosphere of Phoenix dactylifera. Rivas R(1), Mateos PF, Martínez-Molina E, Velázquez E. Author information: (1)Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain. [email protected] A bacterial strain, designated PALXIL04(T), was isolated from the phyllosphere of Phoenix dactylifera. Phylogenetic analysis placed the isolate within the genus Paenibacillus with the closest relatives being Paenibacillus curdlanolyticus and Paenibacillus kobensis. DNA-DNA hybridization measurements showed low DNA relatedness (15-20 %) between the isolate and its closest relatives. Cells were Gram-variable, facultatively anaerobic, motile, sporulating rods. Catalase and oxidase were produced by the organism. Cellulose, starch, aesculin and xylan were hydrolysed. Growth was supported by many carbohydrates as the carbon source. MK-7 was the predominant menaquinone and anteiso-C(15 : 0) the major 71 fatty acid. The G+C content of the DNA was 50.7 mol%. Phylogenetic, DNA-DNA relatedness and phenotypic analyses indicated that strain PALXIL04(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus phyllosphaerae sp. nov. is proposed. The type strain is PALXIL04(T) (=LMG 22192(T)=CECT 5862(T)). PMID: 15774655 [PubMed - indexed for MEDLINE] 254. Paenibacillus profundus Nat Prod Commun. 2013 Mar;8(3):381-4. A new antimicrobial and anticancer peptide producing by the marine deep sediment strain "Paenibacillus profundus" sp. nov. Sl 79. Kalinovskaya NI(1), Romanenko LA, Kalinovsky AI, Dmitrenok PS, Dyshlovoy SA. Author information: (1)G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Pr. 100-letiya Vladivostoka 159, Russian Federation. [email protected] A new linear glyceryl acid derived heptapeptide (1), together with known isocoumarin antibiotic, Y-05460M-A (2), were isolated from the culture of the deep sea sediment strain SI 79 classified as "Paenibacillus profundus" sp. nov. Their structures were determined by 1D- and 2DNMR techniques and ESI-MS/MS experiments. HPLC analysis of the Marfey derivatives in comparison to their analogs of authentic amino acids revealed that all amino acids in peptide 1, with an exception of Val, have the D-configuration. The compound 1 showed inhibitory activity against Staphylococcus aureus, Staphylococcus epidermidis, Bacillus subtilis, Enterococcus faecium as well as cytotoxic and moderate colony growth inhibitory activity against SK-MEL-28 cell line. PMID: 23678816 [PubMed - indexed for MEDLINE]$$ 255. Paenibacillus tyraminigenes Int J Food Microbiol. 2008 Oct 31;127(3):209-14. doi: 10.1016/j.ijfoodmicro.2008.07.002. Epub 2008 Jul 4. Paenibacillus tyraminigenes sp. nov. isolated from Myeolchi-jeotgal, a traditional Korean salted and fermented anchovy. Mah JH(1), Chang YH, Hwang HJ. Author information: (1)Graduate School of Biotechnology, Korea University, Seoul, Republic of Korea. A bacterial strain H3029, a gram-positive, rod-shaped, oxidase-negative, endospore-forming bacterium that characteristically produces tyramine from tyrosine, was isolated from a Myeolchi-jeotgal, a traditional Korean salted and fermented anchovy (Engraulis japonicus). The H3029 strain showed a high ability to produce 4140 microg/ml of tyramine from the culture broth containing 5000 microg/ml tyrosine. On the other hand, the strain produced a relatively low level of other putrefactive amines, at 973 microg/ml of putrescine and 147 microg/ml of cadaverine from the media, with each 5000 microg/ml of ornithine hydrochloride and lysine hydrochloride. The H3029 strain produced no detectable level of histamine (detection limit of 4 microg/ml) from the media containing 5000 microg/ml of histidine hydrochloride. Meanwhile, tyramine, the main product of the strain, showed the antimicrobial activity at the level of over 1 mg/disk against Staphylococcus aureus by agar diffusion test, and the mutagenicity in Ames test at 0.1 mg/plate using Salmonella typhimurium TA98 and TA1535. On the basis of the polyphasic taxonomic study, the H3029(T) strain was assigned a novel species of the genus Paenibacillus as Paenibacillus tyraminigenes sp. nov. The type strain of which is strain H3029(T) (=KCTC 10694BP(T)). PMID: 18678425 [PubMed - indexed for MEDLINE] 第二十四节 Paraliobacillus 256. Paraliobacillus ryukyuensis J Gen Appl Microbiol. 2002 Oct;48(5):269-79. Paraliobacillus ryukyuensis gen. nov., sp. nov., a new Gram-positive, slightly halophilic, extremely halotolerant, facultative anaerobe isolated from a decomposing marine alga. Ishikawa M(1), Ishizaki S, Yamamoto Y, Yamasato K. Author information: (1)Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, Setagaya-ku, Japan. [email protected] A slightly halophilic, extremely halotolerant, alkaliphilic, and facultatively anaerobic rod bacterium was isolated from a decomposing marine alga collected in Okinawa, Japan. The isolate, designated O15-7(T), was Gram-positive, endospore-forming, catalase-positive, menaquinone-7-possessing bacterium that is motile by peritrichous flagella. The isolate was an inhabitant of marine environments; the optimum NaCl concentration for growth was 0.75-3.0% (w/v) with a range of 0-22.0%, and the optimum pH was 7.0-8.5 with a range of 5.5-9.5. Catalase was produced in aerobic cultivation but not in anaerobic cultivation. Carbohydrate, sugar alcohol or a related carbon compound was required for growth. In aerobic cultivation, the isolate produced pyruvate, acetate and CO(2) from glucose, and in anaerobic cultivation, it produced lactate, formate, acetate and ethanol with a molar ratio of approximately 2 : 1 : 1 for the last three products. No gas was produced anaerobically. Lactate yield per consumed glucose was markedly affected by the pH of the fermentation medium: 51% at pH 6.5 and 8% at pH 9.0. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Phylogenetically, the isolate occupied an independent lineage within the group composed of the halophilic/halotolerant/alkaliphilic and/or alkalitolerant species in Bacillus rRNA group 1 with the highest 16S rRNA gene sequence similarity of 95.2% to the genus Gracilibacillus. For this isolate, Paraliobacillus ryukyuensis gen. nov., sp. nov. was proposed. The type strain, O15-7(T) (G+C535.6 mol%), has been deposited in the DSMZ, IAM, 72 NBRC, and NRIC (DSM 15140(T)=IAM 15001(T)=NBRC 10001(T)=NRIC 0520(T)). PMID: 12501437 [PubMed - indexed for MEDLINE] 第二十五节 Pelagibacillus 257. Pelagibacillus goriensis Int J Syst Evol Microbiol. 2007 Jul;57(Pt 7):1554-60. Pelagibacillus goriensis gen. nov., sp. nov., a moderately halotolerant bacterium isolated from coastal water off the east coast of Korea. Kim YG(1), Hwang CY, Yoo KW, Moon HT, Yoon JH, Cho BC. Author information: (1)School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, San 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea. A Gram-positive, moderately halotolerant bacterium, designated CL-GR16(T), was isolated from coastal water off the east coast of Korea. The strain was strictly aerobic, rod-shaped, motile by means of peritrichous flagella and produced ellipsoidal spores. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represented an independent lineage within Bacillus rRNA group 1, showing 93.6-94.6 % similarity with respect to the genus Ornithinibacillus, 94.0 % with respect to Paucisalibacillus, 91.0-93.5 % with respect to Virgibacillus, 93.2-93.3 % with respect to Salinibacillus and 92.8-93.2 % with respect to Oceanobacillus. The optimum temperature and pH for growth were 30 degrees C and pH 7.5. Strain CL-GR16(T) was able to grow at NaCl concentrations from 0 to 14 %, with optimum growth occurring at 0-2 % NaCl. The strain lacked oxidase. The major fatty acids were anteiso-C(15 : 0) (65.6 %), anteiso-C(17 : 0) (11.0 %) and iso-C(15 : 0) (9.1 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The predominant menaquinone was MK-7. The G+C content of the DNA was 43 mol%. On the basis of the results of the polyphasic analysis, strain CL-GR16(T) represents a novel genus and species, for which the name Pelagibacillus goriensis gen. nov., sp. nov. is proposed. The type strain is strain CL-GR16(T) (=KCCM 42329(T)=DSM 18252(T)). PMID: 17625193 [PubMed - indexed for MEDLINE] 第二十六节 Pontibacillus 258. Pontibacillus chungwhensis Int J Syst Evol Microbiol. 2005 Jan;55(Pt 1):165-70. Pontibacillus chungwhensis gen. nov., sp. nov., a moderately halophilic Gram-positive bacterium from a solar saltern in Korea. Lim JM(1), Jeon CO, Song SM, Kim CJ. Author information: (1)Korea Research Institute of Bioscience and Biotechnology (KRIBB), 52 Oeundong, Yusong, Daejon 305-333, Republic of Korea. Three moderately halophilic, spore-forming strains, designated BH030062T, BH030049 and BH030080, were isolated from a solar saltern in Korea. Phylogenetic analyses and comparative 16S rRNA gene sequence studies revealed that the isolates represent a novel distinct monophyletic lineage within the phyletic group classically defined as the genus Bacillus and are most closely related to members of the genera Gracilibacillus (93.7-95.1 % similarity), Virgibacillus (93.5-94.8 %), Halobacillus (94.8-95.9 %), Filobacillus (94.4-94.8 %) and Lentibacillus (93.3-93.7 %). Strain BH030062T was strictly aerobic, rod-shaped, Gram-positive and motile by means of peritrichous flagella. It grew in the presence of 1-15 % (w/v) NaCl and at temperatures of 15-45 degrees C. The cell wall peptidoglycan contained A1gamma-meso-diaminopimelic acid as the diagnostic diamino acid. The predominant cellular fatty acids were iso-C(15 : 0), anteiso-C(15 : 0) and iso-C(16 : 0). DNA G+C content was about 41 mol% and the major isoprenoid quinone was MK-7. On the basis of their physiological and molecular properties, the isolates represent a new genus, Pontibacillus gen. nov., and novel species, Pontibacillus chungwhensis sp. nov. The type strain is BH030062T (=KCTC 3890T=DSM 16287T). PMID: 15653871 [PubMed - indexed for MEDLINE] 第二十七节 Psychrobacillus 259. Psychrobacillus gen. nov. Syst Appl Microbiol. 2010 Nov;33(7):367-73. doi: 10.1016/j.syapm.2010.06.003. Epub 2010 Jul 21. Psychrobacillus gen. nov. and proposal for reclassification of Bacillus insolitus Larkin & Stokes, 1967, B. psychrotolerans Abd-El Rahman et al., 2002 and B. psychrodurans Abd-El Rahman et al., 2002 as Psychrobacillus insolitus comb. nov., Psychrobacillus psychrotol- 73 erans comb. nov. and Psychrobacillus psychrodurans comb. nov. Krishnamurthi S(1), Ruckmani A, Pukall R, Chakrabarti T. Author information: (1)Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology, Sector 39A, Chandigarh 160 036, India. The taxonomic status of three Bacillus species, Bacillus insolitus, B. psychrodurans and B. psychrotolerans was reexamined using a polyphasic approach. In our analysis, these three Bacillus species formed a cluster separate from other members of Bacillus rRNA group 2 [5] and from Bacillus sensu stricto. These three species shared high 16S rRNA gene sequence similarities between them (97.8-99.7%) and showed closest sequence similarity (95.3-96.3%) to Paenisporosarcina quisquiliarum gen. nov., sp. nov. [18]. Sequence similarities with other related genera ranged between 90.9% and 94.5%. Phylogenetic coherence of the three species was supported by phenotypic characteristics, such as growth at low temperatures, negative oxidation and assimilation of many carbohydrates, MK8 as the major isoprenoid quinine and broadly similar polar lipid profiles. All three species had a similar peptidoglycan type of the variation A4β and similar genomic G+C contents (35.7-36.6 mol% [1]). Genomic relatedness among them was shown to be less than 70% and justified their separate species status [1]. These three species could be differentiated from each other and from related taxa on the basis of phenotypic, including chemotaxonomic, characteristics and ribotype patterns. On the basis of our analysis, we propose a new genus Psychrobacillus gen. nov. and to transfer B. insolitus, B. psychrodurans and B. psychrotolerans to the new genus as Psychrobacillus insolitus comb. nov. (type species of the genus; type strain W16B(T)=DSM 5(T)), P. psychrodurans comb. nov. (type strain 68E3(T)=DSM 11713(T)) and P. psychrotolerans comb. nov. (type strain 3H1(T)=DSM 11706(T)). Copyright © 2010 Elsevier GmbH. All rights reserved. PMID: 20650590 [PubMed - indexed for MEDLINE] 第二十八节 Rummeliibacillus 260. Rummeliibacillus stabekisii Int J Syst Evol Microbiol. 2009 May;59(Pt 5):1094-9. doi: 10.1099/ijs.0.006098-0. Description of Rummeliibacillus stabekisii gen. nov., sp. nov. and reclassification of Bacillus pycnus Nakamura et al. 2002 as Rummeliibacillus pycnus comb. nov. Vaishampayan P(1), Miyashita M, Ohnishi A, Satomi M, Rooney A, La Duc MT, Venkateswaran K. Author information: (1)Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA. Strains of aerobic, Gram-positive, rod-shaped, round-spore-forming bacteria were isolated from different geographical locations and a subsequent polyphasic study was undertaken to clarify the taxonomic position of the round-spore-forming isolates strain KSC-SF6g(T), strain M32 and strain NBRC 12622. 16S rRNA gene sequence similarities demonstrated that these strains were most closely affiliated with Bacillus pycnus NRRL NRS-1691(T) (98 %), with species of Kurthia (96 %) and Viridibacillus (94-96 %) as the next nearest relatives. However, while DNA-DNA hybridization studies showed approx. 70 % reassociation among strains KSC-SF6g(T), M32 and NBRC 12622, DNA-DNA hybridization values between these strains and B. pycnus NRRL NRS-1691(T) never exceeded 13 %. Differences in the molecular structure of the cell-wall peptidoglycan could not differentiate these strains sufficiently from other closely related genera (Viridibacillus and Kurthia). However, Lys-Asp was present in strains KSC-SF6g(T), M32 and NBRC 12622, whereas l-Lys-d-Glu was reported in B. pycnus NRRL NRS-1691(T). The menaquinone MK-7 was dominant in strains KSC-SF6g(T), M32 and NBRC 12622 and members of the genus Kurthia, whereas MK-8 was abundant in Viridibacillus species. Strains KSC-SF6g(T), M32 and NBRC 12622 exhibited fatty acid profiles consisting of major amounts of anteiso-C(15 : 0) ( approximately 50 %) and iso-C(15 : 0) ( approximately 25 %) and moderate amounts of anteiso-C(17 : 0) ( approximately 7 %), which discriminated them from closely related B. pycnus NRRL NRS-1691(T) and species of Viridibacillus (iso-C(15 : 0); 46-74 %). The authors propose that strains KSC-SF6g(T), M32 and NBRC 12622 and B. pycnus NRRL NRS-1691(T) be reclassified into a separate genus based on clear-cut differences in discriminative taxonomic markers and the distant placement of B. pycnus and the novel strains described herein from other species of this clade according to current 16S rRNA gene sequence-based relatedness ( approximately 4 % difference in sequence). We propose the placement of these isolates into the novel genus Rummeliibacillus gen. nov. For the new taxon comprising strains KSC-SF6g(T), M32 and NBRC 12622, we propose the name Rummeliibacillus stabekisii gen. nov., sp. nov. (the type species of Rummeliibacillus), represented by the type strain KSC-SF6g(T) (=NRRL B-51320(T) =NBRC 104870(T)). In addition, Bacillus pycnus, which bears traits distinct from other round-spore-forming species [i.e. absence of growth at high NaCl (7 %), positive reaction for gelatin liquefaction], is reclassified as Rummeliibacillus pycnus comb. nov. (type strain JCM 11075(T) =NRRL NRS-1691(T)) based on phylogenetic affiliations and phenotypic characterization. PMID: 19406799 [PubMed - indexed for MEDLINE] 74 第二十九节 Salinibacillus 261. Salinibacillus aidingensis Int J Syst Evol Microbiol. 2005 Mar;55(Pt 2):949-53. Salinibacillus aidingensis gen. nov., sp. nov. and Salinibacillus kushneri sp. nov., moderately halophilic bacteria isolated from a neutral saline lake in Xin-Jiang, China. Ren PG(1), Zhou PJ. Author information: (1)State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China. Three Gram-positive, moderately halophilic, heterotrophic bacterial strains were isolated from a neutral saline lake in the Xin-Jiang area of China. The strains, designated 8-2(T), W11-1 and 25-7(T), were motile, spore-forming, aerobic rods and contained meso-diaminopimelic acid in their cell walls. Their DNA G+C contents were 37.4, 37.2 and 39.9 mol%, respectively. The main fatty acids in the cellular membranes of these novel strains were C(15) and C(17) methyl-branched. No species with validly published names showed 16S rRNA gene sequence similarity of more than 95 % with respect to these novel isolates; the most closely related species was a halophilic denitrifier, Bacillus halodenitrificans (94.6 %). Polyphasic taxonomic studies revealed that these strains belong to the Bacillaceae and are distantly related to other genera of the family. It is proposed that a new genus, Salinibacillus, should be created, with Salinibacillus aidingensis (type strain, 25-7(T)=AS 1.3565(T)=JCM 12389(T)) as the type species. Another species, Salinibacillus kushneri, is also proposed, with 8-2(T) (=AS 1.3566(T)=JCM 12390(T)) as the type strain. PMID: 15774690 [PubMed - indexed for MEDLINE] 第三十节 Salsuginibacillus 262. Salsuginibacillus kocurii Int J Syst Evol Microbiol. 2007 Oct;57(Pt 10):2381-6. Salsuginibacillus kocurii gen. nov., sp. nov., a moderately halophilic bacterium from soda-lake sediment. Carrasco IJ(1), Márquez MC, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A. Author information: (1)Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain. A Gram-positive, endospore-forming, alkali-tolerant, moderately halophilic bacterium, designated strain CH9d(T), was isolated from the sediment of Lake Chagannor in the Inner Mongolia Autonomous Region, China. The cells were rod-shaped and motile. Isolate CH9d(T) grew at pH 5.8-10.0 (optimally at pH 8.5), at salinities of 3-20 % (w/v) marine salts (optimally at 10.0 %, w/v) and between 20 and 50 degrees C (optimally at 37 degrees C). The cell wall contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was MK-7. The predominant cellular fatty acids of strain CH9d(T) were anteiso-C(15 : 0), anteiso-C(17 : 0), iso-C(17 : 0) and iso-C(15 : 0) and its polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unknown phospholipids. The G+C content of the DNA was 44.7 mol%. Strain CH9d(T) exhibited a 16S rRNA gene sequence similarity value of only 91 % with respect to Thalassobacillus devorans DSM 16966(T) and showed values below 91 % with respect to members of the genera Bacillus, Halobacillus and Marinococcus. Strain CH9d(T) could be clearly differentiated from its closest phylogenetic neighbours on the basis of several phenotypic, genotypic and chemotaxonomic features. Therefore, data from the polyphasic study support the placement of strain CH9d (T) in a novel genus and species, for which the name Salsuginibacillus kocurii gen. nov., sp. nov. is proposed. The type strain is CH9d(T) (=CCM 7365(T)=CECT 7154(T)=CGMCC 1.6287(T)=DSM 18087(T)). PMID: 17911315 [PubMed - indexed for MEDLINE] 第三十一节 Sulfobacillus 263. Sulfobacillus sibiricus Mikrobiologiia. 2003 Sep-Oct;72(5):681-8. [Sulfobacillus sibiricus sp. nov., a new moderately thermophilic bacterium]. [Article in Russian] Melamud VS(1), Pivovarova TA, Turova TP, Kolganova TV, Osipov GA, Lysenko AM, Kondrat'eva TF, Karavaĭko GI. Author information: (1)Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7, k. 2., Moscow, 117312 Russia. In the course of pilot industrial testing of a biohydrometallurgical technology for processing goldarsenic concentrate obtained from the Nezhdaninskoe ore deposit (East Siberia, Sakha, Yakutiya), a new gram-positive rod-shaped spore-forming moderately thermophilic bacterium (designated as strain N1) oxidizing Fe2+, S0, and sulfide minerals in the presence of yeast extract (0.02%) was isolated from a dense pulp. Physiologically, strain N1 differs from previously described species of the genus Sulfobacillus in having a somewhat higher optimal growth temperature (55 degrees C). Unlike the type strain of S. thermosulfidooxidans, strain 75 N1 could grow on medium with 1 mM thiosulfate or sodium tetrathionate as a source of energy only within several passages and failed to grow, in the absence of an inorganic energy source, on media with sucrose, fructose, glucose, reduced glutathione, alanine, cysteine, sorbitol, sodium acetate, or pyruvate. The G + C content of the DNA of strain N1 was 48.2 mol %. The strain showed 42% homology after DNA-DNA hybridization with the type strain of S. thermosulfidooxidans and 10% homology with the type strain of S. acidophilus. The isolate differed from previously studied strains of S. thermosulfidooxidans in the structure of its chromosomal DNA (determined by the method of pulsed-field gel electrophoresis) which remained stable as growth conditions were changed. According to the results of the 16S rRNA gene analysis, the new strain forms a single cluster with the bacteria of the species Sulfobacillus thermosulfidooxidans (sequence similarity of 97.9-98.6%). Based on these genetic and physiological features, strain N1 is described as a new species Sulfobacillus sibiricus sp. nov. PMID: 14679908 [PubMed - indexed for MEDLINE] 第三十二节 Tenuibacillus 264. Tenuibacillus multivorans Int J Syst Evol Microbiol. 2005 Jan;55(Pt 1):95-9. Tenuibacillus multivorans gen. nov., sp. nov., a moderately halophilic bacterium isolated from saline soil in Xin-Jiang, China. Ren PG(1), Zhou PJ. Author information: (1)State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China. [email protected] Two Gram-positive, rod-shaped, spore-forming and moderately halophilic bacteria (strains 28-1T, 28-4), isolated from a soil sample from a neutral salt lake in Xin-Jiang, China, were characterized polyphasically. On the basis of fasta (ungapped) analyses of 16S rRNA gene sequences, strains 28-1T and 28-4 were shown to belong to the Bacillaceae and to be closely related to Filobacillus milensis DSM 13259T (97.0 %) and Bacillus haloalkaliphilus DSM 5271T (95.7 %). 16S rRNA gene sequence similarity with other recognized species was not more than 94.1 %. Phylogenetic, chemotaxonomic, physiological and biochemical data supported the differentiation of these novel strains from F. milensis and B. haloalkaliphilus. Therefore these two previously unidentified strains are considered to represent a new genus and species, for which the name Tenuibacillus multivorans gen. nov., sp. nov. is proposed. The type strain is 28-1T (=AS 1.3442T=NBRC 100370T). PMID: 15653860 [PubMed - indexed for MEDLINE] 第三十三节 Texcoconibacillus 265. Texcoconibacillus texcoconensis Int J Syst Evol Microbiol. 2013 Sep;63(Pt 9):3336-41. doi: 10.1099/ijs.0.048447-0. Epub 2013 Apr 5. Texcoconibacillus texcoconensis gen. nov., sp. nov., alkalophilic and halotolerant bacteria isolated from soil of the former lake Texcoco (Mexico). Ruiz-Romero E(1), Coutiño-Coutiño Mde L, Valenzuela-Encinas C, López-Ramírez MP, Marsch R, Dendooven L. Author information: (1) Laboratory of Soil Ecology, Cinvestav, Mexico. A novel Gram-positive, rod-shaped, spore-forming bacterium, designated 13CC(T) was isolated from soil of the former lake Texcoco. The strain was aerobic, catalase-positive and oxidase-negative. It grew at salinities of 0-26% (w/v) NaCl with an optimum at 9-16% (w/v) NaCl. The cells contain peptidoglycan type A1γ, A1γ' with glycine instead of l-alanine and three variations of peptidoglycan type A4γ. The only quinone detected was MK-7. The major fatty acid was anteiso-C(15:0). The polar lipids fraction consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three different phospholipids. The DNA G+C content was 37.5 mol%. Maximum-likelihood phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 13CC(T) was closely related to members of the genus Bacillus and shared 92.35% similarity with Bacillus agaradhaerens, 92.28% with Bacillus neizhouensis and 92.21% with Bacillus locisalis. It is proposed based on the phenotypic, genotypic and phylogenetic analyses that the novel isolate should be classified as a representative of a new genus and novel species, for which the name Texcoconibacillus texcoconensis gen. nov., sp. nov. is proposed. The type strain of Texcoconibacillus texcoconensis is 13CC(T) ( =JCM 17654(T) =DSM 24696(T)). PMID: 23563229 [PubMed - indexed for MEDLINE]$$ 76 第三十四节 Thermobacillus 266. Thermobacillus xylanilyticus Int J Syst Evol Microbiol. 2000 Jan;50 Pt 1:315-20. Thermobacillus xylanilyticus gen. nov., sp. nov., a new aerobic thermophilic xylan-degrading bacterium isolated from farm soil. Touzel JP(1), O'Donohue M, Debeire P, Samain E, Breton C. Author information: (1)INRA, Unité de Physicochimie et Biotechnologie des Polymères, Equipe de Fractionnement Enzymatique, Reims, France. [email protected] An aerobic, thermophilic, xylanolytic, spore-forming bacterium, XETP (T = type strain; P = patent strain), has been isolated from farm soil situated underneath a manure heap in northern France. Strain XETP, which stained negative in the Gram test, occurs as short rods which sometimes form chains. Its spores are ellipsoidal, central to subterminal and occur in swollen sporangia. It grows at temperatures up to 63 degrees C and in the pH range 6.5-8.5. When grown on glucose in optimal conditions, its doubling time was found to be 33 min. CO2 was observed to have a growth-stimulating effect at the start of the culture. In addition to glucose, the isolate utilizes xylose, arabinose, mannose, cellobiose, galactose, maltose, sucrose, xylan and starch. Growth is inhibited by 5% NaCl. The G+C content of strain XETP is 57.5 mol%. The 16S rDNA sequence analysis indicated that strain XETP falls into the radiation of the Bacillus-Lactobacillus-Streptococcus subdivision of the Gram-positive phylum. Its three closest phylogenetic relatives are 'Bacillus viscosus', Paenibacillus curdlanolyticus and Bacillus popilliae with identity values of 91.15, 90.94 and 90.92%, respectively. The major cellular fatty acids are 14-methyl pentadecanoic acid (16:0 iso), hexadecanoic acid (16:0) and 14-methyl hexadecanoic acid (17:0 anteiso). On the basis of 16S rRNA sequence and chemotaxonomic characteristics, the isolate is different enough for it to be considered as a member of a new genus. It is therefore proposed that this isolate represents a new genus and species: Thermobacillus xylanilyticus. Strain XETP, the type strain of Thermobacillus xylanilyticus, has been deposited in the Collection Nationale de Cultures Microbiennes (CNCM I-1017) as a patent strain. PMID: 10826818 [PubMed - indexed for MEDLINE] 第三十五节 Tuberibacillus 267. Tuberibacillus calidus Int J Syst Evol Microbiol. 2006 Nov;56(Pt 11):2545-51. Tuberibacillus calidus gen. nov., sp. nov., isolated from a compost pile and reclassification of Bacillus naganoensis Tomimura et al. 1990 as Pullulanibacillus naganoensis gen. nov., comb. nov. and Bacillus laevolacticus Andersch et al. 1994 as Sporolactobacillus laevolacticus comb. nov. Hatayama K(1), Shoun H, Ueda Y, Nakamura A. Author information: (1)Division of Integrative Environmental Sciences, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, and Institute of Hyperthermophiles, Motobu-Noge Hospital, Okinawa, Japan. Two thermophilic strains, designated 607T and 606b, were isolated from a compost pile in Japan. The novel strains were Gram-positive, aerobic, spore-forming rods. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains 607T and 606b were closely related to Bacillus naganoensis (94.0-94.1% similarity) and separated from clusters of the related genera Bacillus (<91.9%) and Sporolactobacillus (91.0-92.5%). In addition, some chemotaxonomic and physiological characteristics of strains 607T and 606b differed from those of B. naganoensis and the two related genera. Several differences in physiological characteristics and 16S-23S rRNA gene internal transcribed spacer region nucleotide sequences were observed between strains 607T and 606b; however, DNA-DNA hybridization indicated that these two strains belonged to the same species. From these results, it is proposed that strains 607T and 606b represent the type species of a new genus, Tuberibacillus calidus gen. nov., sp. nov., with strain 607T (=JCM 13397T=DSM 17572T) as the type strain. In addition, the results of phylogenetic analyses, as well as chemotaxonomic and physiological characterization, indicated that B. naganoensis and Bacillus laevolacticus did not belong to the genus Bacillus. Based on these results, it is proposed that B. naganoensis and B. laevolacticus should be transferred to Pullulanibacillus naganoensis gen. nov., comb. nov. and Sporolactobacillus laevolacticus comb. nov., respectively. PMID: 17082388 [PubMed - indexed for MEDLINE] 77 第三十六节 Ureibacillus 268. Ureibacillus suwonensis Int J Syst Evol Microbiol. 2006 Mar;56(Pt 3):663-6. Ureibacillus suwonensis sp. nov., isolated from cotton waste composts. Kim BY(1), Lee SY, Weon HY, Kwon SW, Go SJ, Park YK, Schumann P, Fritze D. Author information: (1)Korean Agricultural Culture Collection (KACC), Genetic Resources Division, National Institute of Agricultural Biotechnology, Rural Development Administration (RDA), Suwon 441-707, Korea. The taxonomic position of two spore-forming strains 6T19T and 6T29, isolated from cotton composts for the cultivation of oyster mushroom (Pleurotus ostreatus), was investigated by a polyphasic approach. Cells of strains 6T19(T) and 6T29 were rod-shaped, Gram-negative and strictly aerobic. Sequencing and comparative analyses for the 16S rRNA genes of these strains clearly showed their phylogenetic affiliation to the genus Ureibacillus. Their closest relatives Ureibacillus thermosphaericus and Ureibacillus terrenus have sequence similarity of 96.9 and 97.5%, respectively. The isoprenoid quinones of isolate 6T19T were MK-9, MK-8, MK-7, MK-10 and MK-6 (45:27:18:5:4%), the peptidoglycan type was L-lys<--D-Asp and the main cellular fatty acid was i-C(16:0). DNA-DNA hybridization experiments resulted in relatedness values of 37% between 6T19T and U. thermosphaericus DSM 10633T and 41% between 6T19T and U. terrenus DSM 12654T. Based on the polyphasic data, strains 6T19T and 6T29 can be described as members of a novel species of the genus Ureibacillus, for which the name Ureibacillus suwonenesis sp. nov. is proposed. The type strain is 6T19T (= KACC 11287T = DSM 16752T). PMID: 16514046 [PubMed - indexed for MEDLINE] 269. Ureibacillus terrenus Int J Syst Evol Microbiol. 2001 Mar;51(Pt 2):447-55. Ureibacillus gen. nov., a new genus to accommodate Bacillus thermosphaericus (Andersson et al. 1995), emendation of Ureibacillus thermosphaericus and description of Ureibacillus terrenus sp. nov. Fortina MG(1), Pukall R, Schumann P, Mora D, Parini C, Manachini PL, Stackebrandt E. Author information: (1)Department of Food Science and Microbiology, University of Milan, Italy. [email protected] Erratum in Int J Syst Evol Microbiol. 2009 May;59(Pt 5):1258. A polyphasic taxonomic study was performed on the type strain of Bacillus thermosphaericus DSM 10633T and three related soil isolates. On the basis of phenotypic characteristics, chemotaxonomic profiles and phylogenetic data a new genus, Ureibacillus gen. nov., is proposed for the strains in the Bacillus thermosphaericus cluster. Strains of this cluster fall into two DNA-DNA similarity groups: while one group contains the type strain of Ureibacillus thermosphaericus comb. nov. and a single soil isolate, the other contains two soil isolates. The two groups differed in the composition of isoprenoid quinones and some phenotypic properties. These data support the description of a novel species of Ureibacillus for which the name Ureibacillus terrenus is proposed. The type strain of this new species is TH9AT (= DSM 12654T = LMG 19470T). PMID: 11321090 [PubMed - indexed for MEDLINE] 第三十七节 Virgibacillus 270. Virgibacillus carmonensis Int J Syst Evol Microbiol. 2003 Mar;53(Pt 2):501-11. Virgibacillus carmonensis sp. nov., Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov., three novel species isolated from deteriorated mural paintings, transfer of the species of the genus salibacillus to Virgibacillus, as Virgibacillus marismortui comb. nov. and Virgibacillus salexigens comb. nov., and emended description of the genus Virgibacillus. Heyrman J(1), Logan NA, Busse HJ, Balcaen A, Lebbe L, Rodriguez-Diaz M, Swings J, De Vos P. Author information: (1)Vakgroep BFM WE10V, Laboratorium voor Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium. [email protected] A group of 13 strains was isolated from samples of biofilm formation on the mural paintings of the Servilia tomb (necropolis of Carmona, Spain) and the Saint-Catherine chapel (castle at Herberstein, Austria). The strains were subjected to a polyphasic taxonomic study, including (GTG)5-PCR, 16S rDNA sequence analysis, DNA-DNA hybridizations, DNA base ratio determination, analysis of fatty acids, polar lipids and menaquinones and morphological and biochemical characterization. In a phylogenetic tree based on neighbour-joining of 16S rDNA sequences, the strains are divided in two major groups, representing three novel species according to DNA-DNA relatedness, that are positioned at approximately equal distances from Virgibacillus and Salibacillus. After comparison of the novel results with existing data, the transfer of the species of Salibacillus to Virgibacillus is proposed, with the resulting new combinations Virgibacillus marismortui comb. nov. and Virgibacillus salexigens comb. nov. Additionally, three novel species are described, for which the names Virgibacillus carmonensis sp. nov., Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov. are proposed. The respective type strains are LMG 20964T (=DSM 14868T), LMG 19488T (=DSM 14866T) and LMG 19492T (= DSM 14867T). Finally, an emended description of the genus Virgibacillus is given. PMID: 12710619 [PubMed - indexed for MEDLINE] 78 271. Virgibacillus proomii Int J Syst Bacteriol. 1999 Jul;49 Pt 3:1083-90. Proposal of Virgibacillus proomii sp. nov. and emended description of Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998. Heyndrickx M(1), Lebbe L, Kersters K, Hoste B, De Wachter R, De Vos P, Forsyth G, Logan NA. Author information: (1)Vakgroep BFM WE10V, Laboratorium voor Microbiologie, Universiteit Gent, Belgium. A polyphasic study of strains originally received as Bacillus (now Virgibacillus) pantothenticus, along with strains representing species belonging to Bacillus, Halobacillus and Paenibacillus, was undertaken using amplified rDNA restriction analysis (ARDRA), fatty acid methyl ester (FAME) analysis, SDS-PAGE of whole-cell proteins and routine diagnostic characters comprising 61 biochemical tests in the API system and 15 observations of vegetative cell and sporangial morphology. It revealed the presence within Virgibacillus of an as yet undescribed new species, for which the name Virgibacillus proomii is proposed; V. proomii can be distinguished from V. pantothenticus and members of Bacillus sensu stricto, and from members of Paenibacillus and other aerobic endospore-forming bacteria, by routine phenotypic tests. The type strain of Virgibacillus proomii is LMG 12370T. PMID: 10425765 [PubMed - indexed for MEDLINE] 272. Virgibacillus siamensis J Gen Appl Microbiol. 2010 Oct;56(5):369-79. Identification of moderately halophilic bacteria from Thai fermented fish ( pla-ra ) and proposal of Virgibacillus siamensis sp. nov. Tanasupawat S(1), Chamroensaksri N, Kudo T, Itoh T. Author information: (1)Department of Biochemistry and Microbiology, Chulalongkorn University, Bangkok, Thailand. [email protected] Forty-one isolates of moderately halophilic bacteria were isolated from fermented fish (pla-ra) in Thailand. On the basis of their phenotypic and chemotaxonomic characteristics, DNA-DNA relatedness and 16S rRNA gene sequences analyses, they were divided into six groups. The isolates in Group I to V were Gram-positive rod-shaped bacteria. They contained meso-diaminopimelic acid in the cell-wall peptidoglycan and menaquinone with seven isoprene units (MK-7). An isolate in Group VI was a Gram-negative rod-shaped bacterium. The DNA G+C contents of tested strains ranged from 36.5-63 mol%. Ten strains (Group I) were identified as Virgibacillus dokdonensis, 13 isolates (Group II) as V. halodenitrificans, 14 isolates (Group III) as V. marismortui, 1 isolate (Group IV) as Virgibacillus sp., 2 isolates (Group V) as Bacillus vietnamnensis, and 1 isolate (Group VI) as Chromohalobacter salexigens. Isolate MS3-4 in Group IV was closely related to V. carmonensis KCTC 3819(T) (95.9%). This strain contained anteiso-C(15:0) (55.8%) and anteiso-C(17:0) (17.7%) as major cellular fatty acids and had phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid as polar lipids. The DNA G+C content of MS3-4 was 38.0 mol%. The strain from Group IV is proposed as Virgibacillus siamensis sp. nov. and MS3-4(T) is the type strain (JCM 15395(T) =PCU 312(T) =TISTR 1957(T)). PMID: 21099133 [PubMed - indexed for MEDLINE] 79 第二章芽胞杆菌基因组学(Bacillus genomics) 1 2 3 100. Appl Environ Microbiol. 2010 May;76(10):3244-54. doi: 10.1128/AEM.03069-09. Epub 2010 Mar 19.Denitrifying bacteria isolated from terrestrial subsurface sediments exposed tomixed-waste contamination.Green SJ(1), Prakash O, Gihring TM, Akob DM, Jasrotia P, Jardine PM, Watson DB,Brown SD, Palumbo AV, Kostka JE.Author information: (1)Department of Oceanography, Florida State University, Tallahassee, FL 32306-4470,USA.In terrestrial subsurface environments where nitrate is a critical groundwatercontaminant, few cultivated representatives are available to verify themetabolism of organisms that catalyze denitrification. In this study, fivespecies of denitrifying bacteria from three phyla were isolated from subsurfacesediments exposed to metal radionuclide and nitrate contamination as part of the U.S. Department of Energy's Oak Ridge Integrated Field Research Challenge(OR-IFRC). Isolates belonged to the genera Afipia and Hyphomicrobium(Alphaproteobacteria), Rhodanobacter (Gammaproteobacteria), Intrasporangium(Actinobacteria), and Bacillus (Firmicutes). Isolates from the phylumProteobacteria were complete denitrifiers, whereas the Gram-positive isolatesreduced nitrate to nitrous oxide. rRNA gene analyses coupled with physiologicaland genomic analyses suggest that bacteria from the genus Rhodanobacter are adiverse population of denitrifiers that are circumneutral to moderatelyacidophilic, with a high relative abundance in areas of the acidic source zone atthe OR-IFRC site. Based on genome analysis, Rhodanobacter species contain twonitrite reductase genes and have not been detected in functional-gene surveys of denitrifying bacteria at the OR-IFRC site. Nitrite and nitrous oxide reductasegene sequences were recovered from the isolates and from the terrestrialsubsurface by designing primer sets mined from genomic and metagenomic data andfrom draft genomes of two of the isolates. We demonstrate that a combination ofcultivation and genomic and metagenomic data is essential to the in situcharacterization of denitrifiers and that current PCR-based approaches are notsuitable for deep coverage of denitrifiers. Our results indicate that thediversity of denitrifiers is significantly underestimated in the terrestrialsubsurface.PMCID: PMC2869116PMID: 20305024 [PubMed - indexed for MEDLINE] 101. Curr Microbiol. 2010 May;60(5):315-20. doi: 10.1007/s00284-009-9542-4. Epub 2009 Nov 19.Analysis of bacterial and fungal communities in Japanese- and Chinese-fermentedsoybean pastes using nested PCR-DGGE.Kim TW(1), Lee JH, Park MH, Kim HY.Author information: (1)Kyung Hee University, Suwon, Republic of Korea .The microbial diversity of Japanese- and Chinese-fermented soybean pastes wasinvestigated using nested PCR-denaturing gradient gel electrophoresis (DGGE).Five Japanese-fermented soybean paste samples and three Chinese-fermented soybeanpaste samples were analyzed for bacteria and fungi. Extracted DNA was used as atemplate for PCR to amplify 16S rRNA and 18S rRNA genes. The nearly complete 16S rRNA and 18S rRNA genes were amplified using universal primers, and the resultingproducts were subsequently used as a template in a nested PCR to obtain suitable fragments for DGGE. Tetragenococcus halophilus and Staphylococcus gallinarum werefound to dominate the bacterial microbiota in Japanese samples, whereas Bacillus sp. was detected as the predominant species in Chinese samples. DGGE analysis of fungi in soybean pastes determined the presence of Aspergillus oryzae andZygosaccharomyces rouxii in most of the Chinese and Japanese samples. Somedifferences were observed in the bacterial diversity of Japanese- andChinese-fermented soybean pastes.PMID: 19924476 [PubMed - indexed for MEDLINE] 102. Nucleic Acids Res. 2010 Jan;38(Database issue):D408-14. doi: 10.1093/nar/gkp850. Epub 2009 Oct 20.Pathema: a clade-specific bioinformatics resource center for pathogen research.Brinkac LM(1), Davidsen T, Beck E, Ganapathy A, Caler E, Dodson RJ, Durkin AS,Harkins DM, Lorenzi H, Madupu R, Sebastian Y, Shrivastava S, Thiagarajan M, OrvisJ, Sundaram JP, Crabtree J, Galens K, Zhao Y, Inman JM, Montgomery R, Schobel S, Galinsky K, Tanenbaum DM, Resnick A, Zafar N, White O, Sutton G.Author information: (1)J Craig Venter Institute, Rockville, MD 20850, USA.Pathema (http://pathema.jcvi.org) is one of the eight Bioinformatics ResourceCenters (BRCs) funded by the National Institute of Allergy and Infectious Disease(NIAID) designed to serve as a core resource for the bio-defense and infectiousdisease research community. Pathema strives to support basic research andaccelerate scientific progress for understanding, detecting, diagnosing andtreating an established set of six target NIAID Category A-C pathogens: Category A priority pathogens; Bacillus anthracis and Clostridium botulinum, and Category B priority pathogens; Burkholderia mallei, Burkholderia pseudomallei, Clostridiumperfringens and Entamoeba histolytica. Each target pathogen is represented in oneof four distinct clade-specific Pathema web resources and underlying databasesdeveloped to target the specific data and analysis needs of each scientificcommunity. All publicly available complete genome projects of phylogeneticallyrelated organisms are also represented, providing a comprehensive collection oforganisms for comparative analyses. Pathema facilitates the scientificexploration of genomic and related data through its integration with web-basedanalysis tools, customized to obtain, display, 80 4 5 6 7 and compute results relevant toongoing pathogen research. Pathema serves the bio-defense and infectious disease research community by disseminating data resulting from pathogen genomesequencing projects and providing access to the results of inter-genomiccomparisons for these organisms.PMCID: PMC2808925PMID: 19843611 [PubMed - indexed for MEDLINE] 103. J Microbiol. 2009 Aug;47(4):466-72. doi: 10.1007/s12275-009-0020-2. Epub 2009 Sep9.Cloning and molecular characterization of a novel rolling-circle replicatingplasmid, pK1S-1, from Bacillus thuringiensis subsp. kurstaki K1.Li MS(1), Roh JY, Tao X, Yu ZN, Liu ZD, Liu Q, Xu HG, Shim HJ, Kim YS, Wang Y,Choi JY, Je YH.Author information: (1)State Key Laboratory of Agricultural Microbiology, Huazhong AgriculturalUniversity, Wuhan 430070, P. R. China.Bacillus thuringiensis, an entomopathogenic bacterium belonging to the B. cereus group, harbors numerous extra-chromosomal DNA molecules whose sizes range from 2 to 250 kb. In this study, we used a plasmid capture system (PCS) to clone threesmall plasmids from B. thuringiensis subsp. kurstaki Kl which were not found inB. thuringiensis subsp. kurstaki HD-1, and determined the complete nucleotidesequence of plasmid pKlS-1 (5.5 kb). Of the six putative open reading frames(ORF2-ORF7) in pKlS-1, ORF2 (MobKl) showed approximately 90% aa identity with theMob-proteins of pGI2 and pTX14-2, which are rolling circle replicating group VII (RCR group VII) plasmids from B. thuringiensis. In addition, a putative origin oftransfer (oriT) showed 95.8% identity with those of pGI2 and pTX14-2. ORF3(RepK1) showed relatively low aa identity (17.8-25.2%) with the Rep protein codedby RCR plasmids, however. The putative double-strand origin of replication (dso) and single-strand origin of replication (sso) of pKlS-1 exhibited approximately70% and 64% identities with those of pGI2 and pTX14-2. ORF6 and 7 showed greater than 50% similarities with alkaline serine protease, which belongs to thesubtilase family. The other 2 ORFs were identified as hypothetical proteins. Todetermine the replicon of pKlS-1, seven subclones were contructed in the B.thuringiensis ori-negative pHTIK vector and were electroporated into a plasmidcured B. thuringiensis strain. The 1.6 kb region that included the putative ORF3 (ReplK), dso and ORF4, exhibited replication ability. These findings identifiedpKlS-1 as a new RCR group VII plasmid, and determined its replication region.PMID: 19763421 [PubMed - indexed for MEDLINE] 104. FEMS Microbiol Lett. 2009 Oct;299(2):205-13. doi:10.1111/j.1574-6968.2009.01749.x. Epub 2009 Aug 6.Biosynthesis and transcriptional analysis of thurincin H, a tandem repeatedbacteriocin genetic locus, produced by Bacillus thuringiensis SF361.Lee H(1), Churey JJ, Worobo RW.Author information: (1)Department of Food Science and Technology, New York State Agricultural ExperimentStation, Cornell University, 630 W North St., Geneva, NY 14456, USA.Thurincin H, a bacteriocin produced by Bacillus thuringiensis SF361 isolated fromhoney, strongly inhibited the growth of Bacillus cereus F4552. The bacteriocinwas purified by 65% ammonium sulfate precipitation of the culture supernatant,followed by octyl-sepharose CL-4B and reverse-phase HPLC. The molecular mass ofthe bacteriocin was determined to be 3139.51 Da and the 14 amino acids of thebacteriocin at the N-terminus were identified. The complete amino acid sequenceof mature thurincin H was deduced from three structural genes, thnA1, thnA2, and thnA3 found in tandem repeats on the chromosome, all of which encode for the samebacteriocin, thurincin H. The genetic determinants for thurincin H biosynthesisconsist of 10 ORFs, including three thurincin H structural genes. Northernhybridization elucidated that the transcription of all three bacteriocinstructural genes was regulated by a putative promoter located upstream of thnA1.PMID: 19732155 [PubMed - indexed for MEDLINE] 105. Appl Environ Microbiol. 2009 Oct;75(19):6352-60. doi: 10.1128/AEM.00470-09. Epub 2009 Aug 7.Intra- and interspecies conjugal transfer of Tn916-like elements from Lactococcuslactis in vitro and in vivo.Boguslawska J(1), Zycka-Krzesinska J, Wilcks A, Bardowski J.Author information: (1)Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106Warsaw, Poland.Tetracycline-resistant Lactococcus lactis strains originally isolated from Polishraw milk were analyzed for the ability to transfer their antibiotic resistancegenes in vitro, using filter mating experiments, and in vivo, using germfreerats. Four of six analyzed L. lactis isolates were able to transfer tetracycline resistance determinants in vitro to L. lactis Bu2-60, at frequencies ranging from10(-5) to 10(-7) transconjugants per recipient. Three of these four strains couldalso transfer resistance in vitro to Enterococcus faecalis JH2-2, whereas notransfer to Bacillus subtilis YBE01, Pseudomonas putida KT2442, Agrobacteriumtumefaciens UBAPF2, or Escherichia coli JE2571 was observed. Rats were initially inoculated with the recipient E. faecalis strain JH2-2, and after a week, the L. lactis IBB477 and IBB487 donor strains were introduced. The first transconjugantswere detected in fecal samples 3 days after introduction of the donors. Asubtherapeutic concentration of tetracycline did not have any significant effect on the number of transconjugants, but transconjugants were observed earlier inanimals dosed with this antibiotic. Molecular analysis of in vivo transconjugantscontaining the tet(M) gene showed that this gene was identical to tet(M)localized on the conjugative transposon Tn916. Primer-specific PCR confirmed thatthe Tn916 transposon was complete in all analyzed transconjugants and donors.This is the first study showing in vivo transfer of a Tn916-like antibioticresistance transposon from L. lactis to E. faecalis. These data suggest that incertain cases food lactococci might be involved in the spread of antibioticresistance genes to other lactic acid bacteria.PMCID: PMC2753074PMID: 19666731 [PubMed - indexed for MEDLINE] 106. J Bacteriol. 2009 Sep;191(18):5775-84. doi: 10.1128/JB.00521-09. Epub 2009 Jun19.Role of the sigmaD-dependent autolysins in Bacillus subtilis populationheterogeneity.Chen R(1), Guttenplan SB, Blair KM, Kearns DB.Author information: (1)Department of Biology, Indiana University, 1001 East Third Street, Bloomington,IN 47405, USA.Exponentially growing populations of Bacillus subtilis contain twomorphologically and functionally distinct cell types: motile individuals andnonmotile multicellular chains. Motility differentiation arises because RNApolymerase and the alternative sigma factor sigma(D) activate expression offlagellin in a subpopula- 81 8 9 10 tion of cells. Here we demonstrate that thepeptidoglycan-remodeling autolysins under sigma(D) control, LytC, LytD, and LytF,are expressed in the same subpopulation of cells that complete flagellarsynthesis. Morphological heterogeneity is explained by the expression of LytFthat is necessary and sufficient for cell separation. Moreover, LytC is required for motility but not at the level of cell separation or flagellum biosynthesis.Rather, LytC appears to be important for flagellar function, and motility wasrestored to a LytC mutant by mutation of either lonA, encoding the LonA protease,or a gene encoding a previously unannotated swarming motility inhibitor, SmiA. Weconclude that heterogeneous activation of sigma(D)-dependent gene expression issufficient to explain both the morphological heterogeneity and functionalheterogeneity present in vegetative B. subtilis populations.PMCID: PMC2737971PMID: 19542270 [PubMed - indexed for MEDLINE] 107. Infect Genet Evol. 2009 Sep;9(5):1010-9. doi: 10.1016/j.meegid.2009.05.014. Epub 2009 May 27.Phylogenetic understanding of clonal populations in an era of whole genomesequencing.Pearson T(1), Okinaka RT, Foster JT, Keim P.Author information: (1)Center for Microbial Genetics and Genomics, Northern Arizona University,Flagstaff, AZ, USA.Phylogenetic hypotheses using whole genome sequences have the potential forunprecedented accuracy, yet a failure to understand issues associated withdiscovery bias, character sampling, and strain sampling can lead to highlyerroneous conclusions. For microbial pathogens, phylogenies derived from wholegenome sequences are becoming more common, as large numbers of charactersdistributed across entire genomes can yield extremely accurate phylogenies,particularly for strictly clonal populations. The availability of whole genomesis increasing as new sequencing technologies reduce the cost and time requiredfor genome sequencing. Until entire sample collections can be fully sequenced,harnessing the phylogenetic power from whole genome sequences in more than asmall subset of fully sequenced strains requires the integration of whole genome and partial genome genotyping data. Such integration involves discoveringevolutionarily stable polymorphic characters by whole genome comparisons, thendetermining allelic states across a wide panel of isolates using high-throughput genotyping technologies. Here, we demonstrate how such an approach using singlenucleotide polymorphisms (SNPs) yields highly accurate, but biased phylogeneticreconstructions and how the accuracy of the resulting tree is compromised byincomplete taxon and character sampling. Despite recent phylogenetic workdetailing the strengths and biases of integrating whole genome and partial genomegenotype data, these issues are relatively new and remain poorly understood bymany researchers. Here, we revisit these biases and provide strategies formaximizing phylogenetic accuracy. Although we write this review with bacterialpathogens in mind, these concepts apply to any clonally reproducing population orindeed to any evolutionarily stable marker that is inherited in a strictly clonalmanner. Understanding the ways in which current and emerging technologies can be used to maximize phylogenetic knowledge is advantageous only with a completeunderstanding of the strengths and weaknesses of these methods.PMID: 19477301 [PubMed - indexed for MEDLINE] 108. Mol Biotechnol. 2009 Jul;42(3):341-9. doi: 10.1007/s12033-009-9168-6. Epub 2009Apr 8.Expression of Cry1Ac in transgenic tobacco plants under the control of awound-inducible promoter (AoPR1) isolated from Asparagus officinalis to controlHeliothis virescens and Manduca sexta.Gulbitti-Onarici S(1), Zaidi MA, Taga I, Ozcan S, Altosaar I.Author information: (1)Department of Biochemistry Microbiology & Immunology, University of Ottawa,Ottawa, ON, K1H 8M5, Canada.Expression of cry1Ac gene from Bacillus thuringiensis (Bt) was evaluated underthe control of a wound-inducible AoPR1 promoter from Asparagus officinalis intransgenic tobacco plants. The leaves of transgenic plants were mechanicallywounded to evaluate the activity of the AoPR1 promoter in driving the expression of Cry1Ac protein at the wound site. Our results indicate that mechanicalwounding of transgenic plants was effective in inducing the expression of Cry1Ac protein. As a result of this induction, the accumulated levels of Cry1Ac protein increased during 6-72 h post-wounding period. The leaves of transgenic tobaccoplants were evaluated for resistance against Heliothis virescens and Manducasexta in insect bioassays in two different ways. The detached tobacco leaves wereeither fed directly to the insect larvae or they were first mechanically wounded followed by a 72 h post-wounding feeding period. Complete protection ofmechanically wounded leaves of transgenic plants was observed within 24 h of the bioassay. The leaves of transgenic plants fed directly (without pre-wounding) to the larvae achieved the same level of protection between 24 and 72 h of thebioassay.PMID: 19353306 [PubMed - indexed for MEDLINE] 109. J Bacteriol. 2009 May;191(10):3350-8. doi: 10.1128/JB.01728-08. Epub 2009 Mar 20.Identification of a polymyxin synthetase gene cluster of Paenibacillus polymyxaand heterologous expression of the gene in Bacillus subtilis.Choi SK(1), Park SY, Kim R, Kim SB, Lee CH, Kim JF, Park SH.Author information: (1)Industrial Biotechnology & Bioenergy Research Center, Korea Research Institute ofBioscience and Biotechnology, 111 Gwahangno, Yuseong-gu, Daejeon 305-806,Republic of Korea.Polymyxin, a long-known peptide antibiotic, has recently been reintroduced inclinical practice because it is sometimes the only available antibiotic for thetreatment of multidrug-resistant gram-negative pathogenic bacteria. Lack ofinformation on the biosynthetic genes of polymyxin, however, has limited thestudy of structure-function relationships and the development of improvedpolymyxins. During whole genome sequencing of Paenibacillus polymyxa E681, aplant growth-promoting rhizobacterium, we identified a gene cluster encodingpolymyxin synthetase. Here, we report the complete sequence of the gene clusterand its function in polymyxin biosynthesis. The gene cluster spanning the 40.6-kbregion consists of five open reading frames, designated pmxA, pmxB, pmxC, pmxD,and pmxE. The pmxC and pmxD genes are similar to genes that encode transportproteins, while pmxA, pmxB, and pmxE encode polymyxin synthetases. Theinsertional disruption of pmxE led to a loss of the ability to produce polymyxin.Introduction of the pmx gene cluster into 82 11 12 13 the amyE locus of the Bacillus subtilischromosome resulted in the production of polymyxin in the presence ofextracellularly added L-2,4-diaminobutyric acid. Taken together, our findingsdemonstrate that the pmx gene cluster is responsible for polymyxin biosynthesis.PMCID: PMC2687177PMID: 19304848 [PubMed - indexed for MEDLINE] 110. J Mol Biol. 2009 Apr 24;388(1):48-70. doi: 10.1016/j.jmb.2009.03.009. Epub 2009Mar 10.The genome of Bacillus subtilis bacteriophage SPO1.Stewart CR(1), Casjens SR, Cresawn SG, Houtz JM, Smith AL, Ford ME, Peebles CL,Hatfull GF, Hendrix RW, Huang WM, Pedulla ML.Author information: (1)Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251, USA.We report the genome sequence of Bacillus subtilis phage SPO1. The unique genome sequence is 132,562 bp long, and DNA packaged in the virion (the chromosome) has a 13,185-bp terminal redundancy, giving a total of 145,747 bp. We predict 204protein-coding genes and 5 tRNA genes, and we correlate these findings with theextensive body of investigations of SPO1, including studies of the functions ofthe 61 previously defined genes and studies of the virion structure. Sixty-ninepercent of the encoded proteins show no similarity to any previously knownprotein. We identify 107 probable transcription promoters; most are members ofthe promoter classes identified in earlier studies, but we also see a new classthat has the same sequence as the host sigma K promoters. We find three genesencoding potential new transcription factors, one of which is a distant homologueof the host sigma factor K. We also identify 75 probable transcription terminatorstructures. Promoters and terminators are generally located between genes andtogether with earlier data give what appears to be a rather complete picture ofhow phage transcription is regulated. There are complete genome sequencesavailable for five additional phages of Gram-positive hosts that are similar toSPO1 in genome size and in composition and organization of genes. Comparativeanalysis of SPO1 in the context of these other phages yields insights about SPO1 and the other phages that would not be apparent from the analysis of any onephage alone. These include assigning identities as well as probable functions forseveral specific genes and inferring evolutionary events in the phages'histories. The comparative analysis also allows us to put SPO1 into aphylogenetic context. We see a pattern similar to what has been noted in phage T4and its relatives, in which there is minimal successful horizontal exchange ofgenes among a "core" set of genes that includes most of the virion structuralgenes and some genes of DNA metabolism, but there is extensive horizontaltransfer of genes over the remainder of the genome. There is a correlationbetween genes in rapid evolutionary flux through these genomes and genes that aresmall.PMCID: PMC2666789PMID: 19285085 [PubMed - indexed for MEDLINE] 111. PLoS Genet. 2009 Mar;5(3):e1000416. doi: 10.1371/journal.pgen.1000416. Epub 2009 Mar 13.The complete genome and proteome of Laribacter hongkongensis reveal potentialmechanisms for adaptations to different temperatures and habitats.Woo PC(1), Lau SK, Tse H, Teng JL, Curreem SO, Tsang AK, Fan RY, Wong GK, HuangY, Loman NJ, Snyder LA, Cai JJ, Huang JD, Mak W, Pallen MJ, Lok S, Yuen KY.Author information: (1)State Key Laboratory of Emerging Infectious Diseases, The University of HongKong, Hong Kong, Special Administrative Region, People's Republic of China.Laribacter hongkongensis is a newly discovered Gram-negative bacillus of theNeisseriaceae family associated with freshwater fish-borne gastroenteritis andtraveler's diarrhea. The complete genome sequence of L. hongkongensis HLHK9,recovered from an immunocompetent patient with severe gastroenteritis, consistsof a 3,169-kb chromosome with G+C content of 62.35%. Genome analysis revealsdifferent mechanisms potentially important for its adaptation to diverse habitatsof human and freshwater fish intestines and freshwater environments. The genecontents support its phenotypic properties and suggest that amino acids and fattyacids can be used as carbon sources. The extensive variety of transporters,including multidrug efflux and heavy metal transporters as well as genes involvedin chemotaxis, may enable L. hongkongensis to survive in different environmental niches. Genes encoding urease, bile salts efflux pump, adhesin, catalase,superoxide dismutase, and other putative virulence factors-such as hemolysins,RTX toxins, patatin-like proteins, phospholipase A1, and collagenases-arepresent. Proteomes of L. hongkongensis HLHK9 cultured at 37 degrees C (human bodytemperature) and 20 degrees C (freshwater habitat temperature) showeddifferential gene expression, including two homologous copies of argB, argB-20,and argB-37, which encode two isoenzymes of N-acetyl-L-glutamate kinase(NAGK)-NAGK-20 and NAGK-37-in the arginine biosynthesis pathway. NAGK-20 showedhigher expression at 20 degrees C, whereas NAGK-37 showed higher expression at 37degrees C. NAGK-20 also had a lower optimal temperature for enzymatic activities and was inhibited by arginine probably as negative-feedback control. Similarduplicated copies of argB are also observed in bacteria from hot springs such as Thermus thermophilus, Deinococcus geothermalis, Deinococcus radiodurans, andRoseiflexus castenholzii, suggesting that similar mechanisms for temperatureadaptation may be employed by other bacteria. Genome and proteome analysis of L. hongkongensis revealed novel mechanisms for adaptations to survival at different temperatures and habitats.PMCID: PMC2652115PMID: 19283063 [PubMed indexed for MEDLINE] 112. Biophys Chem. 2009 May;141(2-3):203-13. doi: 10.1016/j.bpc.2009.02.003. Epub 2009Feb 20.Statistical scales of order in DNA.Poland D.Author information: Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, USA. [email protected] the present paper we examine the statistics of occurrence of A-T and C-G base pairs in DNA. We focus on the net base composition in blocks of base pairs ofvarious sizes. This paper extends our previous work on randomness and order inDNA sequences and examines order on various scales. For structure on the localscale (10(0)-10(1) bp) we have seen that the net base composition in given block sizes is fitted very accurately by the discrete binomial distribution for arandom system. If the statistics were random for larger block sizes then theappropriate distribution would be the standard normal (Gaussian) distributionwhich is the 83 14 15 16 continuous analog of the discrete binomial distribution. However, wehave found that at the intermediate scale (10(2)-10(4) bp) the compositiondistribution is not fit by a standard normal distribution but rather by amodified normal distribution with a standard deviation that is a marked nonrandomfunction of block size. In particular, the standard deviation accurately follows a power law with a characteristic exponent. This behavior can be interpreted interms of a random walk model due to Mandelbrot that is characterized by atendency for the walk to persist in direction. The DNA analog of the walk modelis the tendency of blocks of base pairs with a given net composition to befollowed by blocks of a similar composition (persistence of composition). A modelbased on a generating function constructed from a matrix of conditionalprobabilities (incorporating persistence) explains the overall order in a givengenome at the intermediate scale. In the present paper we examine the blockstatistics in DNA using the genomes of two organisms, namely Bacillus anthracisand Escherichia coli both of which have a chain length of slightly over fivemillion base pairs. We find that the distributions in B. anthracis are well fitby a Mandelbrot-like distribution. On the other hand, the distributions in E.coli are not so well fit by this distribution which is based on two moments.Using the maximum-entropy method we construct an improved distribution for E.coli based on four moments. Finally we look at the order on the scale of theentire molecule (global scale). Applying the model of a random walk to thecomplete DNA genome we find that the Mandelbrot distribution on an intermediatelevel cannot explain the global character of the random walk, there beingstructure to the walk with features on the scale of the total length of themolecule (10(5)-10(7) bp). To understand the three scales of order (local,intermediate and global) we construct a model sequence based on the incorporationof Mandelbrot-type order on the intermediate scale in a single size block. Wethen find that the character of the order on the local and global scales follows naturally from this single feature. Thus all three scales of order in DNA areincorporated into our model sequence.PMID: 19254822 [PubMed - indexed for MEDLINE] 113. Vaccine. 2009 Mar 10;27(11):1710-6. doi: 10.1016/j.vaccine.2009.01.034. Epub 2009Feb 4.Whole genome sequence analysis of Mycobacterium bovis bacillus Calmette-Guérin(BCG) Tokyo 172: a comparative study of BCG vaccine substrains.Seki M(1), Honda I, Fujita I, Yano I, Yamamoto S, Koyama A.Author information: (1)Japan BCG Laboratory, Research of Product, 3-1-5 Matsuyama, Kiyose City, Tokyo204-0022, Japan. [email protected] investigate the molecular characteristics of bacillus Calmette-Guérin (BCG)vaccines, the complete genomic sequence of Mycobacterium bovis BCG Tokyo 172 was determined, and the results were compared with those for BCG Pasteur and other M.tuberculosis complex. The genome of BCG Tokyo had a length of 4,371,711bp andcontained 4033 genes, including 3950 genes coding for proteins (CDS). There were 18 regions of difference (showing differences of more than 20bp), 20 insertion ordeletion (ins/del) mutations of less than 20bp, and 68 SNPs between the two BCGsubstrains. These findings are useful for better understanding of the geneticdifferences in BCG substrains due to in vitro evolution of BCG.PMID: 19200449 [PubMed - indexed for MEDLINE] 114. DNA Repair (Amst). 2009 May 1;8(5):612-9. doi: 10.1016/j.dnarep.2008.12.011.Characterization in vitro and in vivo of the DNA helicase encoded by Deinococcus radiodurans locus DR1572.Cao Z(1), Julin DA.Author information: (1)Department of Chemistry and Biochemistry, University of Maryland, College Park,MD 20742, United States.Deinococcus radiodurans survives extremely high doses of ionizing and ultravioletradiation and treatment with various DNA-damaging chemicals. As an effort toidentify and characterize proteins that function in DNA repair in this organism, we have studied the protein encoded by locus DR1572. This gene is predicted toencode a Superfamily I DNA helicase, except that genome sequencing indicated thatit has a one-base frameshift and would not encode a complete helicase. We havecloned the gene from two different D. radiodurans strains and find that theframeshift mutation is not present. The corrected gene encodes a 755 residueprotein that is similar to the Bacillus subtilis YvgS protein and to helicase IV of Escherichia coli. The purified protein (helicase IV(Dr)) has ATP hydrolysisand DNA helicase activity. A truncated protein that lacks 214 residues from theN-terminus, which precede the conserved helicase domain, has greater ATPaseactivity than the full-length protein but has no detectable helicase activity.Disruption of locus DR1572 in the D. radiodurans chromosome causes greatersensitivity to hydrogen peroxide and methyl-methanesulfonate compared towild-type cells, but no change in resistance to gamma and ultraviolet radiationand to mitomycin C. The results indicate that locus DR1572 encodes a completeprotein that contributes to DNA metabolism in D. radiodurans.PMID: 19179120 [PubMed - indexed for MEDLINE] 115. BMC Genomics. 2009 Jan 11;10:16. doi: 10.1186/1471-2164-10-16.Conservation in the face of diversity: multistrain analysis of an intracellularbacterium.Dark MJ(1), Herndon DR, Kappmeyer LS, Gonzales MP, Nordeen E, Palmer GH, Knowles DP Jr, Brayton KA.Author information: (1)Program in Genomics, Department of Veterinary Microbiology and Pathology, School for Global Animal Health, Washington State University, Pullman, WA 99164-7040,USA. [email protected]: With the recent completion of numerous sequenced bacterial genomes,notable advances have been made in understanding the level of conservationbetween various species. However, relatively little is known about the genomicdiversity among strains. We determined the complete genome sequence of theFlorida strain of Anaplasma marginale, and near complete (>96%) sequences for an additional three strains, for comparative analysis with the previously fullysequenced St. Maries strain genome.RESULTS: These comparisons revealed that A. marginale has a closed-core genomewith few highly plastic regions, which include the msp2 and msp3 genes, as wellas the aaap locus. Comparison of the Florida and St. Maries genome sequencesfound that SNPs comprise 0.8% of the longer Florida genome, with 33.5% of thetotal SNPs between all five strains present in at least two strains and 3.0% ofSNPs present in all strains except Florida. Comparison of genomes from threestrains of Mycobacterium tuberculosis, Bacillus anthracis, and Nessieriameningiditis, as 84 17 18 19 20 21 well as four Chlamydophila pneumoniae strains found that98.8%-100% of SNPs are unique to each strain, suggesting A. marginale, with76.0%, has an intermediate level of strain-specific SNPs. Comparison of genomesfrom other organisms revealed variation in diversity that did not segregate with the environmental niche the bacterium occupies, ranging from 0.00% to 8.00% ofthe larger pairwise-compared genome.CONCLUSION: Analysis of multiple A. marginale strains suggests intracellularbacteria have more variable SNP retention rates than previously reported, and mayhave closed-core genomes in response to the host organism environment and/orreductive evolution.PMCID: PMC2649000PMID: 19134224 [PubMed - indexed for MEDLINE] 116. Appl Environ Microbiol. 2009 Feb;75(4):1144-55. doi: 10.1128/AEM.02518-08. Epub2008 Dec 19.Characterization of the complete zwittermicin A biosynthesis gene cluster fromBacillus cereus.Kevany BM(1), Rasko DA, Thomas MG.Author information: (1)Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive,Madison, WI 53706, USA.Bacillus cereus UW85 produces the linear aminopolyol antibiotic zwittermicin A(ZmA). This antibiotic has diverse biological activities, such as suppression of disease in plants caused by protists, inhibition of fungal and bacterial growth, and amplification of the insecticidal activity of the toxin protein from Bacillusthuringiensis. ZmA has an unusual chemical structure that includes a d amino acidand ethanolamine and glycolyl moieties, as well as having an unusual terminalamide that is generated from the modification of the nonproteinogenic amino acid beta-ureidoalanine. The diverse biological activities and unusual structure ofZmA have stimulated our efforts to understand how this antibiotic isbiosynthesized. Here, we present the identification of the complete ZmAbiosynthesis gene cluster from B. cereus UW85. A nearly identical gene cluster isidentified on a plasmid from B. cereus AH1134, and we show that this strain isalso capable of producing ZmA. Bioinformatics and biochemical analyses of the ZmAbiosynthesis enzymes strongly suggest that ZmA is initially biosynthesized aspart of a larger metabolite that is processed twice, resulting in the formationof ZmA and two additional metabolites. Additionally, we propose that thebiosynthesis gene cluster for the production of the amino sugar kanosamine iscontained within the ZmA biosynthesis gene cluster in B. cereus UW85.PMCID: PMC2643575PMID: 19098220 [PubMed - indexed for MEDLINE] 117. J Bacteriol. 2009 Feb;191(4):1180-90. doi: 10.1128/JB.01058-08. Epub 2008 Dec 12.Complete genome sequence of Macrococcus caseolyticus strain JCSCS5402,[corrected] reflecting the ancestral genome of the human-pathogenicstaphylococci.Baba T(1), Kuwahara-Arai K, Uchiyama I, Takeuchi F, Ito T, Hiramatsu K.Author information: (1)Department of Microbiology and Infection Control Science, Juntendo University,2-1-1 Hongo, Bunkyo, Tokyo 113-8421, Japan. [email protected] in J Bacteriol. 