Download Chapter 4: 4b-prokoutl

MICR V01: The Prokaryotes (Ch 4b with 18-21, 26-7)
© copyright 2013 Marta D. de Jesus
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{FunFacts: human gut has ~10 bacteria; 75% are unknown species (The Scientist 7/5/99 p31); 10% of the
cells of the human body are eukaryotic…}
I. Review criteria for classification and identification of microorganisms
A. morphology: shapes of cells & colonies (with interaction with media)
B. staining
C. other biochemical tests
D. comparing nucleic acids
E. phage typing
F. reference cultures
II. Survey of the prokaryotes
A. Bergey’s Manual categories
1. What is Bergey’s Manual?
a) Systematic Bacteriology - now working to finish 2nd ed.; enyclopedic
b) Determinative Bacteriology – for ID
B. Archaeal phyla - as of 200?
I. Crenarchaeota
III. Korarcheota
II. Euryarchaeota
IV. Nanoarcheota
C. Bacterial phyla (discuss the bolded groups) - as of 2008
I. Aquificae
XIV. Bacteroidetes
II. Thermotogae
XV. Spirochaetes
III. Thermodesulfobacteria
XVI. Tenericutes (Mollicutes) (new)
IV. Deinococcus-Thermus
XVII. Acidobacteria
V. Chrysiogenetes
XVIII. Fibrobacteres
VI. Chloroflexi
XIX. Fusobacteria
VII. Thermomicrobia
XX. Dictyoglomi
VIII. Nitrospira
XXI. Gemmatimonadetes
IX. Deferribacteres
XXII. Lentisphaerae (new)
X. Cyanobacteria
XXIII. Verrucomicrobia
XI. Chlorobi
XXIV. Chlamydiae
XII. Proteobacteria
XXV. Planctomycetes
XIII. Firmicutes
XXVI. Actinobacteria
D. most microbes are not out to GET you…
III. Domain & Kingdom Archaea
A. myths
B. truths
C. P: Crenarch(a)eota
Geogemma barossi
Ignicoccus
Pyrodictium
D. P: Euryarch(a)eota
1. methanogens
Methanobacterium smithii
Methanopyrus
2. halophiles
Halobacterium salinarium
Haloarcula (square)
3. acidophiles: Ferroplasma acidamarnus
4. also some thermophiles & hyperthermophiles
E. P: Korarchaeota
F: P: Nanoarch(a)eota
Nanoarcheum equitans
III. A closer look at important groups of Bacteria († = human pathogen); NOT inclusive
A. Some Gram Negative Bacteria
1. Deeply branching
P: Aquificae (I)
Aquifex
P: ‘Deinococcus-Thermus’ (IV)
Kineococcus radiodurans
Thermus
Thermus aquaticus
2. Green bacteria
P: Chloroflexi (VI)
Chloroflexus
P: Chlorobi (XI)
Chlorobium
3. P: Cyanobacteria (X)
heterocysts
examples
Anabaena
Oscillatoria
Spirulina
†Microcystis
chloroplast
B. Gram Positive Bacteria
1. Low G+C = P: ‘Firmicutes’ (XIII)
a. C: Clostridia
Clostridium:
† C. botulinum
† C. tetani
† C. perfringens
(†) C. difficile
Epulopiscium
b. C: Bacilli
Bacillus
† B. anthraci
B. cereus
B. thuringiensis
Lactobacillus
L. acidophilus
Lactococcus
Streptococcus
1) 1 classification based on appearance on blood agar
-hemolytic
ß-hemolytic
-hemolytic
2) classification by (Rebecca) Lancefield groups
Group A (GAS): †S. pyogenes
Group B (GBS): † S. agalactiae
Group D: Enterococci & others eg: (†) Enterococcus
MRE, VRE
No Lancefield group: (†) S. pneumoniae
Viridans group: eg: †S. mutans
Staphylococcus
(†) S. aureus
MRSA, VRSA & LRSA
(†) S. epidermidis
†Listeria monocytogenes
2. P: Tenericutes (Mollicutes, XVI)
Mycoplasma
† M. pneumoniae
† M. hominis
(†) M. genitalium
(†) Ureaplasma urealyticum
3. high G+C = P: Actinobacteria (XXVI)
Mycobacterium
† M. tuberculosis
MDR-TB & XDR-TB
† M. leprae
† Corynebacterium diphtheriae
† Propionibacterium acnes
† Gardnerella vaginalis
Actinomycetes
(†) Actinomyces israeli
(†) Nocardia asteroides
Micrococcus luteus
Streptomyces
C. More Gram Negative Bacteria
1. P: Proteobacteria (XII)
a. Alpha
1) N fixers:
Azospirillum
Rhizobium
2) purple non-sulfur
eg: Rhodospirillum
3) Hu pathogens
†Rickettsia
R. prowazekii
R. rickettsia
R. typhi
†Ehrlichia
E. chaffeensis
†Anaplasma phagocytophilum
†Bartonella
B. henselea
B. quintana
†Brucella
4) vinegar-makers: Acetobacter
5) prosthecate:
Hyphomicrobium
Caulobacter
6) others
Agrobacterium tumefaciens
Wolbachia
7) mitochondrion
b. Beta
1) Thiobacillus
2) Hu pathogens
†Neisseria
N. gonorrhoeae
N. meningitides
†Bordetella pertussis
Burkholderia
(†) B. cepacia
c. Gamma
1) purple sulfur:
eg: Chromatium
2) other S cycler
Thiomargarita namibiensis
3) Hu intracellular pathogens
†Legionella
†Coxiella burnetii
4) Family Enterobacteriaceae
- coliforms
Escherichia (5 spp. ?) aka. E. coli (some †)
(†) Klebsiella pneumoniae
(†) Serratia marcescens
(†) Enterobacter spp., Hafnia spp., Citrobacter spp.
- non-coliform
(†) Proteus vulgaris
(†) Morganella, Providencia
-frank pathogens
† Salmonella
Kauffman-White system of ID by antigens
K:
O:
H:
Vi:
†S. enterica
serovars
S. typhi
S. paratyphi
†Shigella
†Yersinia pestis
5) Family Vibrionaceae
Vibrio
†V. cholerae
†V. parahaemolyticus
†V. vulnificus
6) Family Pasteurellaceae
†Pasteurella multocida
†Haemophilus
H. influenzae
H. ducreyi
9) Others
Pseudomonas aeruginosa
† Moraxella
M. lacunata
M. catarrhalis
† Acinetobacter
† Francisella tularensis
d. Delta
Bdellovibrio
Desulfovibrio
Myxobacteria
eg: Stigmatella
e. Epsilon
† Campylobacter jejuni
(†) Helicobacter pylori
2. P: Chlamydiae (XVI)
† Chlamydia
C. trachomatis
C. pneumoniae
3. P: Spirochetes (XV)
†Treponema
T. pallidum pallidum
†Borrelia
B. burgdorferi
B. recurrenti
†Leptospira interrogans
4. P: Bacteroidetes (XIV)
Bacteroides (can be†)
(†) Prevotella
5. P: Fusobacteria (XIX)
† Fusobacterium
(Note: this is by no means a complete list of prokaryotic species or bacterial pathogens of humans)