Download Table S1. - BioMed Central

Table S1 Syntenical placement of the UNSWCD plasmid genes across the C. concisus strains. A group of eight UNSWCD plasmid
genes including the exotoxin 9 displayed syntenical conservation and are highlighted in grey.
a. Plasmid from UNSWCD
Gene ID/Description
UNSW2
UNSWCD_11|hypothetical protein
UNSWCD_18|StbE
UNSWCD_25|StbE replicon stabilization toxin
UNSWCD_8|MobA-like protein
UNSWCD_14|exotoxin 9
UNSWCD_23|R.Ecl18kI
UNSWCD_7|DNA-cytosine methyltransferase
UNSWCD_13|site-specific recombinase2C resolvase family2C
UNSWCD_19|Site-specific recombinase
UNSW3
UNSWCD_10|hypothetical protein
UNSWCD_11|hypothetical protein
UNSWCD_9|Mature parasite-infected erythrocyte surface antigen
UNSWCD_1|hypothetical protein
UNSWCD_3|hypothetical protein
UNSWCD_22|Sodium/solute symporter
UNSWCD_15|hypothetical protein
UNSWCD_20|Radical SAM
UNSWCD_4|Fe-S oxidoreductase
UNSWCD_16|glycosyl transferase2C family 2
UNSWCD_12|Membrane spanning protein
UNSWCD_26|DedA family inner membrane protein YdjZ
UNSWCD_6|Choline kinase
Scaffold
Position co-ordinates
Orientation
8
8
8
8
8
8
8
8
8
66131, 65691
69276, 69028
69553, 69269
71891, 70302
73405, 73097
76956, 76321
78237, 77059
78807, 78502
80085, 79132
+
+
+
+
+
-
10
10
10
10
10
10
10
10
10
10
10
10
10
45655, 45533
50533, 50012
52411, 51002
53390, 52686
56622, 55723
58007, 56625
58429, 58010
59382, 58450
60341, 59382
61023, 60322
61654, 60995
62342, 61635
63850, 62342
+
1
UNSWCD_21|hypothetical protein
UNSWCD_24|hypothetical protein
UNSWCD_17|hypothetical protein
UNSWCD_18|StbE
UNSWCD_25|StbE replicon stabilization toxin
UNSWCD_8|MobA-like protein
UNSWCD_14|exotoxin 9
UNSWCD_23|R.Ecl18kI
UNSWCD_7|DNA-cytosine methyltransferase
UNSWCD_13|site-specific recombinase2C resolvase family2C
UNSWCD_19|Site-specific recombinase
UNSW1
UNSWCD_9|Mature parasite-infected erythrocyte surface antigen
UNSWCD_1|hypothetical protein
UNSWCD_15|hypothetical protein
UNSWCD_20|Radical SAM
UNSWCD_4|Fe-S oxidoreductase
UNSWCD_2|hypothetical protein
UNSWCD_16|glycosyl transferase2C family 2
UNSWCD_12|Membrane spanning protein
UNSWCD_26|DedA family inner membrane protein YdjZ
UNSWCD_6|Choline kinase
UNSWCD_21|hypothetical protein
UNSWCD_24|hypothetical protein
UNSWCD_17|hypothetical protein
UNSWCD_18|StbE
UNSWCD_25|StbE replicon stabilization toxin
UNSWCD_8|MobA-like protein
UNSWCD_14|exotoxin 9
10
10
10
10
10
10
10
10
10
10
10
64224, 63850
64862, 64227
67299, 65332
67632, 67384
67909, 67625
70224, 68635
71738, 71430
75318, 74404
76599, 75421
77174, 76869
78440, 77499
+
+
+
+
+
-
13
13
13
13
13
13
13
13
13
13
13
13
13
13
13
13
13
3143, 1734
4131, 3427
8607, 8188
9559, 8627
10521, 9559
11178, 10567
11904, 11203
12535, 11876
13223, 12516
14731, 13223
15105, 14731
15743, 15108
18173, 16215
18507, 18259
18784, 18500
21120, 19528
22639, 22331
+
+
+
+
2
UNSWCD_23|R.Ecl18kI
UNSWCD_7|DNA-cytosine methyltransferase
UNSWCD_13|site-specific recombinase2C resolvase family2C
UNSWCD_19|Site-specific recombinase
UNSWCD_11|hypothetical protein
UNSWCS
UNSWCD_7|DNA-cytosine methyltransferase
UNSWCD_11|hypothetical protein
UNSWCD_18|StbE
UNSWCD_25|StbE replicon stabilization toxin
UNSWCD_9|Mature parasite-infected erythrocyte surface antigen
ATCC 51562
UNSWCD_11|hypothetical protein
UNSWCD_9|Mature parasite-infected erythrocyte surface antigen
UNSWCD_25|StbE replicon stabilization toxin
UNSWCD_18|StbE
UNSWCD_7|DNA-cytosine methyltransferase
UNSWCD_17|hypothetical protein
UNSWCD_5|TonB-dependent receptor
ATCC 51561
UNSWCD_9|Mature parasite-infected erythrocyte surface antigen
UNSWCD_1|hypothetical protein
UNSWCD_3|hypothetical protein
UNSWCD_22|Sodium/solute symporter
UNSWCD_15|hypothetical protein
UNSWCD_20|Radical SAM
UNSWCD_4|Fe-S oxidoreductase
UNSWCD_16|glycosyl transferase2C family 2
UNSWCD_12|Membrane spanning protein
13
13
13
13
3
26484, 25579
27791, 26613
28361, 28056
29640, 28660
68423, 67749
+
+
1
10
10
10
10
49030, 48335
64873, 64433
68007, 67759
68284, 68000
69682, 68885
+
+
+
+
3
3
3
3
3
3
3
261351, 260929
266894, 265332
267495, 267211
267736, 267488
276317, 275316
277450, 276551
306958, 305537
+
+
10
10
10
10
10
10
10
10
10
4607, 3204
5596, 4892
6551, 5634
7954, 6551
8376, 7957
9328, 8396
10287, 9328
10969, 10268
11600, 10941
3
UNSWCD_8|MobA-like protein
UNSWCD_26|DedA family inner membrane protein YdjZ
UNSWCD_6|Choline kinase
UNSWCD_21|hypothetical protein
UNSWCD_24|hypothetical protein
UNSWCD_11|hypothetical protein
UNSWCD_17|hypothetical protein
BAA-1457
UNSWCD_18|StbE
UNSWCD_17|hypothetical protein
13
10
10
10
10
7
7
12577, 11612
12288, 11581
13796, 12288
14170, 13796
14808, 14173
126329, 125916
173836, 171911
+
+
+
NC_009802.1
NC_009802.1
343056, 342835
346650, 344533
+
+
b. Plasmids from BAA-1457
pCCON31
Gene ID
Description
UNSW2
YP_001456653.1
YP_001456658.1
YP_001456659.1
YP_001456657.1
YP_001456654.1
YP_001456648.1
YP_001456650.1
hypothetical protein
hypothetical protein
hypothetical protein
putative phytanoyl-CoAdioxygenase
hypothetical protein
hypothetical protein
putative periplasmic protein
Contig
Position coordinates
40
103
64
102
30
1
Orientation
549, 1
193, 2
544, 218
1014, 709
14386, 13778
49107, 48466
332965, 331196
+
+
+
-
5 336571, 332978
+
5
YP_001456651.1
filamentous haemagglutinin family protein
UNSW3
4
YP_001456654.1
hypothetical protein
UNSW1
YP_001456650.1
putative periplasmic protein
13 19909, 19301
+
2310, 541
+
20 5742, 2323
1 9056, 8448
13 22688, 20388
+
+
20
YP_001456651.1
YP_001456654.1
YP_001456661.1
filamentous haemagglutinin family protein
hypothetical protein
hypothetical protein
UNSWCS
YP_001456650.1
YP_001456658.1
YP_001456659.1
YP_001456649.1
YP_001456661.1
YP_001456648.1
YP_001456657.1
YP_001456656.1
YP_001456655.1
YP_001456651.1