2009 May;191(10):3429.We isolated the methicillin-resistant Macrococcus caseolyticus strain JCSC5402from animal meat in a supermarket and determined its whole-genome nucleotidesequence. This is the first report on the genome analysis of a macrococcalspecies that is evolutionarily closely related to the human pathogensStaphylococcus aureus and Bacillus anthracis. The essential biological pathwaysof M. caseolyticus are similar to those of staphylococci. However, the specieshas a small chromosome (2.1 MB) and lacks many sugar and amino acid metabolismpathways and a plethora of virulence genes that are present in S. aureus. On the other hand, M. caseolyticus possesses a series of oxidative phosphorylationmachineries that are closely related to those in the family Bacillaceae. We also discovered a probable primordial form of a Macrococcus methicillin resistancegene complex, mecIRAm, on one of the eight plasmids harbored by the M.caseolyticus strain. This is the first finding of a plasmid-encoding methicillin resistance gene. Macrococcus is considered to reflect the genome of ancestralbacteria before the speciation of staphylococcal species and may be closelyassociated with the origin of the methicillin resistance gene complex of thenotorious human pathogen methicillin-resistant S. aureus.PMCID: PMC2632007PMID: 19074389 [PubMed - indexed for MEDLINE] 118. J Bacteriol. 2009 Feb;191(3):1120-1. doi: 10.1128/JB.01629-08. Epub 2008 Dec 5.Complete genome sequence of the extremophilic Bacillus cereus strain Q1 withindustrial applications.Xiong Z(1), Jiang Y, Qi D, Lu H, Yang F, Yang J, Chen L, Sun L, Xu X, Xue Y, Zhu Y, Jin Q.Author information: (1)State Key Laboratory for Molecular Virology and Genetics Engineering, Instituteof Pathogen Biology, Chinese Academy of Medical Sciences, 6 Rongjing East Street,BDA, Beijing 100176, People's Republic of China.Bacillus cereus strain Q1 was isolated from a deep-subsurface oil reservoir inthe Daqing oil field in northeastern China. This strain is able to producebiosurfactants and to survive in extreme environments. Here we report thefinished and annotated genome sequence of this organism.PMCID: PMC2632077PMID: 19060151 [PubMed - indexed for MEDLINE] 119. Plasmid. 2009 Mar;61(2):126-9. doi: 10.1016/j.plasmid.2008.10.001. Epub 2008 Nov 25.An improved tetracycline-inducible expression vector for Staphylococcus aureus.Corrigan RM(1), Foster TJ.Author information: (1)Department of Microbiology, Moyne Institute of Preventive Medicine, TrinityCollege, Dublin 2, Ireland.The tetracycline-inducible expression vector pALC2073 allowed high levelexpression of the cloned sasG gene but repression by uninduced cells was leaky.The -10 box of the tetR promoter was mutated to the Bacillus subtitlis consensus,which resulted in complete repression of SasG protein expression.Anhydrotetracycline at 1.28 microg ml(-1) gave the same high level of inductionthat was obtained with pALC2073sasG using 160 ng ml(-1) tetracycline, the highestconcentration that could be used without inhibiting bacterial growth. Thisvariant of pALC2073 thus offers almost complete repression when uninduced andhigh levels of expression when induced.PMID: 18996145 [PubMed - indexed for MEDLINE] 120. Nucleic Acids Res. 2009 Jan;37(1):e1. doi: 10.1093/nar/gkn883. Epub 2008 Nov 6.Using shotgun sequence data to find active restriction enzyme genes.Zheng Y(1), Posfai J, Morgan RD, Vincze T, Roberts RJ.Author information: (1)New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.Whole genome shotgun sequence analysis has become the standard method forbegin- 85 22 23 24 25 ning to determine a genome sequence. The preparation of the shotgun sequenceclones is, in fact, a biological experiment. It determines which segments of the genome can be cloned into Escherichia coli and which cannot. By analyzing thecomplete set of sequences from such an experiment, it is possible to identifygenes lethal to E. coli. Among this set are genes encoding restriction enzymeswhich, when active in E. coli, lead to cell death by cleaving the E. coli genome at the restriction enzyme recognition sites. By analyzing shotgun sequence datasets we show that this is a reliable method to detect active restriction enzymegenes in newly sequenced genomes, thereby facilitating functional annotation.Active restriction enzyme genes have been identified, and their activitydemonstrated biochemically, in the sequenced genomes of Methanocaldococcusjannaschii, Bacillus cereus ATCC 10987 and Methylococcus capsulatus.PMCID: PMC2615612PMID: 18988632 [PubMed - indexed for MEDLINE] 121. J Mol Microbiol Biotechnol. 2009;16(1-2):53-68. doi: 10.1159/000142894. Epub 2008Oct 29.Cell physiology and protein secretion of Bacillus licheniformis compared toBacillus subtilis.Voigt B(1), Antelmann H, Albrecht D, Ehrenreich A, Maurer KH, Evers S, GottschalkG, van Dijl JM, Schweder T, Hecker M.Author information: (1)Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany. [email protected] genome sequence of Bacillus subtilis was published in 1997 and since thenmany other bacterial genomes have been sequenced, among them Bacilluslicheniformis in 2004. B. subtilis and B. licheniformis are closely related andfeature similar saprophytic lifestyles in the soil. Both species can secretenumerous proteins into the surrounding medium enabling them to usehigh-molecular-weight substances, which are abundant in soils, as nutrientsources. The availability of complete genome sequences allows for the prediction of the proteins containing signals for secretion into the extracellular milieuand also of the proteins which form the secretion machinery needed for proteintranslocation through the cytoplasmic membrane. To confirm the predictedsubcellular localization of proteins, proteomics is the best choice. Theextracellular proteomes of B. subtilis and B. licheniformis have been analyzedunder different growth conditions allowing comparisons of the extracellularproteomes and conclusions regarding similarities and differences of the proteinsecretion mechanisms between the two species.Copyright (c) 2008 S. Karger AG, Basel.PMID: 18957862 [PubMed - indexed for MEDLINE] 122. J Bacteriol. 2009 Jan;191(1):445-6. doi: 10.1128/JB.01347-08. Epub 2008 Oct 24.The complete genome sequence of Bacillus anthracis Ames "Ancestor".Ravel J(1), Jiang L, Stanley ST, Wilson MR, Decker RS, Read TD, Worsham P, KeimPS, Salzberg SL, Fraser-Liggett CM, Rasko DA.Author information: (1)The Institute for Genomic Research, Rockville, Maryland 20850, [email protected] pathogenic bacterium Bacillus anthracis has become the subject of intensestudy as a result of its use in a bioterrorism attack in the United States inSeptember and October 2001. Previous studies suggested that B. anthracis AmesAncestor, the original Ames fully virulent plasmid-containing isolate, was theideal reference. This study describes the complete genome sequence of thatoriginal isolate, derived from a sample kept in cold storage since 1981.PMCID: PMC2612425PMID: 18952800 [PubMed - indexed for MEDLINE] 123. Plasmid. 2009 Jan;61(1):52-64. doi: 10.1016/j.plasmid.2008.09.004. Epub 2008 Oct 26.Bioinformatic and partial functional analysis of pEspA and pEspB, two plasmidsfrom Exiguobacterium arabatum sp. nov. RFL1109.Jakubauskas A(1), Kriukiene E, Trinkunaite L, Sapranauskas R,Jurenaite-Urbanaviciene S, Lubys A.Author information: (1)Institute of Biotechnology, Graiciuno g. 8, Vilnius LT-02241, [email protected] complete nucleotide sequences of two plasmids from Exiguobacterium arabatumsp. nov. RFL1109, pEspA (4563bp) and pEspB (38,945bp), have been determined. FiveORFs were identified in the pEspA plasmid, and putative functions were assignedto two of them. Using deletion mapping approach, the Rep-independent replication region of pEspA, which functions in Bacillus subtilis, was localized within a0.6kb DNA region. Analysis of the pEspB sequence revealed 42 ORFs. From these,function of two genes encoding enzymes of the Lsp1109I restriction-modificationsystem was confirmed experimentally, while putative functions of another 18 ORFs were suggested based on comparative analysis. Three functional regions have been proposed for the pEspB plasmid: the putative conjugative transfer region, theregion involved in plasmid replication and maintenance, and the regionresponsible for transposition of the IS21 family-like transposable elements.PMID: 18848579 [PubMed - indexed for MEDLINE] 124. Arch Virol. 2008;153(10):1855-65. doi: 10.1007/s00705-008-0201-z. Epub 2008 Sep20.Isolation, characterization and genome sequencing of phage MZTP02 from Bacillusthuringiensis MZ1.Liao W(1), Song S, Sun F, Jia Y, Zeng W, Pang Y.Author information: (1)State Key Laboratory of Biocontrol, School of Life Sciences, Institute ofEntomology, Sun Yat-sen Zhongshan University, Guangzhou, People's Republic ofChina. [email protected] lysogenic phage, MZTP02, was produced via induction by mitomycin C fromBacillus thuringiensis (B. thuringiensis) strain MZ1. Plaques were about 3 mm in diameter with a small inner zone consisting of new B. thuringiensis colonies.Electron microscopic analysis showed that MZTP02 had a long tail (220 nm x 18 nm)and an icosahedral head (82 nm x 85 nm). MZTP02 was insensitive to organicsolvents such as chloroform, and infected six B. thuringiensis strains. Itscomplete genome contained 15,717 base pairs (bp) with 37.55% G + C content. Twoinverted terminal repeats consisting of 40 bp were 65% identical. Twenty putativeopen reading frames (ORFs) were found in the MZTP02 genome, and nine predictedproteins, including two terminase subunits, portal protein, minor head protein,scaffold protein, two putative membrane proteins, tail component, and minorstructural protein, showed similarity to other phage proteins. But six ORFs were unique. The presence of a terminal protein at the 5'-terminus was demonstratedusing proteinase K, lambda exonuclease and E. coli exonuclease III to digest the genome DNA. A TMP phylogenetic tree was constructed based on amino acid sequencesfrom ten phages.PMID: 18807113 [Pub- 86 26 27 28 29 30 Med - indexed for MEDLINE] 125. FEMS Microbiol Lett. 2008 Nov;288(2):186-95. doi:10.1111/j.1574-6968.2008.01342.x. Epub 2008 Sep 15.Complete nucleotide sequencing and analysis of the 65-kb highly conjugativeEnterococcus faecium plasmid pMG1: identification of the transfer-related region and the minimum region required for replication.Tanimoto K(1), Ike Y.Author information: (1)Laboratory of Bacterial Drug Resistance, Gunma University Graduate School ofMedicine, Maebashi, Gunma, Japan.pMG1 (65.1 kb) is a highly conjugative, pheromone-independent Enterococcusfaecium plasmid that carries a Tn4001-like transposon encoding gentamicinresistance. The complete nucleotide sequence (65 029 bp) of the pMG1 plasmid was determined and 73 ORFs lying in the same transcription orientation wereidentified. Sixty-one of the 73 ORFs showed a high degree of similarity (90-100% identity at the amino acid level) to the ORFs of the pHTbeta plasmids. Like thepHTbeta plasmid, 22 of the pMG1 plasmid ORFs showed homology with ORFs present onthe pXO2 plasmid (96.2 kb), which is the virulence plasmid essential for capsularformation by Bacillus anthracis. Analysis of tra mutants created by Tn917insertion and Northern analysis of transcripts indicated that ORFs 15-49, lyingin the 31.7 kb region between 13.6 and 45.3 kb on the plasmid map, were relatedto transfer. This region was designated as the Tra I region of pMG1. A 5.9-kbHindIII fragment that replicates autonomously in Enterococcus faecalis was clonedand analysis of this fragment by deletion and in vitro insertion mutations showedthat ORF10 (rep) and the inverted repeat sequence in the noncoding region betweenORF8 and ORF9 were necessary for pMG1 replication.PMID: 18795955 [PubMed - indexed for MEDLINE] 126. J Basic Microbiol. 2008 Dec;48(6):448-54. doi: 10.1002/jobm.200800116.Cloning, sequencing and analysis of dnaK -dnaJ gene cluster of Bacillusmegaterium.Bao F(1), Gong L, Shao W.Author information: (1)Jiangsu Key Laboratory for Biodiversity and Bioresources, Nanjing NormalUniversity, Nanjing, PR China.The DNA fragment of heat shock genes (hrcA-grpE-dnaK-dnaJ) containing completehrcA-grpE-dnaK operon and the transcription unit of dnaJ was cloned, sequensedand analyzed from Bacillus megaterium RF5. The sequence of hrcA, grpE and dnaJwere first time reported, and their coding products exibit 60%, 63% and 81% ofidentities to the homologs of B. subtilis. A sigmaA-type promoter ofGram-positive bacteria (PA1) and a terminator were located upstream of the hrcAand downstream of dnaK, and a Controlling inverted repeat of chaperone expressionelement (CIRCE) was identified between PA1 and hrcA. Another sigmaA-type promoter(PA2) and a terminator were found upstream and downstream of dnaJ, indicating B. megaterium has a transcription unit containing a single gene dnaJ. The structure of dnaJ transcription unit is more similar to that of Listeria monocytogenes thanother species of Bacillus. A partial protein-based phylogenetic tree, derivedfrom Gram-positive bacteria using HrcA sequence, indicated a closer phylogenetic relationship between B. megaterium and Geobacillus species than other twoBacillus species.PMID: 18785662 [PubMed - indexed for MEDLINE] 127. Proteomics. 2008 Jun;8(12):2477-91. doi: 10.1002/pmic.200700971.Deciphering the proteomic profile of Mycobacterium leprae cell envelope.Marques MA(1), Neves-Ferreira AG, da Silveira EK, Valente RH, Chapeaurouge A,Perales J, da Silva Bernardes R, Dobos KM, Spencer JS, Brennan PJ, Pessolani MC.Author information: (1)Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA.The complete sequence of the Mycobacterium leprae genome, an obligateintracellular pathogen, shows a dramatic reduction of functional genes, with acoding capacity of less than 50%. Despite this massive gene decay, the leprosybacillus has managed to preserve a minimal gene set, most of it shared withMycobacterium tuberculosis, allowing its survival in the host with ensuingpathological manifestations. Thus, the identification of proteins that areactually expressed in vivo by M. leprae is of high significance in understanding obligate, intracellular mycobacterial pathogenesis. In this study, ahigh-throughput proteomic approach was undertaken resulting in the identificationof 218 new M. leprae proteins. Of these, 60 were in the soluble/cytosol fraction,98 in the membrane and 104 in the cell wall. Although several proteins wereidentified in more than one subcellular fraction, the majority were unique toone. As expected, a high percentage of these included enzymes responsible forlipid biosynthesis and degradation, biosynthesis of the major components of themycobacterial cell envelope, proteins involved in transportation across lipidbarriers, and lipoproteins and transmembrane proteins with unknown functions. Thedata presented in this study contribute to our understanding of the in vivocomposition and physiology of the mycobacterial cell envelope, a compartmentknown to play a major role in bacterial pathogenesis.PMID: 18563741 [PubMed - indexed for MEDLINE] 128. Curr Microbiol. 2008 Jul;57(1):61-5. doi: 10.1007/s00284-008-9153-5. Epub 2008Apr 30.A nonribosomal peptide synthetase gene tzw1 is involved in zwittermicin Abiosynthesis in Bacillus thuringiensis G03.Shao T(1), Bai L, Zhang J, Wang G, Liu D, Li Z, Liu J, Song F, Huang D.Author information: (1)State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute ofPlant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China.A 4.20-kb SspI fragment from Bacillus thuringiensis G03 was cloned and sequenced.Sequencing analysis revealed two complete open reading frames (ORF; tzw1 andtzw2), and one incomplete ORF (tzw3) (GenBank accession no. EU293887). Tzw1encodes a putative nonribosomal peptide synthetase with thiolation andcondensation domains localized at the C-termini, whereas tzw2 and tzw3 encodeacyl carrier protein and Acyl-CoA dehydrogenase, respectively. To investigate thefunction of tzw1 in zwittermicin A (ZA) biosynthesis, an in-frame deletion of1,461 bp within tzw1 was constructed. The mutant abolished ZA production.Complementation of the mutant with cloned tzw1 restored ZA productivity. Theseresults revealed that tzw1 is required for ZA biosynthesis in B. thuringiensisG03.PMID: 18446411 [PubMed indexed for MEDLINE] 129. J Biol Chem. 2008 Jun 20;283(25):17158-67. doi: 10.1074/jbc.M801461200. Epub 2008Apr 29.Role of Bacillus subtilis RNase 87 31 32 33 J1 endonuclease and 5'-exonuclease activities in trp leader RNA turnover.Deikus G(1), Condon C, Bechhofer DH.Author information: (1)Department of Pharmacology and Systems Therapeutics, Mount Sinai School ofMedicine of New York University, New York, New York 10029, USA.The 140-nucleotide trp leader RNA, which is formed by transcription terminationunder conditions of high intracellular tryptophan, was used to study RNA turnoverin Bacillus subtilis. We showed in vivo that the amount of endonuclease cleavage at approximately nucleotide 100 is decreased under conditions where RNase J1concentration is reduced. In addition, under these conditions the level of3'-terminal RNA fragments, which contain the strong transcription terminatorstructure, increases dramatically. These results implicated RNase J1 in theinitiation of trp leader RNA decay as well as in the subsequent steps leading to complete turnover of the terminator fragment. To confirm a direct role for RNase J1, experiments were performed in vitro with various forms of trp leader RNA and 3'-terminal RNA fragments. Specific endonuclease cleavages, which were restrictedto single-stranded regions not bound by protein, were observed. Degradation ofthe 3'-terminal fragment by the 5' to 3'-exonuclease activity of RNase J1 wasalso demonstrated, although the presence of strong secondary structure impededRNase J1 processivity to some extent. These results are consistent with a modelfor mRNA decay in Bacillus subtilis whereby the downstream products of RNase J1endonucleolytic cleavage become substrates for the 5' to 3'-exoribonucleaseactivity of the enzyme.PMCID: PMC2427345PMID: 18445592 [PubMed - indexed for MEDLINE] 130. Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5803-8. doi:10.1073/pnas.0800981105. Epub 2008 Apr 11.The genome of Bacillus coahuilensis reveals adaptations essential for survival inthe relic of an ancient marine environment.Alcaraz LD(1), Olmedo G, Bonilla G, Cerritos R, Hernández G, Cruz A, Ramírez E,Putonti C, Jiménez B, Martínez E, López V, Arvizu JL, Ayala F, Razo F, Caballero J, Siefert J, Eguiarte L, Vielle JP, Martínez O, Souza V, Herrera-Estrella A,Herrera-Estrella L.Author information: (1)Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Departamentode Ingeniería Genética and Departamento de Biotecnología, Cinvestav, CampusGuanajuato, AP 629 Irapuato, Guanajuato CP36500, México.The Cuatro Ciénegas Basin (CCB) in the central part of the Chihuahan desert(Coahuila, Mexico) hosts a wide diversity of microorganisms contained withinsprings thought to be geomorphological relics of an ancient sea. A major questionremaining to be answered is whether bacteria from CCB are ancient marine bacteriathat adapted to an oligotrophic system poor in NaCl, rich in sulfates, and withextremely low phosphorus levels (<0.3 microM). Here, we report the completegenome sequence of Bacillus coahuilensis, a sporulating bacterium isolated fromthe water column of a desiccation lagoon in CCB. At 3.35 Megabases this is thesmallest genome sequenced to date of a Bacillus species and provides insightsinto the origin, evolution, and adaptation of B. coahuilensis to the CCBenvironment. We propose that the size and complexity of the B. coahuilensisgenome reflects the adaptation of an ancient marine bacterium to a novelenvironment, providing support to a "marine isolation origin hypothesis" that is consistent with the geology of CCB. This genomic adaptation includes theacquisition through horizontal gene transfer of genes involved in phosphorousutilization efficiency and adaptation to high-light environments. The B.coahuilensis genome sequence also revealed important ecological features of thebacterial community in CCB and offers opportunities for a unique glimpse of amicrobe-dominated world last seen in the Precambrian.PMCID: PMC2311347PMID: 18408155 [PubMed - indexed for MEDLINE] 131. J Bacteriol. 2008 Apr;190(8):2892-902. doi: 10.1128/JB.01652-07. Epub 2008 Feb22.Complete genome sequence of the mosquitocidal bacterium Bacillus sphaericus C3-41and comparison with those of closely related Bacillus species.Hu X(1), Fan W, Han B, Liu H, Zheng D, Li Q, Dong W, Yan J, Gao M, Berry C, Yuan Z.Author information: (1)Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.Bacillus sphaericus strain C3-41 is an aerobic, mesophilic, spore-formingbacterium that has been used with great success in mosquito control programsworldwide. Genome sequencing revealed that the complete genome of thisentomopathogenic bacterium is composed of a chromosomal replicon of 4,639,821 bp and a plasmid replicon of 177,642 bp, containing 4,786 and 186 potentialprotein-coding sequences, respectively. Comparison of the genome with otherpublished sequences indicated that the B. sphaericus C3-41 chromosome is mostsimilar to that of Bacillus sp. strain NRRL B-14905, a marine species that, like B. sphaericus, is unable to metabolize polysaccharides. The lack of key enzymesand sugar transport systems in the two bacteria appears to be the main reason forthis inability, and the abundance of proteolytic enzymes and transport systemsmay endow these bacteria with exclusive metabolic pathways for a wide variety of organic compounds and amino acids. The genes shared between B. sphaericus C3-41and Bacillus sp. strain NRRL B-14905, including mobile genetic elements,membrane-associated proteins, and transport systems, demonstrated that these two species are a biologically and phylogenetically divergent group. Knowledge of thegenome sequence of B. sphaericus C3-41 thus increases our understanding of thebacilli and may also offer prospects for future genetic improvement of thisimportant biological control agent.PMCID: PMC2293248PMID: 18296527 [PubMed - indexed for MEDLINE] 132. J AOAC Int. 2007 Nov-Dec;90(6):1517-25.Detection and characterization of cry1Ac transgene construct in Bt cotton:multiple polymerase chain reaction approach.Singh CK(1), Ojha A, Kachru DN.Author information: (1)Industrial Toxicology Research Centre, Post Box No. 80, M.G. Marg Lucknow-226001 U.P., India.To comply with international labeling regulations for genetically modified (GM)crops and food, and to enable proper identification of GM organisms (GMOs),effective methodologies and reliable approaches are needed. The spurious andunapproved GM planting has contributed to crop failures and commercial losses. Toensure effective and genuine GM cultivation, a methodology is needed to detectand identify the trait of interest and concurrently evaluate the struc- 88 34 35 36 tural andfunctional stability of the transgene insert. A multiple polymerase chainreaction (PCR) approach was developed for detection, identification, and genestability confirmation of cry1Ac transgene construct in Bt cotton. As many as 9samples of Bt cotton hybrid seeds comprising 3 approved Bt hybrids, MECH-12Bt,MECH-162Bt, MECH-184Bt, and a batch of 6 nonapproved Bt hybrids were tested.Initially, single standard PCR assays were run to amplify predominant GM DNAsequences (CaMV 35S promoter, nos terminator, and npt-II marker gene); ahousekeeping gene, Gossypium hirsutum fiber-specific acyl carrier protein gene(acp1); a trait-specific transgene (cry1Ac); and a sequence of 7S 3'transcription terminator which specifically borders with 3' region of cry1Actransgene cassette. The concurrent amplification of all sequences of the entirecassette was performed by 3 assays, duplex, triplex, and quadruplex multiplex PCRassays, under common assay conditions. The identity of amplicons was reconfirmed by restriction endonuclease digestion profile. The 2 distinct transgenecassettes, cry1Ac and npt-II, of the Bt cotton were amplified using therespective forward primer of promoter and reverse primer of terminator. Theresultant amplicons were excised, eluted, and purified. The purified ampliconsserved as template for nested PCR assays. The nested PCR runs confirmed thetransgene construct orientation and identity. The limit of detection asestablished by our assay for GM trait (cry1Ac) was 0.1%. This approach can beadopted as a standard procedure for complete molecular characterization of Btcotton. These assays will be of interest and use to importers, breeders, researchlaboratories, safety regulators, and food processors for detection of cry1Acbearing GMOs.PMID: 18193727 [PubMed - indexed for MEDLINE] 133. Proteins. 2008 Jun;71(4):1995-2011. doi: 10.1002/prot.21878.Insights into activation and RNA binding of trp RNA-binding attenuation protein(TRAP) through all-atom simulations.Murtola T(1), Vattulainen I, Falck E.Author information: (1)Laboratory of Physics and Helsinki Institute of Physics, Helsinki University ofTechnology, FI-02015 Espoo, Finland. [email protected] biosynthesis in Bacillus stearothermophilus is regulated by a trp RNA binding attenuation protein (TRAP). It is a ring-shaped 11-mer of identical 74residue subunits. Tryptophan binding pockets are located between adjacentsubunits, and tryptophan binding activates TRAP to bind RNA. Here, we reportresults from all-atom molecular dynamics simulations of the system, complementingexisting extensive experimental studies. We focus on two questions. First, welook at the activation mechanism, of which relatively little is knownexperimentally. We find that the absence of tryptophan allows larger motionsclose to the tryptophan binding site, and we see indication of a conformationalchange in the BC loop. However, complete deactivation seems to occur on muchlonger time scales than the 40 ns studied here. Second, we study the TRAP-RNAinteractions. We look at the relative flexibilities of the different bases in thecomplex and analyze the hydrogen bonds between the protein and RNA. We also studythe role of Lys37, Lys56, and Arg58, which have been experimentally identified asessential for RNA binding. Hydrophobic stacking of Lys37 with the nearby RNA baseis confirmed, but we do not see direct hydrogen bonding between RNA and the othertwo residues, in contrast to the crystal structure. Rather, these residues seemto stabilize the RNA-binding surface, and their positive charge may also play arole in RNA binding. Simulations also indicate that TRAP is able to attract RNAnonspecifically, and the interactions are quantified in more detail using bindingenergy calculations. The formation of the final binding complex is a very slowprocess: within the simulation time scale of 40 ns, only two guanine bases becomebound (and no others), indicating that the binding initiates at these positions. In general, our results are in good agreement with experimental studies, andprovide atomic-scale insights into the processes.(c) 2008 Wiley-Liss, Inc.PMID: 18186477 [PubMed - indexed for MEDLINE] 134. Indian J Lepr. 2007 Apr-Sep;79(2-3):151-66.Recent advances in molecular biology of leprosy.Katoch VM(1), Lavania M, Chauhan DS, Sharma R, Hirawati, Katoch K.Author information: (1)National JALMA Institute for Leprosy and Other Mycobacterial Diseases (ICMR),Tajganj, Agra, India. [email protected] last three decades have witnessed rapid progress in understanding themolecular biology of Mycobacterium leprae. Following the availability of completegenome sequence of leprosy bacillus in 2001, things have drastically changed.With the information about genetic structure, several techniques have beendeveloped for diagnosis, molecular epidemiology and also detection of drugresistance. With the decline in the prevalence of leprosy globally, there hasbeen some reduction in interest in the molecular methods for diagnosis, yetmolecular techniques for studying the transmission dynamics and detection of drugresistance continue to be relevant. Knowledge about complete genome sequence has made it possible to undertake studies that can improve our understanding of thestructure and function of this enigmatic organism. Newer information emergingabout biology of M. leprae would provide insight into mechanisms of its survival and persistence in host and is likely to lead to better diagnostics and alsotherapeutics for mycobacterial infections in general.PMID: 18085172 [PubMed - indexed for MEDLINE] 135. J Microbiol Biotechnol. 2007 Jan;17(1):15-20.Identification and molecular characterization of novel cry1-type toxin genes fromBacillus thuringiensis K1 isolated in Korea.Li MS(1), Choi JY, Roh JY, Shim HJ, Kang JN, Kim YS, Wang Y, Yu ZN, Jin BR, JeYH.Author information: (1)State Key Laboratory of Agricultural Microbiology, Huazhong AgriculturalUniversity, Lion Street, Hongshan District, Wuhan 430070, China.To clone novel cry1-type genes from the Bacillus thuringiensis K1 isolate, about 2.4-kb-long PCR fragments were amplified with two primer sets of ATG1-F/N400-Rand 1BeATG1-F/N400-R. Using PCR-RFLP, three novel cry1-type genes, cry1-1,cry1-7, and cry1-44, were obtained from B. thuringiensis K1 and the completecoding sequences of these novel genes were analyzed. The Cry1-1, Cry1-7, andCry1-44 proteins showed maximum similarities of about 78.0%, 99.7%, and 91.0%with the Cry1Ha1, Cry1Be1, and Cry1Ac2 proteins, respectively. These novelcry1-type genes were expressed using a 89 37 38 39 40 baculovirus expression vector system andtheir insecticidal activities were investigated. Whereas all three novel geneswere toxic to Plutella xylostella larvae, only Cry1-1 showed insecticidalactivity against Spodoptera exigua larvae.PMID: 18051348 [PubMed indexed for MEDLINE] 136. Microbiology. 2007 Nov;153(Pt 11):3645-59.The orotate transporter encoded by oroP from Lactococcus lactis is required fororotate utilization and has utility as a food-grade selectable marker.Defoor E(1), Kryger MB, Martinussen J.Author information: (1)Center for Systems Microbiology, BioCentrum-DTU, Building 301, TechnicalUniversity of Denmark, DK-2800 Kgs. Lyngby, Denmark.A new lactococcal plasmid, pDBORO, was isolated from the Lactococcus lactissubsp. lactis biovar diacetylactis strain DB0410. This plasmid is responsible forthe sensitivity of DB0410 to the toxic pyrimidine analogue 5-fluoroorotate. Thecomplete nucleotide sequence has been determined and amounts to 16 404 bp. Of 15 ORFs encountered, three were found to be insertion sequence (IS) elements,identified as two IS946 and one IS982. Two ORFs are incomplete due to theinsertion of an IS element in their C-terminal region. Homologues for four ORFswere found in the IL1403 sequence: the copB gene, coding for acopper-potassium-transporting ATPase B, and the ysbA, ysbB and ysbC genes. Thestructural organization of the pDBORO replication region is highly similar toother theta-replicating plasmids in both the cis- (repA) and trans-acting (repBand orfX) sequences. By plasmid deletion analysis and molecular cloning, a singlelocus on pDBORO was found to confer sensitivity to 5-fluoroorotate. It wasidentified as ysbC, but renamed oroP in order to reflect its function. The oroPgene was found to be essential for the utilization of orotate as the solepyrimidine source in a strain deficient in pyrimidine de novo synthesis. Theamino acid sequence encoded by the ORF showed the characteristic features of amembrane protein. Therefore, oroP most probably encodes an orotate transporter.Surprisingly, homologues of oroP could be identified in the genomes of both L.lactis MG1363 and L. lactis IL1403 despite the fact that these strains wereunable to significantly utilize orotate. Cloning of oroP in Escherichia coli and Bacillus subtilis showed that the orotate transport phenotype could betransformed to both organisms. The findings presented indicate that oroP can beused as a powerful, food-grade selection/counterselection marker in manydifferent organisms.PMID: 17975072 [PubMed - indexed for MEDLINE] 137. Plant Cell Rep. 2008 Feb;27(2):251-9. Epub 2007 Oct 13.Application of Arabidopsis AGAMOUS second intron for the engineered ablation offlower development in transgenic tobacco.Wang HZ(1), Hu B, Chen GP, Shi NN, Zhao Y, Yin QC, Liu JJ.Author information: (1)Key Laboratory of Biochemistry and Molecular Biology, Hangzhou Normal University,Hangzhou 310018, China. [email protected] explore a new approach to generating reproductive sterility in transgenicplants, the barnase gene from Bacillus amyloliquefaciens was placed under thecontrol of an 1853-bp nucleotide sequence from the 3'end of the second intron of Arabidopsis AGAMOUS and CaMV 35S (-60) minimal promoter [AG-I-35S(-60)::Barnase], and was introduced into tobacco through transformation mediated by Agrobacterium tumefaciens. All AG-I-35S (-60)::Barnase transgenic plantsshowed normal vegetative growth and 28% of the transgenic lines displayedcomplete ablation of flowering. Two transgenic lines, Bar-5 and Bar-15, were 98.1and 98.4% sterile, respectively, as determined by seed production andgermination. When controlled by AG-I-35S (-60) chimeric promoter, barnase mRNAwas detected in the reproductive tissues of transgenic tobacco plants, but not invegetative parts. This study presents the first application of an AG intronsequence in the engineered ablation of sexual reproduction in plants. TheAG-I-35S (-60)::Barnase construct can be useful in diminishing pollen and seedformation in plants, providing a novel bisexual sterility strategy forinterception of transgene escape and has other potentially commercial use fortransgenic engineering.PMID: 17934737 [PubMed - indexed for MEDLINE] 138. J Bacteriol. 2007 Dec;189(23):8616-25. Epub 2007 Oct 5.The yydFGHIJ operon of Bacillus subtilis encodes a peptide that induces the LiaRStwo-component system.Butcher BG(1), Lin YP, Helmann JD.Author information: (1)Department of Microbiology, 370 Wing Hall, Cornell University, Ithaca, NY14853-8101, USA.The Bacillus subtilis LiaRS two-component system (TCS) responds to perturbations of the cell envelope induced by lipid II-interacting antibiotics, such asvancomycin, ramoplanin, nisin, and bacitracin. Here, we characterizeTn7-generated mutations that induce the liaRS TCS. In addition to insertions inliaF, a known negative regulator of the LiaRS TCS, we identified two disruptions in the last two genes of the yydFGHIJ operon. This operon is predicted to encode a 49-amino-acid peptide (YydF), a modification enzyme (YydG), a membrane-embeddedprotease (YydH), and an ATP-binding cassette (ABC) transporter (YydIJ). Genomesequence comparisons suggest that the yydFGHIJ operon may have been acquired byhorizontal transfer. Inactivation of the YydIJ transporter resulted in increased expression from the LiaR-dependent P(liaI) promoter only in the presence of theyydFGH genes. Cells harboring the complete yydFGHIJ operon induced LiaR activity in cocultured cells lacking either this transporter or the complete operon. Theseresults suggest that this operon is involved in the synthesis and export of amodified peptide (YydF*) that elicits cell envelope stress sensed by the LiaRSTCS.PMCID: PMC2168931PMID: 17921301 [PubMed - indexed for MEDLINE] 139. J Appl Microbiol. 2008 Jan;104(1):60-9.Changes in the properties of Bacillus thuringiensis after prolonged culture in a rich medium.Bizzarri MF(1), Bishop AH, Dinsdale A, Logan NA.Author information: (1)School of Science, University of Greenwich, Chatham Maritime, UK.AIM: To investigate the effect of repeated culture in a rich medium on certaingenetic, metabolic, pathogenic and structural characteristics of fresh isolatesof Bacillus thuringiensis.METHODS AND RESULTS: Four strains of B. thuringiensis, which had been isolated invegetative form from leaf surfaces, were grown for 500 generations in batchculture in a rich medium. One of the strains, S4g, differed from the parent inthe following respects: greater cell width; changed plasmid profile; completeloss of ability to 90 41 42 43 44 produce delta-endotoxins; loss of ability to producebeta-exotoxin and disruption of vip3 gene; radically different fatty acidcomposition; and altered metabolic activity. Two of the other evolved strains(S1g and S6g) showed differences in fatty acid profiles compared with theparents. Genetic finger-printing showed that there were also mutations in the crygenes of two of the evolved strains (S1g and S2g). The delta-endotoxins of strainS6g were significantly less toxic to the larvae of Pieris brassica compared with those of the parent and it also differed in the plasmid content.CONCLUSION: Radical and unpredictable changes can occur in fresh isolates of B.thuringiensis when subjected to growth in the laboratory.SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first analysis of a Grampositive and biotechnologically significant bacterium after repeated laboratoryculture. It is of great relevance to the biotechnological exploitation of B.thuringiensis that prolonged growth of environmental isolates on laboratoryculture media can have profound effects on their structure, genome and virulence determinants.PMID: 17850315 [PubMed - indexed for MEDLINE] 140. Appl Environ Microbiol. 2007 Nov;73(21):6939-44. Epub 2007 Sep 7.Mutated cadherin alleles from a field population of Helicoverpa armigera conferresistance to Bacillus thuringiensis toxin Cry1Ac.Yang Y(1), Chen H, Wu Y, Yang Y, Wu S.Author information: (1)Department of Entomology, College of Plant Protection, Nanjing AgriculturalUniversity, Nanjing 210095, China.The cotton bollworm Helicoverpa armigera is the major insect pest targeted bycotton genetically engineered to produce the Bacillus thuringiensis toxin(transgenic Bt cotton) in the Old World. The evolution of this pest's resistance to B. thuringiensis toxins is the main threat to the long-term effectiveness oftransgenic Bt cotton. A deletion mutation allele (r(1)) of a cadherin gene(Ha_BtR) was previously identified as genetically linked with Cry1Ac resistancein a laboratory-selected strain of H. armigera. Using a biphasic screen strategy,we successfully trapped two new cadherin alleles (r(2) and r(3)) associated with Cry1Ac resistance from a field population of H. armigera collected from theYellow River cotton area of China in 2005. The r(2) and r(3) alleles,respectively, were created by inserting the long terminal repeat of aretrotransposon (designated HaRT1) and the intact HaRT1 retrotransposon at thesame position in exon 8 of Ha_BtR, which results in a truncated cadherincontaining only two ectodomain repeats in the N terminus of Ha_BtR. This is thefirst time that the B. thuringiensis resistance alleles of a target insect of Bt crops have been successfully detected in the open field. This study alsodemonstrated that bollworm larvae carrying two resistance alleles can completedevelopment on Bt cotton. The cadherin locus should be an important target forintensive DNA-based screening of field populations of H. armigera.PMCID: PMC2074965PMID: 17827322 [PubMed - indexed for MEDLINE] 141. Nat Biotechnol. 2007 Sep;25(9):1007-14. Epub 2007 Aug 19.Comparative analysis of the complete genome sequence of the plantgrowth-promoting bacterium Bacillus amyloliquefaciens FZB42.Chen XH(1), Koumoutsi A, Scholz R, Eisenreich A, Schneider K, Heinemeyer I,Morgenstern B, Voss B, Hess WR, Reva O, Junge H, Voigt B, Jungblut PR, Vater J,Süssmuth R, Liesegang H, Strittmatter A, Gottschalk G, Borriss R.Author information: (1)Bakteriengenetik, Institut für Biologie, Humboldt Universität, Chausseestrasse117, D-10115 Berlin, Germany.Bacillus amyloliquefaciens FZB42 is a Gram-positive, plant-associated bacterium, which stimulates plant growth and produces secondary metabolites that suppresssoil-borne plant pathogens. Its 3,918-kb genome, containing an estimated 3,693protein-coding sequences, lacks extended phage insertions, which occurubiquitously in the closely related Bacillus subtilis 168 genome. The B.amyloliquefaciens FZB42 genome reveals an unexpected potential to producesecondary metabolites, including the polyketides bacillaene and difficidin. More than 8.5% of the genome is devoted to synthesizing antibiotics and siderophoresby pathways not involving ribosomes. Besides five gene clusters, known from B.subtilis to mediate nonribosomal synthesis of secondary metabolites, weidentified four giant gene clusters absent in B. subtilis 168. The pks2 genecluster encodes the components to synthesize the macrolactin core skeleton.PMID: 17704766 [PubMed - indexed for MEDLINE] 142. Virology. 2007 Nov 25;368(2):405-21. Epub 2007 Jul 30.Complete genomic sequence and mass spectrometric analysis of highly diverse,atypical Bacillus thuringiensis phage 0305phi8-36.Thomas JA(1), Hardies SC, Rolando M, Hayes SJ, Lieman K, Carroll CA, WeintraubST, Serwer P.Author information: (1)Department of Biochemistry, The University of Texas Health Science Center, 7703Floyd Curl Drive, San Antonio, TX 78229-3900, USA.To investigate the apparent genomic complexity of long-genome bacteriophages, we have sequenced the 218,948-bp genome (6479-bp terminal repeat), and identifiedthe virion proteins (55), of Bacillus thuringiensis bacteriophage 0305phi8-36.Phage 0305phi8-36 is an atypical myovirus with three large curly tail fibers. An accurate mode of DNA pyrosequencing was used to sequence the genome and massspectrometry was used to accomplish the comprehensive virion protein survey.Advanced informatic techniques were used to identify classical morphogenesisgenes. The 0305phi8-36 genes were highly diverged; 19% of 247 closely spacedgenes have similarity to proteins with known functions. Genes forvirion-associated, apparently fibrous proteins in a new class were found, inaddition to strong candidates for the curly fiber genes. Phage 0305phi8-36 hastwice the virion protein coding sequence of T4. Based on its genomic isolation,0305phi8-36 is a resource for future studies of vertical gene transmission.PMCID: PMC2171028PMID: 17673272 [PubMed - indexed for MEDLINE] 143. Microbiology. 2007 Aug;153(Pt 8):2553-9.Development of an intermolecular transposition assay system in Bacillus subtilis 168 using IS4Bsu1 from Bacillus subtilis (natto).Takahashi K(1), Sekine Y, Chibazakura T, Yoshikawa H.Author information: (1)Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Tokyo156-8502, Japan.Most of the spontaneous poly-gamma-glutamate (gamma-PGA)-deficient mutants ofBacillus subtilis (natto) appear to have resulted from the insertion of IS4Bsu1exclusively into the comP gene. However, complete genomic analysis of B. subtilis168, a close relative of B. subtilis (natto), revealed no IS4Bsu1 insertion.Preliminary experiments using a transformable 'natto' strain indicated that thefrequency of transposi- 91 45 46 47 48 tion of IS4Bsu1 was exceptionally high undercompetence-developing conditions. On the other hand, such high-frequencytransposition was not observed when cells were grown in a rich medium, such as LBmedium, suggesting that there must be suitable environmental conditions that giverise to the transposition of IS4Bsu1. To assess the behaviour of IS4Bsu1 andexplore any host factors playing roles in IS transposition, an intermoleculartransposition assay system was constructed using a modified IS4Bsu1 element in B.subtilis 168. Here, the details of the intermolecular transposition assay system are given, and the increase in transposition frequency observed underhigh-temperature and competence-inducing conditions is described.PMID: 17660419 [PubMed - indexed for MEDLINE] 144. Microbiology. 2007 Aug;153(Pt 8):2541-52.FlhF, a signal recognition particle-like GTPase, is involved in the regulation offlagellar arrangement, motility behaviour and protein secretion in Bacilluscereus.Salvetti S(1), Ghelardi E, Celandroni F, Ceragioli M, Giannessi F, Senesi S.Author information: (1)Dipartimento di Patologia Sperimentale, Biotecnologie Mediche, Infettivologia ed Epidemiologia, Università di Pisa, via San Zeno 37, 56127 Pisa, Italy.Flagellar arrangement is a highly conserved feature within bacterial species.However, only a few genes regulating cell flagellation have been described inpolar flagellate bacteria. This report demonstrates that the arrangement offlagella in the peritrichous flagellate Bacillus cereus is controlled by flhF.Disruption of flhF in B. cereus led to a reduction in the number of flagella from10-12 to 1-3 filaments per cell in the insertion mutant MP06. Moreover, compared to the parental strain, MP06 exhibited: (i) shorter smooth swimming phases,causing reduced swimming motility but not affecting chemotaxis; (ii) completeinhibition of swarming motility, as differentiated swarm cells were neverdetected; (iii) an increased amount of extracellular proteins; and (iv)differential export of virulence determinants, such as haemolysin BL (HBL),phosphatidylcholine-preferring phospholipase C (PC-PLC) and non-haemolyticenterotoxin (NHE). Introduction of a plasmid harbouring flhF (pDGflhF) into MP06 completely restored the wild-type phenotype in the trans-complemented strainMP07. B. cereus flhF was found to constitute a monocistronic transcriptional unitand its overexpression did not produce abnormal features in the wild-typebackground. Characterization of a B. cereus mutant (MP05) carrying a partial flhFdeletion indicated that the last C-terminal domain of FlhF is involved in proteinexport while not required for flagellar arrangement and motility behaviour. Takentogether, these data suggest that B. cereus FlhF is a promising candidate forconnecting diverse cellular functions, such as flagellar arrangement, motilitybehaviour, pattern of protein secretion and virulence phenotype.PMID: 17660418 [PubMed - indexed for MEDLINE] 145. FEMS Yeast Res. 2007 Oct;7(7):1197-205. Epub 2007 Jul 26.A novel vector element providing multicopy vector integration in Arxulaadeninivorans.Steinborn G(1), Gellissen G, Kunze G.Author information: (1)Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung, Gatersleben,Germany.An Arxula adeninivorans vector element has been identified that providesmulticopy integration in an atrp1 host strain. The element consists of the ATRP1 selection marker fused to a newly generated truncated ALEU2 promoter of 53 bp. Inthe described example eight copies of an amyA expression vector encodingheterologous alpha-amylase from Bacillus amyloliquefaciens are integrated in the genome of the recombinant strain instead of a single copy observed when using theATRP1 element with the complete promoter. The high copy number results in strainsof superior productivity for a secreted recombinant alpha-amylase. The vectordesign enables the integration of a small vector fragment that consists of yeast DNA only providing high transformation frequencies and a high mitotic stability.PMID: 17655689 [PubMed - indexed for MEDLINE] 146. J Biosci Bioeng. 2007 May;103(5):457-63.Molecular cloning and characterization of thermostable beta-lactam acylase withbroad substrate specificity from Bacillus badius.Rajendhran J(1), Gunasekaran P.Author information: (1)Department of Genetics, Centre for Excellence in Genomic Sciences, School ofBiological Sciences, Madurai Kamaraj University, Madurai, India.The gene (pac) encoding beta-lactam acylase from Bacillus badius was cloned andexpressed in Escherichia coli. The pac gene was identified by polymerase chainreaction (PCR) using degenerated primers, on the basis of conserved amino acidresidues. By using single specific primer PCR (SSP-PCR) and direct genomesequencing, a complete pac gene with its promoter region was obtained. The ORFconsisted of 2415 bp and the deduced amino acid sequence indicated that theenzyme is synthesized as a preproenzyme with a signal sequence, an alpha-subunit,a spacer peptide and a beta-subunit. The pac gene was expressed with its ownpromoter in different E. coli host strains and a maximum recombinant PAC (1820 U l(-1)) was obtained in E. coli DH5alpha. The recombinant PAC was purified byNi-NTA chromatography and the purified PAC had two subunits with apparentmolecular masses of 25 and 62 kDa. This enzyme exhibited a high thermostabilitywith a maximum activity at 50 degrees C. This enzyme showed stability over a widepH range (pH 6.0-8.5) with a maximum activity at pH 7.0 and activity on a widebeta-lactam substrate range. The K(m) values obtained for the hydrolysis ofpenicillin G and a chromogenic substrate, 6-nitro-3-phenylacetylamidobenzoicacid, from B. badius PAC were 39 and 41 microM, respectively. The PAC activitywas competitively inhibited by PAA (K(i), 108 microM) and noncompetitively by6-APA (K(i), 17 mM). The constitutive production of B. badius PAC in E. coli and its easier purification together with the advantageous properties, such asthermostability, pH stability and broad substrate specificity, make this as anovel enzyme suitable for beta-lactam industry.PMID: 17609162 [PubMed - indexed for MEDLINE] 147. J Clin Immunol. 2007 Sep;27(5):490-6. Epub 2007 May 21.Two patients with complete defects in interferon gamma receptor-dependentsignaling.Noordzij JG(1), Hartwig NG, Verreck FA, De Bruin-Versteeg S, De Boer T, VanDissel JT, De Groot R, Ottenhoff TH, Van Dongen JJ.Author information: (1)Department of Immunology, Erasmus MC/University Medical Center Rotterdam,Rotterdam, The Netherlands.Unusual susceptibility to mycobacterial infections can be caused by deleteriousmutations in genes 92 49 50 51 that encode the interferon-gamma receptor 1 chain. Suchmutations hamper the activation of macrophages by a type 1 immune response andresult in enhanced survival of intracellular pathogens. We here report twopatients with unusual mycobacterial infections, both diagnosed with homozygousdeleterious interferon-gamma receptor 1 gene mutations. Patient 1 became illafter Bacillus Calmette-Guérin vaccination at the age of 9 months and died at theage of 18 months. She carried a homozygous C71Y mutation in the extracellularpart of the mature interferon-gamma receptor 1 protein, resulting in the lack of detectable protein expression and absence of interferon-gamma dependentsignaling. Patient 2 became ill at the age of 3 years, is still alive at 19 yearsof age, and has suffered from five successive infection episodes with atypicalmycobacteria. A homozygous splice-site mutation in intron 3 was identified,resulting in the deletion of exon 3 at the mRNA level and consequently atruncated interferon-gamma receptor 1 protein with absence of the transmembranedomain. Protein expression and interferon-gamma dependent signaling were notdetectable.PMID: 17514500 [PubMed - indexed for MEDLINE] 148. Appl Environ Microbiol. 2007 Jun;73(12):3803-13. Epub 2007 Apr 20.Plant cell wall degradation by saprophytic Bacillus subtilis strains: geneclusters responsible for rhamnogalacturonan depolymerization.Ochiai A(1), Itoh T, Kawamata A, Hashimoto W, Murata K.Author information: (1)Laboratory of Basic and Applied Molecular Biotechnology, Graduate School ofAgriculture, Kyoto University, Uji, Kyoto 611-0011, Japan.Plant cell wall degradation is a premier event when Bacillus subtilis, a typical saprophytic bacterium, invades plants. Here we show the degradation system ofrhamnogalacturonan type I (RG-I), a component of pectin from the plant cell wall,in B. subtilis strain 168. Strain 168 cells showed a significant growth on plant cell wall polysaccharides such as pectin, polygalacturonan, and RG-I as a carbon source. DNA microarray analysis indicated that three gene clusters(yesOPQRSTUVWXYZ, ytePQRST, and ybcMOPST-ybdABDE) are inducibly expressed instrain 168 cells grown on RG-I. Cells of an industrially important bacterium, B. subtilis strain natto, fermenting soybeans also express the gene clusterincluding the yes series during the assimilation of soybean used as a carbonsource. Among proteins encoded in the yes cluster, YesW and YesX were found to benovel types of RG lyases releasing disaccharide from RG-I. Genetic and enzymatic properties of YesW and YesX suggest that strain 168 cells secrete YesW, whichcatalyzes the initial cleavage of the RG-I main chain, and the resultantoligosaccharides are converted to disaccharides through the extracellular exotypeYesX reaction. The disaccharide is finally degraded into its constituentmonosaccharides through the reaction of intracellular unsaturated galacturonylhydrolases YesR and YteR. This enzymatic route for RG-I degradation in strain 168differs significantly from that in plant-pathogenic fungus Aspergillus aculeatus.This is, to our knowledge, the first report on the bacterial system for complete RG-I main chain degradation.PMCID: PMC1932723PMID: 17449691 [PubMed - indexed for MEDLINE] 149. Wei Sheng Wu Xue Bao. 2007 Feb;47(1):17-21.[Cloning and characterization of gerM gene involved in germination in Bacillusthuringiensis].[Article in Chinese]Yan XH(1), Liu G, Tan HR.Author information: (1)Center for Microbial Genetics and Metabolic Engineering, Institute ofMicrobiology, Chinese Academy of Sciences, Beijing 100080, [email protected] Bacilli, gerM is a very conservative gene. Primers were designed according to the gerM gene sequence of Bacillus cereus, and a 640bp DNA fragment was obtained from Bacillus thuringiensis subsp. kustaki 1. 175 by PCR. Using this fragment as a probe, a 4.5kb DNA fragment was cloned from the partial DNA library of Bacillusthuringiensis subsp. kustaki 1.175. Sequence analysis showed that the fragmentcontains one complete open reading frame (ORF) that encodes a 349-amino acid (aa)protein, which has high homology with GerM protein from Bacillus subtilis. Thisgene was designated gerM (GenBank Accession No. DQ537381 ) . RT-PCR analysisshowed that gerM gene was only expressed in the process of sporulation,suggesting gerM is not required for the vegetative growth. The function of thegerM gene was studied by a strategy of gene disruption, and the resulting gerMdisruption mutant did show normal growth and sporulation. However, gerMdisruption mutant spores germinate slower than wild-type spores when triggered byL-alanine or inosine, indicating that gerM is required for the spore normalgermination initiated by L-alanine or inosine in Bacillus thuringiensis.PMID: 17436617 [PubMed - indexed for MEDLINE] 150. Appl Microbiol Biotechnol. 2007 Jul;75(6):1309-17. Epub 2007 Apr 11.Recombinant expression and characterization of XynD from Bacillus subtilis subsp.subtilis ATCC 6051: a GH 43 arabinoxylan arabinofuranohydrolase.Bourgois TM(1), Van Craeyveld V, Van Campenhout S, Courtin CM, Delcour JA, RobbenJ, Volckaert G.Author information: (1)Laboratory of Gene Technology, Katholieke Universiteit Leuven, KasteelparkArenberg 21, 3001 Leuven, Belgium. [email protected] complete genome sequence of Bacillus subtilis reveals that sequences encodingseveral hemicellulases are co-localised with a gene (xynD) encoding a putativefamily 43 glycoside hydrolase that has not yet been characterised. In this work, xynD has been isolated from genomic DNA of B. subtilis subsp. subtilis ATCC 6051 and cloned for cytoplasmatic expression in Escherichia coli. Recombinant XynD(rXynD) was purified using ion-exchange chromatography and gel permeationchromatography. The enzyme had a molecular mass of approximately 52 kDa, a pIabove 9.0 and releases alpha-L-arabinose from arabinoxylo-oligosaccharides aswell as arabinoxylan polymers with varying degree of substitution. Usingpara-nitrophenyl-alpha-L-arabinofuranoside as substrate, maximum activity wasobserved at pH 5.6 and 45 degrees C. The enzyme retained its activity over alarge pH range, while activity was lost after pre-incubation above 50 degrees C. Gas-liquid chromatography and proton nuclear magnetic resonance spectrometryanalysis indicated that rXynD specifically releases arabinofuranosyl groups from mono-substituted C-(O)-2 and C-(O)-3 xylopyranosyl residues on the xylanbackbone. As rXynD did not display endoxylanase, xylosidase or arabinanaseactivity and was inactive on arabinan, we 93 52 53 54 55 conclude that this enzyme is bestdescribed as an arabinoxylan arabinofuranohydrolase.PMID: 17426966 [PubMed - indexed for MEDLINE] 151. J Bacteriol. 2007 Jun;189(12):4384-90. Epub 2007 Apr 6.Identification of the sigmaB regulon of Bacillus cereus and conservation ofsigmaB-regulated genes in low-GC-content gram-positive bacteria.van Schaik W(1), van der Voort M, Molenaar D, Moezelaar R, de Vos WM, Abee T.Author information: (1)Wageningen Centre for Food Sciences, P.O. Box 557, 6700AN Wageningen, TheNetherlands.The alternative sigma factor sigma(B) has an important role in the acquisition ofstress resistance in many gram-positive bacteria, including the food-bornepathogen Bacillus cereus. Here, we describe the identification of the set ofsigma(B)-regulated genes in B. cereus by DNA microarray analysis of thetranscriptome upon a mild heat shock. Twenty-four genes could be identified asbeing sigma(B) dependent as witnessed by (i) significantly lower expressionlevels of these genes in mutants with a deletion of sigB and rsbY (which encodethe alternative sigma factor sigma(B) and a crucial positive regulator ofsigma(B) activity, respectively) than in the parental strain B. cereus ATCC 14579and (ii) increased expression of these genes upon a heat shock. Newly identified sigma(B)-dependent genes in B. cereus include a histidine kinase and two genesthat have predicted functions in spore germination. This study shows that thesigma(B) regulon of B. cereus is considerably smaller than that of othergram-positive bacteria. This appears to be in line with phylogenetic analyseswhere sigma(B) of the B. cereus group was placed close to the ancestral form ofsigma(B) in gram-positive bacteria. The data described in this study and previousstudies in which the complete sigma(B) regulon of the gram-positive bacteriaBacillus subtilis, Listeria monocytogenes, and Staphylococcus aureus weredetermined enabled a comparison of the sets of sigma(B)-regulated genes in thedifferent gram-positive bacteria. This showed that only three genes (rsbV, rsbW, and sigB) are conserved in their sigma(B) dependency in all four bacteria,suggesting that the sigma(B) regulon of the different gram-positive bacteria has evolved to perform niche-specific functions.PMCID: PMC1913364PMID: 17416654 [PubMed - indexed for MEDLINE] 152. Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5602-7. Epub 2007 Mar 19.Genome and proteome of long-chain alkane degrading Geobacillusthermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir.Feng L(1), Wang W, Cheng J, Ren Y, Zhao G, Gao C, Tang Y, Liu X, Han W, Peng X,Liu R, Wang L.Author information: (1)TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China.The complete genome sequence of Geobacillus thermodenitrificans NG80-2, athermophilic bacillus isolated from a deep oil reservoir in Northern China,consists of a 3,550,319-bp chromosome and a 57,693-bp plasmid. The genome revealsthat NG80-2 is well equipped for adaptation into a wide variety of environmental niches, including oil reservoirs, by possessing genes for utilization of a broad range of energy sources, genes encoding various transporters for efficientnutrient uptake and detoxification, and genes for a flexible respiration systemincluding an aerobic branch comprising five terminal oxidases and an anaerobicbranch comprising a complete denitrification pathway for quick response todissolved oxygen fluctuation. The identification of a nitrous oxide reductasegene has not been previously described in Gram-positive bacteria. The proteomefurther reveals the presence of a long-chain alkane degradation pathway; and the function of the key enzyme in the pathway, the long-chain alkane monooxygenaseLadA, is confirmed by in vivo and in vitro experiments. The thermophilic soluble monomeric LadA is an ideal candidate for treatment of environmental oilpollutions and biosynthesis of complex molecules.PMCID: PMC1838512PMID: 17372208 [PubMed - indexed for MEDLINE] 153. J Bacteriol. 2007 May;189(9):3680-1. Epub 2007 Mar 2.The complete genome sequence of Bacillus thuringiensis Al Hakam.Challacombe JF(1), Altherr MR, Xie G, Bhotika SS, Brown N, Bruce D, Campbell CS, Campbell ML, Chen J, Chertkov O, Cleland C, Dimitrijevic M, Doggett NA, FawcettJJ, Glavina T, Goodwin LA, Green LD, Han CS, Hill KK, Hitchcock P, Jackson PJ,Keim P, Kewalramani AR, Longmire J, Lucas S, Malfatti S, Martinez D, McMurry K,Meincke LJ, Misra M, Moseman BL, Mundt M, Munk AC, Okinaka RT, Parson-Quintana B,Reilly LP, Richardson P, Robinson DL, Saunders E, Tapia R, Tesmer JG, Thayer N,Thompson LS, Tice H, Ticknor LO, Wills PL, Gilna P, Brettin TS.Author information: (1)Department of Energy Joint Genome Institute, Bioscience Division, MS M888, LosAlamos National Laboratory, Los Alamos, NM 87545, USA. [email protected] thuringiensis is an insect pathogen that is widely used as abiopesticide (E. Schnepf, N. Crickmore, J. Van Rie, D. Lereclus, J. Baum, J.Feitelson, D. R. Zeigler, and D. H. Dean, Microbiol. Mol. Biol. Rev. 62:775-806, 1998). Here we report the finished, annotated genome sequence of B. thuringiensisAl Hakam, which was collected in Iraq by the United Nations Special Commission(L. Radnedge, P. Agron, K. Hill, P. Jackson, L. Ticknor, P. Keim, and G.Andersen, Appl. Environ. Microbiol. 69:2755-2764, 2003).PMCID: PMC1855882PMID: 17337577 [PubMed - indexed for MEDLINE] 154. Gene. 2007 Apr 15;391(1-2):171-7. Epub 2007 Jan 19.Direct cloning of full-length mouse mitochondrial DNA using a Bacillus subtilisgenome vector.Yonemura I(1), Nakada K, Sato A, Hayashi J, Fujita K, Kaneko S, Itaya M.Author information: (1)Graduate School of Life and Environmental Sciences, Institute of BiologicalSciences, University of Tsukuba, Ibaraki 305-8572, Japan.The complete mouse mitochondrial genome (16.3 kb) was directly cloned into aBacillus subtilis genome (BGM) vector. Two DNA segments of 2.06 and 2.14 kb that flank the internal 12 kb of the mitochondrial DNA (mtDNA) were subcloned into an Escherichia coli plasmid. Subsequent integration of the plasmid at the cloninglocus of the BGM vector yielded a derivative specific for the targeted cloning ofthe internal 12-kb mtDNA region. The BGM vector took up mtDNA purified from mouseliver and integrated it by homologous recombination at the two preinstalledmtDNA-flanking sequences. The complete cloned mtDNA in the BGM vector wascon- 94 56 57 58 59 verted to a covalently closed circular (ccc) plasmid form via gene conversion in B. subtilis. The mtDNA carried on this plasmid was then isolated andtransferred to E. coli. DNA sequence fidelity and stability through the BGMvector-mediated cloning process were confirmed.PMID: 17317040 [PubMed - indexed for MEDLINE] 155. J Bacteriol. 2007 Apr;189(8):3256-70. Epub 2007 Feb 16.Complete genome sequence of the prototype lactic acid bacterium Lactococcuslactis subsp. cremoris MG1363.Wegmann U(1), O'Connell-Motherway M, Zomer A, Buist G, Shearman C, Canchaya C,Ventura M, Goesmann A, Gasson MJ, Kuipers OP, van Sinderen D, Kok J.Author information: (1)Department of Molecular Genetics, Groningen Biomolecular Sciences andBiotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, TheNetherlands.Lactococcus lactis is of great importance for the nutrition of hundreds ofmillions of people worldwide. This paper describes the genome sequence ofLactococcus lactis subsp. cremoris MG1363, the lactococcal strain mostintensively studied throughout the world. The 2,529,478-bp genome contains 81pseudogenes and encodes 2,436 proteins. Of the 530 unique proteins, 47 belong to the COG (clusters of orthologous groups) functional category "carbohydratemetabolism and transport," by far the largest category of novel proteins incomparison with L. lactis subsp. lactis IL1403. Nearly one-fifth of the 71insertion elements are concentrated in a specific 56-kb region. This integration hot-spot region carries genes that are typically associated with lactococcalplasmids and a repeat sequence specifically found on plasmids and in the "lateralgene transfer hot spot" in the genome of Streptococcus thermophilus. Although theparent of L. lactis MG1363 was used to demonstrate lysogeny in Lactococcus, L.lactis MG1363 carries four remnant/satellite phages and two apparently completeprophages. The availability of the L. lactis MG1363 genome sequence willreinforce its status as the prototype among lactic acid bacteria throughfacilitation of further applied and fundamental research.PMCID: PMC1855848PMID: 17307855 [PubMed - indexed for MEDLINE] 156. RNA. 2007 Apr;13(4):573-82. Epub 2007 Feb 16.Ligand binding and gene control characteristics of tandem riboswitches inBacillus anthracis.Welz R(1), Breaker RR.Author information: (1)Department of Molecular, Cellular, and Developmental Biology, Yale University,New Haven, CT 06520, USA.Most riboswitches are composed of a single metabolite-binding aptamer and asingle expression platform that function together to regulate genes in responseto changing metabolite concentrations. In rare instances, two aptamers orsometimes two complete riboswitches reside adjacent to each other in untranslatedregions (UTRs) of mRNAs. We have examined an example of a tandem riboswitch inthe Gram-positive bacterium Bacillus anthracis that includes two completeriboswitches for thiamine pyrophosphate (TPP). Unlike other complex riboswitchsystems described recently, tandem TPP riboswitches do not exhibit cooperativeligand binding and do not detect two different types of metabolites. In contrast,both riboswitches respond independently to TPP and are predicted to function inconcert to mimic the more "digital" gene control outcome observed when twoaptamers bind ligands cooperatively. Our findings further demonstrate that simplegene control elements made only of RNA can be assembled in differentarchitectures to yield more complex gene control outcomes.PMCID: PMC1831863PMID: 17307816 [PubMed - indexed for MEDLINE] 157. FEMS Microbiol Lett. 2007 Feb;267(1):64-71.Identification of a novel two-peptide lantibiotic, haloduracin, produced by thealkaliphile Bacillus halodurans C-125.Lawton EM(1), Cotter PD, Hill C, Ross RP.Author information: (1)Department of Microbiology, University College Cork, Cork, Ireland.Complete genome sequencing of the alkaliphilic bacterium Bacillus haloduransC-125 revealed the presence of several genes homologous to those involved in the production of lantibiotic peptides. Additional bioinformatic analysis identified a total of eleven genes, spanning a 15 kbp region, potentially involved in theproduction, modification, immunity and transport of a two-peptide lantibiotic.Having established that strain C-125 exhibited antimicrobial activity against awide range of Gram-positive bacteria, it was demonstrated through peptidepurification, MS and site-directed mutagenesis that this activity was indeedattributable to the production of a lantibiotic encoded by these genes. Thisantimicrobial has been designated haloduracin and represents the first occasionwherein production of two-peptide lantibiotic has been associated with a Bacillussp. It is also the first example of a lantibiotic of any kind to be produced byan alkaliphilic species.PMID: 17233677 [PubMed - indexed for MEDLINE] 158. J Bacteriol. 2007 Mar;189(5):1698-710. Epub 2006 Dec 22.Biosynthetic analysis of the petrobactin siderophore pathway from Bacillusanthracis.Lee JY(1), Janes BK, Passalacqua KD, Pfleger BF, Bergman NH, Liu H, Håkansson K, Somu RV, Aldrich CC, Cendrowski S, Hanna PC, Sherman DH.Author information: (1)Life Sciences Institute, Department of Medicinal Chemistry, University ofMichigan, Ann Arbor, MI 48109-2216, USA.The asbABCDEF gene cluster from Bacillus anthracis is responsible forbiosynthesis of petrobactin, a catecholate siderophore that functions in bothiron acquisition and virulence in a murine model of anthrax. We initiated studiesto determine the biosynthetic details of petrobactin assembly based on mutationalanalysis of the asb operon, identification of accumulated intermediates, andaddition of exogenous siderophores to asb mutant strains. As a starting point,in-frame deletions of each of the genes in the asb locus (asbABCDEF) wereconstructed. The individual mutations resulted in complete abrogation ofpetrobactin biosynthesis when strains were grown on iron-depleted medium.However, in vitro analysis showed that each asb mutant grew to a very limitedextent as vegetative cells in iron-depleted medium. In contrast, none of the B.anthracis asb mutant strains were able to outgrow from spores under the sameculture conditions. Provision of exogenous petrobactin was able to rescue thegrowth defect in each asb mutant strain. Taken together, these data providecompelling evidence that AsbA performs the penultimate step in the biosynthesisof petrobactin, involving condensation of 3,4-dihydroxybenzoyl spermidine withcitrate to form 95 60 61 62 63 3,4-dihydroxybenzoyl spermidinyl citrate. As a final step, thedata reveal that AsbB catalyzes condensation of a second molecule of3,4-dihydroxybenzoyl spermidine with 3,4-dihydroxybenzoyl spermidinyl citrate to form the mature siderophore. This work sets the stage for detailed biochemicalstudies with this unique acyl carrier protein-dependent, nonribosomal peptidesynthetase-independent biosynthetic system.PMCID: PMC1855748PMID: 17189355 [PubMed - indexed for MEDLINE] 159. J Bacteriol. 2007 Mar;189(6):2401-10. Epub 2006 Dec 15.The timing of cotE expression affects Bacillus subtilis spore coat morphology butnot lysozyme resistance.Costa T(1), Serrano M, Steil L, Völker U, Moran CP Jr, Henriques AO.Author information: (1)Instituto de Tecnologia Quimica e Biológica, Universidade Nova de Lisboa, Avenidada República, Apartado 127, 2781-901 Oeiras, Portugal.The synthesis of structural components and morphogenetic factors required for theassembly of the Bacillus subtilis spore coat is governed by a mothercell-specific transcriptional cascade. The first two temporal classes of geneexpression, which involve RNA polymerase sigma sigma(E) factor and the ancillary regulators GerR and SpoIIID, are deployed prior to engulfment of the prespore by the mother cell. The two last classes rely on sigma(K), whose activation follows engulfment completion, and GerE. The cotE gene codes for a morphogenetic protein essential for the assembly of the outer coat layer and spore resistance tolysozyme. cotE is expressed first from a sigma(E)-dependent promoter and, in asecond stage, from a promoter that additionally requires SpoIIID and that remainsactive under sigma(K) control. CotE localizes prior to engulfment completionclose to the surface of the developing spore, but formation of the outer coat is a late, sigma(K)-controlled event. We have transplanted cotE to progressivelylater classes of mother cell gene expression. This created an early class ofmutants in which cotE is expressed prior to engulfment completion and a lateclass in which expression of cotE follows the complete engulfment of theprespore. Mutants of the early class assemble a nearly normal outer coatstructure, whereas mutants of the late class do not. Hence, the early expression of CotE is essential for outer coat assembly. Surprisingly, however, all mutants were fully resistant to lysozyme. The results suggest that CotE has geneticallyseparable functions in spore resistance to lysozyme and spore outer coatassembly.PMCID: PMC1899386PMID: 17172339 [PubMed - indexed for MEDLINE] 160. Biotechnol Appl Biochem. 2007 Mar;46(Pt 3):169-78.Bacillus minimum genome factory: effective utilization of microbial genomeinformation.Ara K(1), Ozaki K, Nakamura K, Yamane K, Sekiguchi J, Ogasawara N.Author information: (1)Biological Science Laboratories, Kao Co., Ltd., 2606 Akabane, Ichikaimachi, Haga,Tochigi 321-3497, Japan. [email protected] 1997, the complete genomic DNA sequence of Bacillus subtilis (4.2 Mbp) wasdetermined and 4100 genes were identified [Kunst, Ogasawara, Moszer, Albertini,Alloni, Azevedo, Bertero, Bessieres, Bolotin, Borchert, S. et al. (1997) Nature90, 249-256]. In addition, B. subtilis, which shows an excellent ability tosecrete proteins (enzymes) and antibiotics in large quantities outside the cell, plays an important role in industrial and medical fields. It is necessary toclarify the genes involved in the production of compounds by understanding thenetwork of these 4100 genes and the proceeding analysis of genes of unknownfunctions. In promoting such a study, it is expected that the regulatory systemof B. subtilis can be simplified by the creation of a Bacillus strain with areduced genome by discriminating genes unnecessary for the production of proteinsfrom essential genes, and deleting as many of these unnecessary genes aspossible, which may help to understand this complex network of genes. We havepreviously distinguished essential and non-essential genes by evaluating thegrowth and enzyme-producing properties of strains of B. subtilis in which about3000 genes (except 271 essential genes) have been disrupted or deleted singly,and have successfully utilized the findings from these studies in creating theMG1M strain with an approx. 