Table 4 |
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|
Bacterial species identified by sequencing of cloned 16S rDNA |
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|
Bacterium-derived DNA identified in ST samples |
Number of patients in whom bacterial DNAs were detected |
Accession numbera |
Length of the sequenceb |
% Similarityc |
|
|
||||
|
Bacteria identified in ReA and UA patients (n = 68) |
||||
|
Bacteria previously detected in arthritis |
||||
|
Acinetobacter baumannii |
(1 ReA) |
AY738400 |
1,384 |
99.86 |
|
Acinetobacter schindleri |
(1 UA) |
AJ278311 |
1,367 |
98.83 |
|
Actinomyces sp. |
(1 UA) |
AY008315 |
1,420 |
98.73 |
|
Aeromonas sp. |
(1 UA) |
U88656 |
1,396 |
99.36 |
|
Aeromonas sp. |
(2 UA) |
AF099027 |
1,336 |
98.58 |
|
Afipia genosp 7 |
(1 UA) |
U87773 |
1,336 |
97.38 |
|
Afipia genosp 9 |
(1 ReA) |
U87779 |
1,335 |
99.62 |
|
Afipia genosp 9 |
(1 ReA) |
U87775 |
1,256 |
97.00 |
|
Afipia genosp 9 |
(1 ReA) |
U87777 |
1,337 |
99.55 |
|
Corynebacterium coyleae |
(1 UA) |
X96497 |
1,360 |
99.04 |
|
Escherichia coli |
(1 ReA) |
AP009048 |
1,389 |
99.71 |
|
Escherichia sp. |
(2 ReA) |
DQ337503 |
1,390 |
99.71 |
|
Klebsiella sp. |
(1 UA) |
U32868 |
1,387 |
99.57 |
|
Neisseria flava |
(1 UA) |
AJ239301 |
1,338 |
98.43 |
|
Paracoccus sp. |
(1 UA) |
AY745834 |
1,308 |
99.92 |
|
Propionibacterium acnes |
(1 ReA+ 2 UA) |
AB108477 |
1,377 |
100.00 |
|
Pseudomonas sp. |
(1 UA) |
DQ079062 |
1,388 |
98.63 |
|
Ralstonia sp. |
(1 ReA) |
DQ227340 |
1,382 |
100.00 |
|
Rhodococcus sp. |
(2 UA) |
AF420412 |
1,365 |
99.85 |
|
Shigella flexneri |
(2 ReA + 1 UA) |
X96963 |
1,389 |
99.71 |
|
Shigella sonnei |
(1 ReA) |
X96964 |
1,389 |
99.86 |
|
Shigella sonnei |
(1 UA) |
CP000038 |
1,390 |
97.70 |
|
Sphingomonas sp. |
(2 UA) |
AJ864842 |
1,329 |
99.77 |
|
Staphylococcus aureus |
(1 UA) |
L37597 |
1,400 |
99.93 |
|
Staphylococcus haemolyticus |
(1 ReA) |
AP006716 |
1,400 |
99.93 |
|
Staphylococcus sp. |
(1 ReA) |
AJ704792 |
1,400 |
99.72 |
|
Staphylococcus sp. |
(1 UA) |
AB177642 |
1,399 |
99.71 |
|
Stenotrophomonas sp. |
(1 UA) |
AF409004 |
1,382 |
99.13 |
|
Streptococcus infantis |
(1 UA) |
AY485603 |
1,385 |
99.64 |
|
Streptococcus mitis |
(2 UA) |
AY005045 |
1,385 |
99.57 |
|
Streptococcus sanguinis |
(1 UA) |
AF003928 |
1,397 |
99.79 |
|
Bacteria not previously detected in arthritis |
||||
|
Bosea vestrisii |
(1 UA) |
AF288302 |
1,336 |
99.70 |
|
Brevundimonas diminuta |
(1 ReA) |
X87274 |
1,308 |
99.62 |
|
Corynebacterium durum |
(2 UA) |
AF537593 |
1,364 |
99.05 |
|
Corynebacterium tuberculostearicum |
(2 UA) |
AJ438044 |
1,368 |
99.71 |
|
Enterococcus cecorum |
(1 UA) |
AF061009 |
1,398 |
99.43 |
|
Enterobacter hormaechei |
(1 UA) |
AY995561 |
1,395 |
99.64 |
|
Kingella oralis |
(1 UA) |
L06164 |