YP_001456647.1
YP_001456653.1
YP_001456662.1
YP_001456663.1
YP_001456654.1
YP_001456665.1
YP_001456666.1
YP_001456669.1
YP_001456672.1
putative periplasmic protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
putative phytanoyl-CoAdioxygenase
hypothetical protein
hypothetical protein
filamentous haemagglutinin family protein
Cpp22
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
HipA domain-containing protein
hypothetical protein
phage integrase family site-specific
86
96
181
15
21
15
67
67
67
75
15
67
21
21
90
21
21
21
21
1014, 1
190, 2
255, 1
552, 334
3120, 817
1241, 558
1530, 1159
2029, 1589
2169, 2032
2288, 828
2877, 1588
3755, 2931
6179, 5964
6649, 6197
9306, 8698
23344, 23204
34089, 32920
35238, 35131
36120, 35137
+
+
5
YP_001456673.1
YP_001456674.1
YP_001456675.1
YP_001456678.1
YP_001456679.1
recombinase
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein3
hypothetical protein
21
21
21
21
21
ATCC51562
YP_001456648.1
YP_001456661.1
hypothetical protein
hypothetical protein
10 40472, 39831
9 183476, 180759
+
ATCC51561
YP_001456661.1
YP_001456650.1
YP_001456651.1
YP_001456652.1
hypothetical protein
putative periplasmic protein
filamentous haemagglutinin family protein
hypothetical protein
45
9
9
9
876, 10
3939, 2170
7380, 3952
14216, 13905
+
+
+
+
43
29
113
23
6
769, 17
1176, 37
1279, 161
44106, 43078
70248, 69952
71288, 70302
+
+
+
+
+
+
36510, 36409
38190, 37936
39557, 38361
41064, 40213
41462, 41067
+
+
+
+
+
pCCON16
UNSW2
YP_001456694.1
YP_001456682.1
YP_001456686.1
YP_001456690.1
YP_001456701.1
YP_001456702.1
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
mobilization protein
6
UNSW3
6
YP_001456686.1
YP_001456694.1
YP_001456690.1
YP_001456682.1
YP_001456693.1
YP_001456701.1
YP_001456702.1
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
mobilization protein
43
50
47
36
31
20
20
782, 3
1571, 783
903, 286
1133, 3
11476, 11099
14132, 13836
15127, 14186
+
+
+
+
+
UNSW1
YP_001456682.1
YP_001456694.1
YP_001456686.1
YP_001456690.1
YP_001456701.1
YP_001456702.1
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
mobilization protein
65
49
47
11
18
18
1407, 268
779, 3
1020, 1
1679, 651
19474, 19178
20514, 19528
+
+
+
UNSWCS
YP_001456686.1
YP_001456682.1
YP_001456694.1
YP_001456690.1
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
190
192
122
4
894, 1
403, 2
961, 266
61886, 60858
+
+
+
ATCC51562
YP_001456690.1
YP_001456682.1
YP_001456686.1
hypothetical protein
hypothetical protein
hypothetical protein
1 81348, 80782
1 81519, 80809
3 162724, 162038
-
ATCC51561
YP_001456680.1
putative pNL871104_protein
130 1120, 164
+
7
YP_001456691.1
YP_001456690.1
YP_001456702.1
YP_001456701.1
YP_001456700.1
YP_001456699.1
YP_001456683.1
YP_001456681.1
YP_001456684.1
YP_001456685.1
YP_001456686.1
YP_001456696.1
YP_001456695.1
YP_001456693.1
YP_001456694.1
YP_001456682.1
bacteriocin-type signal sequence domaincontaining protein
hypothetical protein
mobilization protein 22
hypothetical protein
hypothetical protein
hypothetical protein
Cpp12
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
HmcD domain-containing protein
peptidase family protein
hypothetical protein
hypothetical protein
hypothetical protein
30 1619, 1194
+
30
22
22
22
22
30
22
30
30
30
22
22
30
27
12
+
+
+
+
+
+
+
+
+
+
-
2719, 1691
2051, 192
2358, 2044
2527, 2348
2992, 2738
3529, 2969
3532, 3128
3798, 3532
4401, 3844
5641, 4460
5736, 4885
6314, 5724
6405, 5908
9961, 9182
125517, 124378
Table S2 KEGG pathways which show the same sub-set of genes conserved across all eight C. concisus strains.
KEGG ID
Pathway name
00780
00550
00730
00970
00430
Biotin metabolism
Peptidoglycan biosynthesis
Thiamine metabolism
Aminoacyl-tRNA biosynthesis
Taurine and hypotaurine metabolism
Number of pathway gene components
conserved across all C. concisus
strains
7
15
11
47
3
8
00562
00860
00410
02040
00471
00472
00473
00290
03420
03440
03030
00920
00625
00071
00627
00740
00660
00760
00310
00450
00020
00130
00052
00230
00750
00790
03060
03410
01040
Inositol phosphate metabolism
Porphyrin and chlorophyll metabolism
beta-Alanine metabolism
Flagellar assembly
D-Glutamine and D-glutamate metabolism
D-Arginine and D-ornithine metabolism
D-Alanine metabolism
Valine, leucine and isoleucine biosynthesis
Nucleotide excision repair
Homologous recombination
DNA replication
Sulfur metabolism
Chloroalkane and chloroalkene degradation
Fatty acid metabolism
Aminobenzoate degradation
Riboflavin metabolism
C5-Branched dibasic acid metabolism
Nicotinate and nicotinamide metabolism
Lysine degradation
Selenocompound metabolism
Citrate cycle (TCA cycle)
Ubiquinone and other terpenoid-quinone biosynthesis
Galactose metabolism
Purine metabolism
Vitamin B6 metabolism
Folate biosynthesis
Protein export
Base excision repair
Biosynthesis of unsaturated fatty acids
3
11
3
28
5
2
4
11
9
18
14
11
3
3
3
7
7
10
4
9
23
6
4
46
6
16
17
11
3
9
00401
00400
00540
00360
00362
03020
00280
04122
00650
02030
00770
00061
00523
00030
00460
00300
00500
00260
00380
Novobiocin biosynthesis
Phenylalanine, tyrosine and tryptophan biosynthesis
Lipopolysaccharide biosynthesis
Phenylalanine metabolism
Benzoate degradation
RNA polymerase
Valine, leucine and isoleucine degradation
Sulfur relay system
Butanoate metabolism
Bacterial chemotaxis
Pantothenate and CoA biosynthesis
Fatty acid biosynthesis
Polyketide sugar unit biosynthesis
Pentose phosphate pathway
Cyanoamino acid metabolism
Lysine biosynthesis
Starch and sucrose metabolism
Glycine, serine and threonine metabolism
Tryptophan metabolism
4
18
22
7
4
5
2
10
11
13
15
12
3
12
4
14
6
18
3
Table S3 Genes found specific to individual Campylobacter concisus strains are tabulated below and those found in syntenic blocks
are highlighted in grey.