1 Mbp deletion by serially deleting 17 unnecessaryregions from the genome. This strain showed slightly reduced growth inenzyme-production medium, but no marked morphological changes. Moreover, weconfirmed that the MG1M strain had cellulase and protease productivity comparablewith that of the B. subtilis 168 strain, thus demonstrating that genome reductiondoes not contribute to a negative influence on enzyme productivity.PMID: 17115975 [PubMed - indexed for MEDLINE] 161. J Comput Biol. 2006 Oct;13(8):1477-88.A compression-based approach for coding sequences identification. I. Application to prokaryotic genomes.Menconi G(1), Marangoni R.Author information: (1)Dipartimento di Matematica Applicata, Università di Pisa, Italia.Most of the gene prediction algorithms for prokaryotes are based on Hidden MarkovModels or similar machine-learning approaches, which imply the optimization of a high number of parameters. The present paper presents a novel method for theclassification of coding and non-coding regions in prokaryotic genomes, based on a suitably defined compression index of a DNA sequence. The main features of thisnew method are the non-parametric logic and the costruction of a dictionary ofwords extracted from the sequences. These dictionaries can be very useful toperform further analyses on the genomic sequences themselves. The proposedapproach has been applied on some prokaryotic complete genomes, obtaining optimalscores of correctly recognized coding and non-coding regions. Severalfalse-positive and false-negative cases have been investigated in detail, whichhave revealed that this approach can fail in the presence of highly structuredcoding regions (e.g., genes coding for modular proteins) or quasi-randomnon-coding regions (e.g., regions hosting non-functional fragments of copies offunctional genes; regions hosting promoters or other protein-binding sequences). We perform an overall comparison with other gene-finder software, since at thisstep we are not interested in building another gene-finder system, but only inexploring the possibility of the suggested approach.PMID: 17061923 [PubMed - indexed for MEDLINE] 162. J Bacteriol. 2007 Jan;189(1):52-64. Epub 2006 Oct 13.Complete sequence analysis of novel plasmids from emetic and perio- 96 64 65 66 dontal Bacilluscereus isolates reveals a common evolutionary history among the B. cereus-groupplasmids, including Bacillus anthracis pXO1.Rasko DA(1), Rosovitz MJ, Økstad OA, Fouts DE, Jiang L, Cer RZ, Kolstø AB, GillSR, Ravel J.Author information: (1)The Institute for Genomic Research, 9712 Medical Center Drive, Rockville,Maryland 20850, USA. [email protected] plasmids of the members of the Bacillus cereus sensu lato group of organisms are essential in defining the phenotypic traits associated with pathogenesis and ecology. For example, Bacillus anthracis contains two plasmids, pXO1 and pXO2,encoding toxin production and encapsulation, respectively, that define thisspecies pathogenic potential, whereas the presence of a Bt toxin-encoding plasmiddefines Bacillus thuringiensis isolates. In this study the plasmids from B.cereus isolates that produce emetic toxin or are linked to periodontal diseasewere sequenced and analyzed. Two periodontal isolates examined contained almostidentical approximately 272-kb plasmids, named pPER272. The emetictoxin-producing isolate contained one approximately 270-kb plasmid, namedpCER270, encoding the cereulide biosynthesis gene cluster. Comparative sequenceanalyses of these B. cereus plasmids revealed a high degree of sequencesimilarity to the B. anthracis pXO1 plasmid, especially in a putative replicationregion. These plasmids form a newly defined group of pXO1-like plasmids. However,these novel plasmids do not contain the pXO1 pathogenicity island, which in each instance is replaced by plasmid specific DNA. Plasmids pCER270 and pPER272 share regions that are not found in any other pXO1-like plasmids. Evolutionary studies suggest that these plasmids are more closely related to each other than to other identified B. cereus plasmids. Screening of a population of B. cereus groupisolates revealed that pXO1-like plasmids are more often found in associationwith clinical isolates. This study demonstrates that the pXO1-like plasmids maydefine pathogenic B. cereus isolates in the same way that pXO1 and pXO2 definethe B. anthracis species.PMCID: PMC1797222PMID: 17041058 [PubMed - indexed for MEDLINE] 163. Appl Microbiol Biotechnol. 2006 Dec;73(3):559-66. Epub 2006 Sep 15.Expression and characterization of a thermostable sarcosine oxidase (SOX) fromBacillus sp. in Escherichia coli.Guo K(1), Ma X, Sun G, Zhao Y, Li X, Zhao W, Kai L.Author information: (1)College of Life Sciences, Zhejiang University, No. 268 , Kaixuan Road, Hangzhou310029, People's Republic of China.A heat-stable sarcosine oxidase produced by Bacillus sp. BSD-8 (SOX) had beenstudied and its complete gene sequence, which contained 1,164 bp nucleotides and encoded a protein of 387 amino acids, was obtained by DNA Walking method. The soxgene was cloned and functionally overexpressed in E. coli and the recombinant SOX(rSOX) was purified to homogeneity, its properties was studied and compared with the wild type of SOX. The rSOX as well as SOX was stable at 60 degrees C and atpH 7.0 approximately 10.0, respectively. The optimal temperature for this enzyme was 60 degrees C and at pH 8.5, it showed its highest activity. The Km and Kcatof the enzyme was 3.1 mM and 20.3/s, respectively. The difference between theproperties of the SOX and rSOX was that the SOX contained noncovalent FAD,whereas the rSOX contained covalent FAD. The study also showed that an increased number of alanine residues in the rSOX might have some contribution in theenzymatic thermostability.PMID: 16977470 [PubMed indexed for MEDLINE] 164. J Biomol Struct Dyn. 2006 Oct;24(2):189-202.Anticodons, frameshifts, and hidden periodicities in tRNA sequences.Chechetkin VR(1), Lobzin VV.Author information: (1)Troitsk Institute of Innovation and Thermonuclear Investigations (TRINITI),Theoretical Department of Division for Perspective Investigations, 142190Troitsk, Moscow Region, Russia. [email protected] analysis of the short-range periodicities for the complete set ofsequences coding for tRNA genes in genome of Bacillus subtilis proves thatperiodicities with periods p = 2, 3, 4, and 6 sites are the inherent propertiesof tRNAs. The related periodicities should be understood in a broad statisticalsense and their identifying needs the elaborate statistical methods. To improvethe statistics, the analysis of significant periodicities was performed for thebinary R-Y, S-W, and K-M sequences. Generally, such short-range periodicities areproduced via biased positioning of particular nucleotides rather than via thetandem multiplication and subsequent modifications of repeats, though the latter mechanism may also be realized. Quasi-coherently piercing long segments of tRNA, the short-range periodicities create the effective long-range structural couplingbetween the acceptor stem and the anticodon loop and may participate in themechanisms of molecular recognition. The periodicities with p = 2 and 4 providethe natural ground for the translation with spontaneous or programmedframeshifting and are present in tRNAs decoding the most frameshift-prone codons.The observation of short-range periodicities suggests that the mechanisms ofamino-acylation of tRNAs and codon-anticodon pairing are not independent. Theirstudy may also provide the important information related to the origin andevolution of the genetic code.PMID: 16928142 [PubMed - indexed for MEDLINE] 165. Biofizika. 2006 Jul-Aug;51(4):656-60.[InterPro as a new tool for whole genome analysis. A comparative analysis ofMycobacterium tuberculosis, Bacillus subtilis and Escherichia coli as a casestudy].[Article in Russian]Mulder N, Fleischmann W, Kanapin A, Arwailer R.InterPro was developed as a new integrated documentation resource for proteinfamilies, domains and functional sites to rationalize the complementary effortsof the PROSITE, PRINTS, Pfam and ProDom database projects and has applications incomputational functional classification of newly determined sequences lackingbiochemical characterization and in comparative genome analysis. InterProcontains over 3500 entries, with more than 1000000 hits in SWISS-PROT and TrEMBL.The database is accessible for text- and sequence-based searches athttp://www.ebi.ac.uk/interpro/. InterPro was used for whole proteome analysis of the pathogenic microorganism, Mycobacterium tuberculosis, and comparison with thepredicted protein coding sequences of the complete genomes of Bacillus subtilisand Escherichia coli. 64.8% of the M. tuberculosis proteins in the proteomematched InterPro entries, 97 67 68 69 70 and these could be classified according to function.The comparison with B. subtilis and E. coli provided information on the mostcommon protein families and domains, and the most highly represented families in each organism. InterPro thus provides a useful tool for global views of wholeproteomes and their compositions.PMID: 16909843 [PubMed - indexed for MEDLINE] 166. Gene. 2006 Nov 1;382:71-8. Epub 2006 Jul 5.Sporulation-specific expression of the yvgW (cadA) gene and the effect ofblockage on spore properties in Bacillus subtilis.Irigül O(1), Yazgan-Karataş A.Author information: (1)Istanbul Technical University, Department of Molecular Biology and Genetics,Maslak, 34469 Istanbul, Turkey.The yvgW gene of Bacillus subtilis has been reported to encode a product whichresembles CPx-type ATPase having a function related to Cd2+ and Zn2+ resistancethrough efflux of this metal. We recently showed that yvgW gene product is alsoimportant for sporulation in B. subtilis. The present study was focused on thefunctional characterization of yvgW in the sporulation process of B. subtilis.The analysis of yvgW expression showed that a significant expression took placeduring the late stage of sporulation (T5-T8). The deletion of spoIIAC and spoIIGBgenes, encoding for sigmaF and sigmaE, respectively, resulted in the completeelimination of yvgW-lacZ expression while the deletion of the spoIIIG coding for sigmaG decreased the yvgW-lacZ expression to only 37% that of the wild typelevel. In contrast, the deletion of spoIVCB gene coding for sigmaK had nosignificant effects on the yvgW-lacZ expression. Transcription initiation site ofyvgW during sporulation was determined by 5'-RACE-PCR, indicating that -10 and-35 sequences exhibited very good homology with the consensus sequencesrecognized by RNA polymerase containing sigmaE. Moreover, through theconstruction of yvgWDelta537-1351::spc, yvgW mutant cells were investigated fortheir spore properties, such as their resistance profiles against heat,chloroform and lysozyme, pointing out that spores of the mutant cells showed highsensitivity to heat and chloroform, but resistance to lysozyme. The level ofdipicolinic acid was also significantly reduced to approximately 63% in yvgWspores as compared to wild type spores. Furthermore, the analyses of thenutrition-specific germination and outgrowth characteristics of the null mutantand the wild type cells revealed no defect in the initiation of yvgW sporegermination but they returned to vegetative state more slowly than the wild type spores in minimal medium.PMID: 16901659 [PubMed - indexed for MEDLINE] 167. Plasmid. 2007 Jan;57(1):44-54. Epub 2006 Aug 9.Complete nucleotide sequence of pBMB67, a 67-kb plasmid from Bacillusthuringiensis strain YBT-1520.Chao L(1), Qiyu B, Fuping S, Ming S, Dafang H, Guiming L, Ziniu Y.Author information: (1)State Key Laboratory of Agricultural Microbiology and National EngineeringResearch Center of Microbe Pesticides, Huazhong Agricultural University, Wuhan430070, China.The complete nucleotide sequence of a large (67kb) cryptic plasmid pBMB67 fromBacillus thuringiensis strain YBT-1520 was determined. Of the 74 predicted openreading frames (ORFs), 25 (34%) were assigned putative functions, 18 (24%)encoded conserved hypothetical proteins, and 31 (42%) had no homology to anygenes present in the current open databases. The ORFs with similar functions wereorganized in a modular structure; thus, the DNA sequence of pBMB67 could befunctionally divided into three modules, including a 39kb transfer regionencoding homologs of the Agrobacterium tumefaciens VirB/D4 system componentsVirB1, VirB4, VirB11, and VirD4, as well as homologs of Gram-positive conjugationproteins. We also found a potential operon that was analogous to the Rap-Phrcassettes from Bacillus subtilis, which are involved in cell-cell communicationand transcriptional regulation. Thus, we suggest that pBMB67 is likely to beimplicated in cell-cell signaling and plays a role in the regulation of severalcellular processes, with the production of exoprotease being one of thecandidates.PMID: 16901541 [PubMed - indexed for MEDLINE] 168. Mol Microbiol. 2006 Sep;61(6):1569-82. Epub 2006 Aug 8.Involvement of Clp protease activity in modulating the Bacillus subtilissigmawstress response.Zellmeier S(1), Schumann W, Wiegert T.Author information: (1)Institute of Genetics, University of Bayreuth, D-95440 Bayreuth, Germany.The induction of Bacillus subtilis genes controlled by the extracytoplasmicfunction alternative sigma factor sigmaW is strongly impaired in a strain deletedfor the ClpP peptidase gene and in a double knockout of the ClpX and ClpE ATPase genes. Truncated soluble forms of the sigmaW anti-sigma factor RsiW arestabilized in a clpP minus strain as revealed by the green fluorescent reporterprotein fused to the N-terminus of RsiW and by pulse-chase experiments. Conservedalanine residues are present in the transmembrane region of RsiW, and mutationsin these positions abolish induction of sigmaW-controlled genes. Followingalkaline shock, a truncated cytoplasmic form of RsiW is detectable in a strainexpressing a triple alanine mutant allele of rsiW. These data point to amechanism where the trans-membrane segment of RsiW contains a cryptic proteolytictag that is uncovered as a result of intramembrane proteolysis of RsiW by RasP(YluC). After RasP-clipped RsiW is detached from the membrane, this proteolytictag becomes crucial for the complete degradation of RsiW by cytoplasmic proteasesand the release of sigmaW. ClpXP plays a major role in this third proteolyticstep of stress-induced degradation of RsiW. Overexpression of SsrA-tagged greenfluorescent protein as a ClpXP substrate protein reduces alkali induction of asigmaW-controlled gene by a factor of about three, indicating that a titrationmechanism is able to tune the sigmaW-mediated stress response to the cellularstate.PMID: 16899079 [PubMed - indexed for MEDLINE] 169. Microbiol Res. 2008;163(1):39-50. Epub 2006 Jun 16.The expression of the serine proteinase gene of Bacillus intermedius in Bacillus subtilis.Sharipova M(1), Balaban N, Kayumov A, Kirillova Y, Mardanova A, Gabdrakhmanova L,Leshchinskaya I, Rudenskaya G, Akimkina T, Safina D, Demidyuk I, Kostrov S.Author information: (1)Department of Microbiology, Kazan State University, Kazan, [email protected] gene encoding for Bacillus intermedius serine proteinase was cloned and thecomplete nucleotide sequence was determined. Gene expression was explored in the protease-deficient strain Bacillus subtilis AJ73 98 71 72 73 during different stages ofgrowth. Catabolite repression involved in control of proteinase expression duringtransition state and onset of sporulation was not efficient at the latestationary phase. Salt stress leads to induction of serine proteinase production during B. subtilis AJ73(pCS9) post-exponential growth. Expression of proteinasein B. subtilis deg-mutants may be controlled by DegU regulator. B. subtilisspo0-mutants failed to accomplish B. intermedius proteinase production. Thesedata suggest complex network regulation of B. intermedius serine proteinaseexpression, including the action of spo0, degU, catabolite repression anddemonstrate changes in control of enzyme biosynthesis at different stages ofgrowth.PMID: 16782315 [PubMed - indexed for MEDLINE] 170. BMC Bioinformatics. 2006 Jun 13;7:296.Accelerating the reconstruction of genome-scale metabolic networks.Notebaart RA(1), van Enckevort FH, Francke C, Siezen RJ, Teusink B.Author information: (1)Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen,The Netherlands. [email protected]: The genomic information of a species allows for the genome-scalereconstruction of its metabolic capacity. Such a metabolic reconstruction givessupport to metabolic engineering, but also to integrative bioinformatics andvisualization. Sequence-based automatic reconstructions require extensive manual curation, which can be very time-consuming. Therefore, we present a method toaccelerate the time-consuming process of network reconstruction for a queryspecies. The method exploits the availability of well-curated metabolic networks and uses high-resolution predictions of gene equivalency between species,allowing the transfer of gene-reaction associations from curated networks.RESULTS: We have evaluated the method using Lactococcus lactis IL1403, for which a genome-scale metabolic network was published recently. We recovered most of thegene-reaction associations (i.e. 74 - 85%) which are incorporated in thepublished network. Moreover, we predicted over 200 additional genes to beassociated to reactions, including genes with unknown function, genes fortransporters and genes with specific metabolic reactions, which are goodcandidates for an extension to the previously published network. In a comparison of our developed method with the well-established approach Pathologic, wepredicted 186 additional genes to be associated to reactions. We also predicted arelatively high number of complete conserved protein complexes, which are derivedfrom curated metabolic networks, illustrating the potential predictive power ofour method for protein complexes.CONCLUSION: We show that our methodology can be applied to accelerate thereconstruction of genome-scale metabolic networks by taking optimal advantage of existing, manually curated networks. As orthology detection is the first step in the method, only the translated open reading frames (ORFs) of a newly sequencedgenome are necessary to reconstruct a metabolic network. When more manuallycurated metabolic networks will become available in the near future, theusefulness of our method in network prediction is likely to increase.PMCID: PMC1550432PMID: 16772023 [PubMed - indexed for MEDLINE] 171. BMC Genomics. 2006 May 24;7:126.Lactobacillus plantarum gene clusters encoding putative cell-surface proteincomplexes for carbohydrate utilization are conserved in specific gram-positivebacteria.Siezen R(1), Boekhorst J, Muscariello L, Molenaar D, Renckens B, Kleerebezem M.Author information: (1)Wageningen Centre for Food Sciences (WCFS), Wageningen, The [email protected]: Genomes of gram-positive bacteria encode many putative cell-surfaceproteins, of which the majority has no known function. From the rapidlyincreasing number of available genome sequences it has become apparent that many cell-surface proteins are conserved, and frequently encoded in gene clusters oroperons, suggesting common functions, and interactions of multiple components.RESULTS: A novel gene cluster encoding exclusively cell-surface proteins wasidentified, which is conserved in a subgroup of gram-positive bacteria. Each genecluster generally has one copy of four new gene families called cscA, cscB, cscC and cscD. Clusters encoding these cell-surface proteins were found only incomplete genomes of Lactobacillus plantarum, Lactobacillus sakei, Enterococcusfaecalis, Listeria innocua, Listeria monocytogenes, Lactococcus lactis ssp lactisand Bacillus cereus and in incomplete genomes of L. lactis ssp cremoris,Lactobacillus casei, Enterococcus faecium, Pediococcus pentosaceus,Lactobacillius brevis, Oenococcus oeni, Leuconostoc mesenteroides, and Bacillusthuringiensis. These genes are neither present in the genomes of streptococci,staphylococci and clostridia, nor in the Lactobacillus acidophilus group,suggesting a niche-specific distribution, possibly relating to association withplants. All encoded proteins have a signal peptide for secretion by theSec-dependent pathway, while some have cell-surface anchors, novel WxL domains,and putative domains for sugar binding and degradation. Transcriptome analysis inL. plantarum shows that the cscA-D genes are co-expressed, supporting theiroperon organization. Many gene clusters are significantly up-regulated in aglucose-grown, ccpA-mutant derivative of L. plantarum, suggesting catabolitecontrol. This is supported by the presence of predicted CRE-sites upstream orinside the up-regulated cscA-D gene clusters.CONCLUSION: We propose that the CscA, CscB, CscC and CscD proteins formcell-surface protein complexes and play a role in carbon source acquisition.Primary occurrence in plant-associated gram-positive bacteria suggests a possiblerole in degradation and utilization of plant oligo- or poly-saccharides.PMCID: PMC1534035PMID: 16723015 [PubMed - indexed for MEDLINE] 172. J Bacteriol. 2006 Jun;188(11):4024-36.Structural and functional characterization of three polyketide synthase geneclusters in Bacillus amyloliquefaciens FZB 42.Chen XH(1), Vater J, Piel J, Franke P, Scholz R, Schneider K, Koumoutsi A,Hitzeroth G, Grammel N, Strittmatter AW, Gottschalk G, Süssmuth RD, Borriss R.Author information: (1)Institut für Biologie, AG Bakteriengenetik, Humboldt-Universität Berlin,Chausseestrasse 115, D-10115 Berlin, Germany.Although bacterial polyketides are of considerable biomedical interest, themolecular biology of polyketide biosynthesis in Bacillus spp., one of the richestbacterial sources of bioactive natural products, remains largely unexplored. Herewe assign for the first time complete polyketide synthase (PKS) gene clusters to Bacillus antibiotics. Three giant modular PKS systems of thetrans-acyltransferase type were identified in Bacillus amyloliquefaciens 99 74 75 76 FZB 42. One of them, pks1, is an ortholog of the pksX operon with a previously unknownfunction in the sequenced model strain Bacillus subtilis 168, while the pks2 and pks3 clusters are novel gene clusters. Cassette mutagenesis combined withadvanced mass spectrometric techniques such as matrix-assisted laser desorptionionization-time of flight mass spectrometry and liquidchromatography-electrospray ionization mass spectrometry revealed that the pks1(bae) and pks3 (dif) gene clusters encode the biosynthesis of the polyeneantibiotics bacillaene and difficidin or oxydifficidin, respectively. Inaddition, B. subtilis OKB105 (pheA sfp(0)), a transformant of the B. subtilis 168derivative JH642, was shown to produce bacillaene, demonstrating that the pksXgene cluster directs the synthesis of that polyketide. The GenBank accessionnumbers for gene clusters pks1(bae), pks2, and pks3(dif) are AJ 634060.2, AJ6340601.2, and AJ 6340602.2, respectively.PMCID: PMC1482889PMID: 16707694 [PubMed - indexed for MEDLINE] 173. BMC Bioinformatics. 2006 May 5;7:248.Promoter prediction and annotation of microbial genomes based on DNA sequence andstructural responses to superhelical stress.Wang H(1), Benham CJ.Author information: (1)Genome Center, University of California, Davis, CA 95616, USA. [email protected]: In our previous studies, we found that the sites in prokaryoticgenomes which are most susceptible to duplex destabilization under the negativesuperhelical stresses that occur in vivo are statistically highly significantlyassociated with intergenic regions that are known or inferred to containpromoters. In this report we investigate how this structural property, eitheralone or together with other structural and sequence attributes, may be used tosearch prokaryotic genomes for promoters.RESULTS: We show that the propensity for stress-induced DNA duplexdestabilization (SIDD) is closely associated with specific promoter regions. The extent of destabilization in promoter-containing regions is found to be bimodallydistributed. When compared with DNA curvature, deformability, thermostability or sequence motif scores within the -10 region, SIDD is found to be the mostinformative DNA property regarding promoter locations in the E. coli K12 genome. SIDD properties alone perform better at detecting promoter regions than otherprograms trained on this genome. Because this approach has a very low falsepositive rate, it can be used to predict with high confidence the subset ofpromoters that are strongly destabilized. When SIDD properties are combined with -10 motif scores in a linear classification function, they predict promoterregions with better than 80% accuracy. When these methods were tested withpromoter and non-promoter sequences from Bacillus subtilis, they achieved similaror higher accuracies. We also present a strictly SIDD-based predictor forannotating promoter sequences in complete microbial genomes.CONCLUSION: In this report we show that the propensity to undergo stress-induced duplex destabilization (SIDD) is a distinctive structural attribute of manyprokaryotic promoter sequences. We have developed methods to identify promotersequences in prokaryotic genomes that use SIDD either as a sole predictor or incombination with other DNA structural and sequence properties. Although thesemethods cannot predict all the promoter-containing regions in a genome, they dofind large sets of potential regions that have high probabilities of being truepositives. This approach could be especially valuable for annotating thosegenomes about which there is limited experimental data.PMCID: PMC1468432PMID: 16677393 [PubMed - indexed for MEDLINE] 174. J Bacteriol. 2006 Apr;188(8):3037-51.Detailed genomic analysis of the Wbeta and gamma phages infecting Bacillusanthracis: implications for evolution of environmental fitness and antibioticresistance.Schuch R(1), Fischetti VA.Author information: (1)Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY 10021, USA. [email protected] lysis has been an essential laboratory tool for rapidlyidentifying Bacillus anthracis for more than 40 years, relying on the gamma phagederivative of a Bacillus cereus prophage called W. The complete genomic sequencesof the temperate W phage, referred to as Wbeta, and its lytic variant gamma were determined and found to encode 53 open reading frames each, spanning 40,864 bpand 37,373 bp, respectively. Direct comparison of the genomes showed that gammaevolved through mutations at key loci controlling host recognition, lysogenicgrowth, and possibly host phenotypic modification. Included are a cluster ofpoint mutations at the gp14 tail fiber locus of gamma, encoding a protein that,when fused to green fluorescent protein, binds specifically to B. anthracis. Alarge 2,003-bp deletion was also identified at the gamma lysogeny module,explaining its shift from a temperate to a lytic lifestyle. Finally, evidence of recombination was observed at a dicistronic Wbeta locus, encoding putativebacterial cell surface-modifying proteins, replaced in gamma with a locus, likelyobtained from a B. anthracis prophage, encoding demonstrable fosfomycinresistance. Reverse transcriptase PCR analysis confirmed strong induction at the dicistronic Wbeta locus and at four other phage loci in B. anthracis and/or B.cereus lysogens. In all, this study represents the first genomic and functionaldescription of two historically important phages and is part of a broaderinvestigation into contributions of phage to the B. anthracis life cycle. Initialfindings suggest that lysogeny of B. anthracis promotes ecological adaptation,rather than virulence, as with other gram-positive pathogens.PMCID: PMC1446989PMID: 16585764 [PubMed - indexed for MEDLINE] 175. J Immunol. 2006 Apr 15;176(8):5078-83.Human complete Stat-1 deficiency is associated with defective type I and II IFNresponses in vitro but immunity to some low virulence viruses in vivo.Chapgier A(1), Wynn RF, Jouanguy E, Filipe-Santos O, Zhang S, Feinberg J, HawkinsK, Casanova JL, Arkwright PD.Author information: (1)Laboratoire de Génétique Humaine des Maladies Infectieuses, Université de ParisRené Descartes-Institut National de la Santé et de la Recherche Médicale, UnitéMixte de Recherche R550, Faculté de Médecine Necker-Enfants Malades, Paris,France.The autosomal recessive form of human complete Stat-1 deficiency is a raredisorder, thus far reported in two unrelated patients, both of whom developeddisseminated bacillus Calmette-Guérin (BCG) and subsequently died of viralillnesses before detailed studies of the condition could be performed. It isassociated with impaired cellular responses to both IFN-gamma and IFN-alphabetavia Stat-1-containing complexes. We describe a third patient with 100 77 78 79 complete Stat-1deficiency and disseminated BCG infection, who died 3 mo after bone marrowtransplantation. The patient's EBV-transformed B cells did not express Stat-1protein and did not activate Stat-1-containing transcription factors. We alsoreport the ex vivo responses of a Stat-1-deficient patient's fresh blood cells toIFN-gamma and the in vitro responses of a SV40-transformed fibroblastic cell lineto IFN-gamma and IFN-alphabeta. There was no response to IFN-gamma in terms ofIL-12 production and HLA class II induction, accounting for vulnerability to BCG.Moreover, IFN-alphabeta did not suppress HSV and vesicular stomatitis virusreplication in fibroblasts, although in vivo the patient was able to successfullyclear at least some viruses. This study broadens our understanding of completeStat-1 deficiency, a severe form of innate immunodeficiency. Stat-1 deficiencyshould be suspected in children with severe infections, notably but notexclusively patients with mycobacterial or viral diseases.PMID: 16585605 [PubMed - indexed for MEDLINE] 176. BMC Microbiol. 2006 Mar 2;6:20.Cereulide synthetase gene cluster from emetic Bacillus cereus: structure andlocation on a mega virulence plasmid related to Bacillus anthracis toxin plasmid pXO1.Ehling-Schulz M(1), Fricker M, Grallert H, Rieck P, Wagner M, Scherer S.Author information: (1)Lehrstuhl für Mikrobielle Okologie, Department für BiowissenschaftlicheGrundlagen, WZW, Technische Universität München, Freising, [email protected]: Cereulide, a depsipeptide structurally related to valinomycin, isresponsible for the emetic type of gastrointestinal disease caused by Bacilluscereus. Recently, it has been shown that this toxin is produced by a nonribosomalpeptide synthetase (NRPS), but its exact genetic organization and biochemicalsynthesis is unknown.RESULTS: The complete sequence of the cereulide synthetase (ces) gene cluster,which encodes the enzymatic machinery required for the biosynthesis of cereulide,was dissected. The 24 kb ces gene cluster comprises 7 CDSs and includes, besides the typical NRPS genes like a phosphopantetheinyl transferase and two CDSsencoding enzyme modules for the activation and incorporation of monomers in thegrowing peptide chain, a CDS encoding a putative hydrolase in the upstream regionand an ABC transporter in the downstream part. The enzyme modules responsible forincorporation of the hydroxyl acids showed an unusual structure while the modulesresponsible for the activation of the amino acids Ala and Val showed the typical domain organization of NRPS. The ces gene locus is flanked by genetic regionswith high homology to virulence plasmids of B. cereus, Bacillus thuringiensis andBacillus anthracis. PFGE and Southern hybridization showed that the ces genes arerestricted to emetic B. cereus and indeed located on a 208 kb megaplasmid, which has high similarities to pXO1-like plasmids.CONCLUSION: The ces gene cluster that is located on a pXO1-like virulence plasmidrepresents, beside the insecticidal and the anthrax toxins, a third type of B.cereus group toxins encoded on megaplasmids. The ces genes are restricted toemetic toxin producers, but pXO1-like plasmids are also present in emetic-likestrains. These data might indicate the presence of an ancient plasmid in B.cereus which has acquired different virulence genes over time. Due to the unusualstructure of the hydroxyl acid incorporating enzyme modules of Ces, substantialbiochemical efforts will be required to dissect the complete biochemical pathway of cereulide synthesis.PMCID: PMC1459170PMID: 16512902 [PubMed - indexed for MEDLINE] 177. Mikrobiol Z. 2005 Nov-Dec;67(6):12-23.[Polymorphism of nonribosomal polypeptide synthetase genes in representatives of the Bacillus genus].[Article in Russian]Reva ON.Polypeptide antibiotics are synthesized by Bacillus under control of nonribosomalpolypeptide synthetases (NRPS). NRPS genes comprise the sequences of functionalmodules, each being responsible for incorporation of a certain amino acid to the synthesized oligopeptide. Dinucleotide frequency profiles calculated for DNAloci, covering the functional subunits of NRPS genes, were often observed to besignificantly distant from those determined for the complete genome of thestrain-producer, that suggests a possibility of horizontal transferring of theNRPS modules between microorganisms. A comparative analysis of the amino acidsequences of NRPS modules and statistical analysis of oligonucleotide usagefrequencies allows following the pathway of evolution of genes controllingbiosynthesis of antibiotics in Bacillus. A set of primers has been developed for genotyping of Bacillus strains with the purpose to identify producers of newpolypeptide antibiotics among environmental isolates.PMID: 16493881 [PubMed - indexed for MEDLINE] 178. Pest Manag Sci. 2006 Feb;62(2):178-87.Regeneration of sugarcane elite breeding lines and engineering of stem borerresistance.Weng LX(1), Deng H, Xu JL, Li Q, Wang LH, Jiang Z, Zhang HB, Li Q, Zhang LH.Author information: (1)Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore138673.Five elite sugarcane breeding lines were tested for efficiency in embryogenesisand plant regeneration. All of them produced regenerative embryogenic calli butwith varied efficiencies. To engineer strongly insect-resistant sugarcanes, theGC content of a truncated cry1Ac gene, which encodes the active region of Cry1Ac insecticidal delta-endotoxin, was increased from the original 37.4 to 47.5%following the sugarcane codon usage pattern. The synthetic cry1Ac gene (s-cry1Ac)was placed under the control of maize ubiquitin promoter and introduced bymicroprojectile bombardment into the embryogenic calli of sugarcane linesYT79-177 and ROC16. Southern blotting analysis showed that multicopies ofs-cry1Ac were integrated into the genomes of transgenic sugarcane lines.Immunoblotting analysis identified 18 transgenic lines expressing detectablelevels of s-Cry1Ac, which were estimated in the range of 1.8-10.0 ng mg(-1) totalsoluble proteins. Four transgenic and two parental lines were assayed forsugarcane stem borer resistance in leaf tissue feeding trials and greenhouseplant assays. The results showed that, while the untransformed control lines wereseverely damaged in both leaves and stems, the transgenic sugarcane linesexpressing high levels of s-Cry1Ac proteins were highly resistant to sugarcanestem borer attack, resulting in complete mortality of the inoculated insectswithin 1 week after inoculation.Copyright (c) 2006 Society of Chemical Industry.PMID: 16408322 [PubMed 101 80 81 82 83 - indexed for MEDLINE] 179. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D338-43.ICDS database: interrupted CoDing sequences in prokaryotic genomes.Perrodou E(1), Deshayes C, Muller J, Schaeffer C, Van Dorsselaer A, Ripp R, Poch O, Reyrat JM, Lecompte O.Author information: (1)Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et deBiologie Moléculaire et Cellulaire, CNRS/INSERM/ULP BP 163, 67404 Illkirch Cedex,France.Unrecognized frameshifts, in-frame stop codons and sequencing errors lead toInterrupted CoDing Sequence (ICDS) that can seriously affect all subsequent stepsof functional characterization, from in silico analysis to high-throughputproteomic projects. Here, we describe the Interrupted CoDing Sequence databasecontaining ICDS detected by a similarity-based approach in 80 completeprokaryotic genomes. ICDS can be retrieved by species browsing or similaritysearches via a web interface (http://www-bio3d-igbmc.u-strasbg.fr/ICDS/). Thedefinition of each interrupted gene is provided as well as the ICDS genomiclocalization with the surrounding sequence. Furthermore, to facilitate theexperimental characterization of ICDS, we propose optimized primers forre-sequencing purposes. The database will be regularly updated with additionaldata from ongoing sequenced genomes. Our strategy has been validated by threeindependent tests: (i) ICDS prediction on a benchmark of artificially createdframeshifts, (ii) comparison of predicted ICDS and results obtained from thecomparison of the two genomic sequences of Bacillus licheniformis strain ATCC14580 and (iii) re-sequencing of 25 predicted ICDS of the recently sequencedgenome of Mycobacterium smegmatis. This allows us to estimate the specificity andsensitivity (95 and 82%, respectively) of our program and the efficiency ofprimer determination.PMCID: PMC1347423PMID: 16381882 [PubMed - indexed for MEDLINE] 180. Infect Immun. 2006 Jan;74(1):682-93.Genome engineering in Bacillus anthracis using Cre recombinase.Pomerantsev AP(1), Sitaraman R, Galloway CR, Kivovich V, Leppla SH.Author information: (1)Bacterial Toxins and Therapeutics Section, National Institute of Allergy andInfectious Diseases, National Institutes of Health, Bethesda, MD 20892-4349, USA.Genome engineering is a powerful method for the study of bacterial virulence.With the availability of the complete genomic sequence of Bacillus anthracis, it is now possible to inactivate or delete selected genes of interest. However, manycurrent methods for disrupting or deleting more than one gene require use ofmultiple antibiotic resistance determinants. In this report we used an approachthat temporarily inserts an antibiotic resistance marker into a selected regionof the genome and subsequently removes it, leaving the target region (a singlegene or a larger genomic segment) permanently mutated. For this purpose, aspectinomycin resistance cassette flanked by bacteriophage P1 loxP sites orientedas direct repeats was inserted within a selected gene. After identification ofstrains having the spectinomycin cassette inserted by a double-crossover event, athermo-sensitive plasmid expressing Cre recombinase was introduced at thepermissive temperature. Cre recombinase action at the loxP sites excised thespectinomycin marker, leaving a single loxP site within the targeted gene orgenomic segment. The Cre-expressing plasmid was then removed by growth at therestrictive temperature. The procedure could then be repeated to mutateadditional genes. In this way, we sequentially mutated two pairs of genes: pepMand spo0A, and mcrB and mrr. Furthermore, loxP sites introduced at distant genes could be recombined by Cre recombinase to cause deletion of large interveningregions. In this way, we deleted the capBCAD region of the pXO2 plasmid and theentire 30 kb of chromosomal DNA between the mcrB and mrr genes, and in the lattercase we found that the 32 intervening open reading frames were not essential togrowth.PMCID: PMC1346652PMID: 16369025 [PubMed - indexed for MEDLINE] 181. J Bacteriol. 2005 Nov;187(22):7753-64.Assembly and function of a spore coat-associated transglutaminase of Bacillussubtilis.Zilhão R(1), Isticato R, Martins LO, Steil L, Völker U, Ricca E, Moran CP Jr,Henriques AO.Author information: (1)Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras Codex, Portugal.The assembly of a multiprotein coat around the Bacillus subtilis spore confersresistance to lytic enzymes and noxious chemicals and ensures normal germination.Part of the coat is cross-linked and resistant to solubilization. The coatcontains epsilon-(gamma-glutamyl)lysyl cross-links, and the expression of thegene (tgl) for a spore-associated transglutaminase was shown before to berequired for the cross-linking of coat protein GerQ. Here, we have investigatedthe assembly and function of Tgl. We found that Tgl associates, albeit atsomewhat reduced levels, with the coats of mutants that are unable to assemblethe outer coat (cotE), that are missing the inner coat and with a greatly alteredouter coat (gerE), or that are lacking discernible inner and outer coatstructures (cotE gerE double mutant). This suggests that Tgl is present atvarious levels within the coat lattice. The assembly of Tgl occurs independently of its own activity, as a single amino acid substitution of a cysteine to analanine (C116A) at the active site of Tgl does not affect its accumulation orassembly. However, like a tgl insertional mutation, the tglC116A allele causesincreased extractability of polypeptides of about 40, 28, and 16 kDa in addition to GerQ (20 kDa) and affects the structural integrity of the coat. We show thatmost Tgl is assembled onto the spore surface soon after its synthesis in themother cell under sigma(K) control but that the complete insolubilization of atleast two of the Tgl-controlled polypeptides occurs several hours later. We also show that a multicopy allele of tgl causes increased assembly of Tgl and affects the assembly, structure, and functional properties of the coat.PMCID: PMC1280291PMID: 16267299 [PubMed - indexed for MEDLINE] 182. J Bacteriol. 2005 Nov;187(22):7727-37.Genetic analysis of transfer-related regions of the vancomycin resistanceEnterococcus conjugative plasmid pHTbeta: identification of oriT and a putativerelaxase gene.Tomita H(1), Ike Y.Author information: (1)Department of Bacteriology and Bacterial Infection Control, Gunma UniversityGraduate School of Medicine, Maebashi, Japan. [email protected] pHT plasmids pHTalpha (65.9 kbp), pHTbeta (63.7 kbp), and pHTgamma (66.5 kbp)are highly 102 84 85 conjugative pheromone-independent pMG1-like plasmids that carryTn1546-like transposons encoding vancomycin resistance. pHTbeta is the prototype plasmid, and the pHTalpha and pHTgamma plasmids are derivatives of the insertion into pHTbeta of an IS232-like (2.2 kbp) element and a group II intron (2.8 kbp), respectively. The complete nucleotide sequence of the pHTbeta plasmid wasdetermined and, with the exception of the Tn1546-like insertion (10,851 bp), was found to be 52,890 bp. Sixty-one open reading frames (ORFs) having the sametranscript orientation were identified. A homology search revealed that 22 of thepHTbeta (pHT) plasmid ORFs showed similarities to the ORFs identified on the pXO2plasmid (96.2 kbp), which is the virulence plasmid essential for capsuleformation by Bacillus anthracis; however, the functions of most of the ORFsremain unknown. Most other ORFs did not show any significant homology to reportedgenes for which functions have been analyzed. To investigate the highly efficienttransfer mechanism of the pHT plasmid, mutations with 174 unique insertions oftransposon Tn917-lac insertion mutants of pHTbeta were obtained. Of the 174derivatives, 92 showed decrease or loss in transfer frequency, and 74 showednormal transfer frequency and LacZ expression. Eight derivatives showed normaltransfer and no LacZ expression. Inserts within the 174 derivatives were mappedto 124 different sites on pHTbeta. The Tn917-lac insertions which resulted inaltered transfer frequency mapped to three separate regions designated I, II, andIII, which were separated by segments in which insertions of Tn917-lac did notaffect transfer. There was no region homologous to the previously reported oriTsequences in the pHT plasmid. The oriT was cloned by selection for the ability tomobilize the vector plasmid pAM401. The oriT region resided in a noncoding region(192 bp) between ORF31 and ORF32 and contained three direct repeat sequences and two inverted repeat sequences. ORF34, encoding a 506-amino-acid protein which waslocated downstream of the oriT region, contains the three conserved motifs (I to III) of the DNA relaxase/nickase of mobile plasmids. The transfer abilities ofthe Tn917-lac-insertion mutants of ORF34 or a mutant of ORF34 with an in-framemotif III deletion were completely abolished. The sequence of the oriT region andthe deduced relaxase/nickase protein of ORF34 showed no significant similarity tothe oriT and relaxase/nickase of other conjugative plasmids, respectively. Theputative relaxase/nickase protein of ORF34 could be classified as a new member ofthe MOB(MG) family.PMCID: PMC1280310PMID: 16267297 [PubMed - indexed for MEDLINE] 183. Proteomics. 2005 Nov;5(17):4472-82.Proteomics-based consensus prediction of protein retention in a bacterialmembrane.Tjalsma H(1), van Dijl JM.Author information: (1)Department of Clinical Chemistry, Radboud University Nijmegen - Medical Centre,The Netherlands. [email protected] availability of complete bacterial genome sequences allows proteome-widepredictions of exported proteins that are potentially retained in the cytoplasmicmembranes of the corresponding organisms. In practice, however, major problemsare encountered with the computer-assisted distinction between (Sec-type) signal peptides that direct exported proteins into the growth medium and lipoproteinsignal peptides or amino-terminal membrane anchors that cause protein retentionin the membrane. In the present studies, which were aimed at improving methods topredict protein retention in the bacterial cytoplasmic membrane, we have comparedsets of membrane-attached and extracellular proteins of Bacillus subtilis thatwere recently identified through proteomics approaches. The results showed thatthree classes of membrane-attached proteins can be distinguished. Two classesinclude 43 lipoproteins and 48 proteins with an amino-terminal transmembranesegment, respectively. Remarkably, a third class includes 31 proteins that remainmembrane-retained despite the presence of typical Sec-type signal peptides withconsensus signal peptidase recognition sites. This unprecedented findingindicates that unknown mechanisms are involved in membrane retention of thisclass of proteins. A further novelty is a consensus sequence indicative forrelease of certain lipoproteins from the membrane by proteolytic shaving.Finally, using non-overlapping sets of secreted and membrane-retained proteins,the accuracy of different signal peptide prediction algorithms was assessed.Accuracy for the prediction of protein retention in the membrane was increased to82% using a majority-vote approach. Our findings provide important leads forfuture identification of surface proteins from pathogenic bacteria, which areattractive candidate infection markers and potential targets for drugs orvaccines.PMID: 16220534 [PubMed - indexed for MEDLINE] 184. Transgenic Res. 2005 Jun;14(3):261-72.Two different Bacillus thuringiensis toxin genes confer resistance to beetarmyworm (Spodoptera exigua Hübner) in transgenic Bt-shallots (Allium cepa L.).Zheng SJ(1), Henken B, de Maagd RA, Purwito A, Krens FA, Kik C.Author information: (1)Plant Research International, Wageningen University and Research Center, P O Box 16, 6700 AA Wageningen, The Netherlands.Agrobacterium-mediated genetic transformation was applied to produce beetarmyworm (Spodoptera exigua Hübner) resistant tropical shallots (Allium cepa L.group Aggregatum). A cry1Ca or a H04 hybrid gene from Bacillus thuringiensis,driven by the chrysanthemum ribulose-1,5-bisphosphate carboxylase/oxygenase smallsubunit (Rubisco SSU) promoter, along with the hygromycin phosphotransferase gene(hpt) driven by the CaMV 35S promoter, was employed for genetic transformation.An average transformation frequency of 3.68% was obtained from two shallotcultivars, Tropix and Kuning. After transfer of the in vitro plants to thegreenhouse 69% of the cry1Ca and 39% of the H04 transgenic shallots survived the first half year. After one year of cultivation in the greenhouse the remainingcry1Ca and H04 transgenic plants grew vigorously and had a normal bulb formation,although the cry1Ca transgenic plants (and controls) had darker green leavescompared to their H04 counterparts. Standard PCR, adaptor ligation PCR andSouthern analyses confirmed the integration of T-DNA into the shallot genome.Northern blot and ELISA analyses revealed expression of the cry1Ca or H04 gene inthe transgenic plants. The amount of Cry1Ca expressed in transgenic plants washigher than the expression levels of H04 (0.39 vs. 0.16% of the total solubleleaf proteins, respectively). There was a 103 86 87 88 89 good correlation between proteinexpression and beet armyworm resistance. Cry1Ca or H04 gene expression of atleast 0.22 or 0.08% of the total soluble protein in shallot leaves was sufficientto give a complete resistance against beet armyworm. This confirms earlierobservations that the H04 toxin is more toxic to S. exigua than the Cry1Ca toxin.The results from this study suggest that the cry1Ca and H04 transgenic shallotsdeveloped could be used for introducing resistance to beet armyworm in (sub)tropical shallot.PMID: 16145834 [PubMed - indexed for MEDLINE] 185. Plasmid. 2005 Sep;54(2):93-103. Epub 2005 Feb 17.Genetic relationship among Bacillus licheniformis rolling-circle-replicatingplasmids and complete nucleotide sequence of pBL63.1, an atypical replicon.Guglielmetti S(1), Mora D, Manachini PL, Parini C.Author information: (1)Department of Food Science and Microbiology, Industrial Microbiology Section,University of Milan, Via Celoria 2, 20133 Milan, Italy.The degree of biodiversity among Bacillus licheniformis plasmids and theirrelation to other Bacillus subtilis group plasmids has been evaluated. To attain this goal we surveyed the diversity and linkage of replication modules in acollection of 21 naturally occurring plasmids of B. licheniformis strains,isolated from different geographical areas. On the basis of rep gene sequenceanalysis it was possible to group the B. licheniformis plasmids rep genes in two main cluster. Comparison with known rep genes from Bacillusrolling-circle-replicating (RCR) plasmids revealed the presence in B.licheniformis plasmids of replication genes with a DNA sequence peculiar to B.licheniformis species together with rep genes with a very high sequencesimilarity to B. subtilis plasmids. Furthermore, the molecular organization of anatypical replicon, pBL63.1, was shown. This plasmid did not display anysignificant similarity with known Bacillus RCR plasmids. The complete nucleotide sequence evidenced a replication module with an unexpected similarity with Repproteins from RCR plasmids of bacterial species phylogenetically distantlyrelated to Bacillus. pBL63.1 represents an exception to the low-level diversityhypothesis among Bacillus RC replicons.PMID: 16122558 [PubMed indexed for MEDLINE] 186. Can J Microbiol. 2005 Feb;51(2):165-70.Expression of the cry11A gene of Bacillus thuringiensis ssp. israelensis inSaccharomyces cerevisiae.Quintana-Castro R(1), Ramírez-Suero M, Moreno-Sanz F, Ramírez-Lepe M.Author information: (1)UNIDA-Instituto Tecnológico de Veracruz, Veracruz, México.The complete cry11A region gene of Bacillus thuringiensis ssp. israelensis wasfused in frame to the 3' end of the GST gene under the control of theSaccharomyces cerevisiae HXK1 promoter. The fusion protein GST-cry11A wasexpressed in S. cerevisiae strain AMW13C+. The fusion gene GST-cry11A wasexpressed when yeast cells were grown on galactose and a nonfermentable mediumcontaining ethanol as carbon and energy source. When the cells were grown inglucose, mannose, fructose, or glycerol as carbon sources, the GST-cry11A genewas repressed. Thus, a regulated expression in accordance with the regulatoryactivity of the HXK1 gene promoter has been detected. The GST-cry11A fusionprotein was detected in the transformed yeasts as a soluble protein. The fusionprotein was purified by affinity chromatography using glutathione-Sepharosebeads. Cell-free extracts from transformed yeasts grown in ethanol-containingculture media showed insecticidal activity against third-instar Aedes aegyptilarvae. This insecticidal activity was increased about 4-fold when the purifiedfusion protein was assayed.PMID: 16091775 [PubMed - indexed for MEDLINE] 187. BMC Genomics. 2005 Jul 26;6:103.Conjugative plasmid pAW63 brings new insights into the genesis of the Bacillusanthracis virulence plasmid pXO2 and of the Bacillus thuringiensis plasmidpBT9727.Van der Auwera GA(1), Andrup L, Mahillon J.Author information: (1)Université Catholique de Louvain, Croix du Sud 2/12, B-1348 Louvain-la-Neuve,Belgium. [email protected]: Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis belongto the genetically close-knit Bacillus cereus sensu lato group, a family ofrod-shaped Gram-positive bacteria. pAW63 is the first conjugative plasmid fromthe B. cereus group to be completely sequenced.RESULTS: The 71,777 bp nucleotide sequence of pAW63 reveals a modular structure, including a 42 kb tra region encoding homologs of the Type IV secretion systemscomponents VirB11, VirB4 and VirD4, as well as homologs of Gram-positiveconjugation genes from Enterococcus, Lactococcus, Listeria, Streptococcus andStaphylococcus species. It also firmly establishes the existence of a commonbackbone between pAW63, pXO2 from Bacillus anthracis and pBT9727 from thepathogenic Bacillus thuringiensis serovar konkukian strain 97-27. The alignmentof these three plasmids highlights the presence of well conserved segments, incontrast to distinct regions of high sequence plasticity. The study of theirspecific differences has provided a three-point reference framework that can beexploited to formulate solid hypotheses concerning the functionalities and themolecular evolution of these three closely related plasmids. This has providedinsight into the chronology of their divergence, and led to the discovery of two Type II introns on pAW63, matching copies of the mobile element IS231L indifferent loci of pXO2 and pBT9727, and the identification on pXO2 of a 37 kbpathogenicity island (PAI) containing the anthrax capsule genes.CONCLUSION: The complete sequence determination of pAW63 has led to a functional map of the plasmid yielding insights into its conjugative apparatus, whichincludes T4SS-like components, as well as its resemblance to other large plasmidsof Gram-positive bacteria. Of particular interest is the extensive homologyshared between pAW63 and pXO2, the second virulence plasmid of B. anthracis, aswell as pBT9727 from the pathogenic strain B. thuringiensis serovar konkukianstrain 97-27.PMCID: PMC1196294PMID: 16042811 [PubMed - indexed for MEDLINE] 188. Plasmid. 2005 Nov;54(3):288-93. Epub 2005 Jul 22.Insights into the genetic organization of the Bacillus mycoides cryptic plasmids pDx14.2 and pSin9.7 deduced from their complete nucleotide sequence.Di Franco C(1), Santini T, Pisaneschi G, Beccari E.Author information: (1)Dipartimento di Genetica e Biologia Molecolare.Bacillus mycoides, a member of the Bacillus cereus group 104 90 91 92 of bacteria, can beeasily distinguished from close species because of colony shape, made byfilaments of cells, resembling fungal hyphae, curving clock- or counterclockwise depending on the strain. Two plasmids, one from a strain curving to the right(pDx14.2), the other from a strain curving to the left (pSin9.7), were sequenced and analyzed for gene content and replication mode. Rolling-circle replicationmodules and mobilization proteins were found, very similar to those of otherplasmids of the B. cereus group bacilli, mostly Bacillus thuringiensis living in the same ecosystem, suggesting active plasmid exchange in nature.PMID: 16040120 [PubMed - indexed for MEDLINE] 189. J Bacteriol. 2005 Aug;187(15):5437-51.Unusual group II introns in bacteria of the Bacillus cereus group.Tourasse NJ(1), Stabell FB, Reiter L, Kolstø AB.Author information: (1)School of Pharmacy, University of Oslo, PB 1068 Blindern, 0316 Oslo, Norway.A combination of sequence and structure analysis and reverse transcriptase PCRexperiments was used to characterize the group II introns in the complete genomesof two strains of the pathogen Bacillus cereus. While B. cereus ATCC 14579harbors a single intron element in the chromosome, B. cereus ATCC 10987 contains three introns in the chromosome and four in its 208-kb pBc10987 plasmid. The moststriking finding is the presence in B. cereus ATCC 10987 of an intron [B.c.I2(a)]located on the reverse strand of a gene encoding a putative cell surface protein which appears to be correlated to strains of clinical origin. Because of theopposite orientation of B.c.I2(a), the gene is disrupted. Even more striking isthat B.c.I2(a) splices out of an RNA transcript corresponding to the opposite DNAstrand. All other intragenic introns studied here are inserted in the sameorientation as their host genes and splice out of the mRNA in vivo, setting theflanking exons in frame. Noticeably, B.c.I3 in B. cereus ATCC 10987 representsthe first example of a group II intron entirely included within a conservedreplication gene, namely, the alpha subunit of DNA polymerase III. Anotherstriking finding is that the observed 3' splice site of B.c.I4 occurs 56 bp afterthe predicted end of the intron. This apparently unusual splicing mechanism maybe related to structural irregularities in the 3' terminus. Finally, we also showthat the intergenic introns of B. cereus ATCC 10987 are transcribed with theirupstream genes and do splice in vivo.PMCID: PMC1196009PMID: 16030238 [PubMed indexed for MEDLINE] 190. J Bacteriol. 2005 Aug;187(15):5166-78.Bacillus subtilis phosphorylated PhoP: direct activation of the E(sigma)A- andrepression of the E(sigma)E-responsive phoB-PS+V promoters during pho response.Abdel-Fattah WR(1), Chen Y, Eldakak A, Hulett FM.Author information: (1)Laboratory for Molecular Biology, Department of Biological Sciences, Universityof Illinois at Chicago, 900 S. Ashland Avenue (M/C 567), Chicago, IL 60607, USA.The phoB gene of Bacillus subtilis encodes an alkaline phosphatase (PhoB,formerly alkaline phosphatase III) that is expressed from separate promotersduring phosphate deprivation in a PhoP-PhoR-dependent manner and at stage two of sporulation under phosphate-sufficient conditions independent of PhoP-PhoR.Isogenic strains containing either the complete phoB promoter or individual phoB promoter fusions were used to assess expression from each promoter under bothinduction conditions. The phoB promoter responsible for expression duringsporulation, phoB-P(S), was expressed in a wild-type strain during phosphatedeprivation, but induction occurred >3 h later than induction of Pho regulongenes and the levels were approximately 50-fold lower than that observed for the PhoPR-dependent promoter, phoB-P(V). E(sigma)E was necessary and sufficient forP(S) expression in vitro. P(S) expression in a phoPR mutant strain was delayed 2 to 3 h compared to the expression in a wild-type strain, suggesting thatexpression or activation of sigma(E) is delayed in a phoPR mutant underphosphate-deficient conditions, an observation consistent with a role for PhoPRin spore development under these conditions. Phosphorylated PhoP (PhoPapproximately P) repressed P(S) in vitro via direct binding to the promoter, the first example of an E(sigma)E-responsive promoter that is repressed by PhoPapproximately P. Whereas either PhoP or PhoP approximately P in the presence ofE(sigma)A was sufficient to stimulate transcription from the phoB-P(V) promoterin vitro, roughly 10- and 17-fold-higher concentrations of PhoP than of PhoPapproximately P were required for P(V) promoter activation and maximal promoteractivity, respectively. The promoter for a second gene in the Pho regulon, ykoL, was also activated by elevated concentrations of unphosphorylated PhoP in vitro. However, because no Pho regulon gene expression was observed in vivo duringP(i)-replete growth and PhoP concentrations increased only threefold in vivoduring phoPR autoinduction, a role for unphosphorylated PhoP in Pho regulonactivation in vivo is not likely.PMCID: PMC1196004PMID: 16030210 [PubMed - indexed for MEDLINE] 191. J Bacteriol. 2005 Aug;187(15):5108-14.Transcriptional analysis of the Bacillus anthracis capsule regulators.Drysdale M(1), Bourgogne A, Koehler TM.Author information: (1)Department of Microbiology and Molecular Genetics, University of Texas-HoustonMedical School, 6431 Fannin St., MSB 1.206 Houston, TX 77030, USA.The poly-d-glutamic acid capsule of Bacillus anthracis is essential forvirulence. Control of capsule synthesis occurs at the level of transcription and involves positive regulation of the capsule biosynthetic operon capBCAD by aCO2/bicarbonate signal and three plasmid-borne regulators: atxA, acpA, and acpB. Although the molecular mechanism for control of cap transcription is unknown,atxA affects cap expression via positive control of acpA and acpB, two genes withpartial functional similarity. Transcriptional analyses of a genetically completestrain indicate that capB expression is several hundred-fold higher during growthin 5% CO2 compared to growth in air. atxA was expressed appreciably during growthin air and induced only 2.5-fold by CO2. In contrast, expression of acpA and acpBwas induced up to 23-fold and 59-fold, respectively, by CO2. The 5'-end mappingof gene transcripts revealed atxA-regulated and atxA-independent apparenttranscription start sites for capB, acpA, and acpB. Transcripts mapping to allatxA-regulated start sites were increased during growth in elevated CO2. The acpAgene has one atxA-regulated and one atxA-independent start site. acpB liesdownstream of capBCAD. A 105 93 94 95 96 single atxA-independent start site maps immediatelyupstream of acpB. atxA-mediated control of acpB appears to occur viatranscriptional read-through from atxA-dependent start sites 5' of capB. OneatxA-independent and two atxA-regulated start sites map upstream of capB.Transcription from the atxA-regulated start sites of capBCAD was reducedsignificantly in an acpA acpB double mutant but unaffected in mutants withdeletion of only acpA or acpB, in agreement with the current model for epistatic relationships between the regulators.PMCID: PMC1196023PMID: 16030203 [PubMed - indexed for MEDLINE] 192. BMC Bioinformatics. 2005 Jul 12;6:171.Systematic determination of the mosaic structure of bacterial genomes: speciesbackbone versus strain-specific loops.Chiapello H(1), Bourgait I, Sourivong F, Heuclin G, Gendrault-Jacquemard A, PetitMA, El Karoui M.Author information: (1)Mathématique, Informatique & Génome, INRA Domaine de Vilvert, 78352 Jouy-en-JosasCedex, France. [email protected]: Public databases now contain multitude of complete bacterial genomes,including several genomes of the same species. The available data offers newopportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recentanalyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specificsequences called loops.RESULTS: Here, we generalize this approach and propose a strategy that allowssystematic and non-biased genome segmentation based on multiple genomealignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization ofbacterial genomes. Segmentation results are available through a Web interfacepermitting functional analysis, extraction and visualization of thebackbone/loops structure of documented genomes. To illustrate the potential ofthis approach, we performed a precise analysis of the mosaic organization ofthree E. coli strains and functional characterization of the loops.CONCLUSION: The segmentation results including the backbone/loops structure of 13bacterial species genomes are new and available for use by the scientificcommunity at the URL: http://genome.jouy.inra.fr/mosaic.PMCID: PMC1187871PMID: 16011797 [PubMed - indexed for MEDLINE] 193. Microbiology. 2005 Jul;151(Pt 7):2323-30.Genetic characterization of the beta-glucuronidase enzyme from a human intestinalbacterium, Ruminococcus gnavus.Beaud D(1), Tailliez P, Anba-Mondoloni J.Author information: (1)Unité d'Ecologie et de Physiologie du Système Digestif, Institut National de laRecherche Agronomique, Domaine de Vilvert, 78352 Jouy-en-Josas, France.beta-Glucuronidase activity (encoded by the gus gene) has been characterized for the first time from Ruminococcus gnavus E1, an anaerobic bacterium belonging tothe dominant human gut microbiota. beta-Glucuronidase activity plays a major rolein the generation of toxic and carcinogenic metabolites in the large intestine,as well as in the absorption and enterohepatic circulation of many aglyconeresidues with protective effects, such as lignans, flavonoids, ceramide andglycyrrhetinic acid, that are liberated by the hydrolysis of the correspondingglucuronides. The complete nucleotide sequence of a 4537 bp DNA fragmentcontaining the beta-glucuronidase locus from R. gnavus E1 was determined. FiveORFs were detected on this fragment: three complete ORFs (ORF2, gus and ORF3) andtwo partial ORFs (ORF4 and ORF5). The products of ORF2 and ORF3 show strongsimilarities with many beta-glucoside permeases of the phosphoenolpyruvate :beta-glucoside phosphotransferase systems (PTSs), such as Escherichia coli BglC, Bacillus subtilis BglP and Bacillus halodurans PTS Enzyme II. The product of ORF5presents strong similarities with the amino-terminal domain of Clostridiumacetobutylicum beta-glucosidase (bglA). The gus gene product presentssimilarities with several known beta-glucuronidase enzymes, including those ofLactobacillus gasseri (69%), E. coli (61%), Clostridium perfringens (59%) andStaphylococcus aureus (58%). By complementing an E. coli strain in which the uidAgene encoding the enzyme was deleted, it was confirmed that the R. gnavus gusgene encodes the beta-glucuronidase enzyme. Moreover, it was found that the gusgene was transcribed as part of an operon that includes ORF2, ORF3 and ORF5.PMID: 16000722 [PubMed - indexed for MEDLINE] 194. Sheng Wu Gong Cheng Xue Bao. 2004 May;20(3):434-6.[Isolation of thermophilic bacteria Thermus sp. YBJ-1 and cloning of amylasegene].[Article in Chinese]Xiong PJ(1), Wen JJ.Author information: (1)The Key Laboratory of Marine Biotechnology, The Third Institute of Oceanography, SOA, Xiamen 361005, China.Thermophilic bacteria strain YBJ-1 was isolated from hot spring samples collectedfrom Yangbajing, Tibet. The 16sr DNA sequence of YBJ-1 (1511bp in length) shares 98% identity with that of Thermus scotoductus strain ITI-252T. The full-lengthORF of amylase gene of YBJ-1 (amyT) was amplified by PCR technique and clonedinto T-vector. The complete sequence of amyT is 1767bp in length, coding for 588 amino acids. The deduced amino acids share 99% similarity withalpha-cyclodextrinse of Bacillus sterothermophilus, 96% with maltogenic amylse ofThermus. sp IM6501, and 81% with neopullulanase of Bacillus sterothermophlus.PMID: 15971619 [PubMed - indexed for MEDLINE] 195. Biochim Biophys Acta. 2005 Aug 30;1725(1):35-46.Molecular analysis of the nitrile catabolism operon of the thermophile Bacilluspallidus RAPc8.Cameron RA(1), Sayed M, Cowan DA.Author information: (1)Advanced Research Centre for Applied Microbiology, Department of Biotechnology,University of the Western Cape, Bellville 7535, Cape Town, South Africa.The gene cluster containing the nitrile hydratase (NHase) and amidase genes of a moderate thermophile, B. pallidus RAPc8 has been cloned and sequenced. The (5.9kb) section of cloned DNA contained eight complete open reading frames, encoding (in order), amidase (belonging to the nitrilase related aliphatic amidasefamily), nitrile hydratase beta and alpha subunits (of the cobalt containingclass), a 122-amino acid accessory protein, designated P14K, a homologue of the2Fe-2S class of ferredoxins and three putative proteins with distinct homology tothe cobalt uptake proteins cbiM, cbiN and cbiQ of the S. typhimurium LT2cobalamin biosynthesis pathway. The amidase and nitrile hydratase genes weresubcloned and inducibly expressed in Escherichia coli, to levels of approximately37 106 97 98 99 U/mg and 49 U/mg, respectively, without the co-expression of additionalflanking genes. However, co-expression of P14K with the NHase structural genessignificantly enhanced the specific activity of the recombinant NHase. This isthe first description of an accessory protein involved in thermostable NHaseexpression. Modelling of the P14K protein structure has suggested that thisprotein functions as a subunit-specific chaperone, aiding in the folding of theNHase alpha subunit prior to alpha-beta subunit association and the formation of alpha(2)beta(2) NHase holoenzyme.PMID: 15955632 [PubMed - indexed for MEDLINE] 196. FEMS Microbiol Lett. 2005 Jul 1;248(1):9-15.A novel beta-glucanase gene from Bacillus halodurans C-125.Akita M(1), Kayatama K, Hatada Y, Ito S, Horikoshi K.Author information: (1)Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 215 Natsushima,Yokosuka 237 0061, Japan. [email protected] novel endo-beta-1,3(4)-D-glucanase gene was found in the complete genomesequence of Bacillus halodurans C-125. The gene was previously annotated as an"unknown" protein and assigned an incorrect open reading frame (ORF). However,determining the biochemical characteristics has elucidated the function andcorrect ORF of the gene. The gene encodes 231 amino acids, and its calculatedmolecular mass was estimated to be 26743.16 Da. The amino acid sequence alignmentshowed that the highest sequence identity was only 28% with that of thebeta-1,3-1,4-glucanase from Bacillus subtilis. Moreover, the nucleotide sequence did not match any other known Bacillus beta-glucanase gene. The member of thegene cluster that includes this novel gene was apparently different from that of the gene cluster including the putative beta-glucanase genes (bh3231 and bh3232) from B. halodurans C-125. Therefore, the novel gene is not a copy of either ofthese genes, and in B. halodurans cells, the putative role of the encoded proteinmay differ from that of bh3231 and bh3232. To examine the activity of the geneproduct, the gene was cloned as a His-tagged protein and expressed in Escherichiacoli. The purified enzyme showed activity against lichenan, barley beta-glucan,laminarin, and carboxymethyl curdlan. Thin-layer chromatography showed that theenzyme hydrolyzes substrates in an endo-type manner. When beta-glucan was used asa substrate, the pH optimum was between 6 and 8, and the temperature optimum was 60 degrees C. After 2 h incubation at 50 and 60 degrees C, the residual activity remained 100% and 50%, respectively. The enzymatic activity was abolished after30 min incubation at 70 degrees C. Based on the results, the gene encodes anendo-type beta-1,3(4)-D-glucanase (E.C. 3.2.1.6).PMID: 15936898 [PubMed - indexed for MEDLINE] 197. Biochimie. 2005 Jun;87(6):529-37. Epub 2005 Mar 7.In vitro maturation pathway of a glutamyl endopeptidase precursor from Bacilluslicheniformis.Trachuk LA(1), Shcheglov AS, Milgotina EI, Chestukhina GG.Author information: (1)Laboratory of Protein Chemistry, Institute of Genetics and Selection ofIndustrial Microorganisms, 1st Dorozhny, 1, Moscow, 113545, [email protected] gene encoding of glutamyl-specific endopeptidase precursor from Bacilluslicheniformis has been cloned in Escherichia coli cells. The recombinant protein was expressed and accumulated as cytoplasmic insoluble inclusion bodies. Washedinclusion bodies were solubilized in 6 M guanidine-HCL in the presence ofreducing agent. The following precursor renaturation was performed by fastfrequent dilution method. The highest yield of the refolded protein was achieved at pH value of 8.5 and 4 degrees C. The renaturation process was accompanied by agradual splitting of Glu(-48)/Thr(-47) and Glu(-13)/Lys(-12) peptide bonds. A26-kDa protein proved to be an end product of in vitro renaturation. The matureglutamyl endopeptidase with a molecular mass of 25 kDa was obtained after alimited proteolysis of the 26-kDa protein was performed by subtilisin or trypsin.The 26-kDa protein was purified by gel filtration on a Superdex 75 column.Comparative characteristics of the thermal stability and catalytic properties of the 26-kDa and 25-kDa proteins showed that complete cleavage of the N-terminalpro-peptide by exogenous proteinase is necessary for a final packing andactivation of the B. licheniformis glutamyl endopeptidase.PMID: 15935278 [PubMed - indexed for MEDLINE] 198. Appl Environ Microbiol. 