1,389 |
98.78 |
|
Leptotrichia sp. |
(1 UA) |
AY008309 |
1,359 |
99.85 |
|
Microbacterium oxydans |
(1 UA) |
AJ717356 |
1,374 |
98.69 |
|
Oxalobacter sp. |
(1 UA) |
AJ496038 |
1,387 |
98.05 |
|
Paracoccus yeei |
(1 UA) |
AY014169 |
1,309 |
99.77 |
|
Bacteria not previously detected in humans |
||||
|
Aquabacterium commune |
(2 ReA) |
AF035054 |
1,367 |
99.85 |
|
Blastococcus sp. |
(1 UA) |
AJ316573 |
1,357 |
97.27 |
|
Bradyrhizobium japonicum |
(2 UA) |
BA000040 |
1,333 |
99.17 |
|
Halomonas sp. |
(1 UA) |
AJ302088 |
1,389 |
98.85 |
|
Leucobacter luti |
(1 ReA) |
AM072819 |
1,369 |
98.39 |
|
Novosphingobium sp. |
(1 UA) |
AB177883 |
1,335 |
97.00 |
|
Pedomicrobium australicum |
(1 UA) |
X97693 |
1,324 |
98.64 |
|
Pirellula sp. |
(1 UA) |
X81945 |
1,322 |
96.14* |
|
Sphingobacterium asaccharolytica |
(1 ReA) |
Y09639 |
1,324 |
98.11 |
|
Variovorax sp. |
(1 ReA) |
AB196432 |
1,383 |
99.28 |
|
Uncultured bacteria |
||||
|
α Proteobacterium |
(1 ReA) |
AY162046 |
1,308 |
99.62 |
|
α Proteobacterium |
(1 ReA+ 21 UA) |
AY162053 |
1,332 |
99.85 |
|
β Proteobacterium |
(1 UA) |
AF236007 |
1,371 |
99.71 |
|
Caulobacter endosymbiont of Tetranychus urticae |
(1 UA) |
AY753176 |
1,334 |
99.63 |
|
|
||||
|
γ Proteobacterium |
(1 ReA) |
AY162032 |
1,395 |
97.42 |
|
Manganese-oxidizing bacterium |
(2 UA) |
U53824 |
1,320 |
99.85 |
|
Uncultured α proteobacterium |
(1 UA) |
AF445680 |
1,329 |
97.06 |
|
Uncultured β proteobacterium |
(1 ReA) |
AF445700 |
1,372 |
99.78 |
|
Uncultured candidate division OP10 bacterium |
(3 ReA + 4 UA) |
AF418946 |
1,297 |
90.98* |
|
Uncultured γ proteobacterium |
(1 UA) |
AJ318146 |
1,397 |
97.35 |
|
Uncultured γ proteobacterium |
(1 UA) |
AF324537 |
1,387 |
99.71 |
|
Unclassified Enterobacteriaceae |
(1 UA) |
AY375058 |
1,391 |
97.56 |
|
Uncultured eubacterium |
(1 ReA) |
AJ292601 |
1,334 |
96.93 |
|
Uncultured soil bacterium |
(1 UA) |
AF423262 |
1,295 |
96.91 |
|
Unclassified proteobacteria |
(1 ReA) |
AY820722 |
1,383 |
96.46* |
|
Unclassified Rhodocyclaceae |
(2 UA) |
AY328759 |
1,388 |
99.42 |
|
Bacteria identified in control group (RA and OA patients; n = 12) |
||||
|
Bacteria previously detected in arthritis |
||||
|
Actinomyces naeslundii |
(1 RA) |
AJ234050 |
1,392 |
97.84 |
|
Brucellaceae bacterium |
(1 OA) |
AY353698 |
1,333 |
99.17 |
|
Corynebacterium aurimucosum |
(1 RA) |
AY536427 |
1,369 |
99.34 |
|
Streptococcus thermophilis |
(1 RA) |
AY188354 |
1,397 |
99.36 |
|
Bacteria not previously detected in arthritis |
||||
|
Alcaligenes sp. |
(1 OA) |
AF430122 |
1,386 |
98.63 |
|
Caulobacter sp. |
(2 RA) |
AJ227775 |
1,323 |
99.70 |
|
Bacteria not previously detected in humans |
||||
|
Caulobacter leidyia |
(1 OA) |
AJ227812 |
1,324 |
100.00 |
|
Curvibacter gracilis |
(1 OA) |
AB109889 |
1,379 |