Campylobacter concisus UNSWCD
fig|6666666.462.peg.202
fig|6666666.462.peg.252
fig|6666666.462.peg.336
fig|6666666.462.peg.341
fig|6666666.462.peg.342
atp-dependent protease atp-binding subunit
hypothetical protein
lipopolysaccharide biosynthesis protein
glycosyl transferase group 1
glycosyl group 1 family protein
10
fig|6666666.462.peg.343
fig|6666666.462.peg.344
fig|6666666.462.peg.345
fig|6666666.462.peg.346
fig|6666666.462.peg.347
fig|6666666.462.peg.348
fig|6666666.462.peg.349
fig|6666666.462.peg.382
fig|6666666.462.peg.405
fig|6666666.462.peg.654
fig|6666666.462.peg.659
fig|6666666.462.peg.660
fig|6666666.462.peg.745
fig|6666666.462.peg.1170
fig|6666666.462.peg.1216
fig|6666666.462.peg.1360
fig|6666666.462.peg.1490
fig|6666666.462.peg.1491
Campylobacter concisus UNSW2
fig|6666666.10684.peg.40
fig|6666666.10684.peg.41
fig|6666666.10684.peg.42
fig|6666666.10684.peg.43
fig|6666666.10684.peg.600
fig|6666666.10684.peg.601
fig|6666666.10684.peg.788
fig|6666666.10684.peg.789
fig|6666666.10684.peg.902
fig|6666666.10684.peg.903
o-antigen polymerase
glycosyltransferase
heparinase ii iii-like protein
polysaccharide biosynthesis protein
phosphatase
aminotransferase
capk protein
methyl-accepting chemotaxis protein
hypothetical protein
hi0933 family partial
membrane protein
tir protein
surface protein
integrase family protein
hypothetical protein
hypothetical protein
dna mismatch repair protein
dna-cytosine methyltransferase
licd2 protein
Hypothetical protein
integral membrane protein domain protein
transcriptional choline ethanolamine kinase
dgqhr domain protein
adenine-specific dna-methyltransferase
hypothetical protein
restriction endonuclease family protein
1 aminotransferase
hypothetical protein
11
fig|6666666.10684.peg.904
fig|6666666.10684.peg.905
fig|6666666.10684.peg.906
fig|6666666.10684.peg.908
fig|6666666.10684.peg.909
fig|6666666.10684.peg.910
fig|6666666.10684.peg.911
fig|6666666.10684.peg.912
fig|6666666.10684.peg.1075
fig|6666666.10684.peg.1084
fig|6666666.10684.peg.1559
fig|6666666.10684.peg.1561
fig|6666666.10684.peg.1840
fig|6666666.10684.peg.1875
fig|6666666.10684.peg.1892
fig|6666666.10684.peg.2014
fig|6666666.10684.peg.2015
fig|6666666.10684.peg.2017
fig|6666666.10684.peg.2018
fig|6666666.10684.peg.2020
fig|6666666.10684.peg.2021
fig|6666666.10684.peg.2022
fig|6666666.10684.peg.2023
fig|6666666.10684.peg.2025
fig|6666666.10684.peg.2026
Campylobacter concisus UNSW3
fig|6666666.10685.peg.231
fig|6666666.10685.peg.232
fig|6666666.10685.peg.656
haloacid dehalogenase-like hydrolase
cyclase family protein
nad-dependent epimerase dehydratase
acetyltransferase (isoleucine patch superfamily)
udp-glucose 4-epimerase
transferase hexapeptide repeat containing protein
3-deoxy-manno-octulosonate cytidylyltransferase
2-dehydro-3-deoxyglucarate aldolase
arginase
hypothetical protein
hypothetical protein
tetratricopeptide repeat domain protein
atpase family protein
cation diffusion facilitator family transporter
hnh endonuclease
3-oxoacyl-(acyl carrier protein) synthase iii
gnat family
3-oxoacyl-acp reductase
short-chain dehydrogenase reductase sdr
amino acid adenylation domain protein
methyltransferase family
amp-dependent synthetase and ligase
nad dependent epimerase dehydratase family protein
metallo-beta-lactamase domain protein
cytidylyltransferase domain protein
rna methylase
hypothetical protein
replication initiation protein
12
fig|6666666.10685.peg.1004
fig|6666666.10685.peg.1006
fig|6666666.10685.peg.1166
fig|6666666.10685.peg.1167
fig|6666666.10685.peg.1168
fig|6666666.10685.peg.1169
fig|6666666.10685.peg.1171
fig|6666666.10685.peg.1173
fig|6666666.10685.peg.1174
fig|6666666.10685.peg.1175
fig|6666666.10685.peg.1176
fig|6666666.10685.peg.1177
fig|6666666.10685.peg.1179
fig|6666666.10685.peg.1246
fig|6666666.10685.peg.1293
fig|6666666.10685.peg.1911
fig|6666666.10685.peg.1912
fig|6666666.10685.peg.1923
fig|6666666.10685.peg.1924
fig|6666666.10685.peg.1925
fig|6666666.10685.peg.1926
fig|6666666.10685.peg.1927
fig|6666666.10685.peg.1948
fig|6666666.10685.peg.1949
Campylobacter concisus UNSW1
fig|6666666.18222.peg.367
fig|6666666.18222.peg.368
fig|6666666.18222.peg.427
fig|6666666.18222.peg.428
phage-related protein
phage-related protein
glycosyl transferase family 2
probable k5 antigen synthesis
conserved domain protein
lipopolysaccharide biosynthesis protein
formyl transferase
fucosyl transferase
methyltransferase family
polysaccharide biosynthesis protein
2-aminoethylphosphonate aminotransferase
phosphonopyruvate decarboxylase
phosphoenolpyruvate phosphomutase
atp-dependent endonuclease
hypothetical protein
hypothetical protein
hypothetical protein
site-specific phage integrase family
protein
membrane protein
phage protein
hypothetical protein
SigF
uncharacterized conserved protein
f0f1-type atp synthase
hypothetical protein
thiosulfate sulfur transferase
hypothetical protein
13
fig|6666666.18222.peg.531
fig|6666666.18222.peg.532
fig|6666666.18222.peg.720
fig|6666666.18222.peg.845
fig|6666666.18222.peg.911
fig|6666666.18222.peg.1208
fig|6666666.18222.peg.1305
fig|6666666.18222.peg.1306
fig|6666666.18222.peg.1311
fig|6666666.18222.peg.1408
fig|6666666.18222.peg.1473
fig|6666666.18222.peg.1744
fig|6666666.18222.peg.1799
fig|6666666.18222.peg.1811
fig|6666666.18222.peg.1813
fig|6666666.18222.peg.1814
fig|6666666.18222.peg.1815
fig|6666666.18222.peg.1816
fig|6666666.18222.peg.1817
fig|6666666.18222.peg.1820
fig|6666666.18222.peg.1821
fig|6666666.18222.peg.1899
dna methylase n-4 n-6 domain protein
ulcer-associated gene restriction endonuclease
aldo keto reductase
didehydrogluconate reductase
type iii site-specific deoxyribonuclease
cog1691: ncair mutase -related proteins
gnat family
hypothetical protein
transposase is204 is1001 is1096 is1165 protein
transcriptional activator
hypothetical protein
outer membrane adhesin-like protein
methyltransferase type 12
hypothetical protein
glycosyl group 1 family protein
acyltransferase family protein
polysaccharide pyruvyl transferase
capsule polysaccharide biosynthesis protein
integral membrane protein
membrane- metal-dependent hydrolase
glycosyl transferase family 2
hypothetical protein
Campylobacter concisus UNSWCS
fig|6666666.10687.peg.106
fig|6666666.10687.peg.286
fig|6666666.10687.peg.301
fig|6666666.10687.peg.571
fig|6666666.10687.peg.572
hypothetical protein
abi-like protein
dna methylase
restriction endonuclease
resolvase domain containing protein
14
fig|6666666.10687.peg.574
fig|6666666.10687.peg.576
fig|6666666.10687.peg.577
fig|6666666.10687.peg.578
fig|6666666.10687.peg.580
fig|6666666.10687.peg.581
fig|6666666.10687.peg.582
fig|6666666.10687.peg.583
fig|6666666.10687.peg.584
fig|6666666.10687.peg.586
fig|6666666.10687.peg.587
fig|6666666.10687.peg.589
fig|6666666.10687.peg.590
fig|6666666.10687.peg.592
fig|6666666.10687.peg.594
fig|6666666.10687.peg.596
fig|6666666.10687.peg.597
fig|6666666.10687.peg.598
fig|6666666.10687.peg.603
fig|6666666.10687.peg.604
fig|6666666.10687.peg.610
fig|6666666.10687.peg.669
fig|6666666.10687.peg.700
fig|6666666.10687.peg.705
fig|6666666.10687.peg.761
fig|6666666.10687.peg.763
fig|6666666.10687.peg.908
fig|6666666.10687.peg.909
fig|6666666.10687.peg.912
transcriptional regulator
crispr-associated protein motif protein
hypothetical protein
crispr-associated protein
crispr-associated ramp protein
conserved domain protein
crispr-associated ramp protein
crispr-associated tm1811 family
hypothetical protein
crispr-associated protein cas1
crispr-associated protein cas6
gtp-binding protein
small gtp-binding protein domain protein
hypothetical protein
gtp-binding protein
atp gtp binding protein
cell division protein
transcriptional regulator
filamentation induced by camp protein fic
hypothetical protein
phage repressor
hypothetical protein
pf03235 family protein
hypothetical protein
transcriptional
hypothetical protein
hypothetical protein
adenylylsulfate kinase
molybdenum cofactor biosynthesis protein
15
fig|6666666.10687.peg.979
fig|6666666.10687.peg.1104
fig|6666666.10687.peg.1247
fig|6666666.10687.peg.1365
fig|6666666.10687.peg.1398
fig|6666666.10687.peg.1484
fig|6666666.10687.peg.1485
fig|6666666.10687.peg.1901
fig|6666666.10687.peg.1907
fig|6666666.10687.peg.1908
fig|6666666.10687.peg.1914
fig|6666666.10687.peg.1921
fig|6666666.10687.peg.1922
fig|6666666.10687.peg.1923
fig|6666666.10687.peg.1924
fig|6666666.10687.peg.1925
fig|6666666.10687.peg.1927
fig|6666666.10687.peg.1935
fig|6666666.10687.peg.1936
fig|6666666.10687.peg.1938
fig|6666666.10687.peg.1941
fig|6666666.10687.peg.1984
fig|6666666.10687.peg.1985
fig|6666666.10687.peg.2044
fig|6666666.10687.peg.2057
fig|6666666.10687.peg.2120
Campylobacter concisus ATCC 51562
fig|6666666.10688.peg.8