2005 Jun;71(6):3068-76.Molecular characterization of plasmid pBM300 from Bacillus megaterium QM B1551.Kunnimalaiyaan M(1), Vary PS.Author information: (1)Department of Biological Sciences, Northern Illinois University, De Kalb 60115,USA. [email protected] QM B1551 of Bacillus megaterium contains seven compatible plasmids: twosmall rolling circle plasmids and five theta-replicating plasmids withcross-hybridizing replicons. To expand our understanding of these plasmids, thereplicon region (6.7 kb) from pBM300 was cloned, sequenced, and functionallycharacterized. Sequence analysis showed that the replication protein (RepM300)was highly homologous to two other plasmid Rep proteins of the same strain but tono other known proteins. Furthermore, the location of the replication origin was within the RepM300 coding region, and the origin contained three 12-base directrepeats. Deletion analysis of the replicon confirmed the role of the Rep protein and showed that open reading frame 2 (ORF2) was required for stability. However, the protein encoded by ORF2 is entirely different from the replicon stabilityproteins encoded by the other two replicons. The entire plasmid was isolated fromthe plasmid array by integrating a spectinomycin resistance gene and transforminga plasmidless strain, PV361. Complete sequencing showed that pBM300 was 26,300 bplong, had a G+C content of 35.2%, and contained 20 ORFs, two of which encodedproteins that had no similarity to other proteins in the database. The proteinsencoded by the plasmid ORFs had similarity to proteins for mobilization andtransfer, an integrase, a rifampin resistance protein, a cell wall hydrolase,glutathione synthase, and a biotin carboxylase. The similarities were to several gram-positive genera and a few gram-negative genera and archaea. oriT andssoT-like regions were detected near two mob genes. These results suggest thatpBM300 is a mobilizable hybrid plasmid that confers increased metabolic andgermination ability on its host. Its replicon also helps define a new plasmidfamily.PMCID: PMC1151835PMID: 15933003 [PubMed - indexed for MEDLINE] 107 100 199. Crit Rev Microbiol. 2005;31(1):11-8.Clostridium botulinum: a bug with beauty and weapon.Shukla HD(1), Sharma SK.Author information: (1)Center of Marine Biotechnology, University of Maryland Biotechnology Institute,Baltimore, Maryland 21202, USA. [email protected] botulinum, a Gram-positive, anaerobic spore-forming bacteria, isdistinguished by its significant clinical applications as well as its potentialto be used as bioterror agent. Growing cells secrete botulinum neurotoxin (BoNT),the most poisonous of all known poisons. While BoNT is the causative agent ofdeadly neuroparalytic botulism, it also serves as a remarkably effectivetreatment for involuntary muscle disorders such as blepharospasm, strabismus,hemifacial spasm, certain types of spasticity in children, and other ailments.BoNT is also used in cosmetology for the treatment of glabellar lines, and iswell-known as the active component of the anti-aging medications Botox andDysport. In addition, recent reports show that botulinum neurotoxin can be usedas a tool for pharmaceutical drug delivery. However, BoNT remains the deadliestof all toxins, and is viewed by biodefense researchers as a possible agent ofbioterrorism (BT). Among seven serotypes, C. botulinum type A is responsible for the highest mortality rate in botulism, and thus has the greatest potential toact as biological weapon. Genome sequencing of C. botulinum type A Hall strain(ATCC 3502) is now complete, and has shown the genome size to be 3.89 Mb with aG+C content of approximately 28.2%. The bacterium harbors a 16.3 kb plasmid with a 26.8% G+C content--slightly lower than that of the chromosome. Most of thevirulence factors in C. botulinum are chromosomally encoded; bioinformaticanalysis of the genome sequence has shown that the plasmid does not harbor toxin genes or genes for related virulence factors. Interestingly, the plasmid doesharbor genes essential to replication, including dnaE, which encodes the alphasubunit of DNA polymerase III which has close similarity with its counterpart in C. perfringens strain 13. The plasmid also contains similar genes to those thatencode the ABC-type multidrug transport ATPase, and permease. The presence ofABC-type multidrug transport ATPase, and permease suggests putative involvementof efflux pumps in bacteriocin production, modification, and export in C.botulinum. The C. botulinum plasmid additionally harbors genes for LambdaBa04prophage and site-specific recombinase that are similar to those found in theAmes strain of Bacillus anthracis; these genes and their products may play a rolein genomic rearrangement. Completion of genome sequencing for C. botulinum willprovide an opportunity to design genomic and proteomic-based systems fordetecting different serotypes of C. botulinum strains in the environment. Thecompleted sequence may also facilitate identification of potential virulencefactors and drug targets, as well as help characterize neurotoxin-complexingproteins, their polycistronic expression, and phylogenetic relationships between different serotypes.PMID: 15839401 [PubMed - indexed for MEDLINE] 101 200. FEMS Microbiol Rev. 2005 Apr;29(2):281-301.Molecular insights into the initiation of sporulation in Gram-positive bacteria: new technologies for an old phenomenon.Stephenson K(1), Lewis RJ.Author information: (1)School of Biochemistry and Microbiology, Faculty of Biological Sciences,University of Leeds, Leeds LS2 9JT, UK. [email protected] last decade has witnessed extensive, and widespread, changes in scientifictechnologies that have impacted significantly upon the study of the lifesciences. Arguably, the biggest advances in our comprehension of simple andcomplex biological processes have come as a consequence of obtaining the completeDNA sequence of organisms. It is likely that we will become accustomed to hearingof quantum leaps in the study and understanding of the biology of highereukaryotes in the coming years, now that (near) complete genome sequences areavailable for man, mouse and rat. In this review, we will discuss the impact ofgenome sequence data, and the use of new scientific technologies that haveemerged largely as consequence of the availability of this information, on thestudy of the master regulator of sporulation, Spo0A, in low G+C Gram-positiveendospore-forming bacteria.PMID: 15808745 [PubMed - indexed for MEDLINE] 102 201. Archaea. 2003 Oct;1(3):185-90.Remarkable sequence signatures in archaeal genomes.Fadiel A(1), Lithwick S, Ganji G, Scherer SW.Author information: (1)The Center for Applied Genomics, Hospital for Sick Children, Toronto, Ontario M5G1Z8, Canada. [email protected] archaeal genomes were probed for the presence of long (> or = 25 bp)oligonucleotide repeats (words). We detected the presence of many wordsdistributed in tandem with narrow ranges of periodicity (i.e., spacer lengthbetween repeats). Similar words were not identified in genomes of non-archaealspecies, namely Escherichia coli, Bacillus subtilis, Haemophilus influenzae,Mycoplasma genitalium and Mycoplasma pneumoniae. BLAST similarity searchesagainst the GenBank nucleotide sequence database revealed that these words werearchaeal species-specific, indicating that they are of a signature character.Sequence analysis and genome viewing tools showed these repeats to be restricted to non-coding regions. Thus, archaea appear to possess a non-coding genomicsignature that is absent in bacterial species. The identification of aspecies-specific genomic signature would be of great value to archaeal genomemapping, evolutionary studies and analyses of genome complexity.PMCID: PMC2685567PMID: 15803664 [PubMed - indexed for MEDLINE] 103 202. J Bacteriol. 2005 Apr;187(7):2426-38.Insights on evolution of virulence and resistance from the complete genomeanalysis of an early methicillin-resistant Staphylococcus aureus strain and abiofilm-producing methicillin-resistant Staphylococcus epidermidis strain.Gill SR(1), Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J, Paulsen IT,Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty SC, Madupu R, Angiuoli SV, Durkin AS, Haft DH, Vamathevan J, Khouri H, Utterback T, Lee C, Dimitrov G, JiangL, Qin H, Weidman J, Tran K, Kang K, Hance IR, Nelson KE, Fraser CM.Author information: (1)Microbial Genomics, The Institute for Genomic Research, 9712 Medical Center Dr., Rockville, MD 20850, USA. [email protected] aureus is an opportunistic pathogen and the major causative agent of numerous hospital- and community-acquired infections. Staphylococcusepidermidis has emerged as a causative agent of infections often associated with implanted medical devices. We have sequenced the approximately 108 2.8-Mb genome ofS. aureus COL, an early methicillin-resistant isolate, and the approximately2.6-Mb genome of S. epidermidis RP62a, a methicillin-resistant biofilm isolate.Comparative analysis of these and other staphylococcal genomes was used toexplore the evolution of virulence and resistance between these two species. The S. aureus and S. epidermidis genomes are syntenic throughout their lengths andshare a core set of 1,681 open reading frames. Genome islands in nonsyntenicregions are the primary source of variations in pathogenicity and resistance.Gene transfer between staphylococci and low-GC-content gram-positive bacteriaappears to have shaped their virulence and resistance profiles. Integratedplasmids in S. epidermidis carry genes encoding resistance to cadmium andspecies-specific LPXTG surface proteins. A novel genome island encodes multiplephenol-soluble modulins, a potential S. epidermidis virulence factor. S.epidermidis contains the cap operon, encoding the polyglutamate capsule, a major virulence factor in Bacillus anthracis. Additional phenotypic differences arelikely the result of single nucleotide polymorphisms, which are most numerous in cell envelope proteins. Overall differences in pathogenicity can be attributed togenome islands in S. aureus which encode enterotoxins, exotoxins, leukocidins,and leukotoxins not found in S. epidermidis.PMCID: PMC1065214PMID: 15774886 [PubMed - indexed for MEDLINE] 104 203. Biomacromolecules. 2005 Mar-Apr;6(2):532-7.Rapid genetic characterization of poly(hydroxyalkanoate) synthase and itsapplications.Solaiman DK(1), Ashby RD.Author information: (1)United States Department of Agriculture, ARS, ERRC. 600 East Mermaid Lane,Wyndmoor, Pennsylvania 19038, USA. [email protected] containing short-chain-length (scl-) or medium-chain-length (mcl-)poly(hydroxyalkanoates) (PHAs) are commonly screened by applying rapid stainingmethods using lipophilic reagents. These methods provide powerful means forgeneral screening of organisms actively producing and accumulating PHAs. TheSouthern blot hybridization method additionally allows the identification ofpotential PHA-producing microorganisms. Polymerase chain reaction (PCR)-baseddetection methods further afford rapid and sensitive means to screen for PHAbiosynthesis genes. Specific PCR assays had been developed for the simultaneousor individual detection of the class II mcl-PHA synthase genes of Pseudomonas.The amplicons (approximately 0.54 kb) can be directly sequenced or used as probesfor hybridization studies. The sequence information can further be used toinitiate chromosome walking for an eventual cloning of the complete PHAbiosynthesis operon. In addition, the amplification pattern and sequence data canbe used to differentiate subgroups of organisms, as demonstrated for P. corrugataand P. mediterranea. Other researchers reported PCR methods for the detection of scl-PHA synthase genes and those of Bacillus spp., thus greatly expanding thetypes of PHA synthase gene and the organisms that can be characterized by thisapproach. The vast sequence information obtainable through PCR-based studies ofvarious PHA synthase operons should facilitate the identification or constructionof new PHA synthases capable of synthesizing novel PHAs.PMID: 15762609 [PubMed - indexed for MEDLINE] 105 204. Mol Microbiol. 2005 Mar;55(6):1646-57.A magnesium-dependent mreB null mutant: implications for the role of mreB inBacillus subtilis.Formstone A(1), Errington J.Author information: (1)Sir William Dunn School of Pathology, University of Oxford, South Parks Road,Oxford OX1 3RE, UK.MreB shares a common prokaryotic ancestor with actin and is present in almost allrod-shaped bacteria. MreB proteins have been implicated in a range of importantcell processes, including cell morphogenesis, chromosome segregation and cellpolarity. The mreB gene frequently lies at the beginning of a cluster of genes,immediately upstream of the conserved mreC and mreD genes. RNA analysis showedthat in Bacillus subtilis mreB is co-transcribed with mreC and that these genesform part of an operon under the control of a promoter(s) upstream of mreB.Construction of an in-frame deletion of mreB and its complementation by mreB(+)only, in trans, established that the gene is important for maintenance of cellwidth and cell viability under normal growth conditions, independent of polareffects on downstream genes. Remarkably, virtually normal growth was restored to the mreB null mutant in the presence of high concentrations of magnesium,especially when high concentrations of the osmoprotectant, sucrose were alsopresent. Under these conditions, cells could be maintained in the completeabsence of an mreB gene, with almost normal morphology. No detectable effect onchromosome segregation was evident in the mutant, nor was there an effect on the topology of nascent peptidoglycan insertion. A GFP-MreB fusion was used to lookat the localization of MreB in live cells. The pattern of localization wassimilar to that previously described, but no tight linkage to nucleoidpositioning was evident. Propagation of the mreB null mutant in the absence ofmagnesium and sucrose led to a progressive increase in cell width, culminating incell lysis. Cell division was also perturbed but this effect may be secondary to the disturbance in cell width. These results suggest that the major role of MreB in B. subtilis lies in the control of cell diameter.PMID: 15752190 [PubMed - indexed for MEDLINE] 106 205. J Microbiol Methods. 2005 May;61(2):225-34. Epub 2004 Dec 30.Development of a versatile cassette for directional genome walking using cassetteligation-mediated PCR and its application in the cloning of complete lipolyticgenes from Bacillus species.Nthangeni MB(1), Ramagoma F, Tlou MG, Litthauer D.Author information: (1)Department of Microbial, Biochemical and Food Biotechnology, University of theFree State, P.O. Box 339, Bloemfontein, 9300, South [email protected] the invention of the PCR technology, adaptation techniques to clone DNAfragments flanking the known sequence continue to be developed. We describe aperfectly annealed cassette available in almost unlimited quantities withvariable sticky-and blunt-end restriction enzyme recognition sites for efficient restriction and ligation with the restricted target genomic DNA. The cassetteprovides a 200-bp sequence, which is used to design a variety ofcassette-specific primers. The dephosphorylation prevents cassette self-ligation and creates a nick at the cassette: target genome DNA ligation site suppressingunspecific PCR amplifications. We in- 109 107 108 109 110 troduce the single-strand amplification PCR(SSA-PCR) technique where a lone known locus-specific primer is firstly used toenrich the targeted template DNA strand resulting in significant PCR productspecificity during the second round conventional nested PCR. The distance betweenthe known locus-specific primer and the nearest location of the restrictionenzyme used determined the length of the obtained PCR product. We used thistechnique to walk downstream into the isochorismatase and upstream into thehypothetical conserved genes flanking the mature extracellular lipase gene fromBacillus licheniformis. We further demonstrated the potential of the technique asa cost-effective method during PCR-based prospecting for novel genes by designing"universal" degenerate primers that detected homologues of Family VII bacteriallipolytic genes in Bacillus species. The cassette ligation-mediated PCR was used to clone complete nucleotide sequences encoding functional lipolytic genes fromB. licheniformis and Bacillus pumilus.PMID: 15722149 [PubMed - indexed for MEDLINE] 206. FEMS Microbiol Lett. 2005 Feb 1;243(1):73-9.NifH and NifD sequences of heliobacteria: a new lineage in the nitrogenasephylogeny.Enkh-Amgalan J(1), Kawasaki H, Seki T.Author information: (1)The International Center for Biotechnology, Osaka University, 2-1 Yamada-oka,Suita-city, Osaka 565-0871, Japan.We determined almost complete nifH and nifD genes from representatives of allrecognized genera of heliobacteria, the strictly anaerobic phototrophs belonging to the low GC gram-positive bacteria. The heliobacterial sequences formed ahighly supported monophyletic group that is clearly distinct from any knowndiazotrophs, in both NifH and NifD trees. According to the classification ofnitrogenase genes in four major clusters, the clade of heliobacterial sequencesbelonged to cluster I and did not cluster with any of the Clostridium (clusterIII) or Paenibacillus (cluster I) species, the close neighbors of heliobacteriabased on the 16S rRNA phylogeny. One partial anfH or alternative nitrogenasesequence was detected from Heliobacterium gestii. Although Heliophilum fasciatum is known to fix nitrogen based on the acetylene reduction test, nifH and/or nifD genes were not detected by either the PCR amplification or Southern hybridizationmethods.PMID: 15668003 [PubMed - indexed for MEDLINE] 207. J Bacteriol. 2005 Feb;187(3):1022-35.The Enterococcus faecalis sigV protein is an extracytoplasmic function sigmafactor contributing to survival following heat, acid, and ethanol treatments.Benachour A(1), Muller C, Dabrowski-Coton M, Le Breton Y, Giard JC, Rincé A,Auffray Y, Hartke A.Author information: (1)Laboratoire de Microbiologie de l'Environnement, IRBA, Université de Caen, 14032 Caen Cedex, France. [email protected] of the genome sequence of Enterococcus faecalis allowed theidentification of two genes whose protein products showed 33 and 34% identitywith those of sigV and yrhM of Bacillus subtilis, respectively. These genes,named sigV and rsiV, are predicted to encode members of the extracytoplasmicfunction subfamily of eubacterial RNA polymerase sigma and anti-sigma factors,respectively. This group of sigma factors has been shown to regulate geneexpression in response to stress conditions. sigV and rsiV were shown to be underthe control of the same promoter. The transcriptional start site was determined, and the 1.5-kb mRNA transcript was shown to be overexpressed under glucose andcomplete starvation, as well as under physicochemical treatments. Three mutants, affected in sigV, rsiV, and both genes, were constructed by double-crossoverrecombination within the genome of E. faecalis strain JH2-2. Compared with thewild type and the rsiV mutant, the sigV mutants were more susceptible to heatshock, acid, and ethanol treatments and displayed decreased survival duringlong-term starvation. A nisin-inducible sigV gene construction used incomplementation assays restored the wild phenotype of the sigV mutants,confirming the involvement of SigV in the heat shock, ethanol, and acid stressresponses. Northern blot analysis carried out with the three mutant strainsrevealed the inhibition of sigV expression by the related anti-sigma factor gene rsiV. In addition, putative candidates of the sigV regulon determined by computersearch for the sigV promoter sequence were analyzed.PMCID: PMC545719PMID: 15659680 [PubMed - indexed for MEDLINE] 208. Can J Microbiol. 2004 Oct;50(10):779-91.Characterization of Paenibacillus popilliae rRNA operons.Dingman DW.Author information: Department of Biochemistry and Genetics, Connecticut Agricultural ExperimentStation, 123 Huntington Street, PO Box 1106, New Haven, CT 06504, [email protected] terminal 39 nucleotides on the 3' end of the 16S rRNA gene, along with thecomplete DNA sequences of the 5S rRNA, 23S rRNA, tRNA(Ile), and tRNA(Ala) geneswere determined for Paenibacillus popilliae using strains NRRL B-2309 and Dutky1. Southern hybridization analysis with a 16S rDNA hybridization probe andrestriction-digested genomic DNA demonstrated 8 copies of the 16S rRNA gene in P.popilliae strains KLN 3 and Dutky 1. Additionally, the 23S rRNA gene in P.popilliae strains NRRL B-2309, KLN 3, and Dutky 1 was shown by I-CeuI digestionand pulsed-field gel electrophoresis of genomic DNA to occur as 8 copies. It was concluded that these 3 P. popilliae strains contained 8 rrn operons. The 8 operoncopies were preferentially located on approximately one-half of the chromosomeand were organized into 3 different patterns of genes, as follows: 16S-23S-5S,16S-ala-23S-5S, and 16S-5S-ile-ala-23S-5S. This is the first report to identify a5S rRNA gene between the 16S and 23S rRNA genes of a bacterial rrn operon.Comparative analysis of the nucleotides on the 3' end of the 16S rRNA genesuggests that translation of P. popilliae mRNA may occur in Bacillus subtilis andEscherichia coli.PMID: 15644892 [PubMed - indexed for MEDLINE] 209. Biochim Biophys Acta. 2004 Dec 1;1703(1):43-51.Expression and characterization of a heterodimer of Streptomyces chromofuscusphospholipase D.Yang H(1), Roberts MF.Author information: (1)Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, MA02167, USA.Streptomyces chromofuscus phospholipase D (PLD) is secreted by the bacterium and proteolytically cleaved to a more active form (PLD(37/18)) where the two parts ofthe molecule are still tightly associated. Based on previ- 110 ous sequencing resultsof authentic PLD(37/18), we have constructed a vector consisting of separate ORFsfor the N-terminal and C-terminal portions of S. chromofuscus PLD andoverexpressed active heterodimeric PLD. Neither fragment cloned separately foldedproperly. The identity of each peptide was confirmed by peptide-massfingerprinting with MALDI-TOF mass spectrometry. The recombinant complex had aspecific activity about six times higher than that of the recombinant intact PLD enzyme and was no longer activated by phosphatidic acid (PA). Phosphotransferase activity, binding affinity to phospholipid vesicles, loss of product activation, pH profile and pH-related Ca(2+) activation and inhibition were comparable toauthentic PLD(37/18) purified from S. chromofuscus growth medium. PLD(37) alonecould also be isolated; the enzyme was active but not as stable as PLD(37/18).These experimental results strongly support the hypothesis that the C-terminalpeptide is necessary for correct folding and insertion of catalytic metal ions.However, they suggest the ligands involved in Fe(3+) coordination must be alteredupon cleavage of the protein. Asp389, in the C-terminal fragment, whosereplacement impairs Fe(3+) binding to the protein, must be replaced by anotherligand, since the N-terminal fragment, once folded, is active. In the process of cloning the two peptides, the complete signal sequence for this protein was also determined. The signal peptide of S. chromofuscus PLD enzyme contained a twinarginine motif suggesting that S. chromofuscus PLD, like Bacillus subtilis phoD, is most likely secreted by the TAT translocation pathway under thetranscriptional control of the pho regulon.PMID: 15588701 [PubMed - indexed for MEDLINE] 111 210. Nucleic Acids Res. 2004 Dec 1;32(21):6292-303. Print 2004.Thermoadaptation trait revealed by the genome sequence of thermophilicGeobacillus kaustophilus.Takami H(1), Takaki Y, Chee GJ, Nishi S, Shimamura S, Suzuki H, Matsui S,Uchiyama I.Author information: (1)Microbial Genome Research Group, Japan Agency of Marine-Earth Science andTechnology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, [email protected] <[email protected]>We present herein the first complete genome sequence of a thermophilicBacillus-related species, Geobacillus kaustophilus HTA426, which is composed of a3.54 Mb chromosome and a 47.9 kb plasmid, along with a comparative analysis with five other mesophilic bacillar genomes. Upon orthologous grouping of the sixbacillar sequenced genomes, it was found that 1257 common orthologous groupscomposed of 1308 genes (37%) are shared by all the bacilli, whereas 839 genes(24%) in the G.kaustophilus genome were found to be unique to that species. Wewere able to find the first prokaryotic sperm protamine P1 homolog, polyaminesynthase, polyamine ABC transporter and RNA methylase in the 839 unique genes;these may contribute to thermophily by stabilizing the nucleic acids. Contrastingresults were obtained from the principal component analysis (PCA) of the aminoacid composition and synonymous codon usage for highlighting the thermophilicsignature of the G.kaustophilus genome. Only in the PCA of the amino acidcomposition were the Bacillus-related species located near, but weredistinguishable from, the borderline distinguishing thermophiles from mesophiles on the second principal axis. Further analysis revealed some asymmetric aminoacid substitutions between the thermophiles and the mesophiles, which arepossibly associated with the thermoadaptation of the organism.PMCID: PMC535678PMID: 15576355 [PubMed - indexed for MEDLINE] 112 211. Curr Pharm Des. 2004;10(26):3185-94.Identification and validation of novel drug targets in tuberculosis.Duncan K.Author information: GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK. [email protected] is an urgent need for new antimycobacterial drugs, and in particular fornovel agents that will shorten the duration of tuberculosis chemotherapy, orovercome drug-resistant strains of the causative organism, Mycobacteriumtuberculosis. Our knowledge of the tubercle bacillus and its complex interaction with the human host has improved dramatically in recent years, particularly with the determination of its complete genome sequence. New genome-scale tools arebeing applied to aid in drug target identification, alongside traditionalapproaches aimed at understanding the basic biology of M. tuberculosis. Manypotential drug targets have been identified, but very few have been validated by showing that they are essential for growth or survival of the bacterium. In this review, the landscape of potential drug targets is surveyed.StructuralBioinformatic Approaches to the Discovery of New Antimycobacterial Drugs.PMID: 15544508 [PubMed - indexed for MEDLINE] 113 212. J Bacteriol. 2004 Nov;186(22):7714-25.The bcr1 DNA repeat element is specific to the Bacillus cereus group and exhibitsmobile element characteristics.Økstad OA(1), Tourasse NJ, Stabell FB, Sundfaer CK, Egge-Jacobsen W, Risøen PA,Read TD, Kolstø AB.Author information: (1)Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway.Bacillus cereus strains ATCC 10987 and ATCC 14579 harbor an approximately 155-bp repeated element, bcr1, which is conserved in B. cereus, B. anthracis, B.thuringiensis, and B. mycoides but not in B. subtilis and B. licheniformis. Inthis study, we show by Southern blot hybridizations that bcr1 is present in all54 B. cereus group strains tested but absent in 11 Bacillus strains outside thegroup, suggesting that bcr1 may be specific and ubiquitous to the B. cereusgroup. By comparative analysis of the complete genome sequences of B. cereus ATCC10987, B. cereus ATCC 14579, and B. anthracis Ames, we show that bcr1 isexclusively present in the chromosome but absent from large plasmids carried bythese strains and that the numbers of full-length bcr1 repeats for these strains are 79, 54, and 12, respectively. Numerous copies of partial bcr1 elements arealso present in the three genomes (91, 128, and 53, respectively). Furthermore,the genomic localization of bcr1 is not conserved between strains with respect tochromosomal position or organization of gene neighbors, as only six full-lengthbcr1 loci are common to at least two of the three strains. However, theintergenic sequence surrounding a specific bcr1 repeat in one of the threestrains is generally strongly conserved in the other two, even in loci where bcr1is found exclusively in one strain. This finding indicates that bcr1 either hasevolved by differential deletion from a very high number of repeats in a commonan- 111 114 115 116 117 cestor to the B. cereus group or is moving around the chromosome. Theidentification of bcr1 repeats interrupting genes in B. cereus ATCC 10987 andATCC 14579 and the presence of a flanking TTTAT motif in each end show that bcr1 exhibits features characteristic of a mobile element.PMCID: PMC524882PMID: 15516586 [PubMed - indexed for MEDLINE] 213. Biosci Biotechnol Biochem. 2004 Oct;68(10):2007-23.Protein traffic for secretion and related machinery of Bacillus subtilis.Yamane K(1), Bunai K, Kakeshita H.Author information: (1)Institute of Biological Sciences, University of Tsukuba, Ibaraki, [email protected] sporulating Bacillus subtilis secretes high levels of protein. Its complete genome sequence, published in 1997, encodes 4,106 proteins.Bioinformatic searches have predicted that about half of all B. subtilis proteinsare related to the cell membrane through export to the extracellular medium,insertion, and attachment. Key features of the B. subtilis protein secretionmachinery are the absence of an Escherichia coli SecB homolog and the presence ofan SRP (signal recognition particle) that is structurally rather similar to humanSRP. In addition, B. subtilis contains five type I signal peptidases (SipS, T, U,V, and W). Our in vitro assay system indicated that co-operation between theSRP-protein targeting system to the cell membrane and the Sec proteintranslocation machinery across the cytoplasmic membrane constitutes the majorprotein secretion pathway in B. subtilis. Furthermore, the function of theSRP-Sec pathway in protein localization to the cell membrane and spore wasanalyzed.PMID: 15502345 [PubMed - indexed for MEDLINE] 214. DNA Res. 2004 Aug 31;11(4):233-45.Identification and distribution of new insertion sequences in the genome of theextremely halotolerant and alkaliphilic Oceanobacillus iheyensis HTE831.Takaki Y(1), Matsuki A, Chee GJ, Takami H.Author information: (1)Microbial Genome Research Group, Japan Agency for Marine-Earth Science andTechnology, 2-15 Natsushima, Yokosuka 237-0061, Japan.Six kinds of new insertion sequences (ISs), IS667 to IS672, a group II intron(Oi.Int), and an incomplete transposon (Tn852loi) were identified in the3,630,528-bp genome of the extremely halotolerant and alkaliphilic Oceanobacillusiheyensis HTE831. Of 19 ISs identified in the HTE831 genome, 7 were truncated,indicating the occurrence of internal rearrangement of the genome. All ISs exceptIS669 generated a 4- to 8-bp duplication of the target site sequence, and theseISs carried 23- to 28-bp inverted repeats (IRs). Sequence analysis revealed that four ISs (IS669, IS670, IS671, and IS672) were newly identified as belonging toseparate IS families (IS200/IS605, IS30, IS5, and IS3, respectively). IS667 andIS668 were also characterized as new members of the ISL3 family. Tn8521oi, which belongs to the Tn3 family as a new member, generated a 5-bp duplication of thetarget site sequence and carried complete 38-bp IRs. Of the eight protein-coding sequences (CDSs) identified in Tn8521oi, three CDSs (OB481, OB482, and OB483)formed a ger gene cluster, and two other paralogous gene clusters were found inthe HTE831 genome. Most of the ISs and the group II intron widely distributedthroughout the genome were inserted in noncoding regions, while two ISs (IS667-08and IS668-02) and Oi.Int-04 were inserted in the coding regions.PMID: 15500249 [PubMed - indexed for MEDLINE] 215. Biomedica. 2004 Jun;24 Supp 1:228-38.[Perspectives for new anti-tuberculous vaccines in the post-genomic era].[Article in Spanish]García LF(1), Barrera LF.Author information: (1)Grupo de Inmunología Celular e Inmunogenética, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia. [email protected] with attenuated Mycobacterium bovis BCG has been used as the routine procedure to immunize against tuberculosis. Since the efficacy of BCG vaccinationis very controversial, the search for new immunoprophylatic tools againsttuberculosis is an area of intense interest. Knowledge of the complete sequenceof Mycobacterium tuberculosis (Mtb) H37Rv genome and the application of newimmunological, biochemical and genetic technologies has led to a detailedunderstanding of the transcriptome and proteome of this bacterium. Approximately one-third of the human population is infected with Mtb; however, the bacillus is only detected once the symptoms appear and therefore most of the recent effortshave been devoted to the development of a post-infection vaccine. In theory, thisvaccine (1) will give rise to an increase in the long-lasting specific immunityagainst Mtb, (2) will not have significant adverse effects, and (3) will beaffordable for the people in third world countries. The main strategies that havebeen developed include the subunit vaccines, either as a mixture of relevantimmunogenic proteins or DNA constructs, recombinant strains of Mycobacteriumbovis BCG and Mtb, designed to secrete immunogenic proteins or with attenuatedvirulence, respectively, and DNA-based vaccines. The subunit vaccines aredelivered either as mixtures of immunogenic proteins and adjuvants, or as nakedDNA or by viral vectors in order to induce a potent Th1 response. Most of thesevaccines have been tested in several kinds of animal models, but they do notfully reproduce the human pathology. However, the results obtained so far arevery encouraging and have led to the development of phase I trials in humans.PMID: 15495589 [PubMed - indexed for MEDLINE] 216. Biochem J. 2005 Mar 1;386(Pt 2):381-6.Examination of mitochondrial protein targeting of haem synthetic enzymes: in vivoidentification of three functional haem-responsive motifs in 5-aminolaevulinatesynthase.Dailey TA(1), Woodruff JH, Dailey HA.Author information: (1)Department of Microbiology, Biomedical and Health Sciences Institute, University of Georgia, Athens, GA 30602-7229, USA.Erratum in Biochem J. 2005 Nov 1;391(Pt 3):711.The initial and the terminal three enzymes of the mammalian haem biosyntheticpathway are nuclear encoded, cytoplasmically synthesized and post-translationallytranslocated into the mitochondrion. The first enzyme, ALAS (5-aminolaevulinatesynthase), occurs as an isoenzyme encoded on different chromosomes and issynthesized either as a housekeeping protein (ALAS-1) in all non-erythroid celltypes, or only in differentiating erythroid precursor cells (ALAS-2). Both ALASproteins possess mitochondrial targeting sequences that have putativehaem-binding motifs. In the present study, evidence is presented demonstratingthat two haem-binding motifs in the leader sequence, as well as one present inthe N-terminus of 112 the mature ALAS-1 function in vivo in the haem-regulatedtranslocation of ALAS-1. Coproporphyrinogen oxidase, the antepenultimate pathway enzyme, possesses a leader sequence that is approx. 120 residues long. Incontrast with an earlier report suggesting that only 30 residues were requiredfor translocation of the coproporphyrinogen oxidase, we report that the complete leader is necessary for translocation and that this process is not haem-sensitivein vivo. PPO (protoporphyrinogen oxidase) lacks a typical mitochondrial targetingleader sequence and was found to be effectively targeted by just 17 N-terminalresidues. Bacillus subtilis PPO, which is very similar to human PPO at itsN-terminal end, is not targeted to the mitochondrion when expressed in mammalian cells, demonstrating that the translocation is highly specific with regard toboth the length and spacing of charged residues in this targeting region.Ferrochelatase, the terminal enzyme, possesses a typical N-terminal leadersequence and no evidence of a role for the C-terminus was found in mitochondrial targeting.PMCID: PMC1134803PMID: 15482256 [PubMed - indexed for MEDLINE] 118 217. J Appl Microbiol. 2004;97(5):992-1000.Cereulide, the emetic toxin of Bacillus cereus, is putatively a product ofnonribosomal peptide synthesis.Toh M(1), Moffitt MC, Henrichsen L, Raftery M, Barrow K, Cox JM, Marquis CP,Neilan BA.Author information: (1)Food Science and Technology, School of Chemical Engineering and IndustrialChemistry, The University of New South Wales, Sydney, Australia.AIMS: To determine if cereulide, the emetic toxin produced by Bacillus cereus, isproduced by a nonribosomal peptide synthetase (NRPS).METHODS AND RESULTS: NC Y, an emetic strain of Bacillus cereus, was examined for a NRPS gene using PCR with primers recognizing a fragment of a NRPS gene from thecyanobacterium Microcystis. The amplicon was sequenced and compared with othergene sequences using BLAST analysis, which showed that the amplicon from strainNC Y was similar in sequence to peptide synthetase genes in othermicro-organisms, including Bacillus subtilis and B. brevis, while no suchsequence was found in the complete genome sequence of a nonemetic strain of B.cereus. Specific PCR primers were then designed and used to screen 40 B. cereusisolates previously implicated in outbreaks of foodborne illness. The isolateswere also screened for toxin production using the MTT cell cytotoxicity assay.PCR and MTT assay screening of the B. cereus isolates revealed a high correlationbetween the presence of the NRPS gene and cereulide production.CONCLUSIONS: The results indicate that cereulide is produced by a NRPS complex.SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study to provide evidenceidentifying the mechanism of production of cereulide, the emetic toxin of B.cereus. The PCR primers developed in the study allow determination of thepotential for cereulide production among isolates of B. cereus.PMID: 15479414 [PubMed - indexed for MEDLINE] 119 218. Appl Environ Microbiol. 2004 Oct;70(10):6247-56.Comparative analysis of physical maps of four Bacillus subtilis (natto) genomes.Qiu D(1), Fujita K, Sakuma Y, Tanaka T, Ohashi Y, Ohshima H, Tomita M, Itaya M.Author information: (1)Institute for Advanced Biosciences and Bioinformatics Program, Keio University,403-1 Nipponkoku, Daihoji, Tsuruoka, Yamagata 997-0017, Japan.The complete SfiI and I-CeuI physical maps of four Bacillus subtilis (natto)strains, which were previously isolated as natto (fermented soybean) starters,were constructed to elucidate the genome structure. Not only the similarity ingenome size and organization but also the microheterogeneity of the gene context was revealed. No large-scale genome rearrangements among the four strains wereindicated by mapping of the genes, including 10 rRNA operons (rrn) and relevantgenes required for natto production, to the loci corresponding to those of the B.subtilis strain Marburg 168. However, restriction fragment length polymorphismand the presence or absence of strain-specific DNA sequences, such as theprophages SP beta, skin element, and PBSX, as well as the insertion elementIS4Bsu1, could be used to identify one of these strains as a Marburg type and theother three strains as natto types. The genome structure and gene heterogeneitywere also consistent with the type of indigenous plasmids harbored by thestrains.PMCID: PMC522138PMID: 15466572 [PubMed - indexed for MEDLINE] 120 219. Genome Biol. 2004;5(10):R77. Epub 2004 Sep 13.Complete genome sequence of the industrial bacterium Bacillus licheniformis andcomparisons with closely related Bacillus species.Rey MW(1), Ramaiya P, Nelson BA, Brody-Karpin SD, Zaretsky EJ, Tang M, Lopez deLeon A, Xiang H, Gusti V, Clausen IG, Olsen PB, Rasmussen MD, Andersen JT,Jørgensen PL, Larsen TS, Sorokin A, Bolotin A, Lapidus A, Galleron N, Ehrlich SD,Berka RM.Author information: (1)Novozymes Biotech Inc, 1445 Drew Ave, Davis, CA 95616, USA. [email protected]: Bacillus licheniformis is a Gram-positive, spore-forming soilbacterium that is used in the biotechnology industry to manufacture enzymes,antibiotics, biochemicals and consumer products. This species is closely related to the well studied model organism Bacillus subtilis, and produces an assortment of extracellular enzymes that may contribute to nutrient cycling in nature.RESULTS: We determined the complete nucleotide sequence of the B. licheniformisATCC 14580 genome which comprises a circular chromosome of 4,222,336 base-pairs(bp) containing 4,208 predicted protein-coding genes with an average size of 873 bp, seven rRNA operons, and 72 tRNA genes. The B. licheniformis chromosomecontains large regions that are colinear with the genomes of B. subtilis andBacillus halodurans, and approximately 80% of the predicted B. licheniformiscoding sequences have B. subtilis orthologs.CONCLUSIONS: Despite the unmistakable organizational similarities between the B. licheniformis and B. subtilis genomes, there are notable differences in thenumbers and locations of prophages, transposable elements and a number ofextracellular enzymes and secondary metabolic pathway operons that distinguishthese species. Differences include a region of more than 80 kilobases (kb) thatcomprises a cluster of polyketide synthase genes and a second operon of 38 kbencoding plipastatin synthase enzymes that are absent in the B. licheniformisgenome. The availability of a completed genome sequence for B. licheniformisshould facilitate the design and construction of improved industrial strains and allow for comparative genomics and evolutionary studies within this group ofBacillaceae.PMCID: PMC545597PMID: 15461803 [PubMed - indexed for 113 121 122 123 124 125 MEDLINE] 220. Biochim Biophys Acta. 2004 Oct 1;1702(1):125-8.Crystallization and preliminary X-ray diffraction studies of themetal-ion-mediated ternary complex of the HutP protein with L-histidine and itscognate RNA.Kumarevel TS(1), Fujimoto Z, Mizuno H, Kumar PK.Author information: (1)Functional Nucleic Acids Group, Institute for Biological Resources and Function, National Institute of Advanced Industrial Science and Technology, Tsukuba Central6, Tsukuba, Ibaraki 305-8566, Japan.HutP is an RNA-binding protein that regulates the expression of the Bacillussubtilis hut operon by binding to cis-acting regulatory sequences within hutmRNA, exclusively in the presence of L-histidine. We recently solved the crystal structure of a binary complex (HutP with an L-histidine analog) that revealed anovel RNA-binding fold, and identified the important residues that interact with the L-histidine analog. In addition, we have defined the minimal RNA bindingsegment that is required for HutP recognition. Interestingly, we showed thatternary complex formation depends on the availability of not only L-histidine butalso divalent metal ions. Here we report the crystallization and preliminaryX-ray diffraction analysis of the HutP ternary complex. The ternary complex wascrystallized in the presence of Mg2+ along with L-histidine and hut mRNA, usingthe hanging drop vapor diffusion method. The crystal belongs to the R3 spacegroup, with unit cell parameters a=b=75.30 A, c=133.8 A. A complete data set at1.60 A was collected.PMID: 15450857 [PubMed - indexed for MEDLINE] 221. J Mol Microbiol Biotechnol. 2004;7(4):204-11.The complete genome sequence of Bacillus licheniformis DSM13, an organism withgreat industrial potential.Veith B(1), Herzberg C, Steckel S, Feesche J, Maurer KH, Ehrenreich P, Bäumer S, Henne A, Liesegang H, Merkl R, Ehrenreich A, Gottschalk G.Author information: (1)Göttingen Genomics Laboratory and Competence Centre for Genome Research onBacteria, Institute of Microbiology and Genetics, University of Göttingen,Göttingen, Germany.The genome of Bacillus licheniformis DSM13 consists of a single chromosome thathas a size of 4,222,748 base pairs. The average G+C ratio is 46.2%. 4,286 openreading frames, 72 tRNA genes, 7 rRNA operons and 20 transposase genes wereidentified. The genome shows a marked co-linearity with Bacillus subtilis butcontains defined inserted regions that can be identified at the sequence as well as at the functional level. B. licheniformis DSM13 has a well-conserved secretorysystem, no polyketide biosynthesis, but is able to form the lipopeptidelichenysin. From the further analysis of the genome sequence, we identifiedconserved regulatory DNA motives, the occurrence of the glyoxylate bypass and thepresence of anaerobic ribonucleotide reductase explaining that B. licheniformisis able to grow on acetate and 2,3-butanediol as well as anaerobically onglucose. Many new genes of potential interest for biotechnological applicationswere found in B. licheniformis; candidates include proteases, pectate lyases,lipases and various polysaccharide degrading enzymes.Copyright 2004 S. Karger AG, BaselPMID: 15383718 [PubMed - indexed for MEDLINE] 222. Microbiology. 2004 Sep;150(Pt 9):2911-20.Roles and regulation of the glutamate racemase isogenes, racE and yrpC, inBacillus subtilis.Kimura K(1), Tran LS, Itoh Y.Author information: (1)Division of Applied Microbiology, National Food Research Institute, Kannondai2-1-12, Tsukuba, Ibaraki 305-8642, Japan.Many bacteria, including Escherichia coli, have a unique gene that encodesglutamate racemase. This enzyme catalyses the formation of d-glutamate, which is necessary for cell wall peptidoglycan synthesis. However, Bacillus subtilis hastwo glutamate racemase genes, named racE and yrpC. Since racE appears to beindispensable for growth in rich medium, the role of yrpC in d-amino acidsynthesis is vague. Experiments with racE- and yrpC-knockout mutants confirmedthat racE is essential for growth in rich medium but showed that this gene wasdispensable for growth in minimal medium, where yrpC executes the anapleroticrole of racE. LacZ fusion assays demonstrated that racE was expressed in bothtypes of media but yrpC was expressed only in minimal medium, which accounted forthe absence of yrpC function in rich medium. Neither racE nor yrpC was requiredfor B. subtilis cells to synthesize poly-gamma-dl-glutamate (gamma-PGA), acapsule polypeptide of d- and l-glutamate linked through a gamma-carboxylamidebond. Wild-type cells degraded the capsule during the late stationary phasewithout accumulating the degradation products, d-glutamate and l-glutamate, inthe medium. In contrast, racE or yrpC mutant cells accumulated significantamounts of d- but not l-glutamate. Exogenous d-glutamate utilization was somewhatdefective in the mutants and the double mutation of race and yrpc severelyimpaired d-amino acid utilization. Thus, both racemase genes appear necessary to complete the catabolism of exogenous d-glutamate generated from gamma-PGA.PMID: 15347750 [PubMed - indexed for MEDLINE] 223. Biotechniques. 2004 Aug;37(2):218, 220-2.PathoGene: a pathogen coding sequence discovery and analysis resource.Ng KW(1), Lawson J, Garner HR.Author information: (1)The University of Texas Southwestern Medical Center, Dallas, TX 75390-8591, USA.PathoGene is a web-based resource that streamlines the process of predictinggenes in microorganisms and designs PCR primers for amplification to facilitatesequence analysis and experimentation. PathoGene currently supports primer designfor every complete microbial, viral, and fungal genome as cataloged in GenBank bythe National Center for Biotechnology Information (NCBI;http://www.ncbi.nlm.nih.gov/). The resulting primers can then be subjected to astand-alone Basic Local Alignment Search Tool (BLAST) system called PathoBLAST inwhich the predicted PCR product and/or primers can be compared against the genomeof interest or a similar genome to find related genes or estimate primer quality.PMID: 15335212 [PubMed - indexed for MEDLINE] 224. J Nutr Sci Vitaminol (Tokyo). 2004 Apr;50(2):69-77.Recent progress of vitamin B6 biosynthesis.Sakai A(1), Kita M, Tani Y.Author information: (1)Graduate School of Biological Sciences, Nara Institute of Science and Technology,8916-5 Takayama-cho, 114 126 127 128 129 Ikoma, Nara 630-0101, Japan.This review is the current summary of vitamin B6 (B6) biosynthesis in Escherichiacoli and other microorganisms. The de novo biosynthesis of B6 has been studiedextensively for last three decades. However, the de novo biosynthesis of B6 stillremains unclear in spite of its simple structure. For the first two decades, B6biosynthesis had been mainly studied with E. coli using genetic, nutritional, andisotopic labeling experiments. According to these studies, some compoundsincluding glycolaldehyde were identified as the precursor. During the lastdecade, gene manipulate techniques were rapidly developed, and complete genomesequences of some microorganisms became available. Using these new tools,valuable information has been provided. The complete DNA sequence of pdx genesand other genes, which are possibly involved in B6 biosynthesis, were shown. The roles of some genes and precursors were proposed. Besides E. coli, B6biosynthesis in other microorganisms has been also studied. In somemicroorganisms, snz/sno was reported to be involved in B6 biosynthesis.Intriguingly these genes show no similarity to any of the E. coli pdx genes, and are not found in E. coli. Microorganisms having snz/sno gene homologues lackhomologues to pdxA/pdxJ genes, whereas those with homologues to pdxA/pdxJ lacksnz/sno gene homologues. Therefore, it is most likely that there are at least twokinds of B6 biosynthetic pathways in microorganisms. These studies providedimportant clues of B6 biosynthesis, but the entire picture of the B6 biosyntheticpathway remains unclear.PMID: 15242009 [PubMed - indexed for MEDLINE] 225. FEMS Microbiol Lett. 2004 Jun 15;235(2):393-9.Cloning and characterization of the Halobacillus trueperi betH gene, encoding thetransport system for the compatible solute glycine betaine.Lu W(1), Zhao B, Feng D, Yang S.Author information: (1)Department of Microbiology, College of Biological Sciences, China AgriculturalUniversity and Key Laboratory of Agro-Microbial Resources and Application,Ministry of Agriculture, Beijing 100094, PR China.Halobacillus trueperi accumulates glycine betaine under condition of highosmolarity. A fragment of the glycine betaine transporter betH gene was obtained from the genome of H. trueperi with degenerate primers. Through Southern blothybridization and inverse PCR, a 5.1 kb EcoRI fragment containing the completebetH gene was identified and subsequently sequenced. The betH gene was predicted to encode a 55.2 kDa protein (504 amino acid residues) with 12 transmembraneregions. BetH showed 56% identity to the OpuD of Bacillus subtilis which belongs to the betaine/carnitine/choline transporter (BCCT) family. Its putative promoterregion was highly homologous to sigmaB-dependent promoter of B. subtilis. A 2.6kb fragment containing the betH gene was cloned into pUC18 and transformed intothe Escherichia coli MKH13. The accumulation of glycine betaine in transformed E.coli MKH13 bacteria was confirmed using 13C nuclear magnetic resonancespectroscopy.PMID: 15183890 [PubMed - indexed for MEDLINE] 226. Nucleic Acids Res. 2004 May 20;32(9):2853-64. Print 2004.A protein-dependent riboswitch controlling ptsGHI operon expression in Bacillussubtilis: RNA structure rather than sequence provides interaction specificity.Schilling O(1), Langbein I, Müller M, Schmalisch MH, Stülke J.Author information: (1)Abteilung für Allgemeine Mikrobiologie, Georg-August-Universität Göttingen,Grisebachstrasse 8, D-37077 Göttingen, Germany.The Gram-positive soil bacterium Bacillus subtilis transports glucose by thephosphotransferase system. The genes for this system are encoded in the ptsGHIoperon. The expression of this operon is controlled at the level of transcriptelongation by a protein-dependent riboswitch. In the absence of glucose atranscriptional terminator prevents elongation into the structural genes. In the presence of glucose, the GlcT protein is activated and binds and stabilizes analternative RNA structure that overlaps the terminator and prevents termination. In this work, we have studied the structural and sequence requirements for thetwo mutually exclusive RNA structures, the terminator and the RNA antiterminator (the RAT sequence). In both cases, the structure seems to be more important than the actual sequence. The number of paired and unpaired bases in the RAT sequence is essential for recognition by the antiterminator protein GlcT. In contrast,mutations of individual bases are well tolerated as long as the general structureof the RAT is not impaired. The introduction of one additional base in the RATchanged its structure and resulted in complete loss of interaction with GlcT. In contrast, this mutant RAT was efficiently recognized by a different B.subtilisantitermination protein, LicT.PMCID: PMC419612PMID: 15155854 [PubMed - indexed for MEDLINE] 227. Nucleic Acids Res. 2004 May 18;32(9):e71.Genome coverage and sequence fidelity of phi29 polymerase-based multiple stranddisplacement whole genome amplification.Paez JG(1), Lin M, Beroukhim R, Lee JC, Zhao X, Richter DJ, Gabriel S, Herman P, Sasaki H, Altshuler D, Li C, Meyerson M, Sellers WR.Author information: (1)Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115,USA.Major efforts are underway to systematically define the somatic and germlinegenetic variations causally associated with disease. Genome-wide genetic analysisof actual clinical samples is, however, limited by the paucity of genomic DNAavailable. Here we have tested the fidelity and genome representation of phi29polymerase-based genome amplification (phi29MDA) using direct sequencing and highdensity oligonucleotide arrays probing >10,000 SNP alleles. Genome representationwas comprehensive and estimated to be 99.82% complete, although six regionsencompassing a maximum of 5.62 Mb failed to amplify. There was no degradation in the accuracy of SNP genotyping and, in direct sequencing experiments sampling500,000 bp, the estimated error rate (9.5 x 10(-6)) was the same as in pairedunamplified samples. The detection of cancer-associated loss of heterozygosityand copy number changes, including homozygous deletion and gene amplification,were similarly robust. These results suggest that phi29MDA yields high fidelity, near-complete genome representation suitable for high resolution geneticanalysis.PMCID: PMC419624PMID: 15150323 [PubMed - indexed for MEDLINE] 228. Biochem J. 2004 Aug 1;381(Pt 3):795-802.Identification of the first archaeal Type 1 RNase H gene from Halobacterium sp.NRC-1: archaeal RNase HI can cleave an RNA-DNA junction.Ohtani N(1), Yanagawa H, Tomita M, Itaya M.Author information: 115 (1)Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017,Japan. [email protected] the archaeal genomes sequenced to date contain a single Type 2 RNase H gene. We found that the genome of a halophilic archaeon, Halobacterium sp. NRC-1,contains an open reading frame with similarity to Type 1 RNase H. The proteinencoded by the Vng0255c gene, possessed amino acid sequence identities of 33%with Escherichia coli RNase HI and 34% with a Bacillus subtilis RNase HIhomologue. The B. subtilis RNase HI homologue, however, lacks amino acidsequences corresponding to a basic protrusion region of the E. coli RNase HI, andthe Vng0255c has the similar deletion. As this deletion apparently conferred acomplete loss of RNase H activity on the B. subtilis RNase HI homologue protein, the Vng0255c product was expected to exhibit no RNase H activity. However, thepurified recombinant Vng0255c protein specifically cleaved an RNA strand of theRNA/DNA hybrid in vitro, and when the Vng0255c gene was expressed in an E. colistrain MIC2067 it could suppress the temperature-sensitive growth defectassociated with the loss of RNase H enzymes of this strain. These results invitro and in vivo strongly indicate that the Halobacterium Vng0255c is the first archaeal Type 1 RNase H. This enzyme, unlike other Type 1 RNases H, was able tocleave an Okazaki fragment-like substrate at the junction between the 3'-side of ribonucleotide and 5'-side of deoxyribonucleotide. It is likely that the archaealType 1 RNase H plays a role in the removal of the last ribonucleotide of the RNA primer from the Okazaki fragment during DNA replication.PMCID: PMC1133889PMID: 15115438 [PubMed - indexed for MEDLINE] 130 229. Virology. 2004 May 1;322(2):239-52.Genomic organization and molecular analysis of the inducible prophage EJ-1, amosaic myovirus from an atypical pneumococcus.Romero P(1), López R, García E.Author information: (1)Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas,CSIC, 28040 Madrid, Spain.We report the complete genomic sequence of EJ-1, an inducible prophage isolatedfrom an atypical Streptococcus pneumoniae strain that belongs to the Myoviridaemorphology family. The phage and bacterial recombinational sites (attachmentsites) have been also determined. The genome of the EJ-1 prophage (42935 bp) isorganized in 73 open reading frames (ORFs) and in at least five major clusters.Bioinformatic and N-terminal amino acid sequence analyses enabled the assignment of possible functions to 52 ORFs. The predicted proteins coded for the EJ-1genome revealed similarities in the lysogeny, DNA replication, regulation,packaging, and head morphogenesis protein clusters with those from severalsiphoviruses infecting lactic acid bacteria. However, the proteins encoded bygenes orf53 to orf64, corresponding to putative tail proteins of the virion, werevery similar to those of the defective Bacillus subtilis myovirus PBSX with thenotable exception of the gene product of orf56 (the tape measure tail protein)that was similar to proteins from phages infecting Gram-negative bacteria. Thefirst description of the genome of a myovirus infecting a low G + C contentGram-positive bacterium, a member of a group embracing important human pathogens and industrial relevant species, will contribute to expand our current knowledge on phage biology and evolution.PMID: 15110522 [PubMed - indexed for MEDLINE] 131 230. Plasmid. 2004 May;51(3):227-37.Nucleotide sequence of the cryptic plasmid pTT8 from Thermus thermophilus HB8 andisolation and characterization of its high-copy-number mutant.Takayama G(1), Kosuge T, Maseda H, Nakamura A, Hoshino T.Author information: (1)Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki305-8572, Japan.The complete nucleotide sequence of pTT8, a cryptic plasmid from Thermusthermophilus HB8, was determined. pTT8 was 9328bp long and its G+C content was69%. pTT8 contained eight putative open reading frames, three of which showedextensive similarities to the plasmid addiction proteins PasA and PasB of pTC-F14and pAM10.6, and the RepA protein of the ColE2-related plasmids, respectively.During the analysis of pTT8-based plasmid pPP442, which had been obtained during a promoter-screening experiment, we occasionally isolated a plasmid with arelatively high-copy-number. This plasmid, pPP442m, contained a 1025 bp fragment derived from the genome of the HB27 host strain immediately upstream of theputative repA gene. Using the ori region of pPP442m, we constructed an expressionvector, pTEV131m, with an estimated high-copy-number of 30-40. This plasmid wasstably maintained in T. thermophilus HB27 under nonselective conditions for atleast 100 generations. Cloning of the alpha-amylase gene of Bacillusstearothermophilus DY-5 into pTEV131m gave more than twofold production of theenzyme compared with pTEV131, the parental plasmid.Copyright 2004 Elsevier Inc.PMID: 15109829 [PubMed - indexed for MEDLINE] 132 231. Biotechnol Bioeng. 2004 May 5;86(3):344-64.Gene expression in Bacillus subtilis surface biofilms with and withoutsporulation and the importance of yveR for biofilm maintenance.Ren D(1), Bedzyk LA, Setlow P, Thomas SM, Ye RW, Wood TK.Author information: (1)Department of Chemical Engineering, University of Connecticut, 191 AuditoriumRoad, Storrs, CT 06269-3222, USA.Five independent DNA microarray experiments were used to study the geneexpression profile of a 5-day Bacillus subtilis air-liquid interface biofilmrelative to planktonic cells. Both wild-type B. subtilis and its sporulationmutant (DeltaspoIIGB::erm) were investigated to discern the important biofilmgenes (in the presence and absence of sporulation). The microarray resultsindicated that suspension cells were encountering anaerobic conditions, and theair-liquid interface biofilm was metabolically active. For the statisticallysignificant differential expression (P < 0.05), there were 342 genes induced and 248 genes repressed in the wild-type biofilm, whereas 371 genes were induced and 128 genes were repressed in the sporulation mutant biofilm. The microarrayresults were confirmed with RNA dot blotting. A small portion of cells (1.5%) in the wild-type biofilm formed spores and sporulation genes were highly expressed. In the biofilm formed by the sporulation mutant, competence genes (comGA, srfAA, srfAB, srfAD, and comS) were induced which indicate a role for quorum sensing(bacterial gene expression controlled by sensing their population) in biofilms.There were 53 genes consistently induced in the biofilms of both the wild-typestrain and its spoIIGB mutant-those genes have functions for 116 133 134 135 136 transport,metabolism, antibiotic production-and 26 genes with unknown functions. Besidesthe large number of genes with known functions induced in the biofilm (121 genes in the wild-type biofilm and 185 genes in the sporulation mutant biofilm), somegenes with unknown functions were also induced (221 genes in the wild-typebiofilm and 186 genes in the sporulation mutant biofilm), such as the yve operon which appears to be involved in polysaccharide synthesis and the ybc operon whichinhibits the growth of competitors for nutrients. A knockout mutant of yveR wasconstructed, and the mutant showed major defects in biofilm maintenance. Both thewild-type strain and its sporulation mutant formed normal biofilms, suggestingcomplete sporulation is not necessary for biofilm formation. The expressionprofiles of these two strains share more repressed genes than induced genes,suggesting that the biofilm cells repress similar pathways in response tostarvation and high cell density.Copyright 2004 Wiley Periodicals, Inc.PMID: 15083514 [PubMed - indexed for MEDLINE] 232. Microbiology. 2004 Apr;150(Pt 4):967-78.Analysis of genetic polymorphisms affecting the four phospholipase C (plc) genes in Mycobacterium tuberculosis complex clinical isolates.Viana-Niero C(1), de Haas PE, van Soolingen D, Leão SC.Author information: (1)Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federalde São Paulo-Escola Paulista de Medicina (UNIFESP-EPM), Rua Botucatu, 862 3rdandar, 04023-062, São Paulo, Brazil.The Mycobacterium tuberculosis genome contains four highly related genes whichpresent significant similarity to Pseudomonas aeruginosa genes encodingphospholipase C enzymes. Three of these genes, plcA, plcB and plcC, are organizedin tandem (locus plcABC). The fourth gene, plcD, is located in a differentregion. This study investigates variations in plcABC and plcD genes in clinicalisolates of M. tuberculosis, Mycobacterium africanum and 'Mycobacteriumcanettii'. Genetic polymorphisms were examined by PCR, Southern blothybridization, sequence analysis and RT-PCR. Seven M. tuberculosis isolatescontain insertions of IS6110 elements within plcA, plcC or plcD. In 19 of 25 M.tuberculosis isolates examined, genomic deletions were identified, resulting inloss of parts of genes or complete genes from the plcABC and/or plcD loci.Partial plcD deletion was observed in one M. africanum isolate. In each case,deletions were associated with the presence of a copy of the IS6110 element andin all occurrences IS6110 was transposed in the same orientation. A mechanism of deletion resulting from homologous recombination of two copies of IS6110 wasrecognized in a group of genetically related M. tuberculosis isolates. Five M.tuberculosis isolates presented major polymorphisms in the plcABC and plcDregions, along with loss of expression competence that affected all four plcgenes. Phospholipase C is a well-known bacterial virulence factor. The preciserole of phospholipase C in the pathogenicity of M. tuberculosis is unknown, butconsidering the potential importance that the plc genes may have in the virulenceof the tubercle bacillus, the study of isolates cultured from patients withactive tuberculosis bearing genetic variations affecting these genes may provide insights into the significance of phospholipase C enzymes for tuberculosispathogenicity.PMID: 15073306 [PubMed - indexed for MEDLINE] 233. Appl Environ Microbiol. 2004 Apr;70(4):2514-9.Growth and sporulation of Bacillus cereus ATCC 14579 under defined conditions:temporal expression of genes for key sigma factors.de Vries YP(1), Hornstra LM, de Vos WM, Abee T.Author information: (1)Wageningen Centre for Food Sciences, Laboratory of Food Microbiology, Wageningen UR, The Netherlands. [email protected] airlift fermentor system allowing precise regulation of pH and aerationcombined with a chemically defined medium was used to study growth andsporulation of Bacillus cereus ATCC 14579. Sporulation was complete andsynchronous. Expression of sigA, sigB, sigF, and sigG was monitored withreal-time reverse transcription-PCR, and the pattern qualitatively resembled thatof Bacillus subtilis. This method allows reproducible production of stablespores, while the synchronous growth and defined conditions are excellentlysuitable for further gene expression studies of cellular differentiation of B.cereus.PMCID: PMC383076PMID: 15066852 [PubMed - indexed for MEDLINE] 234. Extremophiles. 2004 Feb;8(1):79-87. Epub 2004 Jan 10.A thermostable leucine aminopeptidase from Bacillus kaustophilus CCRC 11223.Lin LL(1), Hsu WH, Wu CP, Chi MC, Chou WM, Hu HY.Author information: (1)Department of Applied Chemistry, National Chiayi University, 60083, Chiayi,Taiwan.Two degenerate primers established from the consensus sequences of bacterialleucine aminopeptidases (LAP) were used to amplify a 360-bp gene fragment fromthe chromosomal DNA of thermophilic Bacillus kaustophilus CCRC 11223 and theamplified fragment was successfully used as a probe to clone a leucineaminopeptidase ( lap) gene from a genomic library of the strain. The geneconsists of an open reading frame (ORF) of 1,494 bp and encodes a protein of 497 amino acid residues with a calculated molecular mass of 53.7 kDa. The completeamino acid sequence of the cloned enzyme showed greater than 30% identity withprokaryotic and eukaryotic LAPs. Phylogenetic analysis showed that B.kaustophilus LAP is closely related to the enzyme from Bacillus subtilis and isgrouped with the M17 family. His6-tagged LAP was generated in Escherichia coli bycloning the coding region into pQE-30 and the recombinant enzyme was purified by nickel-chelate chromatography. The pH and temperature optima for the purifiedenzyme were 8 and 65 degrees C, respectively, and 50% of its activity remainedafter incubation at 60 degrees C for 32 min. The enzyme preferentially hydrolyzedL-leucine- p-nitroanilide ( L-Leu- p-NA) followed by Cys derivative.PMID: 15064993 [PubMed - indexed for MEDLINE] 235. Nucleic Acids Res. 2004 Apr 1;32(6):1973-81. Print 2004.Transcriptional organization of the Clostridium acetobutylicum genome.Paredes CJ(1), Rigoutsos I, Papoutsakis ET.Author information: (1)Department of Chemical and Biological Engineering, Northwestern University,Evanston, IL 60208, USA.Prokaryotic genes are frequently organized in multicistronic operons (ortranscriptional units, TUs), and usually the regulatory motifs for the whole TUare located upstream of the first TU gene. Although the number 117 137 138 139 140 of sequencedgenomes has increased dramatically, experimental information on TU organizationis extremely limited. Even for organisms as extensively studied as Escherichiacoli and Bacillus subtilis, TU annotation is far from complete. It thereforebecomes imperative to rely on computational approaches to complement experimentalinformation. Here we present a TU map for the obligate anaerobe Clostridiumacetobutylicum ATCC 824. This map is largely based on the distance between pairs of consecutive genes but enhanced and refined by predictions of several types of promoters (sigmaA, sigmaE and sigmaF/G) and rho-independent terminatorstructures. Based on the set of known C.acetobutylicum TUs, the presented TU map offers an 88% prediction accuracy.PMCID: PMC390361PMID: 15060177 [PubMed - indexed for MEDLINE] 236. Microbiology. 2004 Mar;150(Pt 3):613-20.Complementation of a Delta ccpA mutant of Lactobacillus casei with CcpA mutantsaffected in the DNA- and cofactor-binding domains.Esteban CD(1), Mahr K, Monedero V, Hillen W, Pérez-Martínez G, Titgemeyer F.Author information: (1)Departamento de Biotecnología, Instituto de Agroquímica y Tecnología deAlimentos-CSIC, Polígono de la Coma s/n, Apartado de Correos (PO Box) 73,46100-Burjassot, Valencia, Spain.In low-G+C Gram-positive bacteria, the regulatory protein CcpA has been shown to play a major part in the so-called carbon catabolite repression (CCR) process, aswell as in the induction of basic metabolic genes, for which it is considered aglobal regulator. A strain of Lactobacillus casei that carried a completedeletion of ccpA has been constructed and used to test the effect of CCR onN-acetylglucosaminidase activity and growth performance of a collection of seven CcpA mutations obtained by site-directed mutagenesis. The replaced amino acidswere located in the DNA- and cofactor (P-Ser-HPr)-binding domains. Mutations inthe DNA-binding domain lacked CCR, as found in Bacillus megaterium. However,mutations in the cofactor-binding domain of L. casei CcpA had a differentphenotype to that observed in the previous studies with B. megaterium. Two ofthem, S80L and T307I, displayed a significant hyper-repression, an effect neverreported before for CcpA. Comparison of growth capabilities provided by thedifferent mutants and their ability to sustain CCR demonstrated that CCR, atleast on the enzymic activity tested, and the growth defect caused by the CcpAmutations are unrelated features.PMID: 14993310 [PubMed - indexed for MEDLINE] 237. J Bacteriol. 2004 Mar;186(5):1229-38.Plasmid-dependent methylotrophy in thermotolerant Bacillus methanolicus.Brautaset T(1), Jakobsen M ØM, Flickinger MC, Valla S, Ellingsen TE.Author information: (1)Department of Biotechnology, Norwegian University of Science and Technology,N-7491 Trondheim. SINTEF Applied Chemistry, SINTEF, N-7043 Trondheim, [email protected] methanolicus can efficiently utilize methanol as a sole carbon sourceand has an optimum growth temperature of 50 degrees C. With the exception ofmannitol, no sugars have been reported to support rapid growth of this organism, which is classified as a restrictive methylotroph. Here we describe the DNAsequence and characterization of a 19,167-bp circular plasmid, designated pBM19, isolated from B. methanolicus MGA3. Sequence analysis of pBM19 demonstrated thepresence of the methanol dehydrogenase gene, mdh, which is crucial for methanolconsumption in this bacterium. In addition, five genes (pfk, encodingphosphofructokinase; rpe, encoding ribulose-5-phosphate 3-epimerase; tkt,encoding transketolase; glpX, encoding fructose-1,6-bisphosphatase; and fba,encoding fructose-1,6-bisphosphate aldolase) with deduced roles in methanolassimilation via the ribulose monophosphate pathway are encoded by pBM19. Ashuttle vector, pTB1.9, harboring the pBM19 minimal replicon (repB and ori) wasconstructed and used to transform MGA3. Analysis of the resulting recombinantstrain demonstrated that it was cured of pBM19 and was not able to grow onmethanol. A pTB1.9 derivative harboring the complete mdh gene could not restoregrowth on methanol when it was introduced into the pBM19-cured strain, suggestingthat additional pBM19 genes are required for consumption of this carbon source.Screening of 13 thermotolerant B. methanolicus wild-type strains showed that theyall harbor plasmids similar to pBM19, and this is the first report describingplasmid-linked methylotrophy in any microorganism. Our findings should have aneffect on future genetic manipulations of this organism, and they contribute to anew understanding of the biology of methylotrophs.PMCID: PMC344432PMID: 14973041 [PubMed - indexed for MEDLINE] 238. Nucleic Acids Res. 2004 Feb 11;32(3):977-88. Print 2004.The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptationsand a large plasmid related to Bacillus anthracis pXO1.Rasko DA(1), Ravel J, Økstad OA, Helgason E, Cer RZ, Jiang L, Shores KA, FoutsDE, Tourasse NJ, Angiuoli SV, Kolonay J, Nelson WC, Kolstø AB, Fraser CM, ReadTD.Author information: (1)The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD20850, USA.We sequenced the complete genome of Bacillus cereus ATCC 10987, a non-lethaldairy isolate in the same genetic subgroup as Bacillus anthracis. Comparison ofthe chromosomes demonstrated that B.cereus ATCC 10987 was more similar toB.anthracis Ames than B.cereus ATCC 14579, while containing a number of uniquemetabolic capabilities such as urease and xylose utilization and lacking theability to utilize nitrate and nitrite. Additionally, genetic mechanisms forvariation of capsule carbohydrate and flagella surface structures wereidentified. Bacillus cereus ATCC 10987 contains a single large plasmid(pBc10987), of approximately 208 kb, that is similar in gene content andorganization to B.anthracis pXO1 but is lacking the pathogenicity-associatedisland containing the anthrax lethal and edema toxin complex genes. Thechromosomal similarity of B.cereus ATCC 10987 to B.anthracis Ames, as well as thefact that it contains a large pXO1-like plasmid, may make it a possible model forstudying B.anthracis plasmid biology and regulatory cross-talk.PMCID: PMC373394PMID: 14960714 [PubMed - indexed for MEDLINE] 239. J Bacteriol. 