99.71 |
|
Rhodococcus fascians |
(1 RA) |
Y11196 |
1,365 |
99.71 |
|
Uncultured bacteria |
||||
|
Antarctic bacterium |
(1 RA) |
AJ440974 |
1,321 |
98.86 |
|
Uncultured α proteobacterium |
(1 RA) |
AJ604541 |
1,324 |
98.60 |
|
Uncultured δ proteobacterium |
(1 RA) |
AY921777 |
1,402 |
97.22 |
|
Common bacteriad (n = 20) |
||||
|
Bacteria previously detected in arthritis |
||||
|
Achromobacter xylosoxidans |
(1 UA + 1 OA) |
AF439314 |
1,378 |
99.71 |
|
Acinetobacter sp. |
(2 ReA + 1 RA) |
Z93442 |
1,365 |
99.35 |
|
Alcaligenes faecalis |
(2 ReA+ 1 UA+ 1 RA+ 1 OA) |
AY548384 |
1,385 |
99.93 |
|
Escherichia coli |
(3 ReA+ 7 UA+ 1 RA+ 2 OA) |
V00348 |
1,393 |
100.00 |
|
Escherichia coli |
(3 ReA+ 9 UA+ 3 RA+ 2 OA) |
U00096 |
1,390 |
100.00 |
|
Flavobacterium mizutaii |
(2 ReA + 7 UA + 1 RA) |
AJ438175 |
1,384 |
94.44* |
|
Pseudomonas sp. |
(2 ReA + 1 UA + 1 RA) |
AJ237965 |
1,376 |
99.56 |
|
Stenotrophomonas maltophilia |
(3 ReA + 4 UA + 1 OA) |
AJ293470 |
1,395 |
99.93 |
|
Shigella sp. |
(2 ReA+ 4 UA+ 2 RA+ 1 OA) |
DQ337523 |
1,392 |
99.93 |
|
Bacteria not previously detected in arthritis |
||||
|
Alcaligenes sp. |
(1 UA + 1 OA) |
AY672759 |
1,345 |
99.11 |
|
Bradyrhizobium elkanii |
(1 ReA+ 2 UA+ 1 RA+ 1 OA) |
AY904749 |
1,338 |
99.93 |
|
Pseudomonas poae |
(1 ReA + 1 OA) |
AJ492829 |
1,386 |
99.93 |
|
Ralstonia sp. |
(5 ReA + 4 UA + 3 RA) |
AB045276 |
1,388 |
100.00 |
|
Serratia proteamaculans |
(1 ReA + 1 RA) |
AJ233435 |
1,387 |
97.76 |
|
Bacteria not previously detected in humans |
||||
|
Uncultured bacteria |
||||
|
Bacteroidetes bacterium |
(2 UA + 1 RA) |
AY395022 |
1,196 |
97.49 |
|
γ proteobacterium |
(2 ReA + 3 UA + 1 OA) |
AY162042 |
1,399 |
99.88 |
|
γ proteobacterium |
(4 ReA + 6 UA + 2 RA) |
AY162068 |
1,397 |
99.93 |
|
Swine manure bacterium |
(6 ReA+ 5 UA+ 2 RA+ 1 OA) |
AY167969 |
1,388 |
100.00 |
|
Uncultured Flavobacterium sp. |
(1 ReA+ 4 UA+ 2 RA+ 1 OA) |
DQ168834 |
1,193 |
97.15 |
|
Uncultured Sphingobacterium sp. |
(2 ReA+ 8 UA+ 1 RA+ 1 OA) |
AB076874 |
1,390 |
94.31* |
|
|
||||
|
Number in brackets after species names indicate the number of patient set from whom bacteria were detected. aAccession number of the bacterial species in the database. bLength of alignment on which the 16S rDNA inserted sequence and the corresponding sequence in the database are similar. cIn the '% similarity' column, asterisks indicate highligh instances where the % similarity is below 97%. dThe 'Common bacteria' row shows the bacteria identified in ReA, UA, RA and OA patients. OA, osteoarthritis; RA, rheumatoid arthritis; ReA, reactive arthritis; ST, synovial tissue; UA, undifferentiated arthritis. |
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|
Siala et al. Arthritis Research & Therapy 2008 10:R40 doi:10.1186/