fig|6666666.10688.peg.11
mafb alternative c-terminus
cytochrome c-type heme-binding periplasmic protein
pf06114 domain protein
hypothetical protein
hypothetical protein
filamentous hemagglutinin family omp
filamentous hemagglutinin omp
adhesin hemagglutinin
appr-1-p processing domain protein
appr-1-p processing domain-containing protein
gp19
phage terminase large subunit
phage structural protein
phage mu protein f-like protein
hypothetical protein
major capsid protein
structural phage protein
phage tape measure protein
tail length tape measure partial
phage minor tail protein l
tail fiber truncation
phage-associated protein
RloG protein, putative
d-arabino-heptulosonate 7-phosphate synthase
hypothetical protein
signal peptide protein
nitrilase cyanide hydratase
general stress protein 14
16
fig|6666666.10688.peg.62
fig|6666666.10688.peg.103
fig|6666666.10688.peg.153
fig|6666666.10688.peg.173
fig|6666666.10688.peg.174
fig|6666666.10688.peg.175
fig|6666666.10688.peg.176
fig|6666666.10688.peg.181
fig|6666666.10688.peg.182
fig|6666666.10688.peg.226
fig|6666666.10688.peg.250
fig|6666666.10688.peg.255
fig|6666666.10688.peg.257
fig|6666666.10688.peg.258
fig|6666666.10688.peg.260
fig|6666666.10688.peg.263
fig|6666666.10688.peg.264
fig|6666666.10688.peg.397
fig|6666666.10688.peg.420
fig|6666666.10688.peg.421
fig|6666666.10688.peg.513
fig|6666666.10688.peg.718
fig|6666666.10688.peg.818
fig|6666666.10688.peg.834
fig|6666666.10688.peg.937
fig|6666666.10688.peg.1047
fig|6666666.10688.peg.1108
fig|6666666.10688.peg.1109
fig|6666666.10688.peg.1110
toxin-antitoxin antitoxin component
hypothetical protein
outer membrane autotransporter barrel protein
abortive phage infection
hypothetical protein
endonuclease
dna mismatch repair enzyme (atpase)
mu c-terminal domain protein
dna transposition protein
4-carboxymuconolactone decarboxylase
methionyl-trna formyltransferase
nad-binding domain protein
acetyltransferase
flagellin modification
conserved domain protein
methyltransferase type 11
glycosyl transferase
aminobenzoyl-glutamate transport protein
phenylalanine and histidine ammonia-lyase
outer membrane domain protein
nucleotide-binding protein
hypothetical protein
protein containing duf88
kap family p-loop domain protein
family protein
type i restriction-modification system
thiazole biosynthesis protein
dependent receptor
periplasmic binding protein
17
fig|6666666.10688.peg.1113
fig|6666666.10688.peg.1114
fig|6666666.10688.peg.1115
fig|6666666.10688.peg.1125
fig|6666666.10688.peg.1130
fig|6666666.10688.peg.1132
fig|6666666.10688.peg.1133
fig|6666666.10688.peg.1135
fig|6666666.10688.peg.1137
fig|6666666.10688.peg.1140
fig|6666666.10688.peg.1142
fig|6666666.10688.peg.1151
fig|6666666.10688.peg.1153
fig|6666666.10688.peg.1163
fig|6666666.10688.peg.1165
fig|6666666.10688.peg.1207
fig|6666666.10688.peg.1208
fig|6666666.10688.peg.1209
fig|6666666.10688.peg.1224
fig|6666666.10688.peg.1232
fig|6666666.10688.peg.1365
fig|6666666.10688.peg.1463
fig|6666666.10688.peg.1466
fig|6666666.10688.peg.1467
fig|6666666.10688.peg.1468
fig|6666666.10688.peg.1481
fig|6666666.10688.peg.1482
fig|6666666.10688.peg.1483
fig|6666666.10688.peg.1608
methyltransferase domain protein
hypothetical protein
hypothetical protein
tail collar domain protein
hypothetical protein
hit family protein
bacteriophage head to tail connecting protein
terminase b
yqey family protein
d12 adenine-specific dna methyltransferase
bacteriophage protein
hypothetical protein
sel1 repeat protein
hypothetical protein
phage protein
phosphate binding protein
phosphate abc permease protein
phosphate abc permease protein
putative lipoprotein
outer membrane autotransporter barrel protein
pf03235 family protein
heme iron utilization protein
hemin uptake system hemin-binding protein
oxygen-independent coproporphyrinogen iii oxidase
flavodoxin family protein
c4-dicarboxylate malic acid transporter
transcriptional crp fnr family protein
sulfide:quinone reductase
hnh endonuclease
18
fig|6666666.10688.peg.1695
fig|6666666.10688.peg.1811
fig|6666666.10688.peg.1813
fig|6666666.10688.peg.1873
Campylobacter concisus ATCC 51561
fig|6666666.18223.peg.376
fig|6666666.18223.peg.592
fig|6666666.18223.peg.593
fig|6666666.18223.peg.595
fig|6666666.18223.peg.618
fig|6666666.18223.peg.811
fig|6666666.18223.peg.866
fig|6666666.18223.peg.1107
fig|6666666.18223.peg.1111
fig|6666666.18223.peg.1112
fig|6666666.18223.peg.1113
fig|6666666.18223.peg.1116
fig|6666666.18223.peg.1117
fig|6666666.18223.peg.1218
fig|6666666.18223.peg.1242
fig|6666666.18223.peg.1243
fig|6666666.18223.peg.1244
fig|6666666.18223.peg.1245
fig|6666666.18223.peg.1719
fig|6666666.18223.peg.1720
Campylobacter concisus BAA-1457
fig|6666666.13147.peg.74
fig|6666666.13147.peg.75
fig|6666666.13147.peg.160
rhs repeat-associated core domain protein
integral membrane protein
hypothetical exported 24-amino acid repeat protein
hypothetical protein
hypothetical protein
helicase domain snf2 family domain protein
pf14335 domain protein
dna (cytosine-5-)-methyltransferase
flavin reductase domain protein
group 1 glycosyl transferase
short-chain dehydrogenase reductase family
family 2 glycosyl transferase
conserved domain protein
tigr04325 family
glycosyltransferase
glucose-1-phosphate thymidylyltransferase
dtdp-glucose -dehydratase
hypothetical protein
hypothetical protein
muramidase (phage lysozyme)
ef hand domain protein
hypothetical protein
putative lysozyme
conserved domain protein
ATPase
smc domain protein
hypothetical protein
19
fig|6666666.13147.peg.225
fig|6666666.13147.peg.349
fig|6666666.13147.peg.359
fig|6666666.13147.peg.360
fig|6666666.13147.peg.361
fig|6666666.13147.peg.362
fig|6666666.13147.peg.363
fig|6666666.13147.peg.368
fig|6666666.13147.peg.376
fig|6666666.13147.peg.377
fig|6666666.13147.peg.414
fig|6666666.13147.peg.415
fig|6666666.13147.peg.416
fig|6666666.13147.peg.738
fig|6666666.13147.peg.942
fig|6666666.13147.peg.949
fig|6666666.13147.peg.951
fig|6666666.13147.peg.952
fig|6666666.13147.peg.954
fig|6666666.13147.peg.990
fig|6666666.13147.peg.1540
fig|6666666.13147.peg.1542
fig|6666666.13147.peg.1543
fig|6666666.13147.peg.1545
fig|6666666.13147.peg.1546
fig|6666666.13147.peg.1547
fig|6666666.13147.peg.1548
fig|6666666.13147.peg.1549
fig|6666666.13147.peg.1550
large extracellular alpha-helical protein
hypothetical protein
dna-cytosine methyltransferase
dna-cytosine methyltransferase
two component transcriptional regulator
5-methylcytosine-specific restriction enzyme b
llaji restriction endonuclease
biopolymer transport protein
hypothetical protein
gtp-binding protein
glycosyl transferase group 1
membrane protein
glycosyl transferase group 1
phenazine biosynthesis protein family protein
two-component regulator
3-oxoacyl-[acyl-carrier-protein] synthase 3
zonula occludens toxin
general secretion pathway protein d
phage integrase
diaminopimelate dehydrogenase
group 1 glycosyl transferase
group 1 glycosyl transferase
lipopolysaccharide n-acetylglucosaminyltransferase
group 1 glycosyl transferase
nad-dependent epimerase dehydratase
polysaccharide biosynthesis protein
group 1 glycosyl transferase
udp-glucuronic acid udp-4-keto-hexauronic acid
hypothetical protein
20
fig|6666666.13147.peg.1551
fig|6666666.13147.peg.1552
fig|6666666.13147.peg.1553
fig|6666666.13147.peg.1554
fig|6666666.13147.peg.1557
fig|6666666.13147.peg.1558
fig|6666666.13147.peg.1560
fig|6666666.13147.peg.1561
fig|6666666.13147.peg.1615
fig|6666666.13147.peg.1616
fig|6666666.13147.peg.1618
fig|6666666.13147.peg.1624
fig|6666666.13147.peg.1656
fig|6666666.13147.peg.1657
fig|6666666.13147.peg.1658
fig|6666666.13147.peg.1674
fig|6666666.13147.peg.1677
fig|6666666.13147.peg.1679
fig|6666666.13147.peg.1680
fig|6666666.13147.peg.1681
fig|6666666.13147.peg.1683
fig|6666666.13147.peg.1769
fig|6666666.13147.peg.1829
fig|6666666.13147.peg.1986
fig|6666666.13147.peg.1987
polysaccharide deacetylase
carbamoyl phosphate synthase-like-protein
mj0936 family
d-mycarose 3-c-methyltransferase
hypothetical protein
nad dependent epimerase dehydratase family protein
transferase hexapeptide repeat containing protein
oxidoreductase domain protein
general secretion pathway protein d
zonula occludens toxin
hypothetical protein
two-component regulator
abc permease protein
twin-arginine translocation pathway signal
carbon-monoxide catalytic subunit
transposase is116 is110 is902 family protein
hypothetical protein
dna-directed rna polymerase alpha chain
hypothetical protein
hypothetical protein
hypothetical protein
arylsulfatase
oxidoreductase family protein
chaperone protein
foldase protein
21
Table S4 Genes found specific to C. concisus strain-pairs are tabulated below and those placed syntenically are highlighted in grey.