2004 Feb;186(4):1120-8.Mechanism of transcription activation at the comG promoter by the competencetranscription factor ComK of Bacillus subtilis.Susanna KA(1), van der Werff AF, den Hengst CD, Calles B, Salas M, Venema G,Hamoen LW, 118 141 142 143 144 Kuipers OP.Author information: (1)Department of Genetics, University of Groningen, NL-9751 NN Haren, TheNetherlands.The development of genetic competence in Bacillus subtilis is regulated by acomplex signal transduction cascade, which results in the synthesis of thecompetence transcription factor, encoded by comK. ComK is required for thetranscription of the late competence genes that encode the DNA binding and uptakemachinery and of genes required for homologous recombination. In vivo and invitro experiments have shown that ComK is responsible for transcriptionactivation at the comG promoter. In this study, we investigated the mechanism of this transcription activation. The intrinsic binding characteristics of RNApolymerase with and without ComK at the comG promoter were determined,demonstrating that ComK stabilizes the binding of RNA polymerase to the comGpromoter. This stabilization probably occurs through interactions with theupstream DNA, since a deletion of the upstream DNA resulted in an almost completeabolishment of stabilization of RNA polymerase binding. Furthermore, a strongrequirement for the presence of an extra AT box in addition to the commonComK-binding site was shown. In vitro transcription with B. subtilis RNApolymerase reconstituted with wild-type alpha-subunits and with C-terminaldeletion mutants of the alpha-subunits was performed, demonstrating that thesedeletions do not abolish transcription activation by ComK. This indicates thatComK is not a type I activator. We also show that ComK is not required for opencomplex formation. A possible mechanism for transcription activation is proposed,implying that the major stimulatory effect of ComK is on binding of RNApolymerase.PMCID: PMC344208PMID: 14762007 [PubMed - indexed for MEDLINE] 240. Acta Crystallogr D Biol Crystallogr. 2004 Feb;60(Pt 2):329-30. Epub 2004 Jan 23.Crystallization of YloQ, a GTPase of unknown function essential for Bacillussubtilis viability.Cladière L(1), Blagova E, Levdikov VM, Brannigan JA, Séror SJ, Wilkinson AJ.Author information: (1)Institut de Génétique et Microbiologie, UMR CNRS 8621, Université Paris-Sud,91405 Orsay CEDEX, France.YloQ is a putative ATP/GTP-binding protein of unknown function identified fromthe complete sequence of the Bacillus subtilis genome. A gene-knockout programme established that yloQ is one of a set of some 270 indispensable genes for theviability of this organism. Crystals of YloQ have been grown from HEPES-buffered solutions at pH 7.5 containing polyethylene glycol and diffraction data have beencollected extending to 2.5 A spacing.PMID: 14747714 [PubMed - indexed for MEDLINE] 241. J Virol Methods. 2004 Mar 15;116(2):209-11.A simple method for cloning the complete begomovirus genome using thebacteriophage phi29 DNA polymerase.Inoue-Nagata AK(1), Albuquerque LC, Rocha WB, Nagata T.Author information: (1)Embrapa Hortaliças, Virology, Km. 9, BR060, C. Postal 218, 70359-970 Brasília,DF, Brazil. [email protected] bacteriophage phiDNA polymerase amplifies circular DNA in a rolling circleamplification mechanism. This characteristic was applied to amplify and clone thecomplete circular DNA genome of a begomovirus. Total DNA extracted from infected tissue was used as the template of an amplification reaction using the commercialkit TempliPhi (Amersham Biosciences). The amplified DNA could be used for direct sequencing and was cloned after digestion with a single cutting restrictionendonuclease. The use of this enzyme simplified the cloning steps and increasedthe cloning efficiency of the complete genome of a circular plant DNA virus.PMID: 14738990 [PubMed - indexed for MEDLINE] 242. Microbiology. 2004 Jan;150(Pt 1):205-15.Chlamydia trachomatis sigma28 recognizes the fliC promoter of Escherichia coliand responds to heat shock in chlamydiae.Shen L(1), Li M, Zhang YX.Author information: (1)Section of Infectious Diseases, Department of Medicine, Boston Medical Center,Boston University School of Medicine, Boston, Massachusetts 02118, USA.The rpsD gene of Chlamydia trachomatis encodes the alternative sigma factorsigma28, which bears strong homology to many bacterial sigma factors, includingEscherichia coli sigma8 and Bacillus subtilis sigmaB and sigmaD. Recently, asigma28 promoter was identified upstream of the late-cycle-expressed gene hctB,which encodes the Chlamydia-histone-like protein 2 (Yu & Tan, 2003). In thisstudy it is shown that the product of chlamydial rpsD is an E. coli sigma28homologue. It was found that recombinant chlamydial sigma8, in combination withE. coli core RNA polymerase, initiates transcription in vitro from the E. colisigma28-dependent promoter of fliC. It was also demonstrated that the recombinantchlamydial sigma28 does not recognize major sigma factor sigma70-consensus-likesequences in vitro. In C. trachomatis-infected cells, two rpsD transcripts weredetected with 5' ends located 18 (transcript I) and 54 bp (transcript II)upstream of the translational initiation codon at 16 and 30 h post-infection.When the temperature of cultures infected with C. trachomatis was shifted from 35to 42 degrees C, the rpsD transcript I increased dramatically. The levels ofchlamydial sigma28, relative to EF-Tu, were greater throughout the exponentialgrowth phase of the reticulate body, but lower late in the developmental cycle.These data support the hypothesis that sigma28 plays a role in the regulatorynetwork that allows chlamydiae to survive changes in its environment, enabling itto complete its unique developmental cycle.PMID: 14702414 [PubMed - indexed for MEDLINE] 243. Comput Biol Chem. 2003 Oct;27(4-5):481-95.Investigating protein domain combinations in complete proteomes.Nikitin F(1), Lisacek F.Author information: (1)Geneva Bioinformatics, Geneva 1206, Switzerland.Protein-related information is more accumulated rather than reduced to asynthetic view. Itemising properties of protein sequences is informative, so isthe list of ingredients to do some cooking, but without a recipe, that is,quantification and chronology, understanding is incomplete. If the goal ofaccumulating information is to discover or reveal the function and relatedbiochemical mechanisms, information has to be weighed and ordered. As aguideline, the weight of a piece of information should reflect how often itconsistently occurs in various contexts. We propose a common sense approach toquantify and put data and information into perspective. Complete bacterialproteomes are individually mapped with the Pfam-A database of domains and proteinfamily signatures in an attempt to assess the modularity of proteins at the levelof a single proteome and the implications of a modular description of proteinsfor a functional interpretation. Poorly annotated 119 145 146 147 148 proteins in the most documentedbacteria (E. coli and B. subtilis) were considered in an attempt to formulatehypothesis on the basis of domain/module content.PMID: 14642756 [PubMed - indexed for MEDLINE] 244. Mol Microbiol. 2003 Nov;50(3):781-93.CotB is essential for complete activation of green light-induced genes duringcomplementary chromatic adaptation in Fremyella diplosiphon.Balabas BE(1), Montgomery BL, Ong LE, Kehoe DM.Author information: (1)Department of Biology, Indiana University, Bloomington, IN 47405, USA.The dramatic modifications of photosynthetic light harvesting antennae calledphycobilisomes that occur during complementary chromatic adaptation incyanobacteria are controlled by two separate photosensory systems. The firstsystem involves the signal transduction components RcaE, RcaF and RcaC, whichappear to make up a complex multistep phosphorelay. This system controls thelight responsive expression of the cpcB2A2H2I2D2, cpeBA and cpeCDE operons, whichencode phycobilisome proteins. The second system, which is not yet characterized,acts in concert with the first but only regulates the light responses of cpeBAand cpeCDE. We have generated and characterized a new mutant class, named the Tanmutants. In at least one member of this class, light-regulated RNA accumulationpatterns are altered for cpeBA and cpeCDE, but not for cpcB2A2H2I2D2. Thus thismutant contains a lesion that may impair the operation of the second system. Wedemonstrate that several Tan mutants are the result of improper expression of thegene cotB. CotB has limited similarity to lyase class proteins, particularlythose related to NblB, which is required for degradation of phycobilisomes inother cyanobacteria. Possible roles of CotB in the biogenesis of phycobilisomesare discussed.PMID: 14617141 [PubMed - indexed for MEDLINE] 245. Appl Environ Microbiol. 2003 Nov;69(11):6888-98.Sequencing and characterization of pBM400 from Bacillus megaterium QM B1551.Scholle MD(1), White CA, Kunnimalaiyaan M, Vary PS.Author information: (1)Present address: Argonne National Laboratory, Bioscience Division, Argonne, IL60439, USA.Bacillus megaterium QM B1551 plasmid pBM400, one of seven indigenous plasmids,has been labeled with a selectable marker, isolated, completely sequenced, andpartially characterized. A sequence of 53,903 bp was generated, revealing a totalof 50 predicted open reading frames (ORFs); 33 were carried on one strand and 17 were carried on the other. These ORFs comprised 57% of the pBM400 sequence.Besides the replicon region and a complete rRNA operon that have previously been described, several interesting genes were found, including genes for predictedproteins for cell division (FtsZ and FtsK), DNA-RNA interaction (FtsK, Int/Rec,and reverse transcriptase), germination (CwlJ), styrene degradation (StyA), andheavy metal resistance (Cu-Cd export and ATPase). Three of the ORF products hadhigh similarities to proteins from the Bacillus anthracis virulence plasmid pXO1.An insertion element with similarity to the IS256 family and several hypotheticalproteins similar to those from the chromosomes of other Bacillus and Lactococcus species were present. This study provides a basis for isolation and sequencing ofother high-molecular-weight plasmids from QM B1551 and for understanding the roleof megaplasmids in gram-positive bacteria. The genes carried by pBM400 suggest a possible role of this plasmid in the survival of B. megaterium in hostileenvironments with heavy metals or styrene and also suggest that there has been anexchange of genes within the gram-positive bacteria, including pathogens.PMCID: PMC262321PMID: 14602653 [PubMed - indexed for MEDLINE] 246. Physiol Genomics. 2003 Dec 16;16(1):19-23.Identification of genomic islands in the genome of Bacillus cereus by comparativeanalysis with Bacillus anthracis.Zhang R(1), Zhang CT.Author information: (1)Department of Epidemiology and Biostatistics, Tianjin Cancer Institute andHospital, Tianjin 300060, China.Comment in Physiol Genomics. 2004 Jan 15;16(2):180-1.Horizontal gene transfer has been recognized as a universal event throughoutbacterial evolution. The availability of both complete genome sequences ofBacillus cereus and B. anthracis provides the possibility to perform comparative analysis based on their genomes. By using a windowless method to display thedistribution of the genomic GC content of B. cereus and B. anthracis, we havefound three genomic islands in the genome of B. cereus, i.e., BCGI-1, BCGI-2, andBCGI-3, respectively, which are absent in the genome of B. anthracis. All thegenomic islands have abrupt changes in GC content compared with that ofsurrounding regions. BCGI-1 has many conserved features of genomic islands, e.g.,a Val-tRNA gene is utilized as the integration site, and a site-specificrecombinase gene is located at the 3' end. BCGI-2 has a large percentage of phageprotein, suggesting a phage-related recombination is involved. BCGI-3 contains a ferric anguibactin transport system, which is likely to be involved in the irontransport that enables the bacterium to overcome the iron limitation in the host.In addition, BCGI-3 also contains a cluster of genes related to lantibiotics,which may play a role during the evolution of the genome. Furthermore, theintegrations of the genomic islands, BCGI-1 and BCGI-3, result in deletions ofDNA sequence fragments; therefore, such integrations lead to both gene gain andgene loss simultaneously.PMID: 14600214 [PubMed - indexed for MEDLINE] 247. Curr Microbiol. 2003 Sep;47(3):226-30.Toxicity of Bacillus sphaericus LP1-G against susceptible and resistant Culexquinquefasciatus and the cloning of the mosquitocidal toxin gene.Shi YX(1), Zheng DS, Yuan ZM.Author information: (1)Wuhan Institute of Virology, Academic Sinica, Wuhan 430071, China.Bacillus sphaericus LP1-G, belonging to flagellar serotype H3, has been found to have moderate toxicity against two resistant Culex quinquefasciatus colonies(RLCq1 and RLCq2) and the susceptible contrast (SLCq). With an aim of screeningmosquitocidal acting factor, a partial genome library was prepared from a partialHindIII digest of the total DNA from Bacillus sphaericus LP1-G. Two thousandtwenty Escherichia coli clones were screened for toxicity against susceptibleSLCq, and a toxic clone, designated E-UL68, was chosen for further study. Therecombinant E-UL68 performed toxicity against both susceptible and two resistant colonies, having the same level of toxicity as that of wide-type strain LP1-G.Sequence analysis revealed that the inserted fragment was composed of 3876nucleotides and contained a complete gene, whose sequence 120 149 150 151 152 was identical to thatof the mtx gene from B. sphaericus SSII-1. Because the binary toxin producedduring sporulation of strain LP1-G has no activity against the target mosquitoes,this indicates that the Mtx toxin or other active factors might perhaps beresponsible for the toxicity of LP1-G against different colonies of mosquitolarvae.PMID: 14570274 [PubMed - indexed for MEDLINE] 248. Vaccine. 2003 Oct 1;21(27-30):4270-4.The in vitro evolution of BCG vaccines.Mostowy S(1), Tsolaki AG, Small PM, Behr MA.Author information: (1)McGill University Health Centre, Montreal, Que., Canada H3G 1A4.The bacillus Calmette-Géurin (BCG) family of vaccines currently implemented toprevent tuberculosis (TB) consist of clonal bacterial strains independentlyshaped by nearly a half-century of evolution. Derived from virulent Mycobacteriumbovis, daughter strains of BCG were additionally passaged under the samelaboratory conditions that resulted in its original attenuation. Genomic loss of the RD1 region has been demonstrated to coincide with attenuation from virulence,while deletions occurring after the loss of RD1 are speculated to be responsible for BCG's over-attenuation. To provide a more complete description of their totalgenomic variation, the genomic content of BCG strains are investigated byAffymetrix GeneChip. Because clinical isolates of M. tuberculosis have previouslybeen characterized via GeneChip interrogation, analysis permits the comparison ofin vivo versus in vitro evolution of M. tuberculosis complex subspecies. Thecontrast between the two modes of evolution are discussed in its relevancetowards TB pathogenicity.PMID: 14505909 [PubMed - indexed for MEDLINE] 249. Microbiology. 2003 Sep;149(Pt 9):2317-29.The Bacillus subtilis YufLM two-component system regulates the expression of the malate transporters MaeN (YufR) and YflS, and is essential for utilization ofmalate in minimal medium.Tanaka K(1), Kobayashi K, Ogasawara N.Author information: (1)Department of Bioinformatics and Genomics, Graduate School of InformationScience, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0101, Japan.The Gram-positive bacterium Bacillus subtilis has a complete set of enzymes forthe tricarboxylic acid (TCA) cycle and can grow aerobically using most of the TCAcycle intermediates (malate, fumarate, succinate and citrate) as a sole carbonsource. The B. subtilis genome sequence contains three paralogous two-componentregulatory systems, CitST, DctSR and YufLM. CitST and DctSR activate theexpression of a transporter of the Mg(2+)-citrate complex (CitM) and a fumarateand succinate transporter (DctP), respectively. These findings prompted aninvestigation of whether the YufL sensor and its cognate regulator, YufM, play a role in malate uptake. This paper reports that the YufM regulator shows in vitro binding to the promoter region of two malate transporter genes, maeN and yflS,and is responsible for inducing their expression in vivo. It was also found that inactivation of the yufM or maeN genes resulted in bacteria that could not growin a minimal salts medium containing malate as a sole carbon source, indicatingthat the induction of the MaeN transporter by the YufM regulator is essential forthe utilization of malate as a carbon source. Inactivation of the yufL generesulted in the constitutive expression of MaeN. This expression was suppressedby reintroduction of the kinase domain of YufL, indicating that the YufL sensoris required for proper signal detection and signalling specificity. The authorspropose that a phosphatase activity of YufL plays an important role in the YufLM two-component regulatory system. The studies reported here have revealed thatmembers of a set of paralogous two-component regulatory systems in B. subtilis,CitST, DctSR and YufLM, are involved in a related function--uptake (andmetabolism) of the TCA cycle intermediates--but with distinct substratespecificities.PMID: 12949159 [PubMed - indexed for MEDLINE] 250. J Bacteriol. 2003 Aug;185(16):4764-71.Transcriptional pausing in the Bacillus subtilis pyr operon in vitro: a role intranscriptional attenuation?Zhang H(1), Switzer RL.Author information: (1)Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA.The genes encoding the enzymes of pyrimidine nucleotide biosynthesis (pyr genes) are regulated in Bacillus subtilis and many other bacterial species bytranscriptional attenuation. When UMP or UTP is bound to the PyrR regulatoryprotein, it binds to pyr mRNA at specific sequences and secondary structures inthe RNA. Binding to this site prevents formation of an antiterminator stem-loopin the RNA and permits formation of a downstream terminator, leading to reducedexpression of the pyr genes lying downstream from the terminator. The functioningof several other transcriptional attenuation systems has been shown to involvetranscriptional pausing; this observation stimulated us to use single-roundtranscription of pyr genes to test for formation of paused transcripts in vitro. Using templates with each of the three known B. subtilis pyr attenuation sites,we identified one major pause site in each in which the half-life of the pausedtranscript was increased four- to sixfold by NusA. In each case pausing at theNusA-stimulated site prevented formation of a complete antiterminator stem-loop, while it resulted in increased time for a PyrR binding loop to form and for PyrR to bind to this loop. Thus, the pausing detected in vitro is potentially capable of playing a role in establishing the correct timing for pyr attenuation in vivo.With two of three pyr templates the combination of NusA with PyrR markedlystimulated termination of transcription at the normal termination sites. Thissuggests that NusA, by stabilizing pausing, plays a role in termination of pyrtranscription in vivo.PMCID: PMC166459PMID: 12896995 [PubMed - indexed for MEDLINE] 251. Science. 2003 Jul 25;301(5632):510-3. Epub 2003 Jun 19.Cannibalism by sporulating bacteria.González-Pastor JE(1), Hobbs EC, Losick R.Author information: (1)Department of Molecular and Cellular Biology, The Biological Laboratories,Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.Comment in Science. 2003 Jul 25;301(5632):467-8.Spore formation by the bacterium Bacillus subtilis is an elaborate developmental process that is triggered by nutrient limitation. Here we report that cells that have entered the pathway to sporulate produce and export a killing factor and asignaling protein that act cooperatively to block sister cells from sporulatingand to cause them to lyse. The sporulating cells feed on the nutrients therebyreleased, which allows them to 121 153 154 155 156 keep growing rather than to completemorphogenesis. We propose that sporulation is a stress-response pathway of lastresort and that B. subtilis delays a commitment to spore formation bycannibalizing its siblings.PMID: 12817086 [PubMed - indexed for MEDLINE] 252. Croat Med J. 2003 Jun;44(3):336-41.Laboratory aspects of bioterrorism-related anthrax--from identification tomolecular subtyping to microbial forensics.Popović T(1), Glass M.Author information: (1)Epidemiologic Investigations Laboratory, Meningitis and Special Pathogens Branch,DBMD/NCID/CDC, Mailstop G34, 1600 Clifton Road, Atlanta, GA 30333, [email protected] the bioterrorism-associated anthrax investigation of 2001 in the UnitedStates, 11 patients were diagnosed with inhalational anthrax and 11 more with thecutaneous forms of the disease. Over 125,000 specimens were processed atlaboratories of the Laboratory Response Network including those at the Centersfor Disease Control and Prevention. Although the 2001 anthrax investigationinitially began as a public health investigation, the forensic aspect quicklybecame a preeminent component of the investigation. Whereas a public healthinvestigation aims primarily to identify the causative agent and its source, sothat appropriate and timely control and preventative measures can be implemented,a forensic investigation goes further to associate the source of the causativeagent with a specific individual or group. In addition to identification andmolecular characterization of the causative agents, which are the crucialcomponents of forensic microbiology, there are many other requirements andactivities that need to be in place for investigators to successfully complete a forensic investigation. These activities include establishment of qualityassurance/quality control criteria and regular proficiency testing for alllaboratories where evidence is analyzed; additional and/or specialized trainingin handling and processing samples in accordance with forensic microbiologycriteria, not only for first responders but also for laboratory and other public health scientists; and establishing and maintaining repositories and databasescontaining isolates of diverse temporal and geographic origins to provide acomparative and diverse background for investigators to identify and track theorigin and source of such agents.PMID: 12808729 [PubMed - indexed for MEDLINE] 253. DNA Cell Biol. 2003 Mar;22(3):209-15.First complete nucleotide sequence and heterologous gene organization of the two rRNA operons in the phytoplasma genome.Jung HY(1), Miyata S, Oshima K, Kakizawa S, Nishigawa H, Wei W, Suzuki S, UgakiM, Hibi T, Namba S.Author information: (1)Division of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi,Bunkyo-ku. Tokyo 113-8657, Japan.Phytoplasmas are cell-wallless Gram-positive low G + C bacteria belonging to the Mollicutes that inhabit the cytoplasm of plants and insects. Althoughphytoplasmas possess two ribosomal RNA (rrn) operons, only one has been fullysequenced. Here, we determined the complete nucleotide sequence of both rrnoperons (designated rrnA and rrnB) of onion yellows (OY) phytoplasma. Bothoperons have rRNA genes organized as 5'-16S-23S-5S-3' with very highly conserved sequences; the 16S, 23S, and 5S rRNA genes are 99.9, 99.8, and 99.1% identicalbetween the two operons. However, the organization of tRNA genes in the upstream region from 16S rRNA gene and in the downstream region from 5S rRNA gene differs markedly. Several promoter candidates were detected upstream from both operons,which suggests that both operons are functional. Interestingly, both have atRNA(Ile) gene in the 16S-23S spacer region, while the reported rrnB operon ofloofah witches' broom phytoplasma does not, indicating heterogenous geneorganization of rrnB within phytoplasmas. The phytoplasma tRNA gene organization is similar to that of acholeplasmas, a closely related mollicute, and differentfrom that of mycoplasmas, another mollicute. Moreover, the organization suggests that the rrn operons were derived from that of a related nonmollicute bacterium, Bacillus subtilis. This data should shed light on the evolutionary relationships and phylogeny of the mollicutes.PMID: 12804119 [PubMed - indexed for MEDLINE] 254. Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7877-82. Epub 2003 Jun 3.The complete genome sequence of Mycobacterium bovis.Garnier T(1), Eiglmeier K, Camus JC, Medina N, Mansoor H, Pryor M, Duthoy S,Grondin S, Lacroix C, Monsempe C, Simon S, Harris B, Atkin R, Doggett J, Mayes R,Keating L, Wheeler PR, Parkhill J, Barrell BG, Cole ST, Gordon SV, Hewinson RG.Author information: (1)Unité de Génétique Moléculaire Bactérienne and PT4 Annotation, Génopole, InstitutPasteur, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France.Mycobacterium bovis is the causative agent of tuberculosis in a range of animalspecies and man, with worldwide annual losses to agriculture of $3 billion. Thehuman burden of tuberculosis caused by the bovine tubercle bacillus is stilllargely unknown. M. bovis was also the progenitor for the M. bovis bacillusCalmette-Guérin vaccine strain, the most widely used human vaccine. Here wedescribe the 4,345,492-bp genome sequence of M. bovis AF2122/97 and itscomparison with the genomes of Mycobacterium tuberculosis and Mycobacteriumleprae. Strikingly, the genome sequence of M. bovis is >99.95% identical to that of M. tuberculosis, but deletion of genetic information has led to a reducedgenome size. Comparison with M. leprae reveals a number of common gene losses,suggesting the removal of functional redundancy. Cell wall components andsecreted proteins show the greatest variation, indicating their potential role inhost-bacillus interactions or immune evasion. Furthermore, there are no genesunique to M. bovis, implying that differential gene expression may be the key to the host tropisms of human and bovine bacilli. The genome sequence thereforeoffers major insight on the evolution, host preference, and pathobiology of M.bovis.PMCID: PMC164681PMID: 12788972 [PubMed - indexed for MEDLINE] 255. J Theor Biol. 2003 Jun 21;222(4):495-503.Gene arrangements and branching orders of gram-positive bacteria.Kunisawa T.Author information: Department of Applied Biological Sciences, Science University of Tokyo, Noda278-8510, Japan. [email protected] availability of complete genomic sequence data allows one to develop newmethods of reconstructing phylogenetic trees. A simple method of reconstructingbranching orders based on gene transposition (or lateral transfer) is presented. 122 It is argued that specific gene arrangements on four different genomes coulddetermine a branching order. A computer search for such gene arrangements wascarried out against gene order data of completely sequenced Gram-positivebacteria. Gene arrangements around ribosomal protein S4 gene, murC(UDP-N-acetylmuramate:alanine ligase) gene and dnaE (DNA polymerase III alphachain) gene each suggest a branching order in which actinobacteria with a highgenomic G+C content first branched off from other Gram-positives with a low G+Ccontent and then a split occurred between Mycoplasma species and a group closely related to Bacillus subtilis. A recently sequenced thermophilic bacteriumThermoanaerobacter tengcongensis is suggested to have branched off from thelineage leading to the low G+C Gram-positives prior to the split between theMycoplasma and Bacillus groups. By contrast to the indel analysis in which asingle evolutionary event of insertion or deletion of a signature sequence isassumed, the present method does not necessarily require such a parsimoniousassumption of gene transposition.PMID: 12781748 [PubMed - indexed for MEDLINE] 157 256. Tuberculosis (Edinb). 2003;83(1-3):201-7.Progress in TB drug development and what is still needed.Duncan K.Author information: GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK. [email protected] effective drugs for treating TB were introduced over 30 years ago, yetdeaths from the disease continue to increase. New tools are needed, includingdrugs with activity against multi-drug resistant strains of Mycobacteriumtuberculosis. Agents that reduce the duration and complexity of the currenttherapy would have a major impact on compliance and overall cure rate. In recent years, our understanding of the tubercle bacillus and its interaction with thehuman host has improved dramatically, particularly with the publication in 1998of the complete genome sequence of M. tuberculosis H37Rv. New genetic tools have been developed and we can now ascertain the function of individual genes. Thus,many potential drug targets have been identified and a number demonstrated to be essential. Several lead compounds have been found, as well as a potential drugcandidate, the nitroimidazopyran PA-824. A far greater effort is needed totranslate basic research into drug discovery programmes. High throughputscreening and rational design must be employed to find lead compounds actingagainst well-validated targets and a substantial increase in resources devoted tomedicinal chemistry is required to take these leads and turn them into drugs.Models of mycobacterial persistence, in which compounds with potent sterilizingactivity can be rapidly analysed, must be characterized. Finally, surrogatemarkers that give an early indication of treatment outcome would facilitateclinical trials.PMID: 12758212 [PubMed - indexed for MEDLINE] 158 257. Plasmid. 2003 May;49(3):205-32.The patchwork nature of rolling-circle plasmids: comparison of six plasmids from two distinct Bacillus thuringiensis serotypes.Andrup L(1), Jensen GB, Wilcks A, Smidt L, Hoflack L, Mahillon J.Author information: (1)National Institute of Occupational Health, Lersø Parkallé 105, DK-2100Copenhagen, Denmark. [email protected] thuringiensis, the entomopathogenic bacteria from the Bacillus cereusgroup, harbors numerous extrachromosomal molecules whose sizes vary from 2 tomore than 200kb. Apart from the genes coding for the biopesticidedelta-endotoxins located on large plasmids, little information has been obtained on these plasmids and their contribution to the biology of their host. In thispaper, we embarked on a detailed comparison of six small rolling-circlereplicating (RCR) plasmids originating from two major B. thuringiensis strains.The complete nucleotide sequences of plasmid pGI1, pGI2, pGI3, pTX14-1, pTX14-2, and pTX14-3 have been obtained and compared. Replication functions, comprising,for each plasmid, the gene encoding the Rep-protein, double-strand origin ofreplication (dso), single-strand origin of replication (sso), have beenidentified and analyzed. Two new families, or homology groups, of RCR plasmidsoriginated from the studies of these plasmids (Group VI based on pGI3 and GroupVII based on pTX14-3). On five of the six plasmids, loci involved in conjugative mobilization (Mob-genes and origin of transfer (oriT)) were identified. Plasmids pTX14-1, pTX14-2, and pTX14-3 each harbor an ORF encoding a polypeptidecontaining a central domain with repetitive elements similar to eukaryoticcollagen (Gly-X-Y triplets). These genes were termed bcol forBacillus-collagen-like genes.PMID: 12749835 [PubMed - indexed for MEDLINE] 159 258. Appl Environ Microbiol. 2003 May;69(5):2684-91.A census of rRNA genes and linked genomic sequences within a soil metagenomiclibrary.Liles MR(1), Manske BF, Bintrim SB, Handelsman J, Goodman RM.Author information: (1)Department of Plant Pathology. Gaylord Nelson Institute of Environmental Studies,University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA.We have analyzed the diversity of microbial genomes represented in a library ofmetagenomic DNA from soil. A total of 24,400 bacterial artificial chromosome(BAC) clones were screened for 16S rRNA genes. The sequences obtained from BACclones were compared with a collection generated by direct PCR amplification and cloning of 16S rRNA genes from the same soil. The results indicated that the BAC library had substantially lower representation of bacteria among the Bacillus,alpha-Proteobacteria, and CFB groups; greater representation among the beta- and gamma-Proteobacteria, and OP10 divisions; and no rRNA genes from the domainsEukaryota and Archaea. In addition to rRNA genes recovered from the bacterialdivisions Proteobacteria, Verrucomicrobia, Firmicutes, Cytophagales, and OP11, weidentified many rRNA genes from the BAC library affiliated with the bacterialdivision Acidobacterium; all of these sequences were affiliated with subdivisionsthat lack cultured representatives. The complete sequence of one BAC clonederived from a member of the Acidobacterium division revealed a complete rRNAoperon and 20 other open reading frames, including predicted gene productsinvolved in cell division, cell cycling, folic acid biosynthesis, substratemetabolism, amino acid uptake, DNA repair, and transcriptional regulation. Thisstudy is the first step in using genomics to reveal the physiology ofas-yet-uncultured members of the Acidobacterium division.PMCID: PMC154537PMID: 12732537 [PubMed - indexed for MEDLINE] 123 160 259. Plasmid. 2003 Mar;49(2):118-29.Sequence and analysis of pBM02, a novel RCR cryptic plasmid from Lactococcuslactis subsp cremoris P8-2-47.Sánchez C(1), Mayo B.Author information: (1)Instituto de Productos Lácteos de Asturias (CSIC), Carretera de Infiesto s/n,33300-Villaviciosa, Asturias, Spain.This paper reports the complete nucleotide sequence of the 3.85 kbp plasmid pBM02from Lactococcus lactis subsp. cremoris P8-2-47. Analysis of the sequencepredicted six ORFs larger than 25 amino acids. They all were transcribed from thesame strand and organized in two functional cassettes: the replication region anda putative mobilization region. In the replication region, two ORFs specifyingproteins homologous to others found in some classes of rolling circle-replicatingplasmids were encountered (copG and repB). In fact, single-stranded DNA wasdetected as a replication intermediate of pBM02. copG and repB, together withsome upstream sequences, formed part of the minimal replication unit of theplasmid. Interestingly, pBM02 shared a 212 bp stretch with plasmids of the pWV01 type, in which the whole single-strand origin of replication is included. In the mobilization region, an ORF coding for a mobilization-like protein was present,preceded by a putative oriT sequence homologous to that of plasmid pMV158. Thereplicon of pBM02 is of the wide-host range type, and functions in bothGram-positive and Gram-negative bacteria, including Lactobacillus casei,Lactobacillus plantarum, Bacillus subtilis, and Escherichia coli.PMID: 12726765 [PubMed - indexed for MEDLINE] 161 260. Nature. 2003 May 1;423(6935):87-91.Genome sequence of Bacillus cereus and comparative analysis with Bacillusanthracis.Ivanova N(1), Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V,Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A, Chu L, Mazur M, Goltsman E,Larsen N, D'Souza M, Walunas T, Grechkin Y, Pusch G, Haselkorn R, Fonstein M,Ehrlich SD, Overbeek R, Kyrpides N.Author information: (1)Integrated Genomics, Chicago, Illinois 60612, USA. [email protected] in Nature. 2003 May 1;423(6935):23-5. Trends Microbiol. 2003 Jul;11(7):297-9.Bacillus cereus is an opportunistic pathogen causing food poisoning manifested bydiarrhoeal or emetic syndromes. It is closely related to the animal and humanpathogen Bacillus anthracis and the insect pathogen Bacillus thuringiensis, theformer being used as a biological weapon and the latter as a pesticide. B.anthracis and B. thuringiensis are readily distinguished from B. cereus by thepresence of plasmid-borne specific toxins (B. anthracis and B. thuringiensis) andcapsule (B. anthracis). But phylogenetic studies based on the analysis ofchromosomal genes bring controversial results, and it is unclear whether B.cereus, B. anthracis and B. thuringiensis are varieties of the same species ordifferent species. Here we report the sequencing and analysis of the type strain B. cereus ATCC 14579. The complete genome sequence of B. cereus ATCC 14579together with the gapped genome of B. anthracis A2012 enables us to performcomparative analysis, and hence to identify the genes that are conserved between B. cereus and B. anthracis, and the genes that are unique for each species. Weuse the former to clarify the phylogeny of the cereus group, and the latter todetermine plasmid-independent species-specific markers.PMID: 12721630 [PubMed - indexed for MEDLINE] 162 261. Nature. 2003 May 1;423(6935):81-6.The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria.Read TD(1), Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J,Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R,Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM,Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, PlautRD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE,White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, KolstøAB, Fraser CM.Author information: (1)The Institute for Genomic Research, 9712 Medical Center Drive, Rockville,Maryland 20850, USA. [email protected]).Comment in Nature. 2003 May 1;423(6935):23-5. Trends Microbiol. 2003 Jul;11(7):297-9.Bacillus anthracis is an endospore-forming bacterium that causes inhalationalanthrax. Key virulence genes are found on plasmids (extra-chromosomal, circular, double-stranded DNA molecules) pXO1 (ref. 2) and pXO2 (ref. 3). To identifyadditional genes that might contribute to virulence, we analysed the completesequence of the chromosome of B. anthracis Ames (about 5.23 megabases). We found several chromosomally encoded proteins that may contribute topathogenicity--including haemolysins, phospholipases and iron acquisitionfunctions--and identified numerous surface proteins that might be importanttargets for vaccines and drugs. Almost all these putative chromosomal virulenceand surface proteins have homologues in Bacillus cereus, highlighting thesimilarity of B. anthracis to near-neighbours that are not associated withanthrax. By performing a comparative genome hybridization of 19 B. cereus andBacillus thuringiensis strains against a B. anthracis DNA microarray, weconfirmed the general similarity of chromosomal genes among this group of closerelatives. However, we found that the gene sequences of pXO1 and pXO2 were morevariable between strains, suggesting plasmid mobility in the group. The complete sequence of B. anthracis is a step towards a better understanding of anthraxpathogenesis.PMID: 12721629 [PubMed - indexed for MEDLINE] 163 262. Appl Environ Microbiol. 2003 Apr;69(4):2116-25.Spatial and temporal analysis of the microbial community in slow sand filtersused for treating horticultural irrigation water.Calvo-Bado LA(1), Pettitt TR, Parsons N, Petch GM, Morgan JA, Whipps JM.Author information: (1)Plant Pathology and Microbiology Department, Horticulture Research International,Wellesbourne, Warwickshire CV35 9EF, United Kingdom.An experimental slow sand filter (SSF) was constructed to study the spatial andtemporal structure of a bacterial community suppressive to an oomycete plantpathogen, Phytophthora cryptogea. Passage of water through the mature sand columnresulted in complete removal of zoospores of the plant pathogen. To monitorglobal changes in the microbial community, 124 bacterial and fungal numbers wereestimated on selective media, direct viable counts of fungal spores were made,and the ATP content was measured. PCR amplification of 16S rRNA genes anddenaturing gradient gel electrophoresis (DGGE) were used to study the dynamics ofthe bacterial community in detail. The top layer (1 cm) of the SSF column wasdominated by a variable and active microbial population, whereas the middle (50cm) and bottom (80 cm) layers were dominated by less active and diverse bacterialpopulations. The major changes in the microbial populations occurred during thefirst week of filter operation, and these populations then remained to the end ofthe study. Spatial and temporal nonlinear mapping of the DGGE bands provided auseful visual representation of the similarities between SSF samples. Accordingto the DGGE profile, less than 2% of the dominating bands present in the SSFcolumn were represented in the culturable population. Sequence analysis of DGGEbands from all depths of the SSF column indicated that a range of bacteria werepresent, with 16S rRNA gene sequences similar to groups such as Bacillusmegaterium, Cytophaga, Desulfovibrio, Legionella, Rhodococcus rhodochrous,Sphingomonas, and an uncharacterized environmental clone. This study describesthe characterization of the performance, and microbial composition, of SSFs used for the treatment of water for use in the horticultural industry. Utilization of naturally suppressive population of microorganisms either directly or bymanipulation of the environment in an SSF may provide a more reproducible controlmethod for the future.PMCID: PMC154832PMID: 12676691 [PubMed - indexed for MEDLINE] 164 263. FEMS Microbiol Lett. 2003 Jan 21;218(1):23-30.The DNA secondary structure of the Bacillus subtilis genome.Tosato V(1), Gjuracic K, Vlahovicek K, Pongor S, Danchin A, Bruschi CV.Author information: (1)Microbiology Group, International Centre for Genetic Engineering andBiotechnology, AREA Science Park, Padriciano 99, 34012, Trieste, Italy.The entire genomic DNA sequence of the Gram-positive bacterium Bacillus subtilis reported in the SubtiList database has been subjected in this work to a complete bioinformatic analysis of the potential formation of secondary DNA structuressuch as hairpins and bending. The most significant of these structures have been mapped with respect to their genomic location and compared to those structuresalready known to have a physiological role, such as the rho-independenttranscription terminators. The distribution of these structures along thebacterial chromosome shows two major features: (i). the concentration of the mostcurved DNA in the intergenic regions rather than within the ORFs, and (ii). adecreasing gradient of large hairpins from the origin towards the terC end ofchromosomal DNA replication. Given the increasing biological relevance ofsecondary DNA structures, these findings should facilitate further studies on theevolution, dynamics and expression of the genetic information stored in bacterialgenomes.PMID: 12583893 [PubMed - indexed for MEDLINE] 165 264. Microbiology. 2003 Jan;149(Pt 1):229-37.Characterization of a nitrate-respiring bacterial community using the nitratereductase gene (narG) as a functional marker.Gregory LG(1), Bond PL, Richardson DJ, Spiro S.Author information: (1)School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.Bacterial cultures capable of reducing nitrate to nitrite, or of completedenitrification, were established from 5, 10, 15 and 20 cm depths of a freshwatersediment. Taxonomic analysis of the 56 isolates using 16S rRNA gene sequencesrevealed an unexpected species richness, which included representatives of thegamma-Proteobacteria, Bacillus spp., Staphylococcus spp. and members of theActinobacteria. Gram-positive species tended to predominate in the lower depthsof the sediment, where there was evidence of active sulphate respiration.Sequences (from the narG gene) potentially encoding the catalytic subunit of the membrane-associated nitrate reductase were successfully amplified from 46 of the isolates, using a nested PCR with four degenerate primers. NarG sequencesclustered into three major groupings that were supported by alternativephylogenetic analyses. The NarG sequences from Gram-positive isolates (according to rRNA gene phylogeny) clustered together within sequences from the low-G+CGram-positive bacteria. However, this cluster also included two sequences frommembers of the genus Pseudomonas. Another group contained mostly NarG sequencesfrom the Proteobacteria (according to rRNA gene phylogeny), but also includedfive sequences from Gram-positive species. The third group of NarG sequencescontained three sequences from Gram-positive species. Thus, the NarG-derivedphylogeny is not entirely consistent with 16S rRNA-based taxonomy, precluding theuse of the narG gene as a taxonomically useful tool for the characterization ofnitrate-respiring bacteria. Total DNA was also extracted from the four depthintervals of the sediment sample and used in similar narG amplifications. Mostsequences amplified directly from environmental DNA clustered in theGram-negative group, and none was in the predominantly Gram-positive group. Thestudy also revealed a degree of spatial organization of a nitrate-respiringcommunity in terms of both microbiology and narG sequences.PMID: 12576596 [PubMed - indexed for MEDLINE] 166 265. J Bacteriol. 2003 Feb;185(3):879-86.Postdivisional synthesis of the Sporosarcina ureae DNA translocase SpoIIIE eitherin the mother cell or in the prespore enables Bacillus subtilis to translocateDNA from the mother cell to the prespore.Chary VK(1), Piggot PJ.Author information: (1)Department of Microbiology and Immunology, Temple University School of Medicine, 3400 N. Broad Street, Philadelphia, PA 19140, USA.The differentiation of vegetative cells of Bacillus subtilis into spores involvesasymmetric cell division, which precedes complete chromosome partitioning. TheDNA translocase SpoIIIE is required to translocate the origin distal 70% of thechromosome from the larger mother cell into the smaller prespore, the two cellsthat result from the division. We have tested the effect of altering the time andlocation of SpoIIIE synthesis on spore formation. We have expressed the spoIIIEhomologue from Sporosarcina ureae in B. subtilis under the control of differentpromoters. Expression from either a weak mother cell-specific (sigma(E)) promoteror a weak prespore-specific (sigma(F)) promoter partly complemented thesporulation defect of a spoIIIE36 mutant; however, expression from a strongprespore-specific (sigma(F)) promoter did not. DNA translocation from the mother cell to the prespore 125 167 168 169 170 was assayed using spoIIQ-lacZ inserted at thrC;transcription of spoIIQ occurs only in the prespore. Translocation ofthrC::spoIIQ-lacZ into the prespore occurred efficiently when spoIIIE(Su) wasexpressed from the weak sigma(E)- or sigma(F)-controlled promoters but not whenit was expressed from the strong sigma(F)-controlled promoter. It is speculatedthat the mechanism directing SpoIIIE insertion into the septum in the correctorientation may accommodate slow postseptational, prespore-specific SpoIIIEsynthesis but may be swamped by strong prespore-specific synthesis.PMCID: PMC142829PMID: 12533463 [PubMed - indexed for MEDLINE] 266. BMC Bioinformatics. 2002 Dec 19;3:40. Epub 2002 Dec 19.ORFer--retrieval of protein sequences and open reading frames from GenBank andstorage into relational databases or text files.Büssow K(1), Hoffmann S, Sievert V.Author information: (1)Protein Structure Factory, Max Planck Institute of Molecular Genetics, Heubnerweg6, 14059 Berlin, Germany. [email protected]: Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading framesas a prerequisite of the cloning and recombinant expression of these proteins.RESULTS: A Java program was developed for retrieval of protein and nucleic acidsequences and annotations from NCBI GenBank, using the XML sequence format.Annotations retrieved by ORFer include sequence name, organism and also thecompleteness of the sequence. The program has a graphical user interface,although it can be used in a non-interactive mode. For protein sequences, theprogram also extracts the open reading frame sequence, if available, and checksits correct translation. ORFer accepts user input in the form of single or lists of GenBank GI identifiers or accession numbers. It can be used to extractcomplete sets of open reading frames and protein sequences from any kind ofGenBank sequence entry, including complete genomes or chromosomes. Sequences are either stored with their features in a relational database or can be exported as text files in Fasta or tabulator delimited format. The ORFer program is freelyavailable at http://www.proteinstrukturfabrik.de/orfer.CONCLUSION: The ORFer program allows for fast retrieval of DNA sequences, proteinsequences and their open reading frames and sequence annotations from GenBank.Furthermore, storage of sequences and features in a relational database issupported. Such a database can supplement a laboratory information system (LIMS) with appropriate sequence information.PMCID: PMC139979PMID: 12493080 [PubMed - indexed for MEDLINE] 267. J Mol Evol. 2002 Dec;55(6):632-7.Simultaneous horizontal gene transfer of a gene coding for ribosomal protein l27 and operational genes in Arthrobacter sp.Garcia-Vallvé S(1), Simó FX, Montero MA, Arola L, Romeu A.Author information: (1)Department of Biochemistry and Biotechnology, Rovira i Virgili University, PlImperial Tàrraco 1, E-43005 Tarragona, Catalonia, Spain.Phylogenetic analysis of bacterial L27 ribosomal proteins showed that, againsttaxonomy, the L27 protein from the Actinobacteria Arthrobacter sp. clusters with protein sequences from the Bacillus group. The L27 gene clusters in theArthrobacter sp. genome with six genes responsible for creatinine and sarcosinedegradation. Phylogenetic analyses of orthologue proteins encoded by three ofthese genes also showed a phylogenetic relationship with Bacillus species.Comparisons between the synonymous codon usage of the Arthrobacter sp. genes and those from complete genomes showed that Arthrobacter genes encoding the L27ribosomal protein and the proteins responsible for the degradation of creatinine and sarcosine have a codon usage that is more similar to that of Bacillus speciesthan that of Arthrobacter. We suggest that the Arthrobacter sp. genes encodingthe L27 ribosomal protein and the proteins responsible for the degradation ofcreatinine and sarcosine were acquired simultaneously through horizontal genetransfer from an unknown Bacillus species.PMID: 12486522 [PubMed - indexed for MEDLINE] 268. Gene. 2002 Oct 30;300(1-2):105-15.Study of statistical correlations in DNA sequences.Bernaola-Galván P(1), Carpena P, Román-Roldán R, Oliver JL.Author information: (1)Departamento de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga, Málaga, Spain. [email protected] we present a study of statistical correlations among different positions in DNA sequences and their implications by directly using the autocorrelationfunction. Such an analysis is possible now because of the availability of largesequences or even complete genomes of many organisms. After describing the way inwhich the autocorrelation function can be applied to DNA-sequence analysis, weshow that long-range correlations, implying scale independence, appear in severalbacterial genomes as well as in long human chromosome contigs. The source forsuch correlations in bacteria, which may extend up to 60 kb in Bacillus subtilis,may be related to massive lateral transfer of compositionally biased genes fromother genomes. In the human genome, correlations extend for more than fivedecades and may be related to the evolution of the 'neogenome', a modernevolutionary acquisition composed by GC-rich isochores displaying long-rangecorrelations and scale invariance.PMID: 12468092 [PubMed - indexed for MEDLINE] 269. Microbiology. 2002 Nov;148(Pt 11):3539-52.Six GTP-binding proteins of the Era/Obg family are essential for cell growth inBacillus subtilis.Morimoto T(1), Loh PC, Hirai T, Asai K, Kobayashi K, Moriya S, Ogasawara N.Author information: (1)Department of Microbial Cell Biology, Graduate school of Biological Sciences,Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0101,Japan.GTP-binding proteins are found in all domains of life and are involved in variousessential cellular processes. With the recent explosion of available genomesequence data, a widely distributed bacterial subfamily of GTP-binding proteinswas discovered, represented by the Escherichia coli Era and the Bacillus subtilisObg proteins. Although only a limited number of the GTP-binding proteinsbelonging to the subfamily have been experimentally characterized, and theirfunction remains unknown, the available data suggests that many of them areessential to bacterial growth. When the complete genomic sequence of B. subtilis was 126 171 172 173 174 surveyed for genes encoding GTP-binding proteins of the Era/Obg family, nine such genes were identified. As a first step in elucidating the functionalnetworks of those nine GTP-binding proteins, data presented here indicates thatsix of them are essential for B. subtilis viability. Additionally, it is shownthat the six essential proteins are able to specifically bind GTP and GDP invitro. Experimental depletion of the essential GTP-binding proteins was examined in the context of cell morphology and chromosome replication, and it was foundthat two proteins, Bex and YqeH, appeared to participate in the regulation ofinitiation of chromosome replication. Collectively, these results suggest thatmembers of the GTP-binding Era/Obg family are important proteins with precise,yet still not fully understood, roles in bacterial growth and viability.PMID: 12427945 [PubMed - indexed for MEDLINE] 270. Plasmid. 2002 Sep;48(2):77-97.The ICESt1 element of Streptococcus thermophilus belongs to a large family ofintegrative and conjugative elements that exchange modules and change theirspecificity of integration.Burrus V(1), Pavlovic G, Decaris B, Guédon G.Author information: (1)Laboratoire de Génétique et Microbiologie, UMR INRA-UHP no. 1128, Faculté desSciences, Université Henri Poincaré (Nancy 1), BP239, 54506 Vandoeuvre-lès-Nancy,France.The 34,734-bp element ICESt1 from Streptococcus thermophilus CNRZ368 issite-specifically integrated into the 3(') end of the gene fda. ICESt1 encodesintegrative functions and putative transfer functions. Six proteins of theputative conjugative system of ICESt1 are related to those encoded by theconjugative transposon Tn916 from Enterococcus faecalis. A comparison of theseproteins with those encoded by the complete or partial genome sequences ofvarious low G+C bacteria including Bacillus subtilis, Clostridium difficile, E.faecalis, Listeria monocytogenes, Staphylococcus aureus, and Streptococcus mutansrevealed the presence of numerous putative site-specific integrative conjugative elements and/or conjugative transposons within these genomes. Sequencecomparisons revealed that these elements possess a modular structure and thatexchanges of unrelated or distantly related modules and genes have occurredbetween these elements, and also plasmids and prophages. These exchanges haveprobably led to modifications in the site specificity of integration of theseelements. Therefore, a distinction between low specificity integrativeconjugative elements (i.e., conjugative transposons) and site-specificintegrative conjugative elements does not appear to be relevant. We propose tocall all the conjugative elements that excise by site-specific recombination and integrate by recombination between a specific site of a circular intermediate andanother site, "Integrative and Conjugative Elements" (ICEs), irrespective of the integration specificity.PMID: 12383726 [PubMed - indexed for MEDLINE] 271. Ann N Y Acad Sci. 2002 Oct;969:112-8.Basis for the extraordinary genetic stability of anthrax.Kiel JL(1), Parker JE, Gifford H, Stribling LJ, Alls JL, Meltz ML, McCreary RP,Holwitt EA.Author information: (1)Directed Energy Bioeffects Division, Human Effectiveness Directorate, Air ForceResearch Laboratory, Brooks Air Force Base, Texas 78235, [email protected] 500 isolates of anthrax bacillus from around the world represent one of the most genetically homogeneous microbes. There are three possibilities for thisgenetic stability: (1) anthrax has an extraordinarily high fidelity repairsystem, (2) genetic damage to anthrax is usually lethal, and/or (3) a highlydemanding and selective process exists in its environment that is necessary forthe completion of its life cycle. Using probes made from genes selected by growthof an Escherichia coli expression vector Bacillus anthracis library onhypertrophic high nitrate concentration medium, genes unique to B. anthracis wereisolated. High nitration conditions generated stable chromosomal mutants thatdisplayed altered morphology and life-cycle progression. Therefore, life-cycleprogression connected to nitration, associated with host inflammatory response,selects for mutants that show life-cycle progression tightly coupled toprogression of the inflammatory response to anthrax. Significant variation fromthis coupled progression leads to failure of anthrax to complete its life-cycleat the death of its host.PMID: 12381574 [PubMed - indexed for MEDLINE] 272. J Biol Chem. 2002 Dec 13;277(50):48949-59. Epub 2002 Oct 9.Comparative genomics of thiamin biosynthesis in procaryotes. New genes andregulatory mechanisms.Rodionov DA(1), Vitreschak AG, Mironov AA, Gelfand MS.Author information: (1)State Scientific Center GosNIIGenetika, Moscow 113545, [email protected] B(1) in its active form thiamin pyrophosphate is an essential coenzymethat is synthesized by coupling of pyrimidine (hydroxymethylpyrimidine; HMP) and thiazole (hydroxyethylthiazole) moieties in bacteria. Using comparative analysis of genes, operons, and regulatory elements, we describe the thiamin biosynthetic pathway in available bacterial genomes. The previously detectedthiamin-regulatory element, thi box (Miranda-Rios, J., Navarro, M., and Soberon, M. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 9736-9741), was extended, resultingin a new, highly conserved RNA secondary structure, the THI element, which iswidely distributed in eubacteria and also occurs in some archaea. Search for THI elements and analysis of operon structures identified a large number of newcandidate thiamin-regulated genes, mostly transporters, in various prokaryoticorganisms. In particular, we assign the thiamin transporter function to yuaJ inthe Bacillus/Clostridium group and the HMP transporter function to an ABCtransporter thiXYZ in some proteobacteria and firmicutes. By analogy to the modelof regulation of the riboflavin biosynthesis, we suggest thiamin-mediatedregulation based on formation of alternative RNA structures involving the THIelement. Either transcriptional or translational attenuation mechanism mayoperate in different taxonomic groups, dependent on the existence of putativehairpins that either act as transcriptional terminators or sequester translation initiation sites. Based on analysis of co-occurrence of the thiamin biosynthetic genes in complete genomes, we predict that eubacteria, archaea, and eukaryotahave different pathways for the HMP and hydroxyethylthiazole biosynthesis.PMID: 12376536 [PubMed - indexed for MEDLINE] 273. J Genet. 2002 Apr;81(1):5-11.Cloning and characterization of an insecticidal crystal protein gene fromBacillus thuringiensis 127 175 176 177 178 subspecies kenyae.Misra HS(1), Khairnar NP, Mathur M, Vijayalakshmi N, Hire RS, Dongre TK, Mahajan SK.Author information: (1)Molecular Biology and Agriculture Division, Bhabha Atomic Research Centre, Mumbai400 085, India. [email protected] sporulating culture of Bacillus thuringiensis subsp. kenyae strain HD549 istoxic to larvae of lepidopteran insect species such as Spodoptera litura,Helicoverpa armigera and Phthorimaea operculella, and a dipteran insect, Culexfatigans. A 1.9-kb DNA fragment, PCR-amplified from HD549 usingcryII-gene-specific primers, was cloned and expressed in E. coli. The recombinantprotein produced 92% mortality in first-instar larvae of Spodoptera litura and86% inhibition of adult emergence in Phthorimaea operculella, but showed very lowtoxicity against Helicoverpa armigera, and lower mortality against third-instarlarvae of dipteran insects Culex fatigans, Anopheles stephensi and Aedes aegypti.The sequence of the cloned crystal protein gene showed almost complete homologywith a mosquitocidal toxin gene from Bacillus thuringiensis var. kurstaki, withonly five mutations scattered in different regions. Amino acid alignment withdifferent insecticidal crystal proteins using the MUTALIN program suggestedpresence of the conserved block 3 region in the sequence of this protein. Amutation in codon 409 of this gene that changes a highly conserved phenylalanine residue to serine lies in this block.PMID: 12357073 [PubMed - indexed for MEDLINE] 274. Tuberculosis (Edinb). 2002;82(2-3):85-90.Is Mycobacterium tuberculosis a closer relative to Gram-positive or Gram-negativebacterial pathogens?Fu LM(1), Fu-Liu CS.Author information: (1)Pacific Tuberculosis and Cancer Research Organization, Los Angeles, California,USA. [email protected] phylogenetic position of Mycobacterium tuberculosis relative to otherbacteria is controversial. Its cell wall has characteristics of bothGram-positive and Gram-negative bacteria. In the standard reference of bacterial phylogeny based on 16S ribosomal RNA sequence comparison, M. tuberculosis belongsto the high G+C Gram-positive bacteria that form a monophyletic group with thelow G+C Gram-positive bacteria such as Bacillus subtilis. Some analyses indicate no particular relationship between these two groups. The availability of thecomplete genome sequence of M. tuberculosis allows us to reexamine this issuefrom genomic perspectives, as genome-based phylogenies may be more representativeof the evolutionary history of whole organisms than molecular trees. In thegenome tree constructed based on conserved gene content, M. tuberculosis is more related to Gram-negative than to Gram-positive bacteria as reflected by theevolutionary distance between nearest ancestral units. This conclusion may besupported by another analysis showing that M. tuberculosis shares relatively moreorthologous genes for energy production and conversion with Gram-negativebacteria, in particular, Escherichia coli and Pseudomonas aeruginosa, than withGram-positive bacteria.PMID: 12356459 [PubMed - indexed for MEDLINE] 275. Appl Environ Microbiol. 2002 Oct;68(10):5082-95.Complete sequence and organization of pBtoxis, the toxin-coding plasmid ofBacillus thuringiensis subsp. israelensis.Berry C(1), O'Neil S, Ben-Dov E, Jones AF, Murphy L, Quail MA, Holden MT, Harris D, Zaritsky A, Parkhill J.Author information: (1)Cardiff School of Biosciences, Cardiff University, Cardiff, United [email protected] entire 127,923-bp sequence of the toxin-encoding plasmid pBtoxis fromBacillus thuringiensis subsp. israelensis is presented and analyzed. In addition to the four known Cry and two known Cyt toxins, a third Cyt-type sequence wasfound with an additional C-terminal domain previously unseen in such proteins.Many plasmid-encoded genes could be involved in several functions other thantoxin production. The most striking of these are several genes potentiallyaffecting host sporulation and germination and a set of genes for the production and export of a peptide antibiotic.PMCID: PMC126441PMID: 12324359 [PubMed - indexed for MEDLINE] 276. Nucleic Acids Res. 2002 Sep 15;30(18):3927-35.Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and itsunexpected adaptive capabilities to extreme environments.Takami H(1), Takaki Y, Uchiyama I.Author information: (1)Japan Marine Science and Technology Center, Microbial Genome Research Group, 2-15Natsushima, Yokosuka, Kanagawa 237-0061, Japan. [email protected] iheyensis HTE831 is an alkaliphilic and extremely halotolerantBacillus-related species isolated from deep-sea sediment. We present here thecomplete genome sequence of HTE831 along with analyses of genes required foradaptation to highly alkaline and saline environments. The genome consists of 3.6Mb, encoding many proteins potentially associated with roles in regulation ofintracellular osmotic pressure and pH homeostasis. The candidate genes involvedin alkaliphily were determined based on comparative analysis with three Bacillus species and two other Gram-positive species. Comparison with the genomes of othermajor Gram-positive bacterial species suggests that the backbone of the genusBacillus is composed of approximately 350 genes. This second genome sequence ofan alkaliphilic Bacillus-related species will be useful in understanding life in highly alkaline environments and microbial diversity within the ubiquitousbacilli.PMCID: PMC137110PMID: 12235376 [PubMed - indexed for MEDLINE] 277. Can J Microbiol. 2002 Jul;48(7):655-74.Molecular characterization of bacterial diversity from British Columbia forestsoils subjected to disturbance.Axelrood PE(1), Chow ML, Radomski CC, McDermott JM, Davies J.Author information: (1)BC Research Inc, Vancouver, Canada. [email protected] in Can J Microbiol 2002 Sep;48(9):853-4.Bacteria from forest soils were characterized by DNA sequence analysis of cloned 16S rRNA gene fragments (16S clones). Surface organic matter and mineral soilsamples from a British Columbia Ministry of Forests Long-Term Soil Productivity(LTSP) installation were collected during winter and summer from two disturbance treatments: whole-tree harvesting with no soil compaction (plot N) and whole-treeharvesting plus complete surface organic matter removal with heavy soilcompaction (plot S). Phylogenetic analyses revealed that 87% of 580 16S cloneswere classified as Proteobacteria, Actinobacteria, Acidobacterium,Verrucomicrobia, Bacil- 128 179 180 181 182 lus/Clostridium group, Cytophaga-Flexibacter-Bacteroidesgroup, green nonsulfur bacteria, Planctomyces, and candidate divisions TM6 andOP10. Seventy-five 16S clones could not be classified into known bacterialdivisions, and five 16S clones were related to chloroplast DNA. Members ofProteobacteria represented 46% of the clone library. A higher proportion of 16Sclones affiliated with y-Proteobacteria were from plot N compared with plot S.16S rRNA gene fragments amplified with Pseudomonas-specific primers and cloned(Ps clones) were examined from mineral-soil samples from plots N and S from threeLTSP installations. A significantly greater proportion of sequenced Ps clonesfrom plot N contained Pseudomonas 16S rRNA gene fragments compared with Ps clonesfrom plot S.PMID: 12224564 [PubMed - indexed for MEDLINE] 278. Can J Microbiol. 2002 Jul;48(7):643-54.Cultivation-dependent characterization of bacterial diversity from BritishColumbia forest soils subjected to disturbance.Axelrood PE(1), Chow ML, Arnold CS, Lu K, McDermott JM, Davies J.Author information: (1)BC Research Inc, Vancouver, Canada. [email protected] from forest surface organic matter and mineral soil horizons werecultivated using four methods and characterized by fatty acid methyl ester (FAME)analysis. Soil samples from a British Columbia Ministry of Forests Long-Term SoilProductivity (LTSP) installation were collected during winter and summer from twodisturbance treatments (whole-tree harvesting with no soil compaction (plot N)and whole-tree harvesting plus complete surface organic matter removal with heavysoil compaction (plot S)) and from an unlogged reference plot (REF). Seventy-fivepercent of 1795 bacterial isolates were affiliated with 42 genera representingbeta- and gamma-Proteobacteria, Actinobacteria, the Bacillus/Clostridium group,and the Cytophaga-Flexibacter-Bacteroides group. Approximately half of theculture collection represented genetic diversity confined to four bacterialgenera: Pseudomonas, Bacillus, Paenibacillus, and Arthrobacter. A significantlyhigher proportion of bacterial isolates belonging to Actinobacteria, and themember genus Arthrobacter, were isolated from plot S soil samples compared withsoil samples from plots N and REF. Twenty-five percent of bacterial isolates werenot conclusively identified to genus with FAME analysis. Sherlock Tracker clusteranalysis and partial 16S rRNA gene sequence analysis enabled classification of a subset of these isolates.PMID: 12224563 [PubMed - indexed for MEDLINE] 279. J Biol Chem. 2002 Nov 15;277(46):44068-78. Epub 2002 Sep 5.Selective contribution of the twin-arginine translocation pathway to proteinsecretion in Bacillus subtilis.Jongbloed JD(1), Antelmann H, Hecker M, Nijland R, Bron S, Airaksinen U, Pries F,Quax WJ, van Dijl JM, Braun PG.Author information: (1)Department of Genetics, Groningen Biomolecular Sciences and BiotechnologyInstitute, Kerklaan 30, 9751 NN Haren, The Netherlands.The availability of the complete genome sequence of Bacillus subtilis has allowedthe prediction of all exported proteins of this Gram-positive eubacterium.Recently, approximately 180 secretory and 114 lipoprotein signal peptides werepredicted to direct protein export from the cytoplasm. Whereas most exportedproteins appear to use the Sec pathway, 69 of these proteins could potentiallyuse the Tat pathway, as their signal peptides contain RR- or KR-motifs. In thepresent studies, proteomic techniques were applied to verify how manyextracellular B. subtilis proteins follow the Tat pathway. Strikingly, theextracellular accumulation of 13 proteins with potential RR/KR-signal peptideswas Tat-independent, showing that their RR/KR-motifs are not recognized by theTat machinery. In fact, only the phosphodiesterase PhoD was shown to be secreted in a strictly Tat-dependent manner. Sodium azide-inhibition of SecA stronglyaffected the extracellular appearance of de novo synthesized proteins, including the lipase LipA and two other proteins with predicted RR/KR-signal peptides. The SecA-dependent export of pre-LipA is particularly remarkable, because itsRR-signal peptide conforms well to stringent criteria for the prediction ofTat-dependent export in Escherichia coli. Taken together, our observations showthat the Tat pathway makes a highly selective contribution to the extracellularproteome of B. subtilis.PMID: 12218047 [PubMed - indexed for MEDLINE] 280. DNA Cell Biol. 2002 Jul;21(7):527-34.Complete nucleotide sequence of the S10-spc operon of phytoplasma: geneorganization and genetic code resemble those of Bacillus subtilis.Miyata S(1), Furuki K, Oshima K, Sawayanagi T, Nishigawa H, Kakizawa S, Jung HY, Ugaki M, Namba S.Author information: (1)Laboratory of Bioresource Technology, Graduate School of Frontier Sciences, TheUniversity of Tokyo, Kashiwa, Chiba Japan.An 11.4-kbp region of genomic DNA containing the complete S10-spc operon wasconstructed by an integrative mapping technique with eight plasmid vectorscarrying ribosomal protein sequences from onion yellows phytoplasma. Southernhybridization analysis indicated that phytoplasmal S10-spc is a single-copyoperon. This is the first complete S10-spc operon of a phytoplasma to bereported, although only a part of six serial genes of the S10 operon is reported previously. The operon has a context of 5'-rps10, rpl3, rpl4, rpl23, rpl2, rps19,rpl22, rps3, rpl16, rpl29, rps17, rpl14, rpl24, rpl5, rps14, rps8, rpl6, rpl18,rps5, rpl30, rpl15, SecY-3', and is composed of 21 ribosomal protein subunitgenes and a SecY protein translocase subunit gene. Resembling Bacillus, thisoperon contains an rpl30 gene that other mollicutes (Mycoplasma genitalium, M.pneumoniae, and M. pulmonis) lack. A phylogenetic tree based on the rps3 sequenceshowed that phytoplasmas are phylogenetically closer to acholeplasmas andbacillus than to mycoplasmas. In the S10-spc operon, translation may start fromeither a GTG codon or an ATG codon, and stop at a TGA codon, as has been reportedfor acholeplasmas and bacillus. However, in mycoplasmas, GTG was found as a startcodon, and TGA was found not as a stop codon, but instead as a tryptophan codon. These data derived from the gene organization, and the genetic code deviationsupport the hypothesis that phytoplasmal genes resemble those of acholeplasmasand Bacillus more than those of other mollicutes.PMID: 12162807 [PubMed - indexed for MEDLINE] 281. Front Biosci. 