Gene ID
BAA-1457 & ATCC
51561
fig|6666666.13147.peg.272
fig|6666666.13147.peg.327
fig|6666666.13147.peg.345
fig|6666666.13147.peg.346
fig|6666666.13147.peg.347
fig|6666666.13147.peg.364
fig|6666666.13147.peg.375
fig|6666666.13147.peg.860
fig|6666666.13147.peg.861
fig|6666666.13147.peg.108
0
fig|6666666.13147.peg.200
2
BAA-1457 & UNSW1
fig|6666666.13147.peg.163
fig|6666666.13147.peg.165
fig|6666666.13147.peg.384
fig|6666666.13147.peg.429
fig|6666666.13147.peg.431
fig|6666666.13147.peg.814
fig|6666666.13147.peg.815
fig|6666666.13147.peg.113
3
fig|6666666.13147.peg.113
Gene definition
Top Blast hit in NCBI nr database
hypothetical protein
pyrimidine dimer dna glycosylase
aaa atpase
phage-related protein
transcriptional xre family
uncharacterized conserved protein
3-isopropylmalate dehydrogenase
creatininase
cytosine permease
peptidase family protein
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
hypothetical protein
Campylobacter concisus BAA-1457
bifunctional dna-directed rna beta chain
hypothetical protein
trna 2-selenouridine synthase
transcriptional regulator
citrate transporter
addiction module txe family
addiction module family
crispr-associated pf09484 family
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
crispr-associated protein hmari subtype
Campylobacter concisus BAA-1457
22
5
fig|6666666.13147.peg.155
5
UNSW2 & UNSW1
fig|6666666.10684.peg.137
fig|6666666.10684.peg.194
8
UNSW2 & ATCC 51561
fig|6666666.10684.peg.699
UNSW2 & ATCC 51562
fig|6666666.10684.peg.630
asparagine synthetase
Campylobacter concisus BAA-1457
methyl-accepting chemotaxis protein
membrane protein
Campylobacter sp. 10_1_50
Campylobacter concisus BAA-1457
phosphoserine phosphatase
Campylobacter showae RM3277
replication protein
Campylobacter fetus subsp. venerealis NCTC
10354
Campylobacter rectus RM3267
Campylobacter rectus RM3267
Campylobacter rectus RM3267
Campylobacter fetus subsp. venerealis NCTC
10354
Campylobacter rectus RM3267
Campylobacter fetus subsp. venerealis NCTC
10354
Campylobacter rectus RM3267
Campylobacter rectus RM3267
Campylobacter rectus RM3267
Campylobacter fetus subsp. venerealis NCTC
10354
Campylobacter fetus subsp. venerealis NCTC
10354
Campylobacter rectus RM3267
Campylobacter fetus subsp. venerealis NCTC
10354
fig|6666666.10684.peg.632
fig|6666666.10684.peg.635
fig|6666666.10684.peg.636
fig|6666666.10684.peg.639
hypothetical protein
plasmid partitioning protein
modification methylase
hypothetical protein
fig|6666666.10684.peg.640
fig|6666666.10684.peg.641
hypothetical protein
hypothetical protein
fig|6666666.10684.peg.642
fig|6666666.10684.peg.643
fig|6666666.10684.peg.644
fig|6666666.10684.peg.645
hypothetical protein
4 coupling protein
hypothetical protein
conjugative transfer regulon protein
fig|6666666.10684.peg.647
protein
fig|6666666.10684.peg.648
fig|6666666.10684.peg.649
dna transformation compentancy
comb8 competence protein
23
fig|6666666.10684.peg.650
hypothetical protein
fig|6666666.10684.peg.651
fig|6666666.10684.peg.653
fig|6666666.10684.peg.656
fig|6666666.10684.peg.841
fig|6666666.10684.peg.842
fig|6666666.10684.peg.843
fig|6666666.10684.peg.844
dna transfer protein
relaxase mobilization nuclease domaincontaining protein
hypothetical protein
bacteriophage-related integrase
cjp29-like protein
hypothetical protein
hypothetical protein
UNSW2 & UNSWCS
fig|6666666.10684.peg.365
fig|6666666.10684.peg.440
fig|6666666.10684.peg.584
fig|6666666.10684.peg.588
fig|6666666.10684.peg.589
fig|6666666.10684.peg.662
fig|6666666.10684.peg.663
fig|6666666.10684.peg.684
fig|6666666.10684.peg.686
fig|6666666.10684.peg.702
fig|6666666.10684.peg.705
fig|6666666.10684.peg.708
fig|6666666.10684.peg.710
fig|6666666.10684.peg.715
fig|6666666.10684.peg.716
fig|6666666.10684.peg.717
fig|6666666.10684.peg.718
ggdef family protein
tetratricopeptide repeat domain protein
hypothetical protein
hypothetical protein
hypothetical protein
protein of unknown function DUF262
protein of hypothetical function duf262
hypothetical protein
appr-1-p processing domain protein
phage protein
bacteriophage head-tail connecting protein
major head protein
tail fiber protein
hypothetical protein
hypothetical protein
lipoprotein
hypothetical protein
Campylobacter fetus subsp. venerealis NCTC
10354
Campylobacter rectus RM3267
Campylobacter rectus RM3267
Campylobacter rectus RM3267
Campylobacter rectus RM3267
Campylobacter rectus RM3267
Campylobacter rectus RM3267
Campylobacter fetus subsp. venerealis NCTC
10354
Shewanella sediminis HAW-EB3
Neisseria wadsworthii 9715
Campylobacter gracilis RM3268
Campylobacter gracilis RM3268
Helicobacter bilis ATCC 43879
Clostridium carboxidivorans P7
Arcobacter butzleri ED-1
Pseudoalteromonas sp. BSi20495
Nautilia profundicola AmH
Hydrogenobacter thermophilus TK6
Campylobacter coli 2680
Hydrogenobacter thermophilus TK6
Campylobacter sp. FOBRC14
Nitratifractor salsuginis DSM 16511
Campylobacter sp. FOBRC14
Campylobacter rectus RM3267
Campylobacter sp. FOBRC14
24
fig|6666666.10684.peg.721
fig|6666666.10684.peg.723
fig|6666666.10684.peg.730
fig|6666666.10684.peg.792
fig|6666666.10684.peg.797
fig|6666666.10684.peg.801
fig|6666666.10684.peg.845
fig|6666666.10684.peg.849
fig|6666666.10684.peg.896
fig|6666666.10684.peg.899
fig|6666666.10684.peg.900
fig|6666666.10684.peg.901
fig|6666666.10684.peg.913
fig|6666666.10684.peg.914
fig|6666666.10684.peg.916
fig|6666666.10684.peg.917
fig|6666666.10684.peg.919
fig|6666666.10684.peg.101
5
fig|6666666.10684.peg.101
6
fig|6666666.10684.peg.131
4
fig|6666666.10684.peg.164
9
fig|6666666.10684.peg.165
0
ATCC 51562 & ATCC
51561
fig|6666666.10688.peg.265
hypothetical protein
hypothetical protein
hypothetical protein
helix-turn-helix domain-containing protein
phage plasmid p4 family
hypothetical protein
hypothetical protein
tetratricopeptide tpr_2 repeat protein
glycosyl family 2
dtdp-4-dehydrorhamnose epimerase
cdp-glucose -dehydratase
glucose-1-phosphate cytidylyltransferase
polysaccharide biosynthesis protein
tigr04331 family
acylneuraminate cytidylyltransferase
cytidylyltransferase domain protein
iron-containing alcohol dehydrogenase
dynamin family protein
Campylobacter sp. FOBRC14
Campylobacter sp. FOBRC14
Corynebacterium efficiens YS-314
Geobacter sp. M21
Sulfuricurvum kujiense DSM 16994
Fusobacterium sp. 11_3_2
Campylobacter gracilis RM3268
Trichoplax adhaerens
Raphidiopsis brookii D9
Sulfuricurvum kujiense DSM 16994
Thiovulum sp. ES
Sulfuricurvum kujiense DSM 16994
Sulfuricurvum kujiense DSM 16994
Thiovulum sp. ES
Desulfovibrio vulgaris str. Hildenborough
Thiovulum sp. ES
Thiovulum sp. ES
Pseudomonas sp. PAMC 25886
elongation factor tu gtp binding protein
Helicobacter pylori F57
hypothetical protein
Campylobacter concisus BAA-1457
restriction endonuclease
Campylobacter coli LMG 23336
type ii modification enzyme
Campylobacter coli LMG 23336
group 2 family protein
Methylomicrobium alcaliphilum 20Z
25
fig|6666666.10688.peg.339
fig|6666666.10688.peg.941
fig|6666666.10688.peg.942
fig|6666666.10688.peg.169
6
UNSW2 & BAA-1457
fig|6666666.10684.peg.256
fig|6666666.10684.peg.676
fig|6666666.10684.peg.703
fig|6666666.10684.peg.704
fig|6666666.10684.peg.104
9
fig|6666666.10684.peg.114
4
fig|6666666.10684.peg.114
5
fig|6666666.10684.peg.114
6
ATCC 51612 & UNSW1
fig|6666666.10688.peg.914
fig|6666666.10688.peg.917
fig|6666666.10688.peg.181
4
fig|6666666.10688.peg.181
5
UNSWCD & UNSW3
fig|6666666.462.peg.748
fig|6666666.462.peg.930
toxin-antitoxin antitoxin xre family
abc transporter
hypothetical protein
hypothetical protein
Campylobacter gracilis RM3268
Helicobacter pullorum MIT 98-5489
Campylobacter gracilis RM3268
Campylobacter rectus RM3267
putative lipoprotein
rare-cutting hnh restriction endonuclease
paci
recombination protein
hypothetical protein
hypothetical protein
Campylobacter concisus BAA-1457
Campylobacter showae RM3277
pf10947 family protein
Campylobacter concisus BAA-1457
hypothetical protein
Campylobacter concisus BAA-1457
pf10947 family protein
Campylobacter concisus BAA-1457
abc atp-binding protein
phage colicin resistance and tellurite
resistance protein
anaerobic c4-dicarboxylate uptake c family
protein
oligoendopeptidase f
Campylobacter curvus 525.92
Campylobacter showae RM3277
conserved domain protein
hypothetical protein
Campylobacter concisus UNSWCD
Campylobacter concisus UNSWCD
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
Campylobacter concisus BAA-1457
Campylobacter rectus RM3267
Campylobacter gracilis RM3268
26
fig|6666666.462.peg.940
fig|6666666.462.peg.1203
fig|6666666.462.peg.1204
fig|6666666.462.peg.1205
fig|6666666.462.peg.1206
fig|6666666.462.peg.1552
fig|6666666.462.peg.1553
fig|6666666.462.peg.1661
UNSWCD & UNSW1
fig|6666666.462.peg.1163
UNSWCD & UNSWCS
fig|6666666.462.peg.992
UNSWCD & ATCC
51562
fig|6666666.462.peg.1154
UNSWCD & BAA-1457
fig|6666666.462.peg.784
ATCC 51562 & BAA1457
fig|6666666.10688.peg.132
0
fig|6666666.10688.peg.132
1
fig|6666666.10688.peg.148
0
UNSW3 & UNSW1
fig|6666666.10685.peg.567
fig|6666666.10685.peg.141
7
fig|6666666.10685.peg.160
signal peptidase i
phage-related protein
hypothetical protein
hypothetical protein
uncharacterised protein
hypothetical protein
hypothetical protein
hypothetical protein
Campylobacter concisus UNSWCD
Campylobacter concisus UNSWCD
Campylobacter concisus UNSWCD
Campylobacter concisus UNSWCD
Campylobacter concisus UNSWCD
Campylobacter concisus UNSWCD
Campylobacter concisus UNSWCD
Campylobacter concisus UNSWCD
hypothetical protein
Peptostreptococcus anaerobius 653-L
hypothetical protein
Campylobacter concisus UNSWCD
s-layer-rtx protein
Campylobacter sp. FOBRC14
hypothetical protein
Campylobacter concisus UNSWCD
methyltransferase type 12
Campylobacter concisus BAA-1457
dependent receptor
Campylobacter sp. FOBRC14
hypothetical protein
Campylobacter concisus BAA-1457
mip family channel protein
hypothetical protein
Finegoldia magna ATCC 53516
Flavobacterium sp. CF136
arsenite methyltransferase
Finegoldia magna ATCC 29328
27
6
fig|6666666.10685.peg.196
4
UNSW3 & UNSWCS
fig|6666666.10685.peg.137
2
fig|6666666.10685.peg.137
3
fig|6666666.10685.peg.137
4
fig|6666666.10685.peg.138
1
fig|6666666.10685.peg.138
2
fig|6666666.10685.peg.138
3
fig|6666666.10685.peg.138
4
fig|6666666.10685.peg.138
5
fig|6666666.10685.peg.138
6
fig|6666666.10685.peg.138
7
fig|6666666.10685.peg.138
8
fig|6666666.10685.peg.138
9
fig|6666666.10685.peg.139
0
fig|6666666.10685.peg.139
protein
Campylobacter rectus RM3267
hypothetical protein
Campylobacter sp. FOBRC14
bacteriophage dna transposition protein
Campylobacter sp. FOBRC14
bacteriophage dna transposition protein
Campylobacter sp. FOBRC14
aaa domain protein
conserved domain protein
Alteromonas macleodii str. 'English Channel
673'
Campylobacter sp. FOBRC14
mor transcription activator domain protein
Campylobacter sp. FOBRC14
hypothetical protein
Campylobacter jejuni subsp. jejuni 414
phage virion morphogenesis
Campylobacter sp. FOBRC14
prophage f
Campylobacter sp. FOBRC14
pf06074 family protein
Campylobacter sp. FOBRC14
hypothetical protein
Campylobacter sp. FOBRC14
atpase gpp-like protein
Campylobacter sp. FOBRC14
conserved domain protein
Campylobacter sp. FOBRC14
phage major capsid protein e
Campylobacter sp. FOBRC14
28
1
fig|6666666.10685.peg.139
2
fig|6666666.10685.peg.139
3
fig|6666666.10685.peg.139
4
fig|6666666.10685.peg.141
0
fig|6666666.10685.peg.193
6
UNSW3 & ATCC 51562
fig|6666666.10685.peg.140
4
UNSW3 & ATCC 51561
fig|6666666.10685.peg.53
fig|6666666.10685.peg.873
fig|6666666.10685.peg.875
fig|6666666.10685.peg.876
fig|6666666.10685.peg.111
8
fig|6666666.10685.peg.116
4
UNSWCS & ATCC
51561
fig|6666666.10687.peg.934
fig|6666666.10687.peg.132
3
UNSWCS & BAA-1457
fig|6666666.10687.peg.2
hypothetical protein
Campylobacter sp. FOBRC14
mu-like prophage i
Campylobacter sp. FOBRC14
hypothetical protein
Campylobacter sp. FOBRC14
mu-like prophage u protein gp41
Campylobacter gracilis RM3268
rare-cutting hnh restriction endonuclease
paci
Campylobacter sp. 10_1_50
bacteriophage tail fiber protein
Campylobacter sp. FOBRC14
type iii restriction-modification system
enzyme res
glycosyl family 9
o-antigen polymerase family
glycosyl family 9
hypothetical protein
Caldithrix abyssi DSM 13497
glycosyl transferase group 1 domaincontaining membrane protein
Caminibacter mediatlanticus TB-2
conserved hypothethical protein
membrane protein
Campylobacter sp. 10_1_50
Campylobacter sp. 10_1_50
hypothetical protein
Campylobacter concisus BAA-1457
Campylobacter rectus RM3267
Campylobacter sp. 10_1_50
Campylobacter sp. 10_1_50
Helicobacter pullorum MIT 98-5489
29
fig|6666666.10687.peg.284
UNSWCS & ATCC
51562
fig|6666666.10687.peg.123
2
fig|6666666.10687.peg.123
4
fig|6666666.10687.peg.124
2
fig|6666666.10687.peg.124
3
fig|6666666.10687.peg.124
5
fig|6666666.10687.peg.190
2
fig|6666666.10687.peg.191
1
fig|6666666.10687.peg.191
3
UNSW3 & BAA-1457
fig|6666666.10685.peg.229
fig|6666666.10685.peg.335
fig|6666666.10685.peg.662
fig|6666666.10685.peg.193
1
fig|6666666.10685.peg.193
3
UNSW1 & ATCC 51561
fig|6666666.18222.peg.242
fig|6666666.18222.peg.244
cobaltochelatase subunit
Campylobacter concisus BAA-1457
tigr01671 family protein
Campylobacter rectus RM3267
hypothetical protein
Sulfurimonas gotlandica GD1
recombinase rect protein
Campylobacter gracilis RM3268
phage anti-repressor protein
Campylobacter rectus RM3267
helix-turn-helix protein
Campylobacter jejuni subsp. doylei 269.97
exonuclease 5 -
Campylobacter gracilis RM3268
peptidase s24-like protein
Campylobacter sp. FOBRC14
winged helix-turn-helix dna-binding protein
Burkholderia phymatum STM815
helix-turn-helix protein
gamma-glutamyl phosphate reductase
type i restriction modification dna specificity
domain protein
hypothetical protein
Campylobacter jejuni subsp. jejuni 1854
Campylobacter concisus BAA-1457
Desulfotomaculum carboxydivorans CO-1-SRB
hypothetical protein
Campylobacter concisus BAA-1457
cytochrome c-type protein
two component transcriptional winged helix
Campylobacter jejuni subsp. jejuni LMG 23216
Campylobacter curvus 525.92
Campylobacter sp. 10_1_50
30
fig|6666666.18222.peg.422
fig|6666666.18222.peg.180
4
fig|6666666.18222.peg.180
6
family
type i site-specific family
acyl dehydratase
Campylobacter sp. 10_1_50
Francisella novicida GA99-3548
family protein
Thioalkalimicrobium aerophilum AL3
Table S5 Percentage of genes specific to each Campylobacter concisus strain.