2002 Aug 1;7:d1815-24.Recent progress in Bacillus subtilis two-component regulation.Ogura M(1), Tanaka T.Author information: (1)Department of Marine Science, School of Marine science and Technology, TokaiUniversity, Orido 3-20-1, 129 183 184 185 186 Shimizu, Shizuoka 424-8610, Japan.Two-component regulatory systems serve to control gene expression in response to environmental and physiological changes. They are widespread among a variety oforganisms and most often found in prokaryotes. One of the gram-positivemicroorganisms Bacillus subtilis is a well-studied bacterium whose completenucleotide sequence has been determined. Thus, it is now possible to studytranscription of the whole genome with microarray analysis. In this review wesummarize the recent progress in B. subtilis two-component regulatory systems by describing the known systems and those for which the function was recentlyassigned. Also included is an attempt to construct a partial transcriptionalnetwork involving several two-component systems. The studies described here arebased on the data from traditional genetics and biochemistry, and from microarrayanalysis of 29 two-component systems.PMID: 12133819 [PubMed - indexed for MEDLINE] 282. Biochem Biophys Res Commun. 2002 Jun 28;294(5):1064-70.The truncated hemoglobin from Mycobacterium leprae.Visca P(1), Fabozzi G, Petrucca A, Ciaccio C, Coletta M, De Sanctis G, Bolognesi M, Milani M, Ascenzi P.Author information: (1)Dipartimento di Biologia e Laboratorio Interdipartimentale di MicroscopiaElettronica, Università Roma Tre, Viale G. Marconi 446, I-00146 Rome, [email protected] hemoglobins (trHb's) form a family of low molecular weight O2 bindinghemoproteins distributed in eubacteria, protozoa, and plants. TrHb's branch in a distinct clade within the hemoglobin (Hb) superfamily. A unique globin gene hasrecently been identified from the complete genome sequence of Mycobacteriumleprae that is predicted to encode a trHb (M. leprae trHbO). Sequence comparison and modelling considerations indicate that monomeric M. leprae trHbO hasstructural features typical of trHb's, such as 20-40 fewer residues thanconventional globin chains, Gly-based sequence consensus motifs, likelyassembling into a 2-on-2 alpha-helical sandwich fold, and hydrophobic residuesrecognized to build up the protein matrix ligand diffusion tunnel. The ferrousheme iron atom of deoxygenated M. leprae trHbO appears to be hexacoordinated,like in Arabidopsis thaliana trHbO-3 (A. thaliana trHbO-3). Accordingly, thevalue of the second-order rate constant for M. leprae trHbO carbonylation (7.3 x 10(3) M(-1) s(-1)) is similar to that observed for A. thaliana trHbO-3 (1.4 x10(4) M(-1) s(-1)) and turns out to be lower than that reported for carbonmonoxide binding to pentacoordinated Mycobacterium tuberculosis trHbN (6.7 x10(6) M(-1) s(-1)). The lower reactivity of M. leprae trHbO as compared to M.tuberculosis trHbN might be related to the higher susceptibility of the leprosybacillus to toxic nitrogen and oxygen species produced by phagocytic cells.PMID: 12074585 [PubMed - indexed for MEDLINE] 283. Genetika. 2002 May;38(5):695-701.[On the problem of genome redundancy in viruses and prokaryotes].[Article in Russian]Sadovskiĭ MG.Author information: Institute of Biophysics, Russian Academy of Sciences, Krasnoyarsk, 660036 [email protected] specific index of nucleotide sequence redundancy, the specific restrictionlength of a finite frequency dictionary, was determined for a complete set ofgenes in some viral genomes and a genome of a bacterium, Bacillus subtilis. Thedistribution of the gene number over the specific restriction length was shown tobe bimodal for viral genomes and unimodal for the Bac. subtilis genome. Theseresults agree with earlier data.PMID: 12068554 [PubMed - indexed for MEDLINE] 284. Genome Res. 2002 May;12(5):689-700.A complete sequence of the T. tengcongensis genome.Bao Q(1), Tian Y, Li W, Xu Z, Xuan Z, Hu S, Dong W, Yang J, Chen Y, Xue Y, Xu Y, Lai X, Huang L, Dong X, Ma Y, Ling L, Tan H, Chen R, Wang J, Yu J, Yang H.Author information: (1)Beijing Genomics Institute/Genomics and Bioinformatics Center, Institute ofGenetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing100101, China.Thermoanaerobacter tengcongensis is a rod-shaped, gram-negative, anaerobiceubacterium that was isolated from a freshwater hot spring in Tengchong, China.Using a whole-genome-shotgun method, we sequenced its 2,689,445-bp genome from anisolate, MB4(T) (Genbank accession no. AE008691). The genome encodes 2588predicted coding sequences (CDS). Among them, 1764 (68.2%) are classifiedaccording to homology to other documented proteins, and the rest, 824 CDS(31.8%), are functionally unknown. One of the interesting features of the T.tengcongensis genome is that 86.7% of its genes are encoded on the leading strandof DNA replication. Based on protein sequence similarity, the T. tengcongensisgenome is most similar to that of Bacillus halodurans, a mesophilic eubacterium, among all fully sequenced prokaryotic genomes up to date. Computational analysis on genes involved in basic metabolic pathways supports the experimental discoverythat T. tengcongensis metabolizes sugars as principal energy and carbon sourceand utilizes thiosulfate and element sulfur, but not sulfate, as electronacceptors. T. tengcongensis, as a gram-negative rod by empirical definitions(such as staining), shares many genes that are characteristics of gram-positivebacteria whereas it is missing molecular components unique to gram-negativebacteria. A strong correlation between the G + C content of tDNA and rDNA genesand the optimal growth temperature is found among the sequenced thermophiles. It is concluded that thermophiles are a biologically and phylogenetically divergent group of prokaryotes that have converged to sustain extreme environmentalconditions over evolutionary timescale.PMCID: PMC186588PMID: 11997336 [PubMed - indexed for MEDLINE] 285. J Bacteriol. 2002 May;184(9):2500-20.Bacillus subtilis functional genomics: global characterization of the stringentresponse by proteome and transcriptome analysis.Eymann C(1), Homuth G, Scharf C, Hecker M.Author information: (1)Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, D-17487Greifswald, Germany.The stringent response in Bacillus subtilis was characterized by using proteomeand transcriptome approaches. Comparison of protein synthesis patterns ofwild-type and relA mutant cells cultivated under conditions which provoke thestringent response revealed significant differences. According to their alteredsynthesis patterns in response to DL-norvaline, proteins were assigned to fourdistinct classes: (i) negative stringent control, i.e., strongly de- 130 creasedprotein synthesis in the wild type but not in the relA mutant (e.g., r-proteins);(ii) positive stringent control, i.e., induction of protein synthesis in the wildtype only (e.g., YvyD and LeuD); (iii) proteins that were induced independentlyof RelA (e.g., YjcI); and (iv) proteins downregulated independently of RelA(e.g., glycolytic enzymes). Transcriptome studies based on DNA macroarraytechniques were used to complement the proteome data, resulting in comparableinduction and repression patterns of almost all corresponding genes. However, acomparison of both approaches revealed that only a subset of RelA-dependent genesor proteins was detectable by proteomics, demonstrating that the transcriptomeapproach allows a more comprehensive global gene expression profile analysis. Thepresent study presents the first comprehensive description of the stringentresponse of a bacterial species and an almost complete map of protein-encodinggenes affected by (p)ppGpp. The negative stringent control concerns reactionstypical of growth and reproduction (ribosome synthesis, DNA synthesis, cell wall synthesis, etc.). Negatively controlled unknown y-genes may also code forproteins with a specific function during growth and reproduction (e.g., YlaG). Onthe other hand, many genes are induced in a RelA-dependent manner, includinggenes coding for already-known and as-yet-unknown proteins. A passive model ispreferred to explain this positive control relying on the redistribution of theRNA polymerase under the influence of (p)ppGpp.PMCID: PMC134987PMID: 11948165 [PubMed - indexed for MEDLINE] 187 286. FEMS Microbiol Lett. 2002 Feb 19;208(1):105-9.Investigation of the yvgW Bacillus subtilis chromosomal gene involved in Cd(2+)ion resistance.Solovieva IM(1), Entian KD.Author information: (1)Molecular and Radiation Biophysics Division, St. Petersburg Nuclear PhysicsInstitute of the Russian Academy of Sciences, PNPI, Gatchina, 188350, St.Petersburg, Russia. [email protected] of the complete genome sequence of Bacillus subtilis has identified the gene yvgW encoding a protein of 703 amino acids with sequence similarity to thecadmium resistance determinant CadA from the Staphylococcus aureus plasmid pI258.Deletion of yvgW (designated cadA) resulted in increased sensitivity of thestrain to cadmium. The cadA gene is expressed from its own promoter, and itsexpression is induced by cadmium. Northern hybridization analysis showed thatcadmium induces the synthesis of a 2.2-kb cadA transcript. These results indicatethat cadA is the chromosomal determinant to cadmium resistance in B. subtilis.PMID: 11934502 [PubMed - indexed for MEDLINE] 188 287. J Mol Biol. 2002 Feb 22;316(3):443-57.Defining the Bacillus subtilis sigma(W) regulon: a comparative analysis ofpromoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches.Cao M(1), Kobel PA, Morshedi MM, Wu MF, Paddon C, Helmann JD.Author information: (1)Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA.The Bacillus subtilis extracytoplasmic function (ECF) sigma factor sigma(W)controls a large regulon that is strongly induced by alkali shock. To define the physiological role of sigma(W) we have sought to identify the complete set ofgenes under sigma(W) control. Previously, we described a promoter consensussearch procedure to identify sigma(W) controlled genes. Herein, we introduce anovel method to identify additional target promoters: run-off transcriptionfollowed by macroarray analysis (ROMA). We compare the resulting list of targets with those identified in conventional transcriptional profiling studies and usingthe consensus search approach. While transcriptional profiling identifies genesthat are strongly dependent on sigma(W) for in vivo expression, somesigma(W)-dependent promoters are not detected due to the masking effects of otherpromoter elements, overlapping recognition with other ECF sigma factors, or both.Taken together, the consensus search, ROMA, and transcriptional profilingapproaches establish a minimum of 30 promoter sites (controlling approximately 60genes) as direct targets for activation by sigma(W). Significantly, no singleapproach identifies more than approximately 80% of the regulon so defined. Wetherefore suggest that a combination of two or more complementary approaches beemployed in studies seeking to achieve maximal coverage when defining bacterialregulons. Our results indicate that sigma(W) controls genes that protect the cellagainst agents that impair cell wall biosynthesis but fail to reveal anyconnection to operons likely to function in adaptation to alkaline growthconditions. This is consistent with the observation that a sigW mutant isunaffected in its ability to survive alkali shock. We conclude that in B.subtilis sudden imposition of alkali stress activates the sigma(W) stressresponse, perhaps by impairing the ability of the cell wall biosyntheticmachinery to function.Copyright 2002 Elsevier Science Ltd.PMID: 11866510 [PubMed - indexed for MEDLINE] 189 288. Int J Syst Evol Microbiol. 2002 Jan;52(Pt 1):101-7.Bacillus endophyticus sp. nov., isolated from the inner tissues of cotton plants (Gossypium sp.).Reva ON(1), Smirnov VV, Pettersson B, Priest FG.Author information: (1)Department of Antibiotics, Institute of Microbiology and Virology, Kiev, Ukraine.Four strains of aerobic, endospore-forming bacteria were isolated from the inner tissues of healthy cotton plants (Gossypium sp., Dushanbe, Tajikistan). Theorganisms had identical randomly amplified polymorphic DNA patterns thatdistinguished them from other bacilli that are commonly isolated from planttissues, e.g. Bacillus amyloliquefaciens, Bacillus licheniformis, Bacilluspumilus and Bacillus subtilis. PCR amplification of 16S-23S rRNA spacer regionssuggested that the four strains could be assigned to two highly related taxa,which correlated with differences in cell morphology. However, the cloned spacer region provided a simple and specific hybridization probe for all four strains.The virtually complete 16S rDNA sequences were prepared for representatives ofthe two groups (strains 2DT(T) and 12DX) and differed by only two bases, thussupporting classification of the four strains in a single taxon at the specieslevel. Phylogenetic analyses indicated that strain 2DT(T) belonged to the genusBacillus and was most closely related to Bacillus sporothermodurans DSM 10599Twith a sequence similarity of 94.8%. It is concluded that the four strains belongto a novel species of Bacillus for which the name Bacillus endophyticus sp. nov. is proposed. The type strain is 2DT(T) (= UCM B-5715T = CIP 106778T).PMID: 11837291 [PubMed - indexed for MEDLINE] 131 190 289. Microbiology. 2002 Feb;148(Pt 2):507-18.The metIC operon involved in methionine biosynthesis in Bacillus subtilis iscontrolled by transcription antitermination.Auger S(1), Yuen WH, Danchin A, Martin-Verstraete I.Author information: (1)Unité de Génétique des Génomes Bactériens, Institut Pasteur, URA CNRS 2171, 28rue du Docteur Roux, 75724 Paris Cedex 15, France.There are two major pathways for methionine biosynthesis in micro-organisms.Little is known about these pathways in Bacillus subtilis. The authors assigned afunction to the metI (formerly yjcI) and metC (formerly yjcJ) genes of B.subtilis by complementing Escherichia coli metB and metC mutants, analysing thephenotype of B. subtilis metI and metC mutants, and carrying out enzyme activity assays. These genes encode polypeptides belonging to the cystathioninegamma-synthase family of proteins. Interestingly, the MetI protein has bothcystathionine gamma-synthase and O-acetylhomoserine thiolyase activities, whereasthe MetC protein is a cystathionine beta-lyase. In B. subtilis, thetranssulfuration and the thiolation pathways are functional in vivo. Due to itsdual activity, the MetI protein participates in both pathways. The metI and metC genes form an operon, the expression of which is subject to sulfur-dependentregulation. When the sulfur source is sulfate or cysteine the transcription ofthis operon is high. Conversely, when the sulfur source is methionine itstranscription is low. An S-box sequence, which is located upstream of the metIgene, is involved in the regulation of the metIC operon. Northern blotexperiments demonstrated the existence of two transcripts: a small transcriptcorresponding to the premature transcription termination at the terminatorpresent in the S-box and a large one corresponding to transcription of thecomplete metIC operon. When methionine levels were limiting, the amount of thefull-length transcript increased. These results substantiate a model ofregulation by transcription antitermination.PMID: 11832514 [PubMed - indexed for MEDLINE] 191 290. Lepr Rev. 2001 Dec;72(4):429-40.Genomics and the chemotherapy of leprosy.Grosset JH(1), Cole ST.Author information: (1)Laboratoire de Bactériologie et Hygiène, Faculté de Médecine Pitié-Salpêtrière,91 Boulevard de l'Hôpital, 75634 Paris, France.The information deduced from the genome sequence of Mycobacterium leprae is ofimmense value for the chemotherapy of leprosy. Knowing the complete set of genes,enzymes and proteins allows us to understand why some drugs are without effectwhereas others are fully active. It may also enable better use to be made ofexisting drugs, such as beta-lactams, and opens new avenues for the developmentof novel compounds. M. leprae is relatively susceptible to a wide range of drugs,unlike the highly related tubercle bacillus, and several new multidrug regimensare in clinical trials. Genomics provides a number of possible explanations forthis broader susceptibility as some of the genes encoding enzymes involved inantibiotic inactivation have decayed whereas the number of transporters availableto contribute to drug efflux is considerably lower than in Mycobacteriumtuberculosis. Several leads for new drug targets have been uncovered.PMID: 11826479 [PubMed - indexed for MEDLINE] 192 291. Antonie Van Leeuwenhoek. 2001 Sep;79(3-4):235-45.Heterologous expression of the naphthocyclinone hydroxylase gene fromStreptomyces arenae for production of novel hybrid polyketides.Brünke P(1), Sterner O, Bailey JE, Minas W.Author information: (1)Institute of Biotechnology, ETH Zürich, [email protected] arenae produces at least four different isochromanequinoneantibiotics, the naphthocyclinones, of which the beta- and gamma-form are active against Gram-positive bacteria. The naphthocyclinone biosynthesis gene clusterwas isolated from Streptomyces arenae DSM 40737 and by sequence analysis theminimal polyketide synthase genes and several genes encoding tailoring enzymeswere identified. Southern blot analysis of the naphthocyclinone gene clusterindicated that a 3.5 kb BamHI fragment located approximately 9 kb downstream ofthe minimal PKS genes hybridizes to the schC hydroxylase DNA probe isolated from S. halstedii. Two complete and one incomplete open reading frames were identifiedon this fragment. Sequence analysis revealed strong homology to the genes of the actVA region of S. coelicolor, to several (suggested) hydroxylases and a putativeFMN-dependent monooxygenase. The proposed hydroxylase, encoded by ncnH, couldhydroxylate aloesaponarin II, a molecule that is produced by the actinorhodinminimal polyketide synthase in combination with the actinorhodin ketoreductase,aromatase and cyclase. Furthermore, this enzyme is capable of acceptingadditional polyketide core structures that contain a 5-hydroxy-1,4-naphthoquinonemoiety as substrates which makes it an interesting tailoring enzyme for themodification of polyketide structures.PMID: 11816965 [PubMed - indexed for MEDLINE] 193 292. Biochemistry. 2001 Dec 25;40(51):15660-8.Copper trafficking: the solution structure of Bacillus subtilis CopZ.Banci L(1), Bertini I, Del Conte R, Markey J, Ruiz-Dueñas FJ.Author information: (1)Centro di Risonanze Magnetiche and Department of Chemistry, University ofFlorence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy.A sequence with a high homology (39% residue identity) with that of thecopper-transport CopZ protein from Enterococcus hirae and with the same MXCXXCmetal-binding motif has been identified in the genome of Bacillus subtilis, andthe corresponding protein has been expressed. The protein, constituted by 73amino acids, does bind copper(I) under reducing conditions and fully folded inboth copper-bound and copper-free forms under the present experimentalconditions. The solution structure of the copper-bound form was determinedthrough NMR spectroscopy on an 15N-labeled sample. A total of 1508 meaningfulnuclear Overhauser effects, 38 dihedral phi angles, and 48 dihedral psi angleswere used in the structural calculations, which lead to a family of 30 conformerswith an average rmsd to the mean structure of 0.32 +/0.06 A for the backboneand of 0.85 +/- 0.07 A for the heavy atoms. NMR data on the apoprotein also show that, also in this form, the protein is in a folded state and essentiallymaintains the complete secondary structure. Some disorder is observed in the loopdevoted to copper binding. These results are compared with those reported forCopZ from E. hirae whose structure is well-defined only in the apo form. Thedifferent behaviors of copper-loaded E. hirae and B. subtilis are tentativelyaccounted for on the basis of the presence of dithiothreitol used in the lattercase, which would stabilize the monomeric form. The comparison is extended 132 194 195 196 197 toother similar proteins, with particular attention to the copper-binding loop. Thenature and the location of conserved residues around the metal-binding site arediscussed with respect to their relevance for the metal-binding process.Proposals for the role of CopZ are also presented.PMID: 11747441 [PubMed - indexed for MEDLINE] 293. J Bacteriol. 2002 Jan;184(1):134-41.Bacillus anthracis pXO1 plasmid sequence conservation among closely relatedbacterial species.Pannucci J(1), Okinaka RT, Sabin R, Kuske CR.Author information: (1)Biosciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico87545, USA.The complete sequencing and annotation of the 181.7-kb Bacillus anthracisvirulence plasmid pXO1 predicted 143 genes but could only assign putativefunctions to 45. Hybridization assays, PCR amplification, and DNA sequencing wereused to determine whether pXO1 open reading frame (ORF) sequences were present inother bacilli and more distantly related bacterial genera. Eighteen Bacillusspecies isolates and four other bacterial species were tested for the presence of106 pXO1 ORFs. Three ORFs were conserved in most of the bacteria tested. Many of the pXO1 ORFs were detected in closely related Bacillus species, and some weredetected only in B. anthracis isolates. Three isolates, Bacillus cereus D-17, B. cereus 43881, and Bacillus thuringiensis 33679, contained sequences that weresimilar to more than one-half of the pXO1 ORF sequences examined. The majority ofthe DNA fragments that were amplified by PCR from these organisms had DNAsequences between 80 and 98% similar to that of pXO1. Pulsed-field gelelectrophoresis revealed large potential plasmids present in both B. cereus 43881(341 kb) and B. thuringiensis ATCC 33679 (327 kb) that hybridized with a DNAprobe composed of six pXO1 ORFs.PMCID: PMC134754PMID: 11741853 [PubMed - indexed for MEDLINE] 294. Microbiology. 2001 Dec;147(Pt 12):3413-9.yveB, Encoding endolevanase LevB, is part of the sacB-yveB-yveA levansucrasetricistronic operon in Bacillus subtilis.Pereira Y(1), Petit-Glatron MF, Chambert R.Author information: (1)Institut Jacques Monod, Laboratoire Génétique et Membranes, CNRS-UniversitésParis 6 et Paris 7, Tour 43, 2 place Jussieu, 75251 Paris Cedex 05, France.Transcription of sacB, yveB and yveA, three clustered genes on the Bacillussubtilis chromosome, is simultaneously induced by sucrose. Northern blottinganalyses with specific probes showed three distinct mRNAs: a monocistronic 1.7 kbsacB mRNA, a bicistronic 3.3 kb sacB-yveB mRNA and a tricistronic 4.9 kbsacB-yveB-yveA mRNA. These results indicate that sacB, encoding levansucrase, is the proximal gene of a sucrose-inducible operon that includes the two othergenes. The yield of the full-length transcript is lower than that of thebicistronic transcript, whose yield is itself lower than that of themonocistronic transcript. This suggested that the 3' terminal parts of sacB andyveB genes worked as internal terminator structures. The protein encoded by yveB,which remains anchored to the membrane, displays an endolevanase activity, which,coupled with exolevanase activity of SacB, leads to a complete degradation oflevan, a branched fructosyl polymer. It is proposed to rename yveB as levB.PMID: 11739774 [PubMed indexed for MEDLINE] 295. J Bacteriol. 2001 Dec;183(24):7329-40.Correlation between Bacillus subtilis scoC phenotype and gene expressiondetermined using microarrays for transcriptome analysis.Caldwell R(1), Sapolsky R, Weyler W, Maile RR, Causey SC, Ferrari E.Author information: (1)Genencor International, Palo Alto, California 94304, USA.The availability of the complete sequence of the Bacillus subtilis chromosome (F.Kunst et al., Nature 390:249-256, 1997) makes possible the construction ofgenome-wide DNA arrays and the study of this organism on a global scale. Because we have a long-standing interest in the effects of scoC on late-stagedevelopmental phenomena as they relate to aprE expression, we studied thegenome-wide effects of a scoC null mutant with the goal of furthering theunderstanding of the role of scoC in growth and developmental processes. In thepresent work we compared the expression patterns of isogenic B. subtilis strains,one of which carries a null mutation in the scoC locus (scoC4). The resultsobtained indicate that scoC regulates, either directly or indirectly, theexpression of at least 560 genes in the B. subtilis genome. ScoC appeared torepress as well as activate gene expression. Changes in expression were observed in genes encoding transport and binding proteins, those involved in amino acid,carbohydrate, and nucleotide and/or nucleoside metabolism, and those associatedwith motility, sporulation, and adaptation to atypical conditions. Changes ingene expression were also observed for transcriptional regulators, along withsigma factors, regulatory phosphatases and kinases, and members of sensorregulator systems. In this report, we discuss some of the phenotypes associatedwith the scoC mutant in light of the transcriptome changes observed.PMCID: PMC95582PMID: 11717292 [PubMed - indexed for MEDLINE] 296. J Bacteriol. 2001 Dec;183(24):7295-307.Regulation of Streptococcus pneumoniae clp genes and their role in competencedevelopment and stress survival.Chastanet A(1), Prudhomme M, Claverys JP, Msadek T.Author information: (1)Unité de Biochimie Microbienne, Institut Pasteur, URA 2172 du Centre National de la Recherche Scientifique, 75724 Paris Cedex 15, France.In vitro mariner transposon mutagenesis of Streptococcus pneumoniae chromosomalDNA was used to isolate regulatory mutants affecting expression of the comCDEoperon, encoding the peptide quorum-sensing two-component signal transductionsystem controlling competence development. A transposon insertion leading toincreased comC expression was found to lie directly upstream from the S.pneumoniae clpP gene, encoding the proteolytic subunit of the Clp ATP-dependentprotease, whose expression in Bacillus subtilis is controlled by the CtsRrepressor. In order to examine clp gene regulation in S. pneumoniae, a detailedanalysis of the complete genome sequence was performed, indicating that there arefive likely CtsR-binding sites located upstream from the clpE, clpP, and clpLgenes and the ctsR-clpC and groESL operons. The S. pneumoniae ctsR gene wascloned under the control of an inducible promoter and used to demonstrateregulation of the S. pneumoniae clpP and clpE genes and the clpC and groESLoperons by using B. 133 198 199 200 201 subtilis as a heterologous host. The CtsR protein of S.pneumoniae was purified and shown to bind specifically to the clpP, clpC, clpE,and groESL regulatory regions. S. pneumoniae Delta ctsR, Delta clpP, Delta clpC, and Delta clpE mutants were constructed by gene deletion/replacement. ClpP wasshown to act as a negative regulator, preventing competence gene expression underinappropriate conditions. Phenotypic analyses also indicated that ClpP and ClpEare both required for thermotolerance. Contrary to a previous report, we foundthat ClpC does not play a major role in competence development, autolysis,pneumolysin production, or growth at high temperature of S. pneumoniae.PMCID: PMC95579PMID: 11717289 [PubMed - indexed for MEDLINE] 297. J Biochem. 2001 Nov;130(5):711-7.nhaG Na(+)/H(+) antiporter gene of Bacillus subtilis ATCC9372, which is missingin the complete genome sequence of strain 168, and properties of the antiporter.Gouda T(1), Kuroda M, Hiramatsu T, Nozaki K, Kuroda T, Mizushima T, Tsuchiya T.Author information: (1)Department of Microbiology, Faculty of Pharmaceutical Sciences, OkayamaUniversity, Tsushima, Okayama, 700-8530, Japan.We cloned a gene which enabled Escherichia coli mutant host cells lacking all of the major Na(+)/H(+) antiporters to grow in the presence of 0.2 M NaCl fromchromosomal DNA of Bacillus subtilis ATCC9372. An Na(+)/H(+) antiport activitywas observed with membrane vesicles prepared from E. coli cells possessing thecloned gene, but not with vesicles from the host cells. Lithium ion was also asubstrate for the antiporter. We sequenced the cloned DNA and found one openreading frame (designated nhaG) preceded by a promoter-like sequence and aShine-Dalgarno sequence, and followed by a terminator-like sequence. The deduced amino acid sequence of NhaG suggested that it consisted of 524 residues and that the calculated molecular mass was 58.1 kDa. None of the bacterial Na(+)/H(+)antiporters so far reported, except NhaP of Pseudomonas aeruginosa and SynNhaP(NhaS1) of Synechocystis sp., showed significant sequence similarity with theNhaG. However, the NhaP, the SynNhaP, animal NHEs (Na(+)/H(+) exchangers), andsome hypothetical Na(+)/H(+) antiporters of several organisms showed significant sequence similarities with the NhaG. Interestingly, the entire DNA regioncorresponding to the nhaG gene is missing in the reported complete genomesequence of B. subtilis strain 168. We detected a band that hybridized with thenhaG DNA in chromosomal DNA from B. subtilis ATCC9372 but not with that fromstrain 168. The missing DNA region (1,774 base pairs) is sandwiched by twoidentical sequences, TTTTCTT.PMID: 11686935 [PubMed - indexed for MEDLINE] 298. Proc Natl Acad Sci U S A. 2001 Oct 23;98(22):12712-7. Epub 2001 Oct 16.Comprehensive identification of conditionally essential genes in mycobacteria.Sassetti CM(1), Boyd DH, Rubin EJ.Author information: (1)Department of Immunology and Infectious Diseases, Harvard School of PublicHealth, 667 Huntington Avenue, Boston, MA 02115, USA.An increasing number of microbial genomes have been completely sequenced, and theidentified genes are categorized based on their homology to genes of knownfunction. However, the function of a large number of genes cannot be determinedon this basis alone. Here, we describe a technique, transposon site hybridization(TraSH), which allows rapid functional characterization by identifying thecomplete set of genes required for growth under different conditions. TraSHcombines high-density insertional mutagenesis with microarray mapping of pools ofmutants. We have made large pools of independent transposon mutants inmycobacteria by using a mariner-based transposon and efficient phagetransduction. By using TraSH, we have defined the set of genes required forgrowth of Mycobacterium bovis bacillus Calmette-Guérin on minimal but not richmedium. Genes of both known and unknown functions were identified. Of the geneswith known functions, nearly all were involved in amino acid biosynthesis. TraSH is a powerful method for categorizing gene function that should be applicable to a variety of microorganisms.PMCID: PMC60119PMID: 11606763 [PubMed - indexed for MEDLINE] 299. Peptides. 2001 Oct;22(10):1555-77.A peptide profile of the Bacillus subtilis genome.Zuber P.Author information: Department of Biochemistry and Molecular Biology, Oregon Graduate Institute ofScience and Technology, 20000 NW Walker Rd, Beaverton, OR 97006, [email protected] subtilis is known to produce an abundance of small polypeptides. Severalof these have antimicrobial activity and others are pheromones or extracellularfactors that affect internal signal transduction systems. The completion of theB. subtilis genomic nucleotide sequence has revealed 345 small polypeptideopen-reading frames (of 85 codons or less), 81% of which are of unknown function.A significant number of these reside in prophage genomes or phage-like elementswhere they can be organized into large operons. It is likely that many more existin the genome of B. subtilis but are "hidden" entirely or partially within other reading frames, or possess non-conventional translation start signals and haveescaped detection. The discovery of so many small polypeptide orfs (SPORFs) andthe likelihood of many more pose a challenging problem for those undertaking the complete functional analysis of genes that constitute prokaryotic genomes. Asurvey of known and potential peptide-encoding reading frames is presented hereinas an attempt to classify those that are found in the B. subtilis genomeaccording to function inferred from homology searches and to conservation amongproducts of other microbial genomes.PMID: 11587785 [PubMed - indexed for MEDLINE] 300. Acta Crystallogr D Biol Crystallogr. 2001 Oct;57(Pt 10):1445-50. Epub 2001 Sep21.ARP/wARP and molecular replacement.Perrakis A(1), Harkiolaki M, Wilson KS, Lamzin VS.Author information: (1)Department of Molecular Carcinogenesis, Plesmanlaan 121, 1066 CX Amsterdam, TheNetherlands. [email protected] aim of ARP/wARP is improved automation of model building and refinement inmacromolecular crystallography. Once a molecular-replacement solution has beenobtained, it is often tedious to refine and rebuild the initial (search) model.ARP/wARP offers three options to automate that task to varying extents: (i)autobuilding of a completely new model based on phases calculated from themolecular-replacement solution, (ii) updating of the initial model by 134 202 203 204 205 atomaddition and deletion to obtain an improved map and (iii) docking of a structure onto a new (or mutated) sequence, followed by rebuilding and refining the sidechains in real space. A few examples are presented where ARP/wARP made aconsiderable difference in the speed of structure solution and/or made possiblerefinement of otherwise difficult or uninterpretable maps. The resolution rangeallowing complete autobuilding of protein structures is currently 2.0 A, but for map improvement considerable advances over more conventional refinementtechniques are evident even at 3.2 A spacing.PMID: 11567158 [PubMed - indexed for MEDLINE] 301. J Bacteriol. 2001 Oct;183(20):5964-73.uvrA is an acid-inducible gene involved in the adaptive response to low pH inStreptococcus mutans.Hanna MN(1), Ferguson RJ, Li YH, Cvitkovitch DG.Author information: (1)Dental Research Institute, University of Toronto, Toronto, Ontario, Canada M5G1G6.The pH-inducible acid tolerance response (ATR) is believed to play a major rolein acid adaptation and virulence of Streptococcus mutans. To study thisphenomenon in S. mutans JH1005, differential display PCR was used to identify andclone 13 cDNA products that had increased expression in response to pH 5.0compared to that of pH 7.5-grown cells. One of these products, confirmed to be pHinducible by RNA dot blot and reverse transcription-PCR analyses, had 67%identity to a uvrA-UV repair excinuclease gene in Bacillus subtilis. Furthersequence analysis of the uvrA homologue using the S. mutans genome databaserevealed that the complete gene was encoded in an open reading frame (ORF) of2,829 bp (944 amino acids; 104.67 kDa). Immediately 3' of uvrA was an ORFencoding a putative aminopeptidase gene (pepP). uvrA knockouts were constructedin S. mutans strains JH1005, NG8, and UA159 using allelic-exchange mutagenesis,replacing the entire gene with an erythromycin resistance cassette. As with uvrA mutants in other bacteria, the S. mutans uvrA mutants were extremely sensitive toUV irradiation. The uvrA mutant of S. mutans JH1005 was also more sensitive than the wild type to growth at pH 5.0, showing a 15% reduction in growth rate and a14% reduction in final resting culture density. Acid-adapted S. mutans JH1005uvrA mutants were shown to be more resistant to UV irradiation than was theparent but were unable to survive exposure to a killing pH of 3.0. Moreover,agarose gel electrophoretic analysis of chromosomal DNA isolated fromuvrA-deficient cells exposed to low pH demonstrated more DNA damage than that forthe wild-type strain. Here we suggest that uvrA and the nucleotide excisionrepair pathway are involved in the repair of acid-induced DNA damage and areassociated with successful adaptation of S. mutans to low pH.PMCID: PMC99675PMID: 11566996 [PubMed - indexed for MEDLINE] 302. Genome Res. 2001 Sep;11(9):1484-502.A proteomic view on genome-based signal peptide predictions.Antelmann H(1), Tjalsma H, Voigt B, Ohlmeier S, Bron S, van Dijl JM, Hecker M.Author information: (1)Institut für Mikrobiologie und Molekularbiologie, Ernst-Moritz-Arndt-UniversiätGreifswald, D-17487 Greifswald, Germany.Comment in Genome Res. 2001 Sep;11(9):1463-8.The availability of complete genome sequences has allowed the prediction of allexported proteins of the corresponding organisms with dedicated algorithms. Even though numerous studies report on genome-based predictions of signal peptides andcell retention signals, they lack a proteomic verification. For example, 180secretory and 114 lipoprotein signal peptides were predicted recently for theGram-positive eubacterium Bacillus subtilis. In the present studies, proteomicapproaches were used to define the extracellular complement of the B. subtilissecretome. Using different growth conditions and a hyper-secreting mutant,approximately 200 extracellular proteins were visualized by two-dimensional (2D) gel electrophoresis, of which 82 were identified by mass spectrometry. Theseinclude 41 proteins that have a potential signal peptide with a type I signalpeptidase (SPase) cleavage site, and lack a retention signal. Strikingly, theremaining 41 proteins were predicted previously to be cell associated because of the apparent absence of a signal peptide (22), or the presence of specific cellretention signals in addition to an export signal (19). To test the importance ofthe five type I SPases and the unique lipoprotein-specific SPase of B. subtilis, the extracellular proteome of (multiple) SPase mutants was analyzed.Surprisingly, only the processing of the polytopic membrane protein YfnI wasstrongly inhibited in Spase I mutants, showing for the first time that a nativeeubacterial membrane protein is a genuine Spase I substrate. Furthermore, amutation affecting lipoprotein modification and processing resulted in theshedding of at least 23 (lipo-)proteins into the medium. In conclusion, ourobservations show that genome-based predictions reflect the actual composition ofthe extracellular proteome for approximately 50%. Major problems are currentlyencountered with the prediction of extracellular proteins lacking signal peptides(including cytoplasmic proteins) and lipoproteins.PMID: 11544192 [PubMed - indexed for MEDLINE] 303. In Silico Biol. 1999;1(2):69-91.An evolutionary classification of the metallo-beta-lactamase fold proteins.Aravind L.Author information: National Center for Biotechnology Information, National Library of Medicine,National Institutes of Health, Bldg. 38A, Bethesda, MD 20894, USA.All the detectable metallo-beta-lactamase fold proteins were identified in thepublicly available sequence databases and complete genome sequences usingiterative profile searches with the PSI-BLAST program and motif searches withposition specific weight matrices. The catalytic site/mechanism and thecorresponding structural elements were characterized for these proteins based on the available structure of the Bacillus zinc-dependent beta-lactamase. Based onpair-wise sequence and phylogenetic analysis an evolutionary classification forenzymes of this fold was developed and discussed in terms of implications forsubstrate specificity. Finally, some predicted inactive members which have beenrecruited for non-enzymatic functions such as microtubule binding in acytoskeletal MAP1 are described.PMID: 11471246 [PubMed - indexed for MEDLINE] 304. J Bacteriol. 2001 Aug;183(16):4823-38.Genome sequence and comparative analysis of the solvent-producing bacteriumClostridium acetobutylicum.Nölling J(1), Breton G, Omelchenko MV, Makarova KS, Zeng Q, Gibson R, Lee HM,Dubois J, Qiu D, Hitti J, Wolf YI, Tatusov RL, Sabathe F, Doucette-Stamm L,Soucaille P, Daly MJ, Bennett GN, Koonin EV, Smith DR.Author infor- 135 206 207 208 209 mation: (1)GTC Sequencing Center, Genome Therapeutics Corporation, Waltham, Massachusetts02453, USA.The genome sequence of the solvent-producing bacterium Clostridium acetobutylicumATCC 824 has been determined by the shotgun approach. The genome consists of a3.94-Mb chromosome and a 192-kb megaplasmid that contains the majority of genesresponsible for solvent production. Comparison of C. acetobutylicum to Bacillussubtilis reveals significant local conservation of gene order, which has not beenseen in comparisons of other genomes with similar, or, in some cases closer,phylogenetic proximity. This conservation allows the prediction of manypreviously undetected operons in both bacteria. However, the C. acetobutylicumgenome also contains a significant number of predicted operons that are sharedwith distantly related bacteria and archaea but not with B. subtilis.Phylogenetic analysis is compatible with the dissemination of such operons byhorizontal transfer. The enzymes of the solventogenesis pathway and of thecellulosome of C. acetobutylicum comprise a new set of metabolic capacities notpreviously represented in the collection of complete genomes. These enzymes show a complex pattern of evolutionary affinities, emphasizing the role of lateralgene exchange in the evolution of the unique metabolic profile of the bacterium. Many of the sporulation genes identified in B. subtilis are missing in C.acetobutylicum, which suggests major differences in the sporulation process.Thus, comparative analysis reveals both significant conservation of the genomeorganization and pronounced differences in many systems that reflect uniqueadaptive strategies of the two gram-positive bacteria.PMCID: PMC99537PMID: 11466286 [PubMed - indexed for MEDLINE] 305. Trends Microbiol. 2001 Jul;9(7):302-7; discussion 308.An abundance of bacterial ADP-ribosyltransferases--implications for the origin ofexotoxins and their human homologues.Pallen MJ(1), Lam AC, Loman NJ, McBride A.Author information: (1)Microbial Genomics and Pathogenesis Unit, Division of Immunity and Infection, TheMedical School, University of Birmingham, B15 2TT, Birmingham, [email protected] is a post-translational modification that can be seen in manycontexts, including as the primary mechanism of action of many importantbacterial exotoxins. By data-mining complete and incomplete bacterial genomesequences, we have discovered >20 novel putative ADP-ribosyltransferases,including several new potential toxins.PMID: 11435081 [PubMed - indexed for MEDLINE] 306. Nucleic Acids Res. 2001 Jul 1;29(13):2747-56.Ribosomal protein gene cluster analysis in eubacterium genomics: homology betweenSinorhizobium meliloti strain 1021 and Bacillus subtilis.Barloy-Hubler F(1), Lelaure V, Galibert F.Author information: (1)Laboratoire Génétique et Développement, UMR6061-CNRS, 2 Avenue du Pr LéonBernard, 35043 Rennes Cedex, France.The first whole genome sequence of a symbiotic soil bacterium, Sinorhizobiummeliloti (formely named Rhizobium meliloti) strain 1021, is due in 2001. As anactive participant in the European and North American consortium that hascompleted this work, our group has sequenced a region on the chromosomecontaining clusters rpoBC, str, S10, spc and alpha corresponding to 30 proteingenes. The structural organization and function of these genes were compared withthose of orthologs in another 15 complete eubacterial genomes available indatabases. This study, involving the DNA and amino acid sequences as well as the organization of the whole region (gene order, cluster order, etc.), has shownthat the phylogenetic tree resulting from a comparison of the amino acid sequenceis rather similar to that derived from 16S rRNA sequence data. However, the tree achieved by aligning DNA sequences groups the organisms with a high GC content(>60% GC), while that based on a comparison of gene cluster orientation andorganization reveals a greater level of correspondence between thealpha-proteobacteria S.meliloti and the firmicute Bacillus subtilis.PMCID: PMC55768PMID: 11433019 [PubMed - indexed for MEDLINE] 307. Microbiol Mol Biol Rev. 2001 Jun;65(2):261-87 ; second page, table of contents.Phi29 family of phages.Meijer WJ(1), Horcajadas JA, Salas M.Author information: (1)Centro de Biología Molecular Severo Ochoa, Universidad Autónoma, Canto Blanco,28049 Madrid, Spain.Continuous research spanning more than three decades has made the Bacillusbacteriophage phi29 a paradigm for several molecular mechanisms of generalbiological processes, such as DNA replication, regulation of transcription, phagemorphogenesis, and phage DNA packaging. The genome of bacteriophage phi29consists of a linear double-stranded DNA (dsDNA), which has a terminal protein(TP) covalently linked to its 5' ends. Initiation of DNA replication, carried outby a protein-primed mechanism, has been studied in detail and is considered to bea model system for the protein-primed DNA replication that is also used by mostother linear genomes with a TP linked to their DNA ends, such as other phages,linear plasmids, and adenoviruses. In addition to a continuing progress inunraveling the initiation of DNA replication mechanism and the role of variousproteins involved in this process, major advances have been made during the last few years, especially in our understanding of transcription regulation, thehead-tail connector protein, and DNA packaging. Recent progress in all thesetopics is reviewed. In addition to phi29, the genomes of several other Bacillusphages consist of a linear dsDNA with a TP molecule attached to their 5' ends.These phi29-like phages can be divided into three groups. The first groupincludes, in addition to phi29, phages PZA, phi15, and BS32. The second groupcomprises B103, Nf, and M2Y, and the third group contains GA-1 as its solemember. Whereas the DNA sequences of the complete genomes of phi29 (group I) and B103 (group II) are known, only parts of the genome of GA-1 (group III) weresequenced. We have determined the complete DNA sequence of the GA-1 genome, whichallowed analysis of differences and homologies between the three groups ofphi29-like phages, which is included in this review.PMCID: PMC99027PMID: 11381102 [PubMed - indexed for MEDLINE] 308. Microbiology. 2001 May;147(Pt 5):1343-51.A general strategy for identification of S-layer genes in the Bacillus cereusgroup: molecular characterization of such a gene in Bacillus thuringiensis subsp.galleriae NRRL 4045.Mesnage S(1), Haustant M, Fouet A.Author information: (1)Toxines et Pathogénie Bactériennes (URA 2172, CNRS), Institut Pasteur, 28 rue du Dr Roux, 75724, Paris 136 210 211 212 213 cédex 15, France. [email protected] its possible role in virulence, there has been little molecularcharacterization of members of the S-layer protein family of the Bacillus cereus group. It is hypothesized that the components of the S-layers are likely todisplay similar anchoring structures in Bacillus thuringiensis and Bacillusanthracis. Based on inferred sequence similarities, a DNA fragment encoding thecell-wall-anchoring domain of an S-layer component of BAC: thuringiensis subsp.galleriae NRRL 4045 was isolated. The complete gene was identified and sequenced.An ORF of 2463 nt was identified, which was predicted to encode a protein of 821 aa, SlpA. The mature SlpA protein (792 residues) carries three S-layer homology(SLH) motifs towards its amino terminus, each about 50 aa long. These motifs weresufficient to bind Bac. thuringiensis and Bac. anthracis cell walls in vitro byinteracting with peptidoglycan-associated polymers, confirming a commonwall-anchoring mechanism. The slpA null-allele mutant was constructed and shownto possess no other abundant surface protein. It is proposed that the methoddescribed in this paper could be applied to the identification and deletion ofany Bac. cereus S-layer gene and is of great value for the molecular andfunctional characterization of these genes.PMID: 11320137 [PubMed - indexed for MEDLINE] 309. Genomics. 2001 Apr 15;73(2):223-31.Genetic, physical, and transcript map of the Ltxs1 region of mouse chromosome 11.Watters JW(1), Dietrich WF.Author information: (1)Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.Erratum in Genomics 2002 Mar;79(3):462.Lethal factor (LF) is a toxin secreted by Bacillus anthracis that plays animportant role in the pathogenesis of anthrax. Intoxication with LF results in a macrophage-specific cytolysis that is not well understood. Interestingly, inbred mouse strains exhibit dramatic differences in the susceptibility of theircultured macrophages to killing by LF, and a gene that influences this phenotype,called Ltxs1, has been mapped to mouse chromosome 11. Here we report ahigh-resolution genetic map that confines the Ltxs1 region to a 0.51-cM interval between D11Mit90 and D11Die37/D11Die38. We have also constructed a completephysical map of YAC and BAC clones covering the Ltxs1 region. In conjunction withsynteny homology searching, BLAST searches of sequences obtained from the clones in the physical map have revealed 14 known genes and five ESTs that reside in thecritical interval. Additionally, a region of 100 kb or more is deleted in theLtxs1 interval of some strains. Our genetic, physical, and transcript mapprovides an important resource for the molecular cloning of Ltxs1.Copyright 2001 Academic Press.PMID: 11318612 [PubMed - indexed for MEDLINE] 310. Mikrobiologiia. 2000 Sep-Oct;69(5):686-93.[Establishment of the phylogenetic relationship between the microbial producersof cyclodextrin glucanotransferases using their complete amino acid sequences].[Article in Russian]Bikbulatova SM(1), Chemeris AV, Usanov NG, Vakhitov VA.Author information: (1)Department of Biochemistry and Cytochemistry, Ufa Research Center, RussianAcademy of Sciences, Ufa, 450054 Russia.A phylogenetic tree was constructed on the basis of the amino acid sequences ofthe known cyclodextrin glucanotransferases (CDGTs), including those deduced from the nucleotide sequences of Bacillus sp. strain 6.6.3 and Paenibacillus macerans IB-7 genes encoding alpha- and beta-CDGTs. The tree clearly demonstrates theexistence of distinct phylogenetic groups of CDGT-producing microorganisms andthe divergence of the alpha-, beta-, and gamma-CDGT produced by microorganismsfrom the genera Bacillus, Paenibacillus, Brevibacillus, and Thermoanaerobacterfrom a common ancestor, whereas the CDGT of Klebsiella pneumoniae is independent and results from the convergence of different ancestors. The degree of homologyof the leader peptide sequences of CDGTs may serve as a criterion of intraspeciesrelatedness between CDGT-producing microorganisms.PMID: 11315672 [PubMed - indexed for MEDLINE] 311. Genome Biol. 2001;2(4):RESEARCH0013. Epub 2001 Mar 22.Conservation of the binding site for the arginine repressor in all bacteriallineages.Makarova KS(1), Mironov AA, Gelfand MS.Author information: (1)Department of Pathology, Uniformed Services University of the Health Sciences,Bethesda, MD 20814, USA.BACKGROUND: The arginine repressor ArgR/AhrC is a transcription factoruniversally conserved in bacterial genomes. Its recognition signal (the ARG box),a weak palindrome, is also conserved between genomes, despite a very low degreeof similarity between individual sites within a genome. Thus, the argininerepressor is different from two other universal transcription factors - HrcA,whose recognition signal is very strongly conserved both within and betweengenomes, and LexA/DinR, whose signal is strongly conserved within, but notbetween, genomes. The arginine regulon is well studied in Escherichia coli and tosome extent in Bacillus subtilis and some other genomes. Here, we apply thecomparative genomic approach to the prediction of the ArgR-binding sites in allcompletely sequenced bacterial genomes.RESULTS: Orthologs of ArgR/AhrC were identified in the complete genomes of E.coli, Haemophilus influenzae, Vibrio choleras, B. subtilis, Mycobacteriumtuberculosis, Thermotoga maritima, Chlamydia pneumoniae and Deinococcusradiodurans. Candidate arginine repressor binding sites were identified upstream of arginine transport and metabolism genes.CONCLUSIONS: We found that the ArgR/AhrC recognition signal is conserved in allgenomes that contain genes encoding orthologous transcription factors of thisfamily. All genomes studied except M. tuberculosis contain ABC transportcassettes (related to the Art system of E. coli) belonging to the candidatearginine regulons.PMCID: PMC31482PMID: 11305941 [PubMed - indexed for MEDLINE] 312. Biosci Biotechnol Biochem. 2001 Jan;65(1):226-8.A cryptic plasmid, pAO1, from a compost bacterium, Bacillus sp.Karita S(1), Ohtaki A, Noborikawa M, Nakasaki K.Author information: (1)Center for Molecular Biology and Genetics, Mie University, Tsu, [email protected] complete nucleotide sequence of a new cryptic plasmid, pAO1 isolated from acompost bacterium Bacillus sp., has been analyzed. Analysis of the PCR-based 16S rRNA sequence showed the bacterium harboring pAO1 was closely related to Bacilluspallidus. The plasmid pAO1 was 3,325 bp in size. Two open reading frames, ORF1and ORF2, encoding 137 214 215 216 217 putative polypeptides of 248 and 290 amino acids,respectively, were identified within the sequence. The ORF1 has a limitedsequence similarity to an integrase/recombinase, while the ORF2 has highsimilarity with the replication protein of pBC1 from Bacillus coagulans. Aputative origin sequence for a plus-strand was located between ORFs. Southernblot analysis indicates this plasmid replicates via a rolling circle-typemechanism.PMID: 11272838 [PubMed - indexed for MEDLINE] 313. Biochim Biophys Acta. 2001 Mar 19;1518(1-2):87-94.Tn10 insertional mutations of Bacillus subtilis that block the biosynthesis ofbacilysin.Yazgan A(1), Ozcengiz G, Marahiel MA.Author information: (1)Biology Department, Middle East Technical University, Ankara 06531, Turkey.Transposon mutagenesis was employed to isolate the gene(s) related with thebiosynthesis of dipeptide antibiotic in Bacillus subtilis PY79 (a prototrophicderivative of the standard 168 strain). The blocked mutants were phenotypicallyselected from the transposon library by bioassay and the complete loss ofbiosynthetic ability was verified through ESI-mass spectrometry analysis. Fourdifferent bacilysin nonproducer mutants (Bac(-)::Tn10(ori-spc)) were isolatedfrom the transposon library. The genes involved in bacilysin biosynthesis wereidentified as thyA (thymidilate synthetase), ybgG (unknown; similar tohomocysteine methyl transferase) and oppA (oligopeptide permease), respectively. The other blocked gene was yvgW (unknown; similar to heavy metal-transportingATPase); however, backcross studies did not verify its involvement in bacilysinbiosynthesis. This gene, on the other hand, appeared to be necessary forefficient sporulation and transformation. Opp involvement was significant as itsuggested that bacilysin biosynthesis is under or a component of the quorumsensing pathway which has been shown to be responsible for the establishment ofsporulation, competence development and onset of surfactin biosynthesis. Forverification, it was necessary to check the involvement of peptide pheromones(PhrA or PhrC) internalized by the Opp system and response regulator ComA as the essential components of this global control. phrA, phrC and comA deleted mutants of PY79 were thus constructed and the latter two genes were shown to be essentialfor bacilysin biosynthesis.PMID: 11267663 [PubMed - indexed for MEDLINE] 314. Mol Microbiol. 2001 Feb;39(4):1010-21.Analysis of the replicon region and identification of an rRNA operon on pBM400 ofBacillus megaterium QM B1551.Kunnimalaiyaan M(1), Stevenson DM, Zhou Y, Vary PS.Author information: (1)Department of Biological Sciences, Northern Illinois University, DeKalb, IL60115, USA.An 18 633 bp region containing the replicon from the approximately 53 kb pBM400plasmid of Bacillus megaterium QM B1551 has been sequenced and characterized.This region contained a complete rRNA operon plus 10 other potential open readingframes (ORFs). The replicon consisted of an upstream promoter and threecontiguous genes (repM400, orfB and orfC) that could encode putative proteins of 428, 251 and 289 amino acids respectively. A 1.6 kb minimal replicon was defined and contained most of repM400. OrfB was shown to be required for stability. Three12 bp identical tandem repeats were located within the coding region of repM400, and their presence on another plasmid caused incompatibility with their owncognate replicon. Nonsense, frameshift and deletion mutations in repM400prevented replication, but each mutation could be complemented in trans. RepM400 had no significant similarity to sequences in the GenBank database, whereas five other ORFs had some similarity to gene products from other plasmids and theBacillus genome. An rRNA operon was located upstream of the replication regionand is the first rRNA operon to be sequenced from B. megaterium. Its unusuallocation on non-essential plasmid DNA has implications for systematics andevolutionary biology.PMID: 11251820 [PubMed - indexed for MEDLINE] 315. J Mol Evol. 2001 Feb;52(2):164-70.Correlation between Shine--Dalgarno sequence conservation and codon usage ofbacterial genes.Sakai H(1), Imamura C, Osada Y, Saito R, Washio T, Tomita M.Author information: (1)Laboratory for Bioinformatics, Keio University, 5322 Endo, Fujisawa, 252-8520,Japan.In this study, we analyzed the correlation between codon usage bias andShine--Dalgarno (SD) sequence conservation, using complete genome sequences ofnine prokaryotes. For codon usage bias, we adopted the codon adaptation index(CAI), which is based on the codon usage preference of genes encoding ribosomalproteins, elongation factors, heat shock proteins, outer membrane proteins, andRNA polymerase subunit proteins. To compute SD sequence conservation, we used SD motif sequences predicted by Tompa and systematically aligned them with 5'UTRsequences. We found that there exists a clear correlation between the CAI values and SD sequence conservation in the genomes of Escherichia coli, Bacillussubtilis, Haemophilus influenzae, Archaeoglobus fulgidus, Methanobacteriumthermoautotrophicum, and Methanococcus jannaschii, and no relationship is foundin M. genitalium, M. pneumoniae, and Synechocystis. That is, genes with higherCAI values tend to have more conserved SD sequences than do genes with lower CAI values in these organisms. Some organisms, such as M. thermoautotrophicum, do notclearly show the correlation. The biological significance of these results isdiscussed in the context of the translation initiation process and translationefficiency.PMID: 11231896 [PubMed - indexed for MEDLINE] 316. Appl Environ Microbiol. 2001 Feb;67(2):834-9.Molecular characterization and identification of Bacillus clausii Strainsmarketed for use in oral bacteriotherapy.Senesi S(1), Celandroni F, Tavanti A, Ghelardi E.Author information: (1)Dipartimento di Patologia Sperimentale, Biotecnologie Mediche, Infettivologia ed Epidemiologia, Università degli Studi di Pisa, Pisa, [email protected] substantial number of Bacillus species have been marketed for use in oralbacteriotherapy because of their purported ability to prevent or treat variousgastrointestinal disorders. Recently, some of the Bacillus strains inEnterogermina, which is made up of aqueous suspensions of viable Bacillus spores,have been partially characterized and aligned with members of the Bacillusalcalophilus subgroup rather than with Bacillus subtilis, as previously reported.With a view toward verifying the original taxonomic position of the Enterogerminastrains, we catalogued both phenotypic and genotypic traits exhibited by the fourBacillus 138 218 219 220 221 strains isolated from the spore mixtures found in original commercialpreparations dated 1975 and 1984 and commercial preparations now being propagatedindustrially. Analyses of physiological and biochemical traits, complete 16S rRNAgene sequences, DNA-DNA reassociation, tRNA intergenic spacer lengthpolymorphism, single-strand conformation polymorphism of PCR-amplified spacerregions of tRNA genes, and randomly amplified polymorphic DNA led to the finding that all of the Enterogermina strains belong to a unique genospecies, which isunequivocally identified as the alkalitolerant species Bacillus clausii.Moreover, we provide evidence that in contrast to several reference strains of B.clausii, the strains constituting Enterogermina are characterized by a notablelow level of intraspecific genome diversity and that each strain has remained thesame for the last 25 years.PMCID: PMC92655PMID: 11157251 [PubMed - indexed for MEDLINE] 317. Genetica. 2000;108(1):25-34.Specific expansion of protein families in the radioresistant bacteriumDeinococcus radiodurans.Makarova KS(1), Aravind L, Daly MJ, Koonin EV.Author information: (1)Uniformed Services University of the Health Sciences, Bethesda, MD 20814, [email protected] analysis of the complete genome of Deinococcus radiodurans R1 reveals a number of protein families, which are over-represented in this organism, comparedto most other bacteria with known genome sequences. These families include bothpreviously characterized and uncharacterized proteins. Most of the families whosefunctions are known or could be predicted seem to be related to stress-responseand elimination of damage products (cell-cleaning). The two most prominent familyexpansions are the Nudix (MutT) family of pyrophosphohydrolases and a previously unnoticed family of proteins related to Bacillus subtilis DinB that could possessa metal-dependent enzymatic activity whose exact nature remains to be determined.Several proteins of the expanded families, particularly the Nudix family, arefused to other domains and form multidomain proteins that are so far unique forDeinococcus. The domain composition of some of these proteins indicates that theycould be involved in novel DNA-repair pathways. Such unique proteins are goodtargets for knock-out and gene expression studies, which are aimed to shed light on the unusual features of this interesting bacterium.PMID: 11145417 [PubMed - indexed for MEDLINE] 318. Curr Microbiol. 2001 Feb;42(2):96-9.PCR analysis of cry7 genes in Bacillus thuringiensis by the five conserved blocksof toxins.Ben-Dov E(1), Manasherob R, Zaritsky A, Barak Z, Margalith Y.Author information: (1)Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653,Be'er-Sheva 84105, Israel. [email protected] alternative PCR analysis to screen for cry7 genes is proposed, based on thefive conserved blocks of amino acids of Bacillus thuringiensis toxins and theirencoding DNA sequences. A complete set of five primers was constructed, fourdirect and one reverse, yielding four specific amplicons. Modified profiles canidentify new cry genes.PMID: 11136129 [PubMed - indexed for MEDLINE] 319. Eur J Biochem. 2000 Dec;267(24):7058-64.Temporal secretion of a multicellulolytic system in Myxobacter sp. AL-1.Molecular cloning and heterologous expression of cel9 encoding a modularendocellulase clustered in an operon with cel48, an exocellobiohydrolase gene.Avitia CI(1), Castellanos-Juárez FX, Sánchez E, Téllez-Valencia A,Fajardo-Cavazos P, Nicholson WL, Pedraza-Reyes M.Author information: (1)Institute of Investigation in Experimental Biology, Faculty of Chemistry,University of Guanajuato, Mexico.The Gram-negative soil micro-organism Myxobacter sp. AL-1 possesses at least fiveextracellular cellulases, the production of which is regulated by the growthcycle. We cloned the complete gene for one of these cellulases, termed cel9,which encoded a 67-kDa modular family 9 endoglycohydrolase, which was producedduring the stationary phase of growth and was strongly enhanced by avicel. Thepredicted product of cel9 matches the structural architecture of family 9cellulases such as Thermonospora fusca endo/exocellulase E4. Cel9 protein wassynthesized in Escherichia coli from a multicopy plasmid and in Bacillus subtilisfrom the isopropyl thiogalactoside-inducible Pspac promoter and was purified fromthe culture medium. Thermal stability, optimum pH and temperature dependence ofCel9 were similar when expressed from either source, and were indistinguishablefrom related cellulases produced by thermophilic bacteria. Downstream from cel9was found a partial ORF, designated cel48, the deduced product of which washighly similar to bacterial exocellobiohydrolases and processive endoglucanasesbelonging to family 48 of the glycosyl hydrolases. The cel9 and cel48 genesappear to be arranged as part of an operon.PMID: 11106416 [PubMed - indexed for MEDLINE] 320. Appl Environ Microbiol. 2000 Dec;66(12):5213-20.Biochemical and genetic characterization of coagulin, a new antilisterialbacteriocin in the pediocin family of bacteriocins, produced by Bacilluscoagulans I(4).Le Marrec C(1), Hyronimus B, Bressollier P, Verneuil B, Urdaci MC.Author information: (1)Unité Sécurité Microbiologique des Aliments, ISTAB, Université Bordeaux I,F-33405 Talence, France. [email protected] plasmid-linked antimicrobial peptide, named coagulin, produced by Bacilluscoagulans I(4) has recently been reported (B. Hyronimus, C. Le Marrec and M. C.Urdaci, J. Appl. Microbiol. 85:42-50, 1998). In the present study, the complete, unambiguous primary amino acid sequence of the peptide was obtained by acombination of both N-terminal sequencing of purified peptide and the completesequence deduced from the structural gene harbored by plasmid I(4). Data revealedthat this peptide of 44 residues has an amino acid sequence similar to thatdescribed for pediocins AcH and PA-1, produced by different Pediococcusacidilactici strains and 100% identical. Coagulin and pediocin differed only by asingle amino acid at their C terminus. Analysis of the genetic determinantsrevealed the presence, on the pI(4) DNA, of the entire 3.5-kb operon of fourgenes described for pediocin AcH and PA-1 production. No extended homology wasobserved between pSMB74 from P. acidilactici and pI(4) when analyzing the regionsupstream and downstream of the operon. An oppositely oriented gene immediatelydowstream of the bacteriocin operon specifies a 474-amino-acid protein whichshows homology to Mob-Pre (plasmid recombination en- 139 zyme) proteins encoded byseveral small plasmids extracted from gram-positive bacteria. This is the firstreport of a pediocin-like peptide appearing naturally in a non-lactic acidbacterium genus.PMCID: PMC92446PMID: 11097892 [PubMed - indexed for MEDLINE] 222 321. FEMS Microbiol Lett. 2000 Dec 1;193(1):63-8.Cloning and characterization of the gene encoding penicillin-binding protein A ofStreptomyces griseus.Jiang H(1), Kendrick KE.Author information: (1)Department of Microbiology, The Ohio State University, Columbus, OH 43210, [email protected] internal segment of the penicillin-binding protein gene, pbpA, of Streptomycesgriseus was amplified from genomic DNA using the polymerase chain reaction andused as a hybridization probe to isolate the complete gene from a cosmid library.pbpA encodes a 485 amino acid sequence that conserves three motifs of PBPs, SXXK,SXN, and KTG. The pbpA gene was located downstream of a gene homologous to theBacillus subtilis spoVE gene. The pbpA gene was disrupted by replacing an ApaIfragment of the pbpA gene in S. griseus chromosome with an apramycin resistancegene cassette or directly inserting this apramycin resistance gene cassette atthe NcoI site of pbpA penicillin-binding domain. No obvious defects in growth,sporulation, or spore sonication resistance were observed in the constructed pbpAmutants, suggesting that PBPA is not essential for growth and sporulation undernormal laboratory conditions in S. griseus.PMID: 11094280 [PubMed - indexed for MEDLINE] 223 322. Genome Inform Ser Workshop Genome Inform. 1998;9:3-12.Genomic Analysis of the Genes Encoding Ribosomal Proteins in Eight EubacterialSpecies and Saccharomyces cerevisiae.Fujita K, Baba T, Isono K.The complete genomic nucleotide sequence data of more than 10 unicellularorganisms have become available. During the past years, we have been focusing ourattention to the analysis of the structure and function of the ribosome and itsprotein components. By making use of the genomic sequence data, our work can now be extended to comparative analysis of the ribosomal components at the genomiclevel. Such analysis will contribute to our understanding of thestructure-function relationship of the ribosome that is vital to the expressionof genetic information. Bearing these in mind, the ribosomal protein genes oforganisms whose genomic sequence data are available were analyzed, which includedAquifex aeolicus; Archaeoglobus fulgidus; Borrelia burgdorferi; Bacillussubtilis; Escherichia coli; Haemophilus influenzae; Helicobacter pylori;Methanococcus jannaschii; Mycoplasma genitalium; Mycoplasma pneumoniae;Synechosystis sp., and Saccharomyces cerevisiae. In addition, the amino acidsequence data of Bacillus stearothermophilus ribosomal proteins were used in the evolutionary evaluation. The results indicate that, in eubacteria including twospecies of Mycoplasma, the operon structure of ribosomal protein genes is wellconserved, while their relative orientation and chromosomal location are divergedinto several classes. The operon structure in M. jannaschii on the other hand is quite different from the eubacterial one and we noticed that its many genes show similarity to rat ribosomal protein genes. The degrees of sequence conservationdiffer from one ribosomal protein gene to another, but several genes encodingproteins that are considered to be of structural importance are conservedthroughout the bacterial species including archaebacteria and further in S.cerevisiae.PMID: 11072316 [PubMed - as supplied by publisher]323. Nucleic Acids Res. 2000 Nov 1;28(21):4317-31.Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans andgenomic sequence comparison with Bacillus subtilis.Takami H(1), Nakasone K, Takaki Y, Maeno G, Sasaki R, Masui N, Fuji F, Hirama C, Nakamura Y, Ogasawara N, Kuhara S, Horikoshi K.Author information: (1)Japan Marine Science and Technology Center, Deep-Sea Microorganisms ResearchGroup, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan. [email protected] 4 202 353 bp genome of the alkaliphilic bacterium Bacillus halodurans C-125contains 4066 predicted protein coding sequences (CDSs), 2141 (52.7%) of whichhave functional assignments, 1182 (29%) of which are conserved CDSs with unknown function and 743 (18. 3%) of which have no match to any protein database. Amongthe total CDSs, 8.8% match sequences of proteins found only in Bacillus subtilis and 66.7% are widely conserved in comparison with the proteins of variousorganisms, including B.subtilis. The B. halodurans genome contains 112transposase genes, indicating that transposases have played an importantevolutionary role in horizontal gene transfer and also in internal geneticrearrangement in the genome. Strain C-125 lacks some of the necessary genes forcompetence, such as comS, srfA and rapC, supporting the fact that competence has not been demonstrated experimentally in C-125. There is no paralog of tupA,encoding teichuronopeptide, which contributes to alkaliphily, in the C-125 genomeand an ortholog of tupA cannot be found in the B.subtilis genome. Out of 11 sigmafactors which belong to the extracytoplasmic function family, 10 are unique to B.halodurans, suggesting that they may have a role in the special mechanism ofadaptation to an alkaline environment.PMCID: PMC113120PMID: 11058132 [PubMed - indexed for MEDLINE] 224 324. Int J Med Microbiol. 2000 May;290(2):123-34.Proteomics, DNA arrays and the analysis of still unknown regulons and unknownproteins of Bacillus subtilis and pathogenic gram-positive bacteria.Hecker M(1), Engelmann S.Author information: (1)Ernst-Moritz-Arndt Universität, Institut für Mikrobiologie, Greifswald, Germany. [email protected] complete sequence of the bacterial genomes provides new perspectives for the study of gene expression and gene function. By the combination of the highlysensitive 2-dimensional (2D) protein gel electrophoresis with the identification of the protein spots by microsequencing or mass spectrometry we established a 2D protein index of Bacillus subtilis that currently comprises almost 400 proteinentries. A computer-aided evaluation of the 2D gels loaded withradioactively-labelled proteins from growing or stressed/starved cells proved to be a powerful tool in the analysis of global regulation of the expression of the entire genome. For the general stress regulon it is demonstrated how theproteomics approach can be used to analyse the regulation, structure and functionof still unknown 140 225 226 227 228 regulons. The application of this approach is illustrated forthe sigmaB dependent general stress regulon. For the comprehensive description ofproteins/genes belonging to stimulons or regulons it is generally recommended to complement the proteome approach with DNA array techniques in order to identifyand allocate still undiscovered members of individual regulons. This approach is also very attractive to uncover the function of still unknown global regulatorsand regulons and to dissect the entire genome into its basic modules of globalregulation. The same strategy can be used to analyse the regulation, structureand function of regulons encoding virulence factors of pathogenic bacteria for a comprehensive understanding of the pathogenicity and for the identification ofnew antibacterial targets.PMID: 11045917 [PubMed - indexed for MEDLINE] 325. J Bacteriol. 2000 Nov;182(21):6169-76.Nonspecific adherence by Actinobacillus actinomycetemcomitans requires geneswidespread in bacteria and archaea.Kachlany SC(1), Planet PJ, Bhattacharjee MK, Kollia E, DeSalle R, Fine DH,Figurski DH.Author information: (1)Department of Microbiology, College of Physicians and Surgeons, ColumbiaUniversity, New York, New York 10032, USA.The gram-negative coccobacillus, Actinobacillus actinomycetemcomitans, is theputative agent for localized juvenile periodontitis, a particularly destructiveform of periodontal disease in adolescents. This bacterium has also been isolatedfrom a variety of other infections, notably endocarditis. Fresh clinical isolatesof A. actinomycetemcomitans form tenacious biofilms, a property likely to becritical for colonization of teeth and other surfaces. Here we report theidentification of a locus of seven genes required for nonspecific adherence of A.actinomycetemcomitans to surfaces. The recently developed transposon IS903phikan was used to isolate mutants of the rough clinical isolate CU1000 that aredefective in tight adherence to surfaces (Tad(-)). Unlike wild-type cells, Tad(-)mutant cells adhere poorly to surfaces, fail to form large autoaggregates, andlack long, bundled fibrils. Nucleotide sequencing and genetic complementationanalysis revealed a 6.7-kb region of the genome with seven adjacent genes(tadABCDEFG) required for tight adherence. The predicted TadA polypeptide issimilar to VirB11, an ATPase involved in macromolecular transport. The predicted amino acid sequences of the other Tad polypeptides indicate membrane localizationbut no obvious functions. We suggest that the tad genes are involved in secretionof factors required for tight adherence of A. actinomycetemcomitans. Remarkably, complete and highly conserved tad gene clusters are present in the genomes of thebubonic plague bacillus Yersinia pestis and the human and animal pathogenPasteurella multocida. Partial tad loci also occur in strikingly diverse Bacteriaand Archaea. Our results show that the tad genes are required for tight adherenceof A. actinomycetemcomitans to surfaces and are therefore likely to be essential for colonization and pathogenesis. The occurrence of similar genes in a widearray of microorganisms indicates that they have important functions. We propose that tad-like genes have a significant role in microbial colonization.PMCID: PMC94753PMID: 11029439 [PubMed - indexed for MEDLINE] 326. J Bacteriol. 2000 Nov;182(21):6114-22.Cloning and characterization of the str operon and elongation factor Tuexpression in Bacillus stearothermophilus.Krásný L(1), Vacík T, Fucík V, Jonák J.Author information: (1)Department of Protein Biosynthesis, Institute of Molecular Genetics, Academy ofSciences of the Czech Republic, 166 37 Prague 6, Czech Republic.The complete primary structure of the str operon of Bacillus stearothermophiluswas determined. It was established that the operon is a five-gene transcriptionalunit: 5'-ybxF (unknown function; homology to eukaryotic ribosomal proteinL30)-rpsL (S12)-rpsG (S7)-fus (elongation factor G [EF-G])-tuf (elongation factorTu [EF-Tu])-3'. The main operon promoter (strp) was mapped upstream of ybxF, and its strength was compared with the strength of the tuf-specific promoter (tufp)located in the fus-tuf intergenic region. The strength of the tufp region toinitiate transcription is about 20-fold higher than that of the strp region, asdetermined in chloramphenicol acetyltransferase assays. Deletion mappingexperiments revealed that the different strengths of the promoters are theconsequence of a combined effect of oppositely acting cis elements, identifiedupstream of strp (an inhibitory region) and tufp (a stimulatory A/T-rich block). Our results suggest that the oppositely adjusted core promoters significantlycontribute to the differential expression of the str operon genes, as monitoredby the expression of EF-Tu and EF-G.PMCID: PMC94746PMID: 11029432 [PubMed - indexed for MEDLINE] 327. Nucleic Acids Res. 2000 Oct 15;28(20):4021-8.A heuristic graph comparison algorithm and its application to detect functionallyrelated enzyme clusters.Ogata H(1), Fujibuchi W, Goto S, Kanehisa M.Author information: (1)Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.The availability of computerized knowledge on biochemical pathways in the KEGGdatabase opens new opportunities for developing computational methods tocharacterize and understand higher level functions of complete genomes. Ourapproach is based on the concept of graphs; for example, the genome is a graphwith genes as nodes and the pathway is another graph with gene products as nodes.We have developed a simple method for graph comparison to identify localsimilarities, termed correlated clusters, between two graphs, which allows gapsand mismatches of nodes and edges and is especially suitable for detectingbiological features. The method was applied to a comparison of the completegenomes of 10 microorganisms and the KEGG metabolic pathways, which revealed, notsurprisingly, a tendency for formation of correlated clusters called FRECs(functionally related enzyme clusters). However, this tendency variedconsiderably depending on the organism. The relative number of enzymes in FRECswas close to 50% for Bacillus subtilis and Escherichia coli, but was <10% forSYNECHOCYSTIS: and Saccharomyces cerevisiae. The FRECs collection is reorganized into a collection of ortholog group tables in KEGG, which represents conservedpathway motifs with the information about gene clusters in all the completelysequenced genomes.PMCID: PMC110779PMID: 11024183 [PubMed - indexed for MEDLINE] 328. Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):12176-81.Genome sequence of Halobacterium species NRC-1.Ng WV(1), Ken- 141 nedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, BaligaNS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, Goo YA,Leithauser B, Keller K, Cruz R, Danson MJ, Hough DW, Maddocks DG, Jablonski PE,Krebs MP, Angevine CM, Dale H, Isenbarger TA, Peck RF, Pohlschroder M, SpudichJL, Jung KW, Alam M, Freitas T, Hou S, Daniels CJ, Dennis PP, Omer AD, Ebhardt H,Lowe TM, Liang P, Riley M, Hood L, DasSarma S.Author information: (1)Department of Molecular Biotechnology, University of Washington, Seattle, WA98195, USA. tment of Microbiology, University of Massachusetts, Amherst, MA01003; Centre for Extremophile Research, Department of Biology and Biochemistry, Univer.We report the complete sequence of an extreme halophile, Halobacterium sp. NRC-1,harboring a dynamic 2,571,010-bp genome containing 91 insertion sequencesrepresenting 12 families and organized into a large chromosome and 2 relatedminichromosomes. The Halobacterium NRC-1 genome codes for 2,630 predictedproteins, 36% of which are unrelated to any previously reported. Analysis of the genome sequence shows the presence of pathways for uptake and utilization ofamino acids, active sodium-proton antiporter and potassium uptake systems,sophisticated photosensory and signal transduction pathways, and DNA replication,transcription, and translation systems resembling more complex eukaryoticorganisms. Whole proteome comparisons show the definite archaeal nature of thishalophile with additional similarities to the Gram-positive Bacillus subtilis andother bacteria. The ease of culturing Halobacterium and the availability ofmethods for its genetic manipulation in the laboratory, including construction ofgene knockouts and replacements, indicate this halophile can serve as anexcellent model system among the archaea.PMCID: PMC17314PMID: 11016950 [PubMed - indexed for MEDLINE] 229 329. FEMS Microbiol Rev. 2000 Oct;24(4):449-67.The ATP binding cassette (ABC) transport systems of Mycobacterium tuberculosis.Braibant M(1), Gilot P, Content J.Author information: (1)Pasteur Institute, Department of Virology, Engelandstraat 642, B-1180, Brussels, Belgium. [email protected] in FEMS Microbiol Rev 2002 Mar;26(1):109.We have undertaken the inventory and assembly of the typical subunits of the ABC transporters encoded by the complete genome of Mycobacterium tuberculosis. These subunits, i.e. the nucleotide binding domains (NBDs), the membrane-spanningdomains (MSDs) and the substrate binding proteins (SBPs), were identified on the basis of their characteristic stretches of amino acids and/or conservedstructure. A total of 45 NBDs present in 38 proteins, of 47 MSDs present in 44proteins and of 15 SBPs were found to be encoded by M. tuberculosis. Analysis of transcriptional clusters and searches of homology between the identified subunitsof the transporters and proteins characterized in other organisms allowed thereconstitution of at least 26 complete (including at least one NBD and one MSD)and 11 incomplete ABC transporters. Sixteen of them were unambiguously classifiedas importers whereas 21 were presumed to be exporters. By searches of homologywith already known transporters from other organisms, potential substrates(peptides, macrolides, carbohydrates, multidrugs, antibiotics, iron, anions)could be attributed to 30 of the ABC transporters identified in M. tuberculosis. The ABC transporters have been further classified in nine different sub-families according to a tree obtained from the clustering of their NBDs. Contrary toEscherichia coli and similarly to Bacillus subtilis, there is an equalrepresentation of extruders and importers. Many exporters were found to bepotentially implicated in the transport of drugs, probably contributing to theresistance of M. tuberculosis to many antibiotics. Interestingly, a transporter(absent in E. coli and in B. subtilis) potentially implicated in the export of a factor required for the bacterial attachment to the eukaryotic host cells wasalso identified. In comparison to E. coli and B. subtilis, there is anunder-representation of the importers (with the exception of the phosphateimporters) in M. tuberculosis. This may reflect the capacity of this bacterium tosynthesize many essential compounds and to grow in the presence of few externalnutrients. The genes encoding the ABC transporters occupy about 2.5% of thegenome of M. tuberculosis.PMID: 10978546 [PubMed - indexed for MEDLINE] 230 330. Phys Rev Lett. 2000 Sep 18;85(12):2641-4.Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification.Yanai I(1), Camacho CJ, DeLisi C.Author information: (1)Department of Biomedical Engineering, Boston University, Boston, Massachusetts02215, USA.A universal property of microbial genomes is the considerable fraction of genesthat are homologous to other genes within the same genome. The process by whichthese homologues are generated is not well understood, but sequence analysis of20 microbial genomes unveils a recurrent distribution of gene family sizes. Weshow that a simple evolutionary model based on random gene duplication and point mutations fully accounts for these distributions and permits predictions for the number of gene families in genomes not yet complete. Our findings are consistent with the notion that a genome evolves from a set of precursor genes to a maturesize by gene duplications and increasing modifications.PMID: 10978127 [PubMed - indexed for MEDLINE] 231 331. Extremophiles. 2000 Aug;4(4):209-14.Characterization and comparative study of the rrn operons of alkaliphilicBacillus halodurans C-125.Nakasone K(1), Masui N, Takaki Y, Sasaki R, Maeno G, Sakiyama T, Hirama C, FujiF, Takami H.Author information: (1)Deep-sea Microorganisms Research Group, Japan Marine Science and TechnologyCenter, Yokosuka. [email protected] ribosomal RNA operons (rrn) of alkaliphilic Bacillus halodurans C-125 werecharacterized and compared with those of B. subtilis. We isolated clonescontaining rrn operons from a lambda phage library of the C-125 chromosome, andthe complete nucleotide sequence of each was determined. Eight rrn operons wereidentified by PFGE analysis of the C-125 chromosome digested with I-CeuI. Thetranscriptional orientation of the rrn operons mapped on the chromosome bySouthern hybridization analysis was the same as the direction of replication ofthe chromosome. These operons were designated as rrnA-H, starting from 142 232 233 234 235 the oriClocus in clockwise rotation. Sequence and structural analyses of these operonssuggested that six of the rrn operons in the C-125 chromosome, rrnA, rrnB,rrnC-rrnD, rrnE, and rrnH, correspond to rrnO, rrnA, rrnJ-rrnW, rrnI, and rrnD inB. subtilis, whereas the other rrn operons (rrnF and rrnG) were specificallyobserved in C-125. The rrn loci were positioned from 0 degrees to 90 degrees onthe physical map, with the oriC locus assigned the position zero degrees. TwoORFs annotated as tnpA and ykfC, whose gene products are likely to act astransposases, were found downstream of these six operons. Comparative analysis ofthe 16S-23S and 23S-5S ITS (internally transcribed sequence) regions of B.halodurans C-125 and those of B. subtilis revealed that the ITS regions in C-125 were much longer than those in B. subtilis. There was no substantial differencein the length of potential promoter sequences in B. halodurans and B. subtilis.PMID: 10972189 [PubMed - indexed for MEDLINE] 332. Appl Environ Microbiol. 2000 Sep;66(9):3727-34.Thermostable chitosanase from Bacillus sp. Strain CK4: cloning and expression of the gene and characterization of the enzyme.Yoon HG(1), Kim HY, Lim YH, Kim HK, Shin DH, Hong BS, Cho HY.Author information: (1)Graduate School of Biotechnology, Korea University, Seoul 136-701, Korea.A thermostable chitosanase gene from the environmental isolate Bacillus sp.strain CK4, which was identified on the basis of phylogenetic analysis of the 16SrRNA gene sequence and phenotypic analysis, was cloned, and its complete DNAsequence was determined. The thermostable chitosanase gene was composed of an822-bp open reading frame which encodes a protein of 242 amino acids and a signalpeptide corresponding to a 30-kDa enzyme. The deduced amino acid sequence of the chitosanase from Bacillus sp. strain CK4 exhibits 76.6, 15.3, and 14.2%similarities to those from Bacillus subtilis, Bacillus ehemensis, and Bacilluscirculans, respectively. C-terminal homology analysis shows that Bacillus sp.strain CK4 belongs to cluster III with B. subtilis. The gene was similar in size to that of the mesophile B. subtilis but showed a higher preference for codonsending in G or C. The enzyme contains 2 additional cysteine residues at positions49 and 211. The recombinant chitosanase has been purified to homogeneity by usingonly two steps with column chromatography. The half-life of the enzyme was 90 minat 80 degrees C, which indicates its usefulness for industrial applications. The enzyme had a useful reactivity and a high specific activity for producingfunctional oligosaccharides as well, with trimers through hexamers as the majorproducts.PMCID: PMC92213PMID: 10966383 [PubMed - indexed for MEDLINE] 333. DNA Seq. 2000;11(1-2):1-7.An ORF from Bacillus licheniformis encodes a putative DNA repressor.Naval J(1), Aguilar D, Serra X, Pérez-Pons JA, Piñol J, Lloberas J, Querol E.Author information: (1)Institut de Biologia Fonamental and Departament de Bioquímica i BiologiaMolecular, Universitat Autònoma de Barcelona, Bellaterra, Spain.The complete sequence of a reading frame adjacent to theendo-beta-1,3-1,4-D-glucanase gene from Bacillus licheniformis is reported. Itencodes a putative 171 amino acid residues protein with either, low significantsequence similarity in data banks or the corresponding orthologue in the recentlysequenced Bacillus subtilis genome. Computer analyses predict a canonicalHelix-Turn-Helix motif characteristic of bacterial repressors/DNA bindingproteins. A maxicells assay shows that the encoded polypeptide is expressed. ADNA-protein binding, assay performed by gel electrophoresis shows that theexpressed protein specifically binds to Bacillus licheniformis DNA.PMID: 10902904 [PubMed - indexed for MEDLINE] 334. Microbiol Immunol. 2000;44(5):389-93.Sequence of the gene encoding an alkaline serine proteinase of Bacillus pumilusTYO-67.Aoyama M(1), Toma C, Yasud M, Iwanaga M.Author information: (1)Department of Bioscience and Biotechnology, Faculty of Agriculture, University ofthe Ryukyus, Okinawa, Japan.The complete nucleotide sequence of the gene encoding an alkaline serineproteinase (aprP) of Bacillus pumilus TYO-67 was determined. The sequenceanalysis showed an open reading frame of 1,149 bp (383 amino acids) that encoded a signal peptide consisting of 29 residues and a propeptide of 79 residues. Thededuced 3 amino acid residues, D32, H64, and S221, were identical with 3essential amino acids in the catalytic center of subtilases. The sequence around these residues revealed that APRP was a new member of the true subtilisinsubgroup of the subtilisin family. The highest homology was found in subtilisinNAT at 64.4% in the DNA sequence. The residue S189 of APRP was different fromthose of other subtilases.PMID: 10888358 [PubMed - indexed for MEDLINE] 335. J Bacteriol. 2000 Jul;182(14):3989-97.vrrB, a hypervariable open reading frame in Bacillus anthracis.Schupp JM(1), Klevytska AM, Zinser G, Price LB, Keim P.Author information: (1)Department of Biological Sciences, Northern Arizona University, Flagstaff86011-5640, USA.Bacillus anthracis appears to be the most molecularly homogeneous bacterialspecies known. Extensive surveys of worldwide isolates have revealed vanishingly small amounts of genomic variation. The biological importance of theresting-stage spore may lead to very low evolutionary rates and, perhaps, to the lack of potentially adaptive genetic variation. In contrast to the overallhomogeneity, some gene coding regions contain hypervariability that is translatedinto protein variation. During marker analysis of diverse strains, we havediscovered a novel ca. 750-nucleotide open reading frame (ORF) that containsin-frame, variable-number tandem-repeat sequences. Four distinct variable regionsexist within vrrB, giving rise to 11 distinct alleles in eight different lengthcategories among B. anthracis strains. This ORF putatively codes for a 241- to265-amino-acid protein, rich in glutamine (13.2%), glycine (23.4%), and histidine(23.0%). The variable-region amino acids of the vrrB ORF are stronglyhydrophilic. Coupled with putative transmembrane domains flanking the variableregions, this suggests a membrane-anchored cytosolic or extracellular locationfor the putative protein. Sequence analysis of the complete ORFs from threeBacillus cereus strains shows maintenance of the ORF across species boundaries,including strong conservation of the amino acid sequence and the capacity to varyamong strains. The presence of 11 different alleles of the vrrB locus is in starkcontrast to the near homogeneity of B. anthracis. Evolution of 143 236 237 238 239 hypervariablegenes can negate the lack of genetic variability in species such as B. anthracis and provide select rapid evolution in other more variable species.PMCID: PMC94584PMID: 10869077 [PubMed - indexed for MEDLINE] 336. Res Microbiol. 2000 Mar;151(2):129-34.Systematic function analysis of Bacillus subtilis genes.Ogasawara N.Author information: Graduate School of Biological Sciences, Nara Institute of Science and Technology,Ikoma, Japan. [email protected] on the complete genome sequence needs to be transformed intoinformation related to function. Toward this goal, research consortia in Japanand Europe have been organized so as to acquire a collection of knockout mutants of genes with no established function. The current status of the Japanese projectconcerning mutant creation and characterization is summarized.PMID: 10865958 [PubMed - indexed for MEDLINE] 337. Genome Res. 2000 Jun;10(6):744-57.Conservation of DNA regulatory motifs and discovery of new motifs in microbialgenomes.McGuire AM(1), Hughes JD, Church GM.Author information: (1)Graduate Program in Biophysics, and Department of Genetics, Lipper Center forComputational Genetics, Harvard Medical School, Boston, MA 02115 USA.Regulatory motifs can be found by local multiple alignment of upstream regionsfrom coregulated sets of genes, or regulons. We searched for regulatory motifsusing the program AlignACE together with a set of filters that helped us choosethe motifs most likely to be biologically relevant in 17 complete microbialgenomes. We searched the upstream regions of potentially coregulated genesgrouped by three methods: (1) genes that make up functional pathways; (2) geneshomologous to regulons from a well-studied species (Escherichia coli); and (3)groups of genes derived from conserved operons. This last group is based on theobservation that genes making up homologous regulons in different species areoften assorted into coregulated operons in different combinations. This allowspartial reconstruction of regulons by looking at operon structure across several species. Unlike other methods for predicting regulons, this method does notdepend on the availability of experimental data other than the genome sequenceand the locations of genes. New, statistically significant motifs were found inthe genome sequence of each organism using each grouping method. The mostsignificant new motif was found upstream of genes in the methane-metabolismfunctional group in Methanobacterium thermoautotrophicum. We found that at least 27% of the known E. coli DNA-regulatory motifs are conserved in one or moredistantly related eubacteria. We also observed significant motifs that differedfrom the E. coli motif in other organisms upstream of sets of genes homologous toknown E. coli regulons, including Crp, LexA, and ArcA in Bacillus subtilis; four anaerobic regulons in Archaeoglobus fulgidus (NarL, NarP, Fnr, and ModE); and thePhoB, PurR, RpoH, and FhlA regulons in other archaebacterial species. We alsoused motif conservation to aid in finding new motifs by grouping upstream regionsfrom closely related bacteria, thus increasing the number of instances of themotif in the sequence to be aligned. For example, by grouping upstream sequences from three archaebacterial species, we found a conserved motif that may regulate ferrous ion transport that was not found in individual genomes. Discovery ofconserved motifs becomes easier as the number of closely related genome sequencesincreases.PMID: 10854408 [PubMed - indexed for MEDLINE] 338. Int J Syst Evol Microbiol. 2000 May;50 Pt 3:1305-13.New psychrophilic and psychrotolerant Bacillus marinus strains from tropical and polar deep-sea sediments and emended description of the species.Rüger HJ(1), Fritze D, Spröer C.Author information: (1)Alfred-Wegener-Institut für Polar- und Meeresforschung, Bremerhaven, Germany.In contrast to the current view that psychrophily combined with an absoluterequirement for NaCl is connected with the Gram-negative cell wall type,psychrophilic and psychrotolerant, NaCl-requiring, Gram-positive bacteria havebeen isolated from tropical Atlantic, Arctic and Antarctic deep-sea sediments.Some of the isolates are even extremely psychrophilic, having maximum growthtemperatures of 4 degrees C. On the basis of phenotypic characteristics, DNA baseanalyses, DNA-DNA hybridizations and partial and complete 16S rRNA gene sequence analyses, the strains from the three distinct geographical regions have beenallocated to the obligately marine species Bacillus marinus. The distribution andorigin of B. marinus are discussed and an emended description of the species ispresented.PMID: 10843076 [PubMed - indexed for MEDLINE] 339. Plasmid. 2000 May;43(3):235-9.Analysis of the complete nucleotide sequence of the tetracycline-resistancetransposon Tn10.Lawley TD(1), Burland V, Taylor DE.Author information: (1)Department of Biological Sciences, University of Alberta, Edmonton, Alberta,Canada.An analysis of the complete nucleotide sequence of the compositetetracycline-resistance transposon Tn10 (9147 bp) from the Salmonella typhiconjugative plasmid R27 is presented. A comparison of the protein sequences from IS10-right and IS10-left transposases has identified four amino acid differences.These residues appear to play an important role in normal transposase functionand may account for the differences in exhibited transposition activities. Thetetracycline determinants encoded by this version of Tn10 share >99% identitywith those of Tn10(R100), demonstrating the conservation that exists betweenthese transposons. A previously uncharacterized approximately 3000-bp region ofTn10 contains four putative open reading frames. One of these open reading framesshares 55% identity with the glutamate permease protein sequence from Haemophilusinfluenzae although it was unable to complement an Escherichia coli glutamatepermease mutant, with which it shares 51% identity. The three remaining putative open reading frames are arranged as a discrete genetic unit adjacent to theglutamate permease homolog and are transcribed in the opposite direction. Two of these open reading frames are homologous with Bacillus subtilis proteins ofunknown functions while the other has no homologs in the database. The presenceof an aminoacyl-tRNA synthetase class II motif in one of these open readingframes in combination with the glutamate permease homolog allows us to postulate that this region of Tn10 could once have played a role in amino acid metabolism.Copyright 2000 Academic Press.PMID: 10783303 [PubMed - in- 144 240 241 242 243 244 dexed for MEDLINE] 340. J Bacteriol. 2000 May;182(10):2970-2.Complete nucleotide sequence of Tn10.Chalmers R(1), Sewitz S, Lipkow K, Crellin P.Author information: (1)Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United [email protected] complete nucleotide sequence of Tn10 has been determined. The dinucleotidesignature and percent G+C of the sequence had no discontinuities, indicating thatTn10 constitutes a homogeneous unit. The new sequence contained three new openreading frames corresponding to a glutamate permease, repressors of heavy metalresistance operons, and a hypothetical protein in Bacillus subtilis. Theglutamate permease was fully functional when expressed, but Tn10 did not protect Escherichia coli from the toxic effects of various metals.PMCID: PMC102010PMID: 10781570 [PubMed - indexed for MEDLINE] 341. J Bacteriol. 2000 May;182(10):2928-36.Multiple-locus variable-number tandem repeat analysis reveals geneticrelationships within Bacillus anthracis.Keim P(1), Price LB, Klevytska AM, Smith KL, Schupp JM, Okinaka R, Jackson PJ,Hugh-Jones ME.Author information: (1)Department of Biological Sciences, Northern Arizona University, Flagstaff,Arizona 86011-5640, USA. [email protected] anthracis is one of the most genetically homogeneous pathogensdescribed, making strain discrimination particularly difficult. In this paper, wepresent a novel molecular typing system based on rapidly evolving variable-numbertandem repeat (VNTR) loci. Multiple-locus VNTR analysis (MLVA) uses the combined power of multiple alleles at several marker loci. In our system, fluorescentlylabeled PCR primers are used to produce PCR amplification products from eightVNTR regions in the B. anthracis genome. These are detected and their sizes aredetermined using an ABI377 automated DNA sequencer. Five of these eight loci werediscovered by sequence characterization of molecular markers (vrrC(1), vrrC(2),vrrB(1), vrrB(2), and CG3), two were discovered by searching complete plasmidnucleotide sequences (pXO1-aat and pXO2-at), and one was known previously (vrrA).MLVA characterization of 426 B. anthracis isolates identified 89 distinctgenotypes. VNTR markers frequently identified multiple alleles (from two tonine), with Nei's diversity values between 0.3 and 0.8. Unweighted pair-groupmethod arithmetic average cluster analysis identified six genetically distinctgroups that appear to be derived from clones. Some of these clones show worldwidedistribution, while others are restricted to particular geographic regions. Humancommerce doubtlessly has contributed to the dispersal of particular clones inancient and modern times.PMCID: PMC102004PMID: 10781564 [PubMed - indexed for MEDLINE] 342. FEMS Microbiol Lett. 2000 May 1;186(1):1-9.The biology of enhancer-dependent transcriptional regulation in bacteria:insights from genome sequences.Studholme DJ(1), Buck M.Author information: (1)Department of Biology, Imperial College of Science Technology and Medicine, SirAlexander Fleming Building, London, UK. [email protected] bacterial transcription factor sigma(N) (sigma-N, sigma-54, RpoN) confersupon RNA polymerase (RNAP) properties distinct from those of the majorhouse-keeping form of RNAP, which contains sigma(70) (sigma-70, RpoD).Transcription by RNAP containing sigma(N) is subject to enhancer-dependentregulation. Far from being an 'oddity' or 'exception to the rule', the occurrenceof sigma(N) in the genome sequences of such diverse bacteria as Aquifex aeolicus,Bacillus subtilis, Chlamydia spp. and Borrelia burgdorferi argues for itsbiological importance. The availability of complete genome sequences of several(eu)bacteria offers an opportunity to extend our understanding of this specialform of transcriptional regulation. By scanning their genome sequences, newfunctions have been predicted for enhancer-dependent transcription in A.aeolicus, Chlamydia trachomatis, Escherichia coli, Treponema pallidum and B.burgdorferi.PMID: 10779705 [PubMed - indexed for MEDLINE] 343. J Bacteriol. 2000 Apr;182(7):1987-94.Mutations in the gerP locus of Bacillus subtilis and Bacillus cereus affectaccess of germinants to their targets in spores.Behravan J(1), Chirakkal H, Masson A, Moir A.Author information: (1)Department of Molecular Biology & Biotechnology, University of Sheffield,Sheffield S10 2TN, United Kingdom.The gerP1 transposon insertion mutation of Bacillus cereus is responsible for adefect in the germination response of spores to both L-alanine and inosine. Themutant is blocked at an early stage, before loss of heat resistance or release ofdipicolinate, and the efficiency of colony formation on nutrient agar from sporesis reduced fivefold. The protein profiles of alkaline-extracted spore coats andthe spore cortex composition are unchanged in the mutant. Permeabilization ofgerP mutant spores by coat extraction procedures removes the block in earlystages of germination, although a consequence of the permeabilization procedurein both wild type and mutant is that late germination events are not complete.The complete hexacistronic operon that includes the site of insertion has beencloned and sequenced. Four small proteins encoded by the operon (GerPA, GerPD,GerPB, and GerPF) are related in sequence. A homologous operon (yisH-yisC) can befound in the Bacillus subtilis genome sequence; null mutations in yisD and yisF, constructed by integrational inactivation, result in a mutant phenotype similarto that seen in B. cereus, though somewhat less extreme and equally repairable byspore permeabilization. Normal rates of germination, as estimated by loss of heatresistance, are also restored to a gerP mutant by the introduction of a cotEmutation, which renders the spore coats permeable to lysozyme. The B. subtilisoperon is expressed solely during sporulation, and is sigma K-inducible. Wehypothesize that the GerP proteins are important as morphogenetic or structuralcomponents of the Bacillus spore, with a role in the establishment of normalspore coat structure and/or permeability, and that failure to synthesize theseproteins during spore formation limits the opportunity for small hydrophilicorganic molecules, like alanine or inosine, to gain access to their normaltarget, the germination receptor, in the spore.PMCID: PMC101904PMID: 10715007 [PubMed - indexed for MEDLINE] 344. Microbiology. 2000 Feb;146 ( Pt 2):263-71.Regulation of the transport system for C4-dicarboxylic acids in Bacillussubtilis.Asai K(1), Baik SH, Kasahara Y, Moriya S, Ogasawara N.Author information: (1)Department of Cell Biology, Graduate School of Biologi- 145 245 246 247 248 cal Sciences, NaraInstitute of Science and Technology, Takayama, Ikoma, Japan.Transport systems for C4-dicarboxylates, such as malate, fumarate and succinate, are poorly understood in Gram-positive bacteria. The whole genome sequence ofBacillus subtilis revealed two genes, ydbE and ydbH, whose deduced products arehighly homologous to binding proteins and transporters for C4-dicarboxylates inGram-negative bacteria. Between ydbE and ydbH, genes ydbF and ydbG encoding asensor-regulator pair, were located. Inactivation of each one of the ydbEFGHgenes caused a deficiency in utilization of fumarate or succinate but not ofmalate. Expression of ydbH, encoding a putative transporter, was stimulated in a minimal salt medium containing 0-05% yeast extract but repressed by the addition of malate to the medium. Inactivation of the putative sensor-regulator pair orsolute-binding protein, ydbFG or ydbE, caused complete loss of ydbH expression.The utilization of fumarate and stimulation of ydbH expression resumed in a ydbE null mutant in which ydbFGH were overproduced. Based on these observations,together with analysis of the sequence similarities of the deduced product, weconclude that YdbH is a C4-dicarboxylate-transport protein and its expression is regulated by a C4-dicarboxylate sensor kinase-regulator pair, YdbF and YdbG.Furthermore, it is suggested that YdbE does not directly participate in transportof C4-dicarboxylates, but plays a sensory role in the ydbF-ydbG two-componentsystem, giving rise to specificity or increased efficiency to the system.Deletion analysis of the promoter region of ydbH revealed that a direct repeatsequence was required for the activation of ydbH expression. Acatabolite-responsive element (CRE) was also found in the -10 region of thepromoter, suggesting negative regulation by a CRE-binding protein.PMID: 10708364 [PubMed - indexed for MEDLINE] 345. Cell Stress Chaperones. 2000 Jan;5(1):21-9.Cloning, sequencing, and transcriptional analysis of the dnaK heat shock operonof Listeria monocytogenes.Hanawa T(1), Kai M, Kamiya S, Yamamoto T.Author information: (1)Department of Microbiology, Kyorin University School of Medicine, Mitaka, Tokyo, Japan.The complete dnaK operon of Listeria monocytogenes was isolated by chromosomewalking using the previously cloned dnaK gene as a probe. Molecular analysis ofthe locus identified 6 genes in the order hrcA, grpE, dnaK, dnaJ, orf35, andorf29. Primer extension analysis revealed 3 transcription start sites-S1, S2, andS3-upstream of the hrcA, grpE, and dnaJ, respectively. The transcription from S1 was heat inducible. Analysis of the sequences revealed the consensus promotersequences of gram-positive bacteria, P1 and P2 upstream of the hrcA and dnaJ,respectively. The hrcA gene and a regulatory sequence, designated CIRCE(controlling inverted repeat of chaperone expression), play a role in theregulation of expression of the dnaK locus in response to heat shock in severalgram-positive bacteria. Their presence upstream of the dnaK locus in L.monocytogenes suggested a similar regulatory mechanism for the transcriptioninitiated at the promoter, P1. Northern blot analysis led to the detection of 4mRNA species of 4.9 kb, 3.6 kb, 3.6 kb, and 1.2 kb; the first 2 species were heatinducible. The current results indicate that 4 distinct transcripts directed by 3promoters are involved in the expression of the dnaK operon of L. monocytogenes.PMCID: PMC312906PMID: 10701836 [PubMed - indexed for MEDLINE] 346. Res Microbiol. 1999 Nov-Dec;150(9-10):725-33.Functional and evolutionary roles of long repeats in prokaryotes.Rocha EP(1), Danchin A, Viari A.Author information: (1)Atelier de bioInformatique, université Paris VI, France. [email protected] recently published complete bacterial genomes have revealed unexpectedlyhigh numbers of long strict repeats. In this article we discuss the variousfunctional and evolutionary roles of these repeats, focusing in particular ontheir role in terms of genome stability, gene transfer, and antigenic variation.PMID: 10673010 [PubMed - indexed for MEDLINE] 347. J Biol Chem. 2000 Feb 11;275(6):4519-24.Effects of mutations in the L-tryptophan binding pocket of the Trp RNA-bindingattenuation protein of Bacillus subtilis.Yakhnin AV(1), Trimble JJ, Chiaro CR, Babitzke P.Author information: (1)Department of Biochemistry and Molecular Biology, The Pennsylvania StateUniversity, University Park, Pennsylvania 16802, USA.The Bacillus subtilis tryptophan biosynthetic genes are regulated by the trpRNA-binding attenuation protein (TRAP). Cooperative binding of L-tryptophanactivates TRAP so that it can bind to RNA. The crystal structure revealed thatL-tryptophan forms nine hydrogen bonds with various amino acid residues of TRAP. We performed site-directed mutagenesis to determine the importance of several of these hydrogen bonds in TRAP activation. We tested both alanine substitutions as well as substitutions more closely related to the natural amino acid atappropriate positions. Tryptophan binding mutations were identified in vivohaving unchanged, reduced, or completely eliminated repression activity. Several of the in vivo defective TRAP mutants exhibited reduced affinity for tryptophanin vitro but did not interfere with RNA binding at saturating tryptophanconcentrations. However, a 10-fold decrease in TRAP affinity for tryptophan ledto an almost complete loss of regulation, whereas increased TRAP affinity fortryptophan had little or no effect on the in vivo regulatory activity of TRAP.One hydrogen bond was found to be dispensable for TRAP activity, whereas twoothers appear to be essential for TRAP function. Another mutant protein exhibitedtryptophan-independent RNA binding activity. We also found that trp leader RNAincreases the affinity of TRAP for tryptophan.PMID: 10660627 [PubMed - indexed for MEDLINE] 348. Microbiology. 2000 Jan;146 ( Pt 1):57-64.Complete spore-cortex hydrolysis during germination of Bacillus subtilis 168requires SleB and YpeB.Boland FM(1), Atrih A, Chirakkal H, Foster SJ, Moir A.Author information: (1)Department of Molecular Biology and Biotechnology, University of Sheffield, FirthCourt, Western Bank, UK.The role of the sleB gene of Bacillus subtilis, which encodes a putativespore-cortex-lytic enzyme, and the downstream ypeB gene were investigated. BothSleB and YpeB were required for normal germination to occur. The correspondingmutants formed phase-bright, heat-resistant spores with no apparent defects indormancy. However, mutant spore suspensions lost optical density slower than the wild-type and spores were phase-grey even 12 h after the 146 triggering ofgermination. Since the loss of heat resistance and release of dipicolinic acidwas similar to the wild-type, these mutants were blocked in the later stages ofgermination. The mutants were nevertheless capable of outgrowth on rich agar toform colonies, indicating that other spore components can compensate for theirfunction sufficiently to allow outgrowth. The expression and regulation of theoperon was examined using a lacZ transcriptional fusion. Expression of the operonbegan 2 h after the onset of sporulation and was under the control of RNApolymerase containing the forespore-specific sigma factor, sigmaG. Theapplication of reverse phase HPLC revealed that the mutants do not have anystructural defect in the dormant spore cortex and therefore these genes are notrequired for normal spore-cortex synthesis. The analysis of peptidoglycandynamics during germination showed, however, that the cortex was only partiallyhydrolysed in both mutants. This analysis also revealed that the likelyhydrolytic bond specificity of SleB is likely to be that of a lytictransglycosylase.PMID: 10658652 [PubMed - indexed for MEDLINE] 249 349. Mol Microbiol. 2000 Jan;35(2):324-40.Complete nucleotide sequence, molecular analysis and genome structure ofbacteriophage A118 of Listeria monocytogenes: implications for phage evolution.Loessner MJ(1), Inman RB, Lauer P, Calendar R.Author information: (1)Institut für Mikrobiologie, FML Weihenstephan, Technische Universität München,Weihenstephaner Berg 3, 85350 Freising, Germany. [email protected] is a temperate phage isolated from Listeria monocytogenes. In this study, wereport the entire nucleotide sequence and structural analysis of its 40 834 bpDNA. Electron microscopic and enzymatic analyses revealed that the A118 genome isa linear, circularly permuted, terminally redundant collection of double-strandedDNA molecules. No evidence for cohesive ends or for a terminase recognition (pac)site could be obtained, suggesting that A118 viral DNA is packaged via a headful mechanism. Partial denaturation mapping of DNA cross-linked to the tail shaftindicated that DNA packaging proceeds from left to right with respect to thearbitrary genomic map and the direction of genes necessary for lytic development.Seventy-two open reading frames (ORFs) were identified on the A118 genome, which are apparently organized in a life cycle-specific manner into at least threemajor transcriptional units. N-terminal amino acid sequencing, bioinformaticanalyses and functional characterizations enabled the assignment of possiblefunctions to 26 ORFs, which included DNA packaging proteins, morphopoeticproteins, lysis components, lysogeny control-associated functions and proteinsnecessary for DNA recombination, modification and replication. Comparativeanalysis of the A118 genome structure with other bacteriophages revealed local,but sometimes extensive, similarities to a number of phages spanning a broaderphylogenetic range of various low G+C host bacteria, which implies relativelyrecent exchange of genes or genetic modules. We have also identified the A118attachment site attP and the corresponding attB in Listeria monocytogenes, andshow that site-specific integration of the A118 prophage by the A118 integraseoccurs into a host gene homologous to comK of Bacillus subtilis, anautoregulatory gene specifying the major competence transcription factor.PMID: 10652093 [PubMed - indexed for MEDLINE] 250 350. Comput Chem. 2000 Jan;24(1):57-70.Detecting localized repeats in genomic sequences: a new strategy and itsapplication to Bacillus subtilis and Arabidopsis thaliana sequences.Klaerr-Blanchard M(1), Chiapello H, Coward E.Author information: (1)Unité de Régulation de l'Expression Génétique, Institut Pasteur, Paris, [email protected] new method for the search of local repeats in long DNA sequences, such ascomplete genomes, is presented. It detects a large variety of repeats varying in length from one to several hundred bases, which may contain many mutations. Bymutations we mean substitutions, insertions or deletions of one or more bases.The method is based on counting occurrences of short words (3-12 bases) insequence fragments called windows. A score is computed for each window, based on calculating exact word occurrence probabilities for all the words of a givenlength in the window. The probabilities are defined using a Bernoulli model(independent letters) for the sequence, using the actual letter frequencies from each window. A plot of the probabilities along the sequence for high-scoringwindows facilitates the identification of the repeated patterns. We applied themethod to the 1.87 Mb sequence of chromosome 4 of Arabidopsis thaliana and to thecomplete genome of Bacillus subtilis (4.2 Mb). The repeats that we found wereclassified according to their size, number of occurrences, distance betweenoccurrences, and location with respect to genes. The method proves particularlyuseful in detecting long, inexact repeats that are local, but not necessarilytandem. The method is implemented as a C program called EXCEP, which is availableon request from the authors.PMID: 10642880 [PubMed - indexed for MEDLINE] 251 351. J Bacteriol. 2000 Jan;182(2):365-70.beta-ketoacyl-acyl carrier protein synthase III (FabH) is a determining factor inbranched-chain fatty acid biosynthesis.Choi KH(1), Heath RJ, Rock CO.Author information: (1)Department of Biochemistry, St. Jude Children's Research Hospital, Memphis,Tennessee 38105, USA.A universal set of genes encodes the components of the dissociated, type II,fatty acid synthase system that is responsible for producing the multitude offatty acid structures found in bacterial membranes. We examined the biochemicalbasis for the production of branched-chain fatty acids by gram-positive bacteria.Two genes that were predicted to encode homologs of the beta-ketoacyl-acylcarrier protein synthase III of Escherichia coli (eFabH) were identified in theBacillus subtilis genome. Their protein products were expressed, purified, andbiochemically characterized. Both B. subtilis FabH homologs, bFabH1 and bFabH2,carried out the initial condensation reaction of fatty acid biosynthesis withacetyl-coenzyme A (acetyl-CoA) as a primer, although they possessed lowerspecific activities than eFabH. bFabH1 and bFabH2 also utilized iso- andanteiso-branched-chain acyl-CoA primers as substrates. eFabH was not able toaccept these CoA thioesters. Reconstitution of a complete round of fatty acidsynthesis in vitro with purified E. coli proteins showed that eFabH was the only E. coli enzyme incapable of using branched-chain substrates. Expression of eitherbFabH1 or bFabH2 in E. coli resulted in the appearance of a 147 252 253 254 255 256 branched-chain17-carbon fatty acid. Thus, the substrate specificity of FabH is an importantdeterminant of branched-chain fatty acid production.PMCID: PMC94284PMID: 10629181 [PubMed - indexed for MEDLINE] 352. Bull Acad Natl Med. 1999;183(7):41-50; discussion 50-1.[What can be expected from sequencing of the Mycobacterium tuberculosis genome?].[Article in French]Cole ST.Author information: Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, Paris.Mycobacterium tuberculosis, the scourge of humanity, is one of the mostsuccessful and scientifically challenging pathogens of all time. To catalyze the conception of new prophylactic and therapeutic interventions againsttuberculosis, and to enhance our understanding of the biology of the tuberclebacillus, the complete genome sequence of the most widely used strain, H37Rv, hasbeen determined. Bioinformatic analysis led to the identification ofapproximately 4,000 genes in the 4.41 Mb genome sequence and provided freshinsight into the biochemistry, physiology, genetics and immunology of thismuch-feared bacterium. Genomic information is centralised in TubercuList(http://www.pasteur.fr/Biol/TubercuList/).PMID: 10622121 [PubMed - indexed for MEDLINE] 353. J Bacteriol. 2000 Jan;182(1):155-63.Genetics of L-sorbose transport and metabolism in Lactobacillus casei.Yebra MJ(1), Veyrat A, Santos MA, Pérez-Martínez G.Author information: (1)Departamento de Biotecnología, Instituto de Agroquímica y Tecnología deAlimentos, CSIC, 46100 Burjassot, Spain.Genes encoding L-sorbose metabolism of Lactobacillus casei ATCC 393 have beenidentified on a 6.8-kb chromosomal DNA fragment. Sequence analysis revealed sevencomplete genes and a partial open reading frame transcribed as two units. Thededuced amino acid sequences of the first transcriptional unit (sorRE) showedhigh similarity to the transcriptional regulator and the L-sorbose-1-phosphatereductase of the sorbose (sor) operon from Klebsiella pneumoniae. The other genesare transcribed as one unit (sorFABCDG) in opposite direction to sorRE. Thededuced peptide sequence of sorF showed homology with the D-sorbitol-6-phosphate dehydrogenase encoded in the sor operon from K. pneumoniae and sorABCD tocomponents of the mannose phosphotransferase system (PTS) family but especiallyto domains EIIA, EIIB, EIIC and EIID of the phosphoenolpyruvate-dependentL-sorbose PTS from K. pneumoniae. Finally, the deduced amino acid sequence of atruncated gene (sorG) located downstream of sorD presented high similarity withketose-1,6-bisphosphate aldolases. Results of studies on enzyme activities andtranscriptional analysis revealed that the two gene clusters, sorRE andsorFABCDG, are induced by L-sorbose and subject to catabolite repression byD-glucose. Data indicating that the catabolite repression is mediated bycomponents of the PTS elements and by CcpA, are presented. Results of sugaruptake assays in L. casei wild-type and sorBC mutant strains indicated thatL-sorbose is taken up by L-sorbose-specific enzyme II and that L. casei contains an inducible D-fructose-specific PTS. Results of growth analysis of those strainsand a man sorBC double mutant suggested that L-sorbose is probably alsotransported by the D-mannose PTS. We also present evidence, from studies on asorR mutant, suggesting that the sorR gene encodes a positive regulator of thetwo sor operons. Sequence alignment of SorR, SorC (K. pneumoniae), and DeoR(Bacillus subtilis) revealed that they might constitute a new group oftranscriptional regulators.PMCID: PMC94252PMID: 10613875 [PubMed - indexed for MEDLINE] 354. Mol Biol (Mosk). 1999 Sep-Oct;33(5):772-8.[Computer analysis of regulatory signals in complete bacterial genomes.Participation of LexA and DinR binding].[Article in Russian]Gel'fand MS, Mironov AA.PMID: 10579181 [PubMed - indexed for MEDLINE] 355. Gene. 1999 Sep 30;238(1):241-52.The role of recombination and mutation in 16S-23S rDNA spacer rearrangements.Gürtler V.Author information: Department of Microbiology, Austin & Repatriation Medical Centre, Heidelberg,Vic., Australia. [email protected] intragenomic heterogeneity of the bacterial intergenic (16S-23S rDNA) spacer region (ISR) was analysed from the following species in which sequences for thecomplete rRNA operon (rrn) set have been determined (rrn number): Enterococcusfaecalis (6) and E. faecium (6), Bacillus subtilis (10), Staphylococcus aureus(9), Vibrio cholerae (4), Haemophilus influenzae (6) and Escherichia coli (7). Itwas found that some spacer sequence blocks were highly conserved between operons of a genome, whereas the presence of others was variable. When these variationswere analysed using the program PLATO and partial likelihood phylogeniesdetermined by DNAml for each operon set, three regions showed significant (Z>3.3)spatial variation [Region I was 78-184 nt long (2.1<Z<49.4), Region II was 10-60 nt long (3.7<Z<23)] and Region III was 6 nt long (3.4<Z>4.4) possibly due torecombination or selection. Within Region I, there was sequence block variationin all operon sets [some operons contained tRNA genes (tRNAala, tRNAile ortRNAglu), whereas others had sequence blocks such as VS2 (S. aureus) or rsl (E.coli)]. Q Analysis of the ISR sequence from E. faecalis and E. faecium showedthat there was more interspecies than intraspecies variation (both in DNAsequence and in the presence or absence of blocks). Dot matrix analysis of thesequence blocks in the nine rrn ISRs from S. aureus showed that there wassignificant homology between VS2 and VS5/VS6. Furthermore, repeat motifs withonly A or T were present in higher copy numbers in VS5/VS6 than in VS2. Sincethese sequence blocks (VS2 and VS5-VS6) are related, intragenic evolutionresulting in AT expansion may have occurred between these two regions. A model isproposed that postulates a role for recombination and AT-expansion inintra-genomic ISR variations. This process may represent a general mechanism ofconcerted evolution for bacterial ISR rearrangements.PMID: 10571000 [PubMed - indexed for MEDLINE] 356. Genome Res. 1999 Nov;9(11):1116-27.Detecting and analyzing DNA sequencing errors: toward a higher quality of theBacillus subtilis genome sequence.Médigue C(1), Rose M, Viari A, Danchin A.Author information: (1)Institut Pasteur REG, F-75724 Paris Cedex 15, France. [email protected] the determination of a DNA sequence, the introduction of artifactualframeshifts and/or in-frame stop codons in putative genes can lead tomisprediction of gene products. Detection of such errors with 148 257 258 259 260 a method based onprotein similarity matching is only possible when related sequences are availablein databases. Here, we present a method to detect frameshift errors in DNAsequences that is based on the intrinsic properties of the coding sequences. Itcombines the results of two analyses, the search for translationalinitiation/termination sites and the prediction of coding regions. This methodwas used to screen the complete Bacillus subtilis genome sequence and the regionsflanking putative errors were resequenced for verification. This procedureallowed us to correct the sequence and to analyze in detail the nature of theerrors. Interestingly, in several cases in-frame termination codons orframeshifts were not sequencing errors but confirmed to be present in thechromosome, indicating that the genes are either nonfunctional (pseudogenes) orsubject to regulatory processes such as programmed translational frameshifts. Themethod can be used for checking the quality of the sequences produced by anyprokaryotic genome sequencing project.PMCID: PMC310837PMID: 10568751 [PubMed - indexed for MEDLINE] 357. Proc Natl Acad Sci U S A. 1999 Nov 9;96(23):13294-9.The mycosubtilin synthetase of Bacillus subtilis ATCC6633: a multifunctionalhybrid between a peptide synthetase, an amino transferase, and a fatty acidsynthase.Duitman EH(1), Hamoen LW, Rembold M, Venema G, Seitz H, Saenger W, Bernhard F,Reinhardt R, Schmidt M, Ullrich C, Stein T, Leenders F, Vater J.Author information: (1)Department of Genetics, Groningen Biomolecular Sciences and BiotechnologyInstitute, Kerklaan 30, 9751 NN Haren, The Netherlands.Bacillus subtilis strain ATCC6633 has been identified as a producer ofmycosubtilin, a potent antifungal peptide antibiotic. Mycosubtilin, which belongsto the iturin family of lipopeptide antibiotics, is characterized by a beta-aminofatty acid moiety linked to the circular heptapeptideAsn-Tyr-Asn-Gln-Pro-Ser-Asn, with the second, third, and sixth position presentin the D-configuration. The gene cluster from B. subtilis ATCC6633 specifying thebiosynthesis of mycosubtilin was identified. The putative operon spans 38 kb and consists of four ORFs, designated fenF, mycA, mycB, and mycC, with stronghomologies to the family of peptide synthetases. Biochemical characterizationshowed that MycB specifically adenylates tyrosine, as expected for mycosubtilinsynthetase, and insertional mutagenesis of the operon resulted in amycosubtilin-negative phenotype. The mycosubtilin synthetase reveals featuresunique for peptide synthetases as well as for fatty acid synthases: (i) Themycosubtilin synthase subunit A (MycA) combines functional domains derived frompeptide synthetases, amino transferases, and fatty acid synthases. MycArepresents the first example of a natural hybrid between these enzyme families.(ii) The organization of the synthetase subunits deviates from that commonlyfound in peptide synthetases. On the basis of the described characteristics ofthe mycosubtilin synthetase, we present a model for the biosynthesis of iturinlipopeptide antibiotics. Comparison of the sequences flanking the mycosubtilinoperon of B. subtilis ATCC6633, with the complete genome sequence of B. subtilis strain 168 indicates that the fengycin and mycosubtilin lipopeptide synthetaseoperons are exchanged between the two B. subtilis strains.PMCID: PMC23941PMID: 10557314 [PubMed - indexed for MEDLINE] 358. Gene. 1999 Nov 1;239(2):361-6.Identification of three merB genes and characterization of a broad-spectrummercury resistance module encoded by a class II transposon of Bacillus megateriumstrain MB1.Huang CC(1), Narita M, Yamagata T, Endo G.Author information: (1)Japan Science and Technology Corporation, 4-1-8 Honcho, Kawaguchi-shi, Japan.The complete structure of a broad-spectrum mercury resistance module was shown bysequencing the Gram-positive bacterial transposon TnMERI1 of Bacillus megaterium MB1. The regions encoding organomercury resistance were identified. Upstream of apreviously identified organomercurial lyase merB (merB1) region of TnMERI1, asecond merR (merR2) and a second merB gene (merB2) were found. These genesconstitute a second operon (mer operon 2) following a promoter/operator(P(merR2)) region. A third organomercurial lyase gene (merB3) was foundimmediately upstream of the mer operon (mer operon 1) followed by apromoter/operator (P(merB3)) region homologous to that of the mer operon 1(P(merR1)-merR1-merE-like-merT-merP-merA). The complete genetic structure of the mercury resistance module is organized asP(merB3)-merB3-P(merR1)-merR1-merE-like-merT+ ++ -merP-merA-P(merR2)-merR2-merB2-merB1. The subcloning analysis of these three merB genes showed distinctsubstrate specificity as different organomercury lyase genes.PMID: 10548738 [PubMed - indexed for MEDLINE] 359. FEMS Microbiol Lett. 1999 Nov 1;180(1):7-14.Complete nucleotide sequence and molecular characterization of hemolysin II gene from Bacillus cereus.Baida G(1), Budarina ZI, Kuzmin NP, Solonin AS.Author information: (1)Institute of Biochemistry and Physiology of Microorganisms, Russian Academy ofSciences, Moscow region, 142292, Pushchino, Russia. [email protected] II gene from Bacillus cereus VKM-B771 has been sequenced. The deducedprimary translation product consists of 412 amino acid residues which correspondsto the protein with an M(r) of 45.6 kDa. The predicted mature Hly-II protein(residues 32 to 412) is of 42.3 kDa, which is in close agreement with themini-cell electrophoresis analysis. Hly-II deletion variant lacking 96 C-terminalresidues still has hemolytic activity. The protein primary structure analysisrevealed no homology with any known Bacillus cytolysins. Significant generalhomology (31-28% identity) was found between the hemolysin II and Staphylococcus aureus alpha-toxin, gamma-hemolysin (HlgB), and leukocidins (LukF, LukF-R,LukF-PV). The data suggest that hemolysin II belongs to the group of beta-channelforming cytolysins.PMID: 10547438 [PubMed - indexed for MEDLINE] 360. Biofizika. 1999 Jul-Aug;44(4):601-10.[Computer analysis of regulatory signals in complete bacterial genomes.Translation initiation of ribosomal protein operons].[Article in Russian]Vitreshchak A(1), Bansal AK, Titov II, Gel'fand MS.Author information: (1)Institute of Problems of Data Transmission, Russian Academy of Sciences, Moscow, Russia.Signals of translation initiation of operons of Haemophilus influenzae ribosomal proteins were predicted. This process is regulated by the formation of secondary RNA structures to which one of the proteins encoded in a particular operon binds.In some cases, these structures imitate the region of 149 261 262 263 264 protein binding to rRNA.Predictions are made by comparing with homologous operons of Escherichia coli andanalogous regions of rRNA and by estimating the energy of secondary structureformation. It is shown that this regulatory mechanism occurs: in operons L11,S10, S15, spc, and alpha of H.influenzae and, probably, in operon S15 ofHelicobacter pylori, Bacillus subtilis, and Mycoplasma genitalium.PMID: 10544808 [PubMed - indexed for MEDLINE] 361. Gene. 1999 Sep 17;237(2):413-9.Sequence analysis and expression of the aspartokinase and aspartate semialdehyde dehydrogenase operon from rifamycin SV-producing amycolatopsis mediterranei.Zhang W(1), Jiang W, Zhao G, Yang Y, Chiao J.Author information: (1)Department of Microbiology, Shanghai Institute of Plant Physiology, AcademiaSinica, 200032 Shanghai, People's Republic of China. [email protected] approximately 4.8 kb KpnI fragment, from the upstream region of themethylmalonyl-CoA mutase gene (mutAB) of rifamycin SV-producing Amycolatopsismediterranei, was cloned and partially sequenced. Codon preference analysisshowed three complete ORFs. ORF2 is internal to ORF1, and encodes a polypeptidecorresponding to 172 amino acids, whereas ORF1 encodes a polypeptide of 421 aminoacids. They were identified as the encoding genes of aspartokinase alphaandbeta-subunits by comparing the amino acid sequences with those in the database.The downstream ORF3, whose start codon was overlapped with the stop codon of bothORF1 and ORF2 by 1 bp, was identified as the aspartate semialdehyde dehydrogenasegene (asd), encoding a polypeptide of 346 amino acids. Subclones containingeither the ask gene or the asd gene were constructed, in which the genes could beexpressed under Lac promoters. Two subclones could transform E. coli CGSC 5074(ask-) and E. coli X6118 (asd-) to prototrophy, supporting the functionalassignments. Southern hybridisation indicated that the approximately 4.8 kbsequenced region represented a continuous segment in the A. mediterraneichromosome. It is concluded that ask and asd genes are present in an operon in A.mediterranei, and therefore that organisation of these two genes is the same asin most gram-positive bacteria, such as Mycobacteria, Corynebacterium glutamicum and Bacillus subtilis, but is different from Streptomyces akiyoshiensis.PMID: 10521665 [PubMed - indexed for MEDLINE] 362. Microb Comp Genomics. 1999;4(1):47-58.Molecular cloning of the dnaK gene region from Bacillus sphaericus in the contextof genomic comparisons.Ahmad S(1), Selvapandiyan A, Gasbarri M, Bhatnagar RK.Author information: (1)International Centre for Genetic Engineering and Biotechnology, New Delhi, India.The dnaK gene region of Bacillus sphaericus was cloned as a 3.8 kb HindIIIfragment and an overlapping 1.7 kb EcoRI fragment by using an internal B.sphaericus specific dnaK gene probe generated by polymerase chain reaction (PCR).Complete DNA sequencing of the two fragments revealed three complete open readingframes (ORFs). These ORFs exhibited a high degree of identity to the grpE dnaK,and dnaJ heat shock genes from other gram-positive bacteria. The order of thegenes was found to be grpE-dnaK-dnaJ. Additionally, the 5'-end and 3'-endcontained amino acid sequences that were homologous to the C-terminal sequence ofthe hrcA gene and the N-terminal sequence of ORF35 (yqeT), respectively, fromBacillus subtilis. The entire hrcA gene from B. sphaericus was then isolated byhigh-fidelity PCR and completely sequenced. A transcription stop site is located between the dnaK and dnaJ genes but not after the dnaJ gene. Consistent with thisobservation, the dnaJ gene is immediately followed by an ORF that shows a highdegree of identity to ORF35 from B. subtilis, Staphylococcus aureus, andClostridium acetobutylicum. The presence of ORF35 is not indicated in othergenera representing the gram-positive bacteria. The amino acid sequence of ORF35 exhibited nearly 30% identity with the methyltransferase for large subunitribosomal protein L11 from gram-negative Proteobacteria and the related proteinfrom cyanobacteria, other gram-negative bacteria, and Archaea, suggesting thepresence of the gene for this protein in the common ancestor of Bacteria andArchaea. The absence of the ORF35 gene in Mycobacterium tuberculosis and othergram-positive bacteria indicates that the loss of this gene must have occurred inan ancestor of other gram-positive bacteria following their divergence from theancestor of Bacillus/Clostridium/staphylococcus lineage.PMID: 10518301 [PubMed - indexed for MEDLINE] 363. J Bacteriol. 1999 Oct;181(20):6230-7.Characterization of a new sigma-K-dependent peptidoglycan hydrolase gene thatplays a role in Bacillus subtilis mother cell lysis.Nugroho FA(1), Yamamoto H, Kobayashi Y, Sekiguchi J.Author information: (1)Department of Applied Biology, Faculty of Textile Science, Shinshu University,Ueda-shi, Nagano 386-8567, Japan.Bacillus subtilis produces a 30-kDa peptidoglycan hydrolase, CwlH, during thelate sporulation phase. Disruption of yqeE led to a complete loss of CwlHformation, indicating the identity of yqeE with cwlH. Northern blot analysis ofcwlH revealed a 0.8-kb transcript after 6 to 7.5 h for the wild-type strain butnot for the sigma(F), sigma(E), sigma(G), and sigma(K) mutants. Expression of thesigma(K)-dependent cwlH gene depended on gerE. Primer extension analysis alsosuggested that cwlH is transcribed by Esigma(K) RNA polymerase. CwlH produced in Escherichia coli harboring a cwlH plasmid is an N-acetylmuramoyl-L-alanineamidase (EC 3.5.1.28) and exhibited an optimum pH of 7.0 and high-level bindingto the B. subtilis cell wall. A cwlC cwlH double mutation led to a lack of mothercell lysis even after 7 days of incubation in DSM medium, but the singlemutations led to mother cell lysis after 24 h.PMCID: PMC103754PMID: 10515909 [PubMed - indexed for MEDLINE] 364. Biochem Biophys Res Commun. 1999 Oct 5;263(3):640-5.Xylanase II from an alkaliphilic thermophilic Bacillus with a distinctlydifferent structure from other xylanases: evolutionary relationship toalkaliphilic xylanases.Kulkarni N(1), Lakshmikumaran M, Rao M.Author information: (1)Biochemical Sciences Division, National Chemical Laboratory, Pune, 411008, India.A 1.0 kilobase gene fragment from the genomic DNA of an alkaliphilic thermophilicBacillus was found to code for a functional xylanase (XynII). The completenucleotide sequence including the structural gene and the 5' and 3' flankingsequences of the xylanase gene have been deter- 150 265 266 267 268 269 mined. An open reading framestarting from ATG initiator codon comprising 402 nucleotides gave a preprotein of133 amino acids of calculated molecular mass 14.090 kDa. The occurrence of three potential N-glycosylation sites in XynII gene is a unique feature for a gene ofbacterial origin. The stop codon was followed by hairpin loop structuresindicating the presence of transcription termination signals. The secondarystructure analysis of XynII predicted that the polypeptide was primarily formedof beta-sheets. XynII appeared to be a member of family G/11 of xylanases basedon its molecular weight and basic pI (8.0). However, sequence homology revealedsimilar identity with families 10 and 11 of xylanases. The conserved triad(Val-Val-Xaa, where Xaa is Asn or Asp) was identified only in the xylanases from alkaliphilic organisms. Our results implicate for the first time the concept ofconvergent evolution for XynII and provide a basis for research in evolutionaryrelationship among the xylanases from alkaliphilic and neutrophilic organisms.Copyright 1999 Academic Press.PMID: 10512731 [PubMed - indexed for MEDLINE] 365. Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11223-8.A cooperative oxygen-binding hemoglobin from Mycobacterium tuberculosis.Couture M(1), Yeh SR, Wittenberg BA, Wittenberg JB, Ouellet Y, Rousseau DL,Guertin M.Author information: (1)Department of Biochemistry, Faculty of Sciences and Engineering, LavalUniversity, Quebec, QC Canada G1K 7P4.Two putative hemoglobin genes, glbN and glbO, were recently discovered in thecomplete genome sequence of Mycobacterium tuberculosis H37Rv. Here, we show that the glbN gene encodes a dimeric hemoglobin (HbN) that binds oxygen cooperatively with very high affinity (P(50) = 0.013 mmHg at 20 degrees C) because of a fastcombination (25 microM(-1).s(-1)) and a slow dissociation (0.2 s(-1)) rate.Resonance Raman spectroscopy and ligand association/dissociation kineticmeasurements, along with mutagenesis studies, reveal that the stabilization ofthe bound oxygen is achieved through a tyrosine at the B10 position in the distalpocket of the heme with a conformation that is unique among the globins.Physiological studies performed with Mycobacterium bovis bacillus Calmette-Guérindemonstrate that the expression of HbN is greatly enhanced during the stationary phase in aerobic cultures but not under conditions of limited oxygenavailability. The results suggest that, physiologically, the primary role of HbN may be to protect the bacilli against reactive nitrogen species produced by thehost macrophage.PMCID: PMC18015PMID: 10500158 [PubMed - indexed for MEDLINE] 366. Mol Biol Evol. 1999 Sep;16(9):1219-30.Analysis of long repeats in bacterial genomes reveals alternative evolutionarymechanisms in Bacillus subtilis and other competent prokaryotes.Rocha EP(1), Danchin A, Viari A.Author information: (1)Atelier de BioInformatique, Université Paris VI, [email protected] genomes seem to be optimized toward compactness and have thereforebeen thought to lack long redundant DNA sequences. However, we identified a largenumber of long strict repeats in eight prokaryotic complete genomes and foundthat their density is negatively correlated with genome size. A detailed analysisof the long repeats present in the genome of Bacillus subtilis revealed a verystrict constraint on the spatial distribution of repeats in this genome. Weinterpret this as the hallmark of selection processes leading to the addition of new genetic information. Such addition is independent of insertion sequences and relies on the nonspecific DNA uptake by the competent cell and its subsequentintegration in the chromosome in a circular form through a Campbell-likemechanism. Similar patterns are found in other competent genomes of Gram-negativebacteria and Archaea, suggesting a similar evolutionary mechanism. Thecorrelation of the spatial distribution of repeats and the absence of insertionsequences in a genome may indicate, in the framework of our model, thatmechanisms aiming at their avoidance/elimination have been developed.PMID: 10486977 [PubMed - indexed for MEDLINE] 367. Tanpakushitsu Kakusan Koso. 1999 Aug;44(10):1512-7.[Impact of the complete genome sequence on biology of Bacillus subtilis].[Article in Japanese]Ogasawara N.Author information: Graduate School of Biological Sciences, Nara Institute of Science and Technology,Japan. [email protected]: 10481607 [PubMed - indexed for MEDLINE] 368. Microbiology. 1999 Aug;145 ( Pt 8):2163-70.A multidomain xylanase from a Bacillus sp. with a region homologous tothermostabilizing domains of thermophilic enzymes.Blanco A(1), Díaz P, Zueco J, Parascandola P, Javier Pastor FI.Author information: (1)Department of Microbiology, Faculty of Biology, University of Barcelona, Spain.The gene xynC encoding xylanase C from Bacillus sp. BP-23 was cloned andexpressed in Escherichia coli. The nucleotide sequence of a 3538 bp DNA fragment containing xynC gene was determined, revealing an open reading frame of 3258 bpthat encodes a protein of 120,567 Da. A comparison of the deduced amino acidsequence of xylanase C with known beta-glycanase sequences showed that theencoded enzyme is a modular protein containing three different domains. Thecentral region of the enzyme is the catalytic domain, which shows high homologyto family 10 xylanases. A domain homologous to family IX cellulose-bindingdomains is located in the C-terminal region of xylanase C, whilst the N-terminal region of the enzyme shows homology to thermostabilizing domains found in severalthermophilic enzymes. Xylanase C showed an activity profile similar to that ofenzymes from mesophilic micro-organisms. Maximum activity was found at 45 degreesC, and the enzyme was only stable at 55 degrees C lower temperatures.Xylotetraose, xylotriose, xylobiose and xylose were the main products frombirchwood xylan hydrolysis, whilst the enzyme showed increasing activity onxylo-oligosaccharides of increasing length, indicating that the cloned enzyme is an endoxylanase. A deletion derivative of xylanase C, lacking the regionhomologous to thermostabilizing domains, was constructed. The truncated enzymeshowed a lower optimum temperature for activity than the full-length enzyme, 35degrees C instead of 45 degrees C, and a reduced thermal stability that resulted in a complete inactivation of the enzyme after 2 h incubation at 55 degrees C.PMID: 10463183 [PubMed - indexed for MEDLINE] 369. Arch Biochem Biophys. 