Disease type
Chronic
Acute
Healthy
Strain
UNSW2
UNSW3
UNSWCD
UNSW1
UNSWCS
ATCC 51562
BAA-1457
ATCC 51561
Strain-specific
1.9
1.4
1.2
1.4
2.8
3.4
2.8
0.99
genes (%)
Table S6 Pathway-specific differences within sequenced C. concisus strains and across C. concisus and C. jejuni species.
00680|Methane metabolism
c c c c c c c c c
j j j j j j j j j
j i n m d e r s u
UN
SW
CD
*
U
NS
W
2
*
U
NS
W
3
*
U
NS
W
1
*
UN AT
SW CC
CS 5156
2
*
*
BA
A145
7
*
AT
CC
5156
1
*
K03781
Y Y Y Y Y Y Y Y Y
K03313
Y Y Y Y Y Y Y Y Y
Y
*
Y
*
Y
Y
Y
Y
katE, CAT, catB, srpA; catalase
[EC:1.11.1.6]
nhaA; Na+:H+ antiporter, NhaA
family
31
K03315
* * * * * * * * *
Y
Y
Y
Y
Y
*
Y
*
BA
A145
7
*
AT
CC
5156
1
Y
nhaC; Na+:H+ antiporter, NhaC
family
02030|Bacterial chemotaxis
K03776
c c c c c c c c c
j j j j j j j j j
j i n m d e r s u
UN
SW
CD
* * * * * * * * *
*
U
NS
W
2
*
U
NS
W
3
*
U
NS
W
1
*
UN AT
SW CC
CS 5156
2
*
*
aer; aerotaxis receptor
00330|Arginine and proline metabolism
c c c c c c c c c
j j j j j j j j j
j i n m d e r s u
UN
SW
CD
*
U
NS
W
2
*
U
NS
W
3
*
U
NS
W
1
*
UN AT
SW CC
CS 5156
2
*
*
BA
A145
7
*
AT
CC
5156
1
Y
K00930
Y Y Y Y Y Y Y Y Y
K00145
Y Y Y Y Y Y Y Y Y
*
*
*
*
*
*
*
Y
K00818
Y * * * Y Y Y * Y
*
*
*
*
*
*
*
Y
argB; acetylglutamate kinase
[EC:2.7.2.8]
argC; N-acetyl-gamma-glutamylphosphate reductase [EC:1.2.1.38]
argD; acetylornithine
aminotransferase [EC:2.6.1.11]
00630|Glyoxylate and dicarboxylate metabolism
c c c c
j j j j
c c c c c
j j j j j
UN
SW
U
U
U
UN AT
NS NS NS SW CC
BA
A-
AT
CC
32
j i
n m d e r s u
CD
K03779
* * * * * * * * *
Y
W
2
*
W
3
Y
W
1
Y
CS
*
5156
2
*
145
7
Y
5156
1
Y
K03780
* * * * * * * * *
Y
*
Y
Y
*
*
Y
Y
K00865
* * * * * * * * *
Y
Y
Y
Y
Y
Y
Y
Y
ttdA; L(+)-tartrate dehydratase alpha
subunit [EC:4.2.1.32]
ttdB; L(+)-tartrate dehydratase beta
subunit [EC:4.2.1.32]
glxK; glycerate kinase [EC:2.7.1.31]
03070|Bacterial secretion system
c c c c c c c c c
j j j j j j j j j
j i n m d e r s u
UN
SW
CD
*
U
NS
W
2
*
U
NS
W
3
*
U
NS
W
1
*
UN AT
SW CC
CS 5156
2
*
*
BA
A145
7
*
AT
CC
5156
1
*
K03197
Y * * * * * * Y *
K03204
Y Y Y * * * * Y *
*
Y
*
*
*
Y
*
Y
K03201
Y Y Y * * * * Y *
*
*
*
*
*
*
*
*
K03203
Y Y Y * * * * Y *
*
Y
*
*
*
Y
*
Y
K03195
Y Y Y * * * * Y *
*
Y
*
*
*
Y
*
Y
K03199
Y Y Y * * * * Y *
*
Y
*
*
*
Y
*
Y
K03196
Y Y Y * * * * Y *
*
Y
*
*
*
Y
*
Y
K03205
Y Y Y * * * * Y *
*
Y
*
*
*
Y
*
Y
K11028
* * * * * * * * *
*
*
*
*
*
*
*
*
virB2, lvhB2; type IV secretion
system protein VirB2
virB9, lvhB9; type IV secretion
system protein VirB9
virB6, lvhB6; type IV secretion
system protein VirB6
virB8, lvhB8; type IV secretion
system protein VirB8
virB10, lvhB10; type IV secretion
system protein VirB10
virB4, lvhB4; type IV secretion
system protein VirB4
virB11, lvhB11; type IV secretion
system protein VirB11
virD4, lvhD4; type IV secretion
system protein VirD4
vacA; vacuolating cytotoxin
33
K11903
* * * * * * * * *
*
*
*
Y
*
*
Y
Y
K11906
* * * * * * * * *
*
*
*
Y
*
*
Y
Y
K11891
* * * * * * * * *
*
*
*
Y
*
*
Y
Y
K11892
* * * * * * * * *
*
*
*
Y
*
*
Y
Y
K12340
* * * * * * * * *
*
*
*
*
*
*
*
*
K03194
* * * * * * * * *
*
*
*
*
*
*
*
Y
K03200
* * * * * * * * *
*
*
*
*
*
*
*
*
K11903, hcp; type VI secretion
system secreted protein Hcp
vasD, lip; type VI secretion system
protein VasD
impL, vasK, icmF; type VI secretion
system protein ImpL
impK, ompA, vasF, dotU; type VI
secretion system protein ImpK
tolC; outer membrane channel protein
TolC
virB1; type IV secretion system
protein VirB1
virB5, lvhB5; type IV secretion
system protein VirB5
02020|Two-component system
c c c c c c c c c
j j j j j j j j j
j i n m d e r s u
UN
SW
CD
Y
U
NS
W
2
Y
U
NS
W
3
Y
U
NS
W
1
Y
UN AT
SW CC
CS 5156
2
Y
Y
BA
A145
7
Y
AT
CC
5156
1
Y
K11688
* * * * * * * * *
K11689
* * * * * * * * *
Y
Y
Y
Y
Y
Y
Y
Y
K11690
* * * * * * * * *
Y
Y
Y
Y
Y
Y
Y
Y
K08357
* * * * * * * * *
*
*
*
Y
*
Y
Y
Y
K08358
* * * * * * * * *
*
*
*
Y
*
Y
Y
Y
dctP; C4-dicarboxylate-binding
protein DctP
dctQ; C4-dicarboxylate transporter,
DctQ subunit
dctM; C4-dicarboxylate transporter,
DctM subunit
ttrA; tetrathionate reductase subunit
A
ttrB; tetrathionate reductase subunit B
34
00920|Sulfur metabolism
c c c c c c c c c
j j j j j j j j j
j i n m d e r s u
UN
SW
CD
Y
U
NS
W
2
Y
U
NS
W
3
Y
U
NS
W
1
Y
UN AT
SW CC
CS 5156
2
Y
Y
BA
A145
7
Y
AT
CC
5156
1
Y
K00641
Y * * * * * Y * *
K00380
* * * * * * * * *
Y
Y
Y
Y
Y
Y
Y
Y
K14155
* * * * * * * * *
Y
Y
Y
Y
Y
Y
Y
Y
metX; homoserine Oacetyltransferase [EC:2.3.1.31]
cysJ; sulfite reductase (NADPH)
flavoprotein alpha-component
[EC:1.8.1.2]