1999 Sep 1;369(1):1-10.Cytochrome P450 and the individuality of species.Nelson DR.Author information: Department of Biochemistry, University of Tennessee, Memphis, Tennessee, 38163,USA. dnel- 151 270 271 272 273 [email protected] P450 superfamily is expanding rapidly on many fronts. Arabidopsis genomicsequencing is producing about 2 to 3 novel P450s per week, with some clusterscontaining 9-14 genes. Bacterial genomes also carry surprises, such as the 20P450s found in Mycobacterium tuberculosis and the 7 in Bacillus subtilis. Therace to finish the human genome has already identified the majority of humanP450s, some by expressed sequence tags only. The rapid discovery of new genes is being complemented by detailed analysis of our human genes to identify andcharacterize the complete set of human P450 polymorphisms and disease-causingmutations, one aspect of our "chemical individuality." Phylogenetic trees areincluded for plant, fungal, animal, and bacterial P450s. Emphasis is given to thehigher order nomenclature of P450 clans, as a tool to see the larger picture ofP450 evolution. Arabidopsis is the current record holder in P450 genes, with 186 named genes and a prediction of 350 in the total genome to be completed nextyear. The biosynthesis of cholesterol in bacteria is discussed in relation toCYP51 as a lanosterol 14 alpha-demethylase. This enzyme may have been the firsteukaryotic P450.Copyright 1999 Academic Press.PMID: 10462435 [PubMed - indexed for MEDLINE] 370. Appl Environ Microbiol. 1999 Aug;65(8):3714-6.Multiplex PCR screening to detect cry9 genes in Bacillus thuringiensis strains.Ben-Dov E(1), Wang Q, Zaritsky A, Manasherob R, Barak Z, Schneider B, Khamraev A,Baizhanov M, Glupov V, Margalith Y.Author information: (1)Department of Life Sciences, Ben-Gurion University of the Negev, Be'er-Sheva84105, Israel.An extended PCR method was established to rapidly identify and classify Bacillus thuringiensis strains containing cry (crystal protein) genes toxic tolepidopteran, coleopteran, and dipteran pests (Ben-Dov et al., Appl. Environ.Microbiol. 63:4883-4890, 1997). To optimize identification of all reported crygenes, this methodology needs a complete PCR set of primers. In the studyreported here, a set of universal (Un9) and specific primers for multiplex rapid screening for all four known genes from the cry9 group was designed. PCR analyseswere performed for cry9 genes on 16 standard strains and 215 field isolates of B.thuringiensis. Among the standard strains, only B. thuringiensis subsp. aizawaiHD-133, which harbors cry1 and cry2 genes, was positive with Un9 but negative to all four specific primers for cry9 genes. DNA of 22 field-collected isolates was also found to be positive with Un9. These isolates were classified into threecry9 profiles using specific primers; all of them harbor cry1 and cry2. Thisnewly designed set of primers complements the existing PCR methodology for mostcurrently known cry genes.PMCID: PMC91556PMID: 10427071 [PubMed - indexed for MEDLINE] 371. J Biochem. 1999 Aug;126(2):333-9.Regulation of the Bacillus subtilis phosphotransacetylase gene.Shin BS(1), Choi SK, Park SH.Author information: (1)Bacterial Molecular Genetics R.U., Korea Research Institute of Bioscience andBiotechnology, Taejon, Korea, 305-333, Japan.The enzyme, phosphotransacetylase (Pta), catalyzes the conversion of acetylcoenzyme A to acetyl phosphate. The putative pta gene of Bacillus subtilis, whichhad been sequenced as part of the Genome Project, was cloned and overexpressed inEscherichia coli. We confirmed that the gene encodes Pta by measuring theenzymatic activity of the purified protein. Insertional mutagenesis of the ptagene resulted in complete loss of the Pta activity, indicating that B. subtiliscontains only one kind of pta gene. Expression of a pta-lacZ fusion was inducedin the presence of excess glucose in the growth medium, and the intact ccpA gene was required for this activation. The transcriptional start site of the pta gene was located at 37 nucleotides upstream of the pta start codon, and a cre(catabolite responsive element) sequence, a cis-acting element that isresponsible for the catabolite repression of a number of carbon utilization genesin B. subtilis, was identified upstream of the tentative promoter site.Experiments involving oligonucleotide-directed mutagenesis showed that the cresequence is involved in glucose-mediated transcriptional activation.PMID: 10423526 [PubMed - indexed for MEDLINE] 372. Plasmid. 1999 Jul;42(1):45-52.Complete nucleotide sequence of a cryptic plasmid from the ruminal bacteriumSelenomonas ruminantium HD4 and identification of two predicted open readingframes.Al-Khaldi SF(1), Evans JD, Martin SA.Author information: (1)Department of Animal and Dairy Science, The University of Georgia, Athens,Georgia 30602-2771, USA.A cryptic plasmid (pSR1) isolated from Selenomonas ruminantium HD4 was previouslycloned into the HindIII site of pBR322 and a restriction map was constructedusing HindIII, ClaI, BamHI, and PvuII (S. A. Martin and R. G. Dean, Appl.Environ. Microbiol. 55(12), 3035-3038, 1989). Analysis of the nucleotide sequenceof pSR1 revealed two major open reading frames (ORFs) located in the minus strandat different frames. Analysis of ORF-1 revealed that it has 325 amino acids with a predicted MW of 36,588, and ORF-2 has 379 amino acids with a predicted MW of42,651. The ORF-1 amino acids showed 30 to 32% sequence homology to thehypothetical protein YtqA in Bacillus subtilis and another hypothetical proteinin the thermophilic bacterium Aquifex aeolicus. ORF-2 showed limited homology(23%) to the hypothetical protein ICFG in the photosynthetic cyanobacteriaSynechocystis PCC6803.Copyright 1999 Academic Press.PMID: 10413665 [PubMed - indexed for MEDLINE] 373. Biochim Biophys Acta. 1999 Jul 13;1432(2):413-8.Nucleotide sequence, heterologous expression and novel purification of DNA ligasefrom Bacillus stearothermophilus(1).Brannigan JA(1), Ashford SR, Doherty AJ, Timson DJ, Wigley DB.Author information: (1)Sir William Dunn School of Pathology, University of Oxford, South Parks Road,Oxford OX1 3RE, UK.The gene for DNA ligase (EC 6.5.1.2) from thermophilic bacterium Bacillusstearothermophilus NCA1503 has been cloned and the complete nucleotide sequencedetermined. The ligase gene encodes a protein 670 amino acids in length. The genewas overexpressed in Escherichia coli and the enzyme has been purified tohomogeneity. Preliminary characterisation confirms that it is a thermostable,NAD(+)-dependent DNA ligase.PMID: 10407164 [PubMed - indexed for MEDLINE] 152 274 374. Comput Chem. 1999 Jun 15;23(3-4):263-74.Sequence complexity and DNA curvature.Gabrielian A(1), Bolshoy A.Author information: (1)National Center for Biotechnology Information, National Library of Medicine,National Institutes of Health, Bethesda, MD 20894, USA.A linguistic complexity measure was applied to the complete genomes of HIV-1,Escherichia coli, Bacillus subtilis, Haemophilus influenzae, Mycoplasmagenitalium, and to long human and yeast genomic fragments. Complexity valuesaveraged over entire genomic sequences were compared, as were predicted averagevalues of intrinsic DNA curvature. We found that both the most curved and theleast complex fragments are located preferentially in non-coding parts of thegenome. Analysis of location of the most curved and the simplest regions inbacteria showed that the low-complexity segments are preferentially located inclose proximity to the highly curved sequences, which are, in turn, placed from100 to 200 bases upstream to the start of the nearest coding sequence. Weconclude that the parallel analysis of sequence complexity and DNA curvaturemight provide important information about sequence-structure-functionrelationship in genomes.PMID: 10404619 [PubMed - indexed for MEDLINE] 275 375. DNA Res. 1999 Apr 30;6(2):75-82.Putative mechanism of natural transformation as deduced from genome data.Yura K(1), Toh H, Go M.Author information: (1)Division of Biological Science, Graduate School of Science, Nagoya University,Japan.Genetic transformation is widely utilized in molecular biology as a tool for genecloning in Escherichia coli and for gene mapping in Bacillus subtilis. Severalstrains of eubacteria can naturally take up exogenous DNA and integrate the DNAinto their own genomes. Molecular details of natural transformation, however,remained to be elucidated. The complete genome of a cyanobacterium, Synechocystissp. PCC6803, has been sequenced. This bacterium has been used to examinefunctions of a particular gene. The genome is considered to carry information on natural transformable characteristics of Synechocystis. The first step in genetictransformation is the uptake of exogenous DNA. Proteins with non-specific DNAbinding features are required, because specificity in the exogenous DNA has notbeen demonstrated. Such proteins have modules interacting with the phosphatebackbone of DNA, including helix-turn-helix modules. Using a consensus pattern ofthe phosphate-binding helix-turn-helix module, we searched through the genomedata of Synechocystis for genes or open reading frame (ORF) products with thepattern in primary structures. We found that an ORF, slr0197, has the pattern in duplicate at the C-terminal region. We also found that the ORF product has ahydrophobic segment at the N-terminal region, which is followed by two internalrepeats of the endonuclease domain. Based on these observations, we propose amodel for the initial stage of genetic transformation. This is apparently thefirst report on molecular mechanisms of natural transformation.PMID: 10382965 [PubMed - indexed for MEDLINE] 276 376. FEBS Lett. 1999 Jun 4;452(1-2):7-10.Learning from the genome sequence of Mycobacterium tuberculosis H37Rv.Cole ST.Author information: Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, Paris, [email protected] tuberculosis, the scourge of humanity, is one of the mostsuccessful and scientifically challenging pathogens of all time. To catalyse the conception of new prophylactic and therapeutic interventions againsttuberculosis, and to enhance our understanding of the biology of the tuberclebacillus, the complete genome sequence of the most widely used strain, H37Rv, hasbeen determined. Bioinformatic analysis led to the identification ofapproximately 4000 genes in the 4.41 Mb genome sequence and provided freshinsight into the biochemistry, physiology. genetics and immunology of thismuch-feared bacterium. Genomic information is centralised in TubercuList(http://www.pasteur.fr/Bio/TubercuList/).PMID: 10376668 [PubMed - indexed for MEDLINE] 277 377. Plasmid. 1999 May;41(3):274-81.Complete sequence of Bacillus subtilis plasmid p1414 and comparison with sevenother plasmid types found in Russian soil isolates of Bacillus subtilis.Thorsted PB(1), Thomas CM, Poluektova EU, Prozorov AA.Author information: (1)School of Biological Sciences, University of Birmingham, Edgbaston, Birmingham,B15 2TT, United Kingdom.We determined the complete sequence of a cryptic 7949-bp plasmid isolated fromnaturally occurring Bacillus subtilis found in Russian soil from Moscow. We found15 putative open reading frames (ORFs), all of which were preceded by a ribosome binding site. One encodes the gene (rep) which should be essential for vegetativerolling circle replication (RCR). The putative double-stranded origin as well as a palT1-like single-stranded origin was also identified. The predicted product ofanother ORF showed similarity to a moblization protein while a third showedsimilarity to a ubiquitous family of small proteins whose members have so farbeen associated with stress response. We used fragments with these latter ORFs toprobe representatives of seven other groups of cryptic RCR plasmids fromgeographically related B. subtilis isolates. All plasmids carried the mobfunction, suggesting a common ancestor for the rep/mob region but the putativehsp was present only on some of the plasmids. This suggests that the putative hspgene is not an essential plasmid component and may therefore be present as aphenotypic marker-perhaps providing response to stress. This adds weight to thegrowing evidence that these small Bacillus plasmids may not be cryptic but mayprovide an adaptive advantage for the host in its natural environment.Copyright 1999 Academic Press.PMID: 10366533 [PubMed - indexed for MEDLINE] 278 378. J Bacteriol. 1999 Jun;181(11):3375-81.Isolation and characterization of two cryptic plasmids in the ammonia-oxidizingbacterium Nitrosomonas sp. strain ENI-11.Yamagata A(1), Kato J, Hirota R, Kuroda A, Ikeda T, Takiguchi N, Ohtake H.Author information: (1)Department of Fermentation Technology, Hiroshima University, Higashi-Hiroshima,Hiroshima 739-8527, Japan.Two plasmids were discovered in the ammonia-oxidizing bacterium Nitrosomonas sp. strain ENI-11, which was isolated from activated sludge. The plasmids, designatedpAYS and pAYL, were relatively small, being approximately 1.9 kb long. They were cryptic plasmids, having no detectable plasmid-linked antibiotic resistance orheavy metal resistance markers. The complete nucleotide sequences of pAYS andpAYL were determined, and their physical maps were constructed. There existed twomajor open reading 153 279 280 281 282 frames, ORF1 in pAYS and ORF2 in pAYL, each of which was more than 500 bp long. The predicted product of ORF2 was 28% identical to part of the replication protein of a Bacillus plasmid, pBAA1. However, no significantsimilarity to any known protein sequences was detected with the predicted productof ORF1. pAYS and pAYL had a highly homologous region, designated HHR, of 262 bp.The overall identity was 98% between the two nucleotide sequences. Interestingly,HHR-homologous sequences were also detected in the genomes of ENI-11 and theplasmidless strain Nitrosomonas europaea IFO14298. Deletion analysis of pAYS and pAYL indicated that HHR, together with either ORF1 or ORF2, was essential forplasmid maintenance in ENI-11. To our knowledge, pAYS and pAYL are the firstplasmids found in the ammonia-oxidizing autotrophic bacteria.PMCID: PMC93803PMID: 10348848 [PubMed - indexed for MEDLINE] 379. Mol Biol Evol. 1999 Mar;16(3):332-46.Evolutionary instability of operon structures disclosed by sequence comparisonsof complete microbial genomes.Itoh T(1), Takemoto K, Mori H, Gojobori T.Author information: (1)Research and Education Center for Genetic Information, Nara Institute of Science and Technology, Japan.Gene orders have been shown to be generally unstable by comprehensive analyses inseveral complete genomes. In this study, we examined instability of genomestructures within operons, where functionally related genes are clustered. Wecompared gene orders of known operons obtained from Escherichia coli and Bacillussubtilis with corresponding those of operons in 11 complete genome sequences. We found that in many cases, gene orders within operons could be shuffled frequentlyduring evolution, although several operon structures, such as ribosomal proteinoperons, were well conserved. This suggests that shuffling of a genome structure is virtually neutral in long-term evolution. Moreover, degrees of instability of the operon structures depended on the genomes examined. Variation in degrees ofinstability of the genome structures was likely to be related to differences inamounts of insertion sequences. Effects on transcription regulation are alsodiscussed in association with operon destruction.PMID: 10331260 [PubMed - indexed for MEDLINE] 380. Int J Syst Bacteriol. 1999 Apr;49 Pt 2:531-40.Transfer of Bacillus lentimorbus and Bacillus popilliae to the genusPaenibacillus with emended descriptions of Paenibacillus lentimorbus comb. nov.and Paenibacillus popilliae comb. nov.Pettersson B(1), Rippere KE, Yousten AA, Priest FG.Author information: (1)Department of Biochemistry and Biotechnology, Royal Institute of Technology,Stockholm, Sweden.Almost complete 16S rRNA gene sequences were generated for the type strains ofthe obligate insect pathogens Bacillus lentimorbus and Bacillus popilliae and asecond strain of Bacillus popilliae (NRRL B-4081) received as 'Bacillus popilliaevar. melolonthae'. A phylogenetic tree was constructed which grouped thesestrains into a well defined subcluster within the genus Paenibacillus. Bacilluspopilliae NRRL B-4081 occupied an intermediate position between the type strains of Bacillus lentimorbus and Bacillus popilliae but with a marked clustering tothe latter. The phylogenetic assignment of these strains to Paenibacillus is incontrast to earlier studies which placed these bacteria in the genus Bacillus,close to Bacillus subtilis. Indeed, the rRNA sequences generated in this studyshare less than 88% similarity to the deposited sequences for Bacillus popilliae ATCC 14706T and Bacillus lentimorbus ATCC 14707T. The results obtained by usingdifferent tree algorithms, bootstrap analysis, branch lengths and verification bysignature nucleotide analysis supported the reclassification of these species in the genus Paenibacillus as Paenibacillus lentimorbus comb. nov. and Paenibacilluspopilliae comb. nov.PMID: 10319474 [PubMed - indexed for MEDLINE] 381. Nucleic Acids Res. 1999 May 15;27(10):2145-55.The complete genome sequence of the Streptomyces temperate phage straight phiC31:evolutionary relationships to other viruses.Smith MC(1), Burns RN, Wilson SE, Gregory MA.Author information: (1)Institute of Genetics, University of Nottingham, Queen's Medical Centre,Nottingham NG7 2UH, UK. [email protected] completed genome sequence of the temperate Streptomyces phage straight phiC31is reported. straight phiC31 contains genes that are related by sequencesimilarities to several other dsDNA phages infecting many diverse bacterialhosts, including Escherichia, Arthrobacter, Mycobacterium, Rhodobacter,Staphylococcus, Bacillus, Streptococcus, Lactobacillus and Lactococcus. Theseobservations provide further evidence that dsDNA phages from diverse bacterialhosts are related and have had access to a common genetic pool. Analysis of thelate genes was particularly informative. The sequences of the head assemblyproteins (portal, head protease and major capsid) were conserved between straightphiC31, coliphage HK97, staphylococcal phage straight phiPVL, two Rhodobactercapsulatus prophages and two Mycobacterium tuberculosis prophages. These phagesand prophages (where non-defective) from evolutionarily diverse hosts are,therefore, likely to share a common head assembly mechanism i.e. that of HK97.The organisation of the tail genes in straight phiC31 is highly reminiscent oftail regions from other phage genomes. The unusual organisation of the putativelysis genes in straight phiC31 is discussed, and speculations are made as to the roles of some inessential early gene products. Similarities between certain phagegene products and eukaryotic dsDNA virus proteins were noted, in particular, the primase/helicases and the terminases (large subunits). Furthermore, the complete sequence clarifies the overall transcription map of the phage during lytic growthand the positions of elements involved in the maintenance of lysogeny.PMCID: PMC148434PMID: 10219087 [PubMed - indexed for MEDLINE] 382. Genetics. 1999 Apr;151(4):1239-44.Genetic and physical maps of the Bacillus subtilis chromosome.Rivolta C(1), Pagni M.Author information: (1)Institut de Génétique et de Biologie Microbiennes, Université de Lausanne,CH-1005 Lausanne, Switzerland.Sequencing of the complete Bacillus subtilis chromosome revealed the presence of approximately 4100 genes, 1000 of which were previously identified and mapped by classical genetic crosses. Comparison of these experimentally determinedpositions to those derived from the nucleotide sequence showed discrepanciesreaching up to 24 degrees (approximately 280 kb). The size of 154 283 284 285 286 these discrepanciesas a function of their position along the chromosome is not random but,apparently, reveals some periodicity. Our analyses demonstrate that thediscrepancies can be accounted for by inaccurate positioning of the earlyreference markers with respect to which all subsequently identified loci weremapped by transduction and transformation. We conclude (i) that specific DNAsequences, such as recombination hotspots or presence of heterologous DNA, had nodetectable effect on the results obtained by classical mapping, and (ii) thatPBS1 transduction appears to be an accurate and unbiased mapping method in B.subtilis.PMCID: PMC1460559PMID: 10101153 [PubMed - indexed for MEDLINE] 383. Extremophiles. 1999 Jan;3(1):21-8.An improved physical and genetic map of the genome of alkaliphilic Bacillus sp.C-125.Takami H(1), Nakasone K, Hirama C, Takaki Y, Masui N, Fuji F, Nakamura Y, InoueA.Author information: (1)Deep-Sea Microorganisms Research Group, Japan Marine Science and TechnologyCenter, Yokosuka. [email protected] alkaliphilic bacteria reported so far, Bacillus sp. C-125 is the strainmost thoroughly characterized physiologically, biochemically, and genetically. A physical map of the chromosome of this strain was constructed to facilitatefurther genome analysis, and the genome size was revised from 3.7 to 4.25Mb.Complete digestion of the chromosomal DNA with two rare cut restrictionendonucleases, AscI and Sse8387I, each yielded 20 fragments ranging in size from 20 to 600 kb. Seventeen linking clones were isolated in each instance to join theadjacent AscI or Sse8387I fragments in the chromosomal map. All AscI linkingclones isolated were sequenced and analyzed by comparison with the BSORF databaseto map the genes in the chromosome of strain C-125. Several ORFs showingsignificant similarities to those of B. subtilis in the AscI linking clones were positioned on the physical map. The oriC region of the C-125 chromosome wasidentified by southern blot analysis with a DNA probe containing the gyrB region.PMID: 10086841 [PubMed indexed for MEDLINE] 384. Genet Anal. 1999 Mar;15(1):9-13.Cloning and nucleotide sequencing of the secA gene from coryneform bacteria.Kobayashi M(1), Fugono N, Asai Y, Yukawa H.Author information: (1)Tsukuba Research Center, Mitsubishi Chemical Corporation, Ibaraki, [email protected] advantage of highly conserved domains present in the secA gene fromEscherichia coli and Bacillus subtilis, we designed degenerate oligonucleotides(oligos) corresponding to these regions. These oligos were used as primers in PCRin order to amplify DNA sequences from Brevibacterium flavum MJ233 chromosomalDNA. The PCR product was used as a probe to recover genomic fragments from alambda library of Br. flavum MJ233. The complete nucleotide sequence (nt) of the cloned 5.3-kb EcoR1 fragment containing the secA homolog from Br. flavum MJ233indicated that the deduced gene product of the Br. flavum secA homolog iscomposed of 845 amino acids (aa) with a deduced molecular weight (MW) of 95429.Comparison of this aa sequence to the corresponding sequences from E. coli and B.subtilis revealed a high degree of conservation and suggested that the Br. flavumsecA homolog has putative ATP binding regions.PMID: 10084122 [PubMed - indexed for MEDLINE] 385. Bioinformatics. 1999 Jan;15(1):2-15.Imagene: an integrated computer environment for sequence annotation and analysis.Médigue C(1), Rechenmann F, Danchin A, Viari A.Author information: (1)Institut Pasteur, REG, 28 rue du Docteur Roux, 75724 Paris Cedex 15,[email protected]: To be fully and efficiently exploited, data coming from sequencingprojects together with specific sequence analysis tools need to be integratedwithin reliable data management systems. Systems designed to manage genome dataand analysis tend to give a greater importance either to the data storage or tothe methodological aspect, but lack a complete integration of both components.RESULTS: This paper presents a co-operative computer environment (calledImagenetrade mark) dedicated to genomic sequence analysis and annotation. Imagenehas been developed by using an object-based model. Thanks to this representation,the user can directly manipulate familiar data objects through icons or lists.Imagene also incorporates a solving engine in order to manage analysis tasks. Aglobal task is solved by successive divisions into smaller sub-tasks. Duringprogram execution, these sub-tasks are graphically displayed to the user and may be further re-started at any point after task completion. In this sense, Imagene is more transparent to the user than a traditional menu-driven package. Imagenealso provides a user interface to display, on the same screen, the resultsproduced by several tasks, together with the capability to annotate these resultseasily. In its current form, Imagene has been designed particularly for use inmicrobial sequencing projects.AVAILABILITY: Imagene best runs on SGI (Irix 6.3 or higher) workstations. It isdistributed free of charge on a CD-ROM, but requires some Ilog licensed software to run. Some modules also require separate license agreements. Please contact theauthors for specific academic conditions and other Unix platforms.CONTACT: imagene home page: http://wwwabi.snv.jussieu.fr/imagenePMID: 10068688 [PubMed - indexed for MEDLINE] 386. J Mol Evol. 1999 Feb;48(2):197-208.Molecular phylogeny of phi29-like phages and their evolutionary relatedness toother protein-primed replicating phages and other phages hosted by gram-positive bacteria.Pecenková T(1), Paces V.Author information: (1)Institute of Molecular Genetics, Academy of Sciences of the Czech Republic,Flemingovo 2, CZ-16637 Prague 6, Czech Republic.The phi29-like phage genus of Podoviridae family contains phages B103, BS32,GA-1, M2, Nf, phi15, phi29, and PZA that all infect Bacillus subtilis. They have very similar morphology and their genomes consist of linear double-stranded DNAof approximately 20 kb. The nucleotide sequences of individual genomes or theirparts determined thus far show that these phages evolved from a common ancestor. A terminal protein (TP) that is covalently bound to the DNA 5'-end primes DNAreplication of these phages. The same mechanism of DNA replication is used by theCp-1 related phages (also members of the Podoviridae family) and by the phagePRD1 (member of the Tectoviridae family). Based on the complete or partialgenomic sequence data of these phages it was 155 287 288 289 290 possible to analyze the evolutionaryrelationship within the phi29-like phage genus as well as to other protein-primedreplicating phages. Noncoding regions containing origins of replication were usedin the analysis, as well as amino acid sequences of DNA polymerases, and with thephi29-like phages also amino acid sequences of the terminal proteins and of thegene 17 protein product, an accessory component of bacteriophage DNA replicating machinery. Included in the analysis are also results of a comparison of thesephage DNAs with the prophages present in the Bacillus subtilis genome. Based onthis complex analysis we define and describe in more detail the evolutionarybranches of phi29-like phages, one branch consisting of phages BS32, phi15,phi29, and PZA, the second branch composed of phages B103, M2, and Nf, and thethird branch having phage GA-1 as its sole member. In addition, amino acidsequences of holins, proteins involved in phage lysis were used to extend theevolutionary study to other phages infecting Gram-positive bacteria. The analysisbased on the amino acid sequences of holins showed several weak points in presentbacteriophage classification.PMID: 9929388 [PubMed - indexed for MEDLINE] 387. J Bacteriol. 1999 Jan;181(2):418-25.Cell wall teichoic acid glycosylation in Listeria monocytogenes serotype 4brequires gtcA, a novel, serogroup-specific gene.Promadej N(1), Fiedler F, Cossart P, Dramsi S, Kathariou S.Author information: (1)Department of Microbiology, University of Hawaii, Honolulu, Hawaii 96822, USA.We have identified a novel gene, gtcA, involved in the decoration of cell wallteichoic acid of Listeria monocytogenes serotype 4b with galactose and glucose.Insertional inactivation of gtcA brought about loss of reactivity with theserotype 4b-specific monoclonal antibody c74.22 and was accompanied by a completelack of galactose and a marked reduction in the amounts of glucose on teichoicacid. Interestingly, the composition of membrane-associated lipoteichoic acid wasnot affected. Complementation of the mutants with the cloned gtcA in transrestored galactose and glucose on teichoic acid to wild-type levels. Thecomplemented strains also recovered reactivity with c74.22. Within L.monocytogenes, sequences homologous to gtcA were found in all serogroup 4isolates but not in strains of any other serotypes. In serotype 4b, gtcA appears to be the first member of a bicistronic operon which includes a gene withhomology to Bacillus subtilis rpmE, encoding ribosomal protein L31. In contrastto gtcA, the latter gene appears conserved among all screened serotypes of L.monocytogenes.PMCID: PMC93394PMID: 9882654 [PubMed - indexed for MEDLINE] 388. Curr Microbiol. 1999 Feb;38(2):107-12.Sequence analysis of small cryptic plasmids isolated from Selenomonas ruminantiumS20.Nakamura M(1), Nagamine T, Ogata K, Tajima K, Aminov RI, Benno Y.Author information: (1)Rumen Microbiology Research Team, STAFF-Institute, 446-1 Ippaizuka, KamiyokobaTsukuba, Ibaraki 305-0854, Japan.Two small cryptic plasmids designated pONE429 and pONE430 were isolated from arumen bacterium, Selenomonas ruminantium S20. The complete sequence of pONE429was 2100 bp and contained one open reading frame (ORF) of 201 amino acids. Thesequence of pONE430 had 1527 bp and one ORF of 171 amino acids with thesimilarity of replication protein (Rep protein) of pOM1, pSN2, and pIM13 isolatedfrom Butyrivibrio fibrisolvens, Staphylococcus aureus, and Bacillus subtilis,respectively. In these plasmids, the upstream nucleotide sequence of Rep protein had the conserved nucleotides which could be double-strand origin (DSO) ofrolling circle replication (RCR) mechanism. The plasmids of pONE429, pONE430,pJJMI, pJDB21, and pS23 were isolated from S. ruminantium strains and had similarregions that were located within a <450-bp nucleotide. These similar regions may be the location that was recognized by the host strain, S. ruminantium.PMID: 9871109 [PubMed - indexed for MEDLINE] 389. J Bacteriol. 1998 Dec;180(24):6729-35.Role of the gerI operon of Bacillus cereus 569 in the response of spores togerminants.Clements MO(1), Moir A.Author information: (1)Department of Molecular Biology and Biotechnology, University of Sheffield,Western Bank, Sheffield S10 2TN, United Kingdom.Bacillus cereus 569 (ATCC 10876) germinates in response to inosine or toL-alanine, but the most rapid germination response is elicited by a combinationof these germinants. Mutants defective in their germination response to eitherinosine or to L-alanine were isolated after Tn917-LTV1 mutagenesis and enrichmentprocedures; one class of mutant could not germinate in response to inosine as asole germinant but still germinated in response to L-alanine, although at areduced rate; another mutant germinated normally in response to inosine but wasslowed in its germination response to L-alanine. These mutants demonstrated that at least two signal response pathways are involved in the triggering ofgermination. Stimulation of germination in L-alanine by limiting concentrationsof inosine and stimulation of germination in inosine by low concentrations ofL-alanine were still detectable in these mutants, suggesting that suchstimulation is not dependent on complete functionality of both these germination loci. Two transposon insertions that affected inosine germination were found tobe located 2.2 kb apart on the chromosome. This region was cloned and sequenced, revealing an operon of three open reading frames homologous to those in the gerA and related operons of Bacillus subtilis. The individual genes of this gerIoperon have been named gerIA, gerIB, and gerIC. The GerIA protein is predicted topossess an unusually long, charged, N-terminal domain containing nine tandemcopies of a 13-amino-acid glutamine- and serine-rich sequence.PMCID: PMC107780PMID: 9852021 [PubMed - indexed for MEDLINE] 390. J Bacteriol. 1998 Dec;180(24):6704-12.New small, acid-soluble proteins unique to spores of Bacillus subtilis:identification of the coding genes and regulation and function of two of thesegenes.Bagyan I(1), Setlow B, Setlow P.Author information: (1)Department of Biochemistry, University of Connecticut Health Center, Farmington, Connecticut 06032, USA.Eleven small, acid-soluble proteins (SASP) which are present in spores but not ingrowing cells of Bacillus subtilis were identified by sequence analysis ofproteins separated by acrylamide gel electrophoresis of acid extracts from sporeswhich lack the three major SASP (alpha, beta, and gamma). Six of these proteinsare encoded by open reading frames identified previously or by analysis of thecomplete sequence of the B. 156 291 292 293 294 subtilis genome, including two minor alpha/beta-type SASP (SspC and SspD) and a putative spore coat protein (CotK). Five proteins are encoded by short open reading frames that were not identified as coding regionsin the analysis of the complete B. subtilis genomic sequence. Studies of theregulation of two of the latter genes, termed sspG and sspJ, showed that both areexpressed only in sporulation. The sspG gene is transcribed in the mother cellcompartment by RNA polymerase with the mother cell-specific sigma factor for RNA polymerase, sigmaK, and is cotranscribed with a downstream gene, yurS; sspGtranscription also requires the DNA binding protein GerE. In contrast, sspJ istranscribed in the forespore compartment by RNA polymerase with theforespore-specific sigmaG and appears to give a monocistronic transcript. Amutation eliminating SspG had no effect on sporulation or spore properties, whileloss of SspJ caused a slight decrease in the rate of spore outgrowth in anotherwise wild-type background.PMCID: PMC107777PMID: 9852018 [PubMed - indexed for MEDLINE] 391. FEMS Microbiol Lett. 1998 Nov 15;168(2):269-76.Cloning and expression of the gene encoding RNA polymerase alpha subunit fromalkaliphilic Bacillus sp. strain C-125.Nakasone K(1), Takaki Y, Takami H, Inoue A, Horikoshi K.Author information: (1)DEEP STAR Group, Japan Marine Science and Technology Center, Kanagawa, [email protected] rpoA gene, encoding the alpha subunit of RNA polymerase, was isolated fromalkaliphilic Bacillus sp. strain C-125 by the PCR method. A 3-kb HindIII fragmentcontaining the complete rpoA gene was cloned and sequenced. The alpha subunitgene was found to encode a protein consisting of 314 amino acid residues with amolecular mass of 34,805 Da. Compared with the amino acid sequences of otherknown eubacterial RNA polymerase alpha subunits, the gene has 84% identity tothat of B. subtilis, while showing 48% and 47% identity to that of Streptomycescoelicolor and Escherichia coli, respectively. Six conserved regions, which areobserved in the case of other eubacteria, were found in the RNA polymerase alpha subunit of this strain. Five of them are located in the N-terminal domaininvolved in assembly of the core enzyme, while one is located in the C-terminaldomain, which interacts with several transcriptional factors and a specific DNAelement. By means of recombinant plasmids, a hexahistidine-tagged derivative ofthe RNA polymerase alpha subunit of strain C-125 and two deletion derivatives (C-and N-terminal domains) of this protein were overexpressed in E. coli cells andpurified to near homogeneity.PMID: 9835038 [PubMed - indexed for MEDLINE] 392. J Bacteriol. 1998 Dec;180(23):6298-305.Role and regulation of Bacillus subtilis glutamate dehydrogenase genes.Belitsky BR(1), Sonenshein AL.Author information: (1)Department of Molecular Biology and Microbiology, Tufts University School ofMedicine, Boston, Massachusetts 02111, USA. [email protected] complete Bacillus subtilis genome contains two genes with the potential toencode glutamate dehydrogenase (GlutDH) enzymes. Mutations in these genes wereconstructed and characterized. The rocG gene proved to encode a major GlutDHwhose synthesis was induced in media containing arginine or ornithine or, to alesser degree, proline and was repressed by glucose. A rocG null mutant wasimpaired in utilization of arginine, ornithine, and proline as nitrogen or carbonsources. The gudB gene was expressed under all growth conditions tested but codesfor a GlutDH that seemed to be intrinsically inactive. Spontaneous mutations ingudB that removed a 9-bp direct repeat within the wild-type gudB sequenceactivated the GudB protein and allowed more-efficient utilization of amino acids of the glutamate family.PMCID: PMC107716PMID: 9829940 [PubMed - indexed for MEDLINE] 393. Nucleic Acids Res. 1998 Dec 1;26(23):5456-63.Analysis of complete genomes suggests that many prokaryotes do not rely onhairpin formation in transcription termination.Washio T(1), Sasayama J, Tomita M.Author information: (1)Laboratory for Bioinformatics, Graduate School of Media and Governance andDepartment of Environmental Information, Keio University, 5322 Endo, Fujisawa252, Japan.Free energy values of mRNA tertiary structures around stop codons weresystematically calculated to surmise the hairpin-forming potential for all genes in each of the 16 complete prokaryote genomes. Instead of trying to detect eachindividual hairpin, we averaged the free energy values around the stop codonsover the entire genome to predict how extensively the organism relies on hairpin formation in the process of transcription termination. The free energy values of Escherichia coli K-12 shows a sharp drop, as expected, at 30 bp downstream of thestop codon, presumably due to hairpin-forming sequences. Similar drops areobserved for Haemophilus influenzae Rd, Bacillus subtilis and Chlamydiatrachomatis, suggesting that these organisms also form hairpins at theirtranscription termination sites. On the other hand, 12 other prokaryotes-Mycoplasma genitalium, Mycoplasma pneumoniae, Synechocystis PCC6803, Helicobacterpylori, Borrelia burgdorferi, Methanococcus jannaschii, Archaeoglobus fulgidus,Methanobacterium thermoautotrophicum, Aquifex aeolicus, Pyrococcus horikoshii,Mycobacterium tuberculosis and Treponema pallidum -show no apparent decrease infree energy value at the corresponding regions. This result suggests that theseprokaryotes, or at least some of them, may never form hairpins at theirtranscription termination sites.PMCID: PMC148011PMID: 9826772 [PubMed - indexed for MEDLINE] 394. Microbiology. 1998 Oct;144 ( Pt 10):2809-17.The conjugative plasmid pSG5 from Streptomyces ghanaensis DSM 2932 differs in itstransfer functions from other Streptomyces rolling-circle-type plasmids.Maas RM(1), Götz J, Wohlleben W, Muth G.Author information: (1)Universität Tübingen, Germany.The Streptomyces ghanaensis plasmid pSG5 is self-transmissible but does not form the growth-retardation zones (pocks) normally characteristic of the Streptomyces plasmid-transfer process. The complete nucleotide sequence of pSG5 was determinedon both strands. pSG5 is 12,208 bp in length and has a GC content of 68 mol%.Characterization of the open reading frames by insertion and deletion analysisrevealed that only a single gene, traB, is involved in the transfer of pSG5. The deduced amino acid sequence of TraB is similar to the SpoIIIE protein that isresponsible for chromosome translocation 157 295 296 297 298 during prespore formation of Bacillussubtilis. In contrast to the tra genes of the other Streptomyces plasmids, thepSG5 traB does not represent a kill function. Although pSG5 transfer is notassociated with pock formation, pSG5 was shown to possess putative spd genes thatare responsible for the pock phenotype of other Streptomyces plasmids. However,promoter-probe experiments revealed that the spd genes of pSG5 are nottranscribed, thus explaining the deficiency in pock formation.PMID: 9802022 [PubMed - indexed for MEDLINE] 395. Proc Natl Acad Sci U S A. 1998 Oct 27;95(22):12838-43.Glutamyl-tRNA(Gln) amidotransferase in Deinococcus radiodurans may be confined toasparagine biosynthesis.Curnow AW(1), Tumbula DL, Pelaschier JT, Min B, Söll D.Author information: (1)Department of Molecular Biophysics and Biochemistry, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8114, USA.Asparaginyl-tRNA (Asn-tRNA) and glutaminyl-tRNA (Gln-tRNA) are essentialcomponents of protein synthesis. They can be formed by direct acylation byasparaginyl-tRNA synthetase (AsnRS) or glutaminyl-tRNA synthetase (GlnRS). Thealternative route involves transamidation of incorrectly charged tRNA.Examination of the preliminary genomic sequence of the radiation-resistantbacterium Deinococcus radiodurans suggests the presence of both direct andindirect routes of Asn-tRNA and Gln-tRNA formation. Biochemical experimentsdemonstrate the presence of AsnRS and GlnRS, as well as glutamyl-tRNA synthetase (GluRS), a discriminating and a nondiscriminating aspartyl-tRNA synthetase(AspRS). Moreover, both Gln-tRNA and Asn-tRNA transamidation activities arepresent. Surprisingly, they are catalyzed by a single enzyme encoded by threeORFs orthologous to Bacillus subtilis gatCAB. However, the transamidation routeto Gln-tRNA formation is idled by the inability of the discriminating D.radiodurans GluRS to produce the required mischarged Glu-tRNAGln substrate. Thepresence of apparently redundant complete routes to Asn-tRNA formation, combined with the absence from the D. radiodurans genome of genes encodingtRNA-independent asparagine synthetase and the lack of this enzyme in D.radiodurans extracts, suggests that the gatCAB genes may be responsible forbiosynthesis of asparagine in this asparagine prototroph.PMCID: PMC23620PMID: 9789001 [PubMed - indexed for MEDLINE] 396. Mol Microbiol. 1998 Sep;29(6):1369-77.A five-nucleotide sequence protects DNA from exonucleolytic degradation by AddAB,the RecBCD analogue of Bacillus subtilis.Chédin F(1), Noirot P, Biaudet V, Ehrlich SD.Author information: (1)Laboratoire de Génétique Microbienne, Institut National de Recherche Agronomique,Domaine de Vilvert, Jouy en Josas, France.Homologous recombination in Bacillus subtilis requires the product of the addAand addB genes, the AddAB enzyme. This enzyme, which is both a helicase and apowerful nuclease, is thought to be the counterpart of the Escherichia coliRecBCD enzyme. From this analogy, it is expected that the nuclease activity ofAddAB can be downregulated by a specific DNA sequence, which would correspond to the chi site in E. coli. Using protection of linear double-stranded DNA as acriterion, we identified the five-nucleotide sequence 5'-AGCGG-3', or itscomplement 5'-CCGCT-3', as being sufficient for AddAB nuclease attenuation. Wehave shown further that this attenuation occurs only if the sequence is properly oriented with respect to the translocating AddAB enzyme. Finally, inspection ofthe complete B. subtilis genome revealed that this five-nucleotide sequence isover-represented and is, in a majority of cases, co-oriented with DNAreplication. Based on these observations, we propose that 5'-AGCGG-3', or itscomplement, is the B. subtilis analogue of the E. coli chi sequence.PMID: 9781875 [PubMed - indexed for MEDLINE] 397. Syst Appl Microbiol. 1998 Aug;21(3):398-407.A DNA probe for the detection and identification of Bacillus sporothermoduransusing the 16S-23S rDNA spacer region and phylogenetic analysis of some fieldisolates of Bacillus which form highly heat resistant spores.de Silva S(1), Petterson B, Aquino de Muro M, Priest FG.Author information: (1)Department of Biological Sciences, Heriot Watt University, Edinburgh, UK.The spacer regions between the 16S and 23S rRNA genes (spacer regions 1) ofBacillus sporothermodurans were PCR-amplified, cloned and sequenced. Six uniquespacer sequences in four size classes were recovered from two strains, rrnA(about 190 bp), rrnB (about 303 bp), rrnC (355 bp) and rrnD (554 bp). rrnDcontained two tRNA genes which were deciphered as tRNA(ala) and tRNA(ile)separated from each other by 13 nucleotides. The primary structures of the tRNAmolecules clearly resembled those found in Bacillus subtilis; the tRNA(ala) geneswere identical and the tRNA(ile) genes were 95% similar. The mixed rrnA and rrnB spacers when PCR-amplified from chromosomal DNA were effective as a hybridizationprobe for identification of B. sporothermodurans strains. However, highbackground signals with DNA from some other bacilli were encountered. A morediscriminating probe was prepared from the cloned rrnB spacer region. Of eightaerobic, endospore-forming bacteria isolated from silage following heatenrichment, one was identified as B. sporothermodurans using the probe and itsidentity was confirmed from partial 16S rDNA analysis (phylotyping). Thisindicated that contamination in milk and dairies by B. sporothermodurans couldoriginate from cattle feeds such as silage. Of the other seven silage strains,only two were identified conclusively by phylotyping and three representedprobable new species. The latter three strains were subjected to phylogeneticanalysis using almost complete 16S rDNA sequences. Branch lengths, bootstrappercentage values, and 16S rDNA similarity to other Bacillus species suggestedthat these isolates are likely to constitute new species within the genusBacillus.PMID: 9779606 [PubMed - indexed for MEDLINE] 398. Biochemistry. 1998 Aug 25;37(34):11745-61.Nuclear magnetic resonance structure of d(GCATATGATAG). d(CTATCATATGC): aconsensus sequence for promoters recognized by sigma K RNA polymerase.Tonelli M(1), Ragg E, Bianucci AM, Lesiak K, James TL.Author information: (1)Department of Pharmaceutical Chemistry, University of California, San Francisco94143-0446, USA.The three-dimensional structure of d(GCATATGATAG).d(CTATCATATGC), from thepromoter region of a gene regulating sporulation in Bacillus subtilis mothercells, was determined utilizing two-dimensional nuclear Overhauser effect (2DNOE) and dou- 158 299 300 301 302 ble-quantum-filtered COSY (2QF-COSY) spectra. To minimize the effect of methods used to obtain restraints and refine structure, several variables werestudied. Interproton distance bounds were calculated very conservatively byrunning the complete relaxation matrix program MARDIGRAS hundreds of times using 2D NOE spectra for exchangeable and for nonexchangeable protons at differentmixing times, assuming different overall correlation times and different startingstructures. The 435 distance restraints were used with two different structuralrefinement methods: restrained molecular dynamics (rMD) and restrained MonteCarlo calculations (rMC). Refinement using different procedures and startingstructures resulted in essentially the same structure (<0.8 A rmsd), indicatingthat the structure is defined by experimental restraints and not the refinementmethod or variables used. R factors indicate the structures fit the experimental NOE data very well. Some helical parameters, notably large negative Xdisplacement, are characteristic of A-DNA, but others are characteristic ofB-DNA. As with TG.CA steps in other duplex DNA sequences studied in ourlaboratory, the two TG.CA steps have a positive roll, with T6-G7 exhibiting thelargest, and consequently a bent helix axis. The converged structure represents atime-averaged structure. However, multiple conformations, especially indeoxyriboses, were evident from vicinal coupling constants obtained fromquantitative simulations of 2QF-COSY cross-peaks and from persistentinconsistencies in experimental distances due to nonlinear conformationalaveraging.PMID: 9718297 [PubMed - indexed for MEDLINE] 399. Appl Microbiol Biotechnol. 1998 Jun;49(6):737-42.Trans activation of the Escherichia coli ato structural genes by a regulatoryprotein from Bacillus megaterium: potential use in polyhydroxyalkanoateproduction.Pettinari MJ(1), Vazquez GJ, Krüger N, Vary PS, Steinbüchel A, Méndez BS.Author information: (1)Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales,Universidad de Buenos Aires, Argentina.A Bacillus megaterium genomic fragment, which encoded an activator homologous to sigma 54 regulators and which was capable of activating Escherichia coli atogenes in trans, was detected in a gene library of B. megaterium screened forbeta-ketothiolase activity. The fragment presented only one complete open readingframe (ORF1), which encoded a protein of 398 amino acids. The recombinant plasmidcomplemented mutations in the Escherichia coli atoC regulatory gene. Theconstitutive expression of the E. coli ato operon mediated by ORF1 could beuseful for the synthesis of polyhydroxyalkanoates with different flexibilityproperties by recombinant E. coli strains.PMID: 9684307 [PubMed - indexed for MEDLINE] 400. DNA Res. 1998 Apr 30;5(2):121-6.An 8 kb nucleotide sequence at the 3' flanking region of the sspC gene (184degrees) on the Bacillus subtilis 168 chromosome containing an intein and anintron.Ghim SY(1), Choi SK, Shin BS, Park SH.Author information: (1)Bacterial Molecular Genetics RU, Korea Research Institute of Bioscience andBiotechnology (KRIBB), Taejon, Korea.As part of the Bacillus subtilis genome sequencing project, we determined thecomplete nucleotide sequence of an 8000-bp fragment downstream of the sspC gene(184 degrees) of the B. subtilis 168 chromosome. The sequence analysis shows thatthe sspC gene is located inside of the SP beta region, which differs from thecurrent genetic map of B. subtilis 168. This region contains 12 putative ORFs(yojQ through yojZ and sspC). A homology search for the deduced products of theORFs shows significant similarities to enzymes involved in deoxyribonucleotidemetabolism: ribonucleotide reductase (Nrd) E, NrdF, thioredoxin and dUTPase.Interestingly, this DNA fragment includes two split genes, yojP containingconserved motifs of an intein and yojQ and yojS with an 808-bp interveningsequence for a putative intron structure. In addition, the yojR gene includes aputative new DNA replication terminator.PMID: 9679200 [PubMed - indexed for MEDLINE] 401. FEBS Lett. 1998 Jun 23;430(1-2):28-36.The complete genome of Bacillus subtilis: from sequence annotation to datamanagement and analysis.Moszer I.Author information: Unité de Régulation de l'Expression Génétique, Institut Pasteur, Paris, [email protected] completion of the entire 4.2-Mb genome sequence of the gram-positivebacterium Bacillus subtilis has been a milestone for biological studies on thismodel organism. This paper describes bioinformatics work related to this jointEuropean and Japanese project: methods and strategies for gene annotation anddetection of sequencing errors, using an integrated cooperative computerenvironment (Imagene); construction of a specialized database for data managementand a WWW server for data retrieval (SubtiList); DNA sequence analysis, yielding striking results on oligonucleotide bias, repeated sequences, and codon usage,all landmarks of evolutionary events shaping the B. subtilis genome.PMID: 9678589 [PubMed - indexed for MEDLINE] 402. J Bacteriol. 1998 Jul;180(14):3548-55.Dual promoters are responsible for transcription initiation of the fla/che operonin Bacillus subtilis.Estacio W(1), Anna-Arriola SS, Adedipe M, Márquez-Magaña LM.Author information: (1)Department of Biology, San Francisco State University, San Francisco, California 94132, USA.The fla/che region contains more than 30 genes required for flagellar synthesisand chemotaxis in Bacillus subtilis, including the gene for theflagellum-specific sigmaD factor, sigD. Sequence and primer extension datademonstrate that a PA promoter immediately upstream of flgB, henceforth referred to as the fla/che PA, and the PD-3 promoter are active in vivo. Transcriptionfrom the PD-3 element is dependent on sigmaD activity and is regulated by theflagellum-specific negative regulator, FlgM. In a strain containing a deletion offla/che PA (PADelta), sigmaD protein was not detected, demonstrating that thefla/che PA is necessary for wild-type expression of the sigD gene. Thus, sigD is part of the >26-kb fla/che operon. Consistent with a lack of detectable sigmaDprotein, the PADelta strain grows as long filaments and does not express asigmaD-dependent hag::lacZ reporter construct. These phenotypes are indicative ofa lack of sigD expression or complete inhibition of sigmaD activity by FlgM.However, sigmaD activity is found in a double mutant containing the PADelta and anull mutation in flgM. The double mutant no longer grows as long filaments, andexpression of hag::lacZ is partially restored. These data demonstrate that a low level of sigmaD activity does exist in the PADelta mutant but can be detectedonly in the presence of a null mutation in flgM. 159 303 304 305 306 Therefore, normal expression of sigD may also involve another promoter(s) within the fla/che operon.PMCID: PMC107321PMID: 9657996 [PubMed - indexed for MEDLINE] 403. Nature. 1998 Jun 11;393(6685):537-44.Deciphering the biology of Mycobacterium tuberculosis from the complete genomesequence.Cole ST(1), Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV,Eiglmeier K, Gas S, Barry CE 3rd, Tekaia F, Badcock K, Basham D, Brown D,Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N,Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K,Osborne J, Quail MA, Rajandream MA, Rogers J, Rutter S, Seeger K, Skelton J,Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG.Author information: (1)Sanger Centre, Wellcome Trust Genome Campus, Hinxton, UK. [email protected] in Nature 1998 Nov 12;396(6707):190.Comment in Nature. 1998 Jun 11;393(6685):515-6.Countless millions of people have died from tuberculosis, a chronic infectiousdisease caused by the tubercle bacillus. The complete genome sequence of thebest-characterized strain of Mycobacterium tuberculosis, H37Rv, has beendetermined and analysed in order to improve our understanding of the biology ofthis slow-growing pathogen and to help the conception of new prophylactic andtherapeutic interventions. The genome comprises 4,411,529 base pairs, containsaround 4,000 genes, and has a very high guanine + cytosine content that isreflected in the biased amino-acid content of the proteins. M. tuberculosisdiffers radically from other bacteria in that a very large portion of its coding capacity is devoted to the production of enzymes involved in lipogenesis andlipolysis, and to two new families of glycine-rich proteins with a repetitivestructure that may represent a source of antigenic variation.PMID: 9634230 [PubMed - indexed for MEDLINE] 404. J Mol Biol. 1998 May 8;278(3):599-608.Protein identification with N and C-terminal sequence tags in proteome projects.Wilkins MR(1), Gasteiger E, Tonella L, Ou K, Tyler M, Sanchez JC, Gooley AA,Walsh BJ, Bairoch A, Appel RD, Williams KL, Hochstrasser DF.Author information: (1)Central Clinical Chemistry Laboratory, Geneva University Hospital, 24 RueMicheli-du-Crest, Geneva 14, 1211, Switzerland.Genome sequences are available for increasing numbers of organisms. The proteomes(protein complement expressed by the genome) of many such organisms are beingstudied with two-dimensional (2D) gel electrophoresis. Here we have investigated the application of short N-terminal and C-terminal sequence tags to theidentification of proteins separated on 2D gels. The theoretical N and C termini of 15, 519 proteins, representing all SWISS-PROT entries for the organismsMycoplasma genitalium, Bacillus subtilis, Escherichia coli, Saccharomycescerevisiae and human, were analysed. Sequence tags were found to be surprisingly specific, with N-terminal tags of four amino acid residues found to be unique forbetween 43% and 83% of proteins, and C-terminal tags of four amino acid residues unique for between 74% and 97% of proteins, depending on the species studied.Sequence tags of five amino acid residues were found to be even more specific. Toutilise this specificity of sequence tags for protein identification, we created a world-wide web-accessible protein identification program, TagIdent(http://www.expasy.ch/www/tools.html), which matches sequence tags of up to sixamino acid residues as well as estimated protein pI and mass against proteins in the SWISS-PROT database. We demonstrate the utility of this identificationapproach with sequence tags generated from 91 different E. coli proteins purifiedby 2D gel electrophoresis. Fifty-one proteins were unambiguously identified byvirtue of their sequence tags and estimated pI and mass, and a further 11proteins identified when sequence tags were combined with protein amino acidcomposition data. We conlcude that the TagIdent identification approach is bestsuited to the identification of proteins from prokaryotes whose complete genomesequences are available. The approach is less well suited to proteins fromeukaryotes, as many eukaryotic proteins are not amenable to sequencing via Edman degradation, and tag protein identification cannot be unambiguous unless anorganism's complete sequence is available.Copyright 1998 Academic Press Limited.PMID: 9600841 [PubMed - indexed for MEDLINE] 405. J Bacteriol. 1998 Jun;180(12):3222-6.The glucose kinase of Bacillus subtilis.Skarlatos P(1), Dahl MK.Author information: (1)Lehrstuhl für Mikrobiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg,Germany.The open reading frame yqgR (now termed glcK), which had been sequenced as partof the genome project, encodes a glucose kinase of Bacillus subtilis. A 1.1-kbDNA fragment containing glcK complemented an Escherichia coli strain deficient inglucose kinase activity. Insertional mutagenesis of glcK resulted in a completeinactivation of glucose kinase activity in crude protein extracts, indicatingthat B. subtilis contains one major glucose kinase. The glcK gene encodes a321-residue protein with a molecular mass of 33.5 kDa. The glucose kinase wasoverexpressed as a fusion protein to a six-His affinity tag and purified tohomogeneity. The enzyme had K(m) values for ATP and glucose of 0.77 and 0.24 mM, respectively, and a Vmax of 93 mumol min-1 mg-1. A B. subtilis strain deficientfor glucose kinase grew at the same rate on different carbon sources tested,including disaccharides such as maltose, trehalose, and sucrose.PMCID: PMC107826PMID: 9620975 [PubMed - indexed for MEDLINE] 406. Nucleic Acids Res. 1998 Jun 15;26(12):2971-80.Oligonucleotide bias in Bacillus subtilis: general trends and taxonomiccomparisons.Rocha EP(1), Viari A, Danchin A.Author information: (1)Atelier de BioInformatique, Université Paris VI, 12 Rue Cuvier, 75005 Paris,France. [email protected] present a general analysis of oligonucleotide usage in the complete genome of Bacillus subtilis . Several datasets were built in order to assign variousbiological contexts to the biased use of words and to reveal local asymmetries inword usage that may be coupled with replication, the control of gene expressionand the restriction/modification system. This analysis was complemented bycross-comparisons with the complete genomes of Escherichia coli , Haemophilusinfluenzae and Methanococcus jannaschii . We have observed a large number ofbiased oligonucleotides for words of size up to 8, 160 307 308 309 310 throughout the datasets andspecies, indicating that such long strict words play an important role asbiological signals. We speculate that some of them are involved in interactionswith DNA and/or RNA polymerases. An extensive analysis of palindrome abundancesand distributions provides the surprising result that prophage-like elementsembedded in the genome exhibit a smaller avoidance of restriction sites. This mayreinforce a recently proposed hypothesis of a selfish gene phenomena in thetransfer of restriction/modification systems in bacteria.PMCID: PMC147636PMID: 9611243 [PubMed - indexed for MEDLINE] 407. Nucleic Acids Res. 1998 Jun 15;26(12):2941-7.Combining diverse evidence for gene recognition in completely sequenced bacterialgenomes.Frishman D(1), Mironov A, Mewes HW, Gelfand M.Author information: (1)Munich Information Center for Protein Sequences (MIPS) of the German NationalCenter for Health and Environment (GSF), Am Klopferspitz 18a, 82152 Martinsried, Germany. [email protected] in Nucleic Acids Res 1998 Aug 15;26(16):following 3870.Analysis of a newly sequenced bacterial genome starts with identification ofprotein-coding genes. Functional assignment of proteins requires the exactknowledge of protein N-termini. We present a new program ORPHEUS that identifies candidate genes and accurately predicts gene starts. The analysis starts with adatabase similarity search and identification of reliable gene fragments. Thelatter are used to derive statistical characteristics of protein-coding regionsand ribosome-binding sites and to predict the complete set of genes in theanalyzed genome. In a test on Bacillus subtilis and Escherichia coli genomes, theprogram correctly identified 93.3% (resp. 96.3%) of experimentally annotatedgenes longer than 100 codons described in the PIR-International database, and forthese genes 96.3% (83.9%) of starts were predicted exactly. Furthermore, 98.9%(99.1%) of genes longer than 100 codons annotated in GenBank were found, and92.9% (75.7%) of predicted starts coincided with the feature table description.Finally, for the complete gene complements of B.subtilis and E.coli , includinggenes shorter than 100 codons, gene prediction accuracy was 88.9 and 87.1%,respectively, with 94.2 and 76.7% starts coinciding with the existing annotation.PMCID: PMC147632PMID: 9611239 [PubMed - indexed for MEDLINE] 408. Genome Res. 1998 Mar;8(3):203-10.Reconstruction of amino acid biosynthesis pathways from the complete genomesequence.Bono H(1), Ogata H, Goto S, Kanehisa M.Author information: (1)Institute for Chemical Research, Kyoto University, Uji, Kyoto 611, Japan.The complete genome sequence of an organism contains information that has notbeen fully utilized in the current prediction methods of gene functions, whichare based on piece-by-piece similarity searches of individual genes. We presenthere a method that utilizes a higher level information of molecular pathways toreconstruct a complete functional unit from a set of genes. Specifically, agenome-by-genome comparison is first made for identifying enzyme genes andassigning EC numbers, which is followed by the reconstruction of selectedportions of the metabolic pathways by use of the reference biochemical knowledge.The completeness of the reconstructed pathway is an indicator of the correctness of the initial gene function assignment. This feature has become possible becauseof our efforts to computerize the current knowledge of metabolic pathways underthe KEGG project. We found that the biosynthesis pathways of all 20 amino acidswere completely reconstructed in Escherichia coli, Haemophilus influenzae, andBacillus subtilis, and probably in Synechocystis and Saccharomyces cerevisiae as well, although it was necessary to assume wider substrate specificity foraspartate aminotransferases.PMID: 9521924 [PubMed - indexed for MEDLINE] 409. FEMS Microbiol Rev. 1998 Feb;21(4):337-68.Rolling-circle plasmids from Bacillus subtilis: complete nucleotide sequences andanalyses of genes of pTA1015, pTA1040, pTA1050 and pTA1060, and comparisons with related plasmids from gram-positive bacteria.Meijer WJ(1), Wisman GB, Terpstra P, Thorsted PB, Thomas CM, Holsappel S, Venema G, Bron S.Author information: (1)Department of Genetics, Groningen Biomolecular Sciences and BiotechnologyInstitute, Haren, The Netherlands.Most small plasmids of Gram-positive bacteria use the rolling-circle mechanism ofreplication and several of these have been studied in considerable detail at the DNA level and for the function of their genes. Although most of the commonlaboratory Bacillus subtilis 168 strains do not contain plasmids, severalindustrial strains and natural soil isolates do contain rolling-circlereplicating (RCR) plasmids. So far, knowledge about these plasmids was mainlylimited to: (i) a classification into seven groups, based on size and restrictionpatterns; and (ii) DNA sequences of the replication region of a limited number ofthem. To increase the knowledge, also with respect to other functions specifiedby these plasmids, we have determined the complete DNA sequence of four plasmids,representing different groups, and performed computer-assisted and experimentalanalyses on the possible function of their genes. The plasmids analyzed arepTA1015 (5.8 kbp), pTA1040 (7.8 kbp), pTA1050 (8.4 kbp), and pTA1060 (8.7 kbp).These plasmids have a structural organization similar to most other known RCRplasmids. They contain highly related replication functions, both for leading andlagging strand synthesis. pTA1015 and pTA1060 contain a mobilization geneenabling their conjugative transfer. Strikingly, in addition to the conservedreplication modules, these plasmids contain unique module(s) with genes which arenot present on known RCR plasmids of other Gram-positive bacteria. Examples aregenes encoding a type I signal peptidase and genes encoding proteins belonging tothe family of response regulator aspartate phosphatases. The latter are likely tobe involved in the regulation of post-exponential phase processes. The presenceof these modules on plasmids may reflect an adaptation to the special conditions to which the host cells were exposed.PMID: 9532747 [PubMed - indexed for MEDLINE] 410. DNA Res. 1997 Oct 31;4(5):325-8.Sequence analysis of a 25-kb segment in the 17 degrees-19 degrees region of theBacillus subtilis chromosome containing ada locus.Liu H(1), Haga K, Kasahara Y, Ogasawara N, Takahashi H, Yoshikawa H.Author information: (1)Institute of Molecular and Cellular Biosciences, University of Tokyo, Japan.As a part of the Bacillus subtilis genome se- 161 311 312 313 314 quencing project, we have determined a 25-kb sequence covering the 17 degrees-19 degrees region. This region contains 26 complete open reading frames (ORFs) including the alkA and adaA/B operon,which encode genes for adaptive response to DNA alkylation. A homology search forthe newly identified 21 ORFs revealed that 4 of them exhibit a significantsimilarity to known proteins, e.g., methicillin-resistant Staphylococcus aureus(MRSA) protein homolog, proteins involved in chloramphenicol resistance,glucosamine synthase and an ABC transporter protein. The remaining 17 ORFs didnot show any significant sequence similarities to known gene products in thedatabase.PMID: 9455480 [PubMed - indexed for MEDLINE] 411. Gene. 1997 Dec 19;204(1-2):201-12.The complete nucleotide sequence and functional organization of Bacillus subtilisbacteriophage SPP1.Alonso JC(1), Lüder G, Stiege AC, Chai S, Weise F, Trautner TA.Author information: (1)Centro Nacional de Biotecnologia, CSIC, Campus Universidad Autónoma de Madrid,Cantoblanco, Spain. [email protected] complete nucleotide sequence of the B. subtilis bacteriophage SPP1 isdescribed. The genome is 44,007 bp in size and has a base composition of 43.7% dG+ dC. Only 32.2 kb are essential for phage amplification under laboratoryconditions. Transcription using only the 'heavy strand' is asymmetric. Eighty-oneorfs organized in five early and four late operons were identified. Experimentshave shown that 25 orfs are essential. Of the remaining orfs, functions could be predicted for the products of five of the orfs on the basis of comparison of the deduced amino acid sequence to known proteins. Intergenic regions include most ofthe 5 PE and the 4 PL promoters. Transcripts are polycistronic. Transcriptionfrom the PE promoters is mediated by host RP, whereas recognition of the PLpromoters requires an additional unidentified phage-encoded product. Translation of mRNA transcribed from most of the orfs seems to be initiated independently,each from its own ribosomal binding and initiation site, although a few cases of coupled translation have been reported. The organization of SPP1 genes involvedin the replication, DNA packaging and phage assembly proteins resembles theorganization of genes of equivalent regions of different E. coli double-stranded DNA phages. Absence of aa sequence similarity between analogous proteins ofdifferent phages suggested that the conserved gene organization is representativeof a primordial bacteriophage.PMID: 9434185 [PubMed - indexed for MEDLINE] 412. Nature. 1997 Nov 20;390(6657):249-56.The complete genome sequence of the gram-positive bacterium Bacillus subtilis.Kunst F(1), Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG,Bessières P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M,Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Carter NM,Choi SK, Codani JJ, Connerton IF, Danchin A, et al.Author information: (1)Institut Pasteur, Unité de Biochimie Microbienne, Paris, [email protected] in Nature. 1997 Nov 20;390(6657):237-8.Bacillus subtilis is the best-characterized member of the Gram-positive bacteria.Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of theseprotein-coding genes, 53% are represented once, while a quarter of the genomecorresponds to several gene families that have been greatly expanded by geneduplication, the largest family containing 77 putative ATP-binding transportproteins. In addition, a large proportion of the genetic capacity is devoted tothe utilization of a variety of carbon sources, including many plant-derivedmolecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes.Many of the genes are involved in the synthesis of secondary metabolites,including antibiotics, that are more typically associated with Streptomycesspecies. The genome contains at least ten prophages or remnants of prophages,indicating that bacteriophage infection has played an important evolutionary rolein horizontal gene transfer, in particular in the propagation of bacterialpathogenesis.PMID: 9384377 [PubMed - indexed for MEDLINE] 413. Microbiology. 1997 Nov;143 ( Pt 11):3443-50.Sequence completion, identification and definition of the fengycin operon inBacillus subtilis 168.Tosato V(1), Albertini AM, Zotti M, Sonda S, Bruschi CV.Author information: (1)Microbiology Group, International Centre for Genetic Engineering andBiotechnology, Trieste, Italy.A 15 kb DNA fragment from the Bacillus subtilis chromosome between citB and ppsC has been sequenced, and new ORFs encoding putative enzymes involved inlipopolypeptide synthesis, which complete a partial operon previously reported,and a new set of enzymes responsible for lipid metabolism have been identified.From the analysis of DNA sequence homology of the fragment it was deduced thatthese new peptide synthetase genes are part of an operon for the biosynthesis of the fungicide fengycin.PMID: 9387222 [PubMed - indexed for MEDLINE] 414. Gene. 1997 Oct 1;198(1-2):149-57.Molecular characterization of the alpha-amylase genes of Lactobacillus plantarum A6 and Lactobacillus amylovorus reveals an unusual 3' end structure with directtandem repeats and suggests a common evolutionary origin.Giraud E(1), Cuny G.Author information: (1)Laboratoire de Biotechnologie, ORSTOM, Montpellier, [email protected] alpha-amylase gene (amyA) of Lactobacillus plantarum A6 was isolated from thegenome by polymerase chain reaction with degenerated oligonucleotides,synthesized according to the tryptic peptide amino acid sequences of the purifiedenzyme. Nucleic acid sequence analysis revealed one open reading frame of 2739 bpencoding a 913 amino acid protein. The amylase appears to be divided into twoequal parts. The N-terminal part has the typical characteristics of thewell-known alpha-amylase family (65% identity with the alpha-amylase of Bacillus subtilis and 97% identity with the partial sequence available for thealpha-amylase of Lactobacillus amylovorus). The C-terminal part displays a fairlyunusual structure. It consists of four direct tandem repeated sequences of 104amino acids sharing 100% similarity. The complete nucleotide sequence of thealpha-amylase gene of L. amylo

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