patB, malY; cystathione beta-lyase
[EC:4.4.1.8]
04146|Peroxisome
c c c c c c c c c
j j j j j j j j j
j i n m d e r s u
UN
SW
CD
Y
U
NS
W
2
Y
U
NS
W
3
Y
U
NS
W
1
Y
UN AT
SW CC
CS 5156
2
Y
Y
BA
A145
7
Y
AT
CC
5156
1
Y
K04565
* * * * * * * * *
K04564
Y Y Y Y Y Y Y Y Y
Y
Y
Y
Y
Y
Y
Y
Y
sodC, SOD1; Cu/Zn superoxide
dismutase [EC:1.15.1.1]
sodA, sodB, SOD2; superoxide
dismutase, Fe-Mn family
[EC:1.15.1.1]
00550|Peptidoglycan biosynthesis
c c c c c c c c c
j j j j j j j j j
j i n m d e r s u
UN
SW
CD
U
NS
W
2
U
NS
W
3
U
UN
NS SW
W CS
1
AT
CC
5156
2
BA
A145
7
AT
CC
5156
1
35
K05367
* * * * * * * * *
Y
Y
Y
Y
Y
Y
Y
Y
pbpC; penicillin-binding protein 1C
[EC:2.4.1.-]
00250|Alanine, aspartate and glutamate metabolism
c c c c c c c c c
j j j j j j j j j
j i n m d e r s u
UN
SW
CD
K00266
YYY Y Y Y Y Y Y
*
U
U
U UN AT BA
NS NS NS SW CC
AW W W CS 5156 145
2
3
1
2
7
*
*
*
*
*
*
K13821
YYY Y Y Y Y Y Y
*
*
*
*
*
*
*
K00262
* * * * * * * * *
Y
Y
Y
Y
Y
Y
Y
AT
CC
5156
1
*
gltD; glutamate synthase
(NADPH/NADH) small chain
[EC:1.4.1.13 1.4.1.14]
*
putA; proline dehydrogenase / delta
1-pyrroline-5-carboxylate
dehydrogenase [EC:1.5.99.8 1.5.1.12]
Y
gdhA; glutamate dehydrogenase
(NADP+) [EC:1.4.1.4]
00910|Nitrogen metabolism
c c c c c c c c c
j j j j j j j j j
j i n m d e r s u
UN
SW
CD
K03385
K15876
K01501
K05601
Y
Y
Y
*
Y
Y
*
*
K10535
* * * * * * * * *
Y
Y
*
*
Y
Y
*
*
Y
Y
*
*
Y
Y
*
*
Y
Y
Y
*
Y
Y
Y
*
Y
Y
*
*
*
*
Y
Y
U
NS
W
2
*
*
Y
Y
U
NS
W
3
*
*
Y
Y
U
NS
W
1
*
*
Y
Y
UN AT
SW CC
CS 5156
2
*
*
*
*
Y
Y
Y
*
BA
A145
7
*
*
Y
Y
AT
CC
5156
1
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
nrfA; cytochrome c-552 [EC:1.7.2.2]
nrfH; cytochrome c-type protein
nitrilase [EC:3.5.5.1]
hcp; hydroxylamine reductase
[EC:1.7.99.1]
hao; hydroxylamine oxidase
[EC:1.7.3.4]
36
K04561
* * * * * * * * *
Y
Y
Y
Y
Y
Y
Y
Y
K00376
* * * * * * * * *
Y
Y
Y
Y
Y
Y
Y
Y
K04014
K04015
K02569
* * * * * * * * *
* * * * * * * * *
* * * * * * * * *
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
norB; nitric oxide reductase subunit B
[EC:1.7.2.5]
nosZ; nitrous-oxide reductase
[EC:1.7.2.4]
nrfC; protein NrfC
nrfD; protein NrfD
napC; cytochrome c-type protein
NapC
00860|Porphyrin and chlorophyll metabolism
K02217
c c c c c c c c c
j j j j j j j j j
j i n m d e r s u
UN
SW
CD
Y YY Y Y Y Y Y Y
*
U
NS
W
2
*
U
NS
W
3
*
U
NS
W
1
*
UN AT
SW CC
CS 5156
2
*
*
BA
A145
7
*
AT
CC
5156
1
*
ftnA, ftn; ferritin [EC:1.16.3.1]
02010|ABC transporters
c c c c c c c c c
j j j j j j j j j
j i n m d e r s u
UN
SW
CD
*
U
NS
W
2
*
U
NS
W
3
*
U
NS
W
1
*
UN AT
SW CC
CS 5156
2
*
*
BA
A145
7
*
AT
CC
5156
1
*
K02012
Y YY Y Y Y Y Y Y
K02011
Y YY Y Y Y Y Y Y
*
*
*
*
*
*
*
*
K02010
Y YY Y Y Y Y Y Y
*
*
*
*
*
*
*
*
K02040
Y YY Y Y Y Y Y Y
*
*
*
*
*
Y
*
Y
afuA, fbpA; iron(III) transport system
substrate-binding protein
afuB, fbpB; iron(III) transport system
permease protein
afuC, fbpC; iron(III) transport system
ATP-binding protein [EC:3.6.3.30]
pstS; phosphate transport system
substrate-binding protein
37
K02037
Y YY Y Y Y Y Y Y
*
*
*
*
*
Y
*
Y
K02038
Y YY Y Y Y Y Y Y
*
*
*
*
*
Y
*
Y
K02036
Y Y* Y Y Y Y Y Y
*
*
*
*
*
Y
*
Y
K01999
Y YY Y Y Y Y Y Y
*
*
*
*
*
*
*
*
K01997
Y YY Y Y Y Y Y Y
*
*
*
*
*
*
*
*
K01998
Y YY Y Y Y Y Y Y
*
*
*
*
*
*
*
*
K01995
Y YY Y Y Y Y Y Y
*
*
*
*
*
*
*
*
K01996
Y YY Y Y Y Y Y Y
*
*
*
*
*
*
*
*
K10107
Y YY Y Y Y Y Y Y
*
*
*
*
*
*
*
*
K09688
Y YY Y Y Y Y Y Y
*
*
*
*
*
*
*
*
K09689
Y YY Y Y Y Y Y Y
*
*
*
*
*
*
*
*
K09687
* * * * * * * * *
Y
Y
Y
Y
Y
Y
Y
Y
pstC; phosphate transport system
permease protein
pstA; phosphate transport system
permease protein
pstB; phosphate transport system
ATP-binding protein [EC:3.6.3.27]
livK; branched-chain amino acid
transport system substrate-binding
protein
livH; branched-chain amino acid
transport system permease protein
livM; branched-chain amino acid
transport system permease protein
livG; branched-chain amino acid
transport system ATP-binding protein
livF; branched-chain amino acid
transport system ATP-binding protein
ABC-2.CPSE.P1; capsular
polysaccharide transport system
permease protein
ABC-2.CPSE.P; capsular
polysaccharide transport system
permease protein
ABC-2.CPSE.A; capsular
polysaccharide transport system
ATP-binding protein
ABC-2.AB.A; antibiotic transport
system ATP-binding protein
38
Figure S1 Phylogenetic analyses of the different pathways within the eight C. concisus strains. a) Bile efflux; b) flagellar
biosynthesis; c) chemotaxis; d) lipopolysaccharide biosynthesis; e) Sulfur relay system; and f) N-glycosylation.
(A)
(B)
(D)
(E)
(C)
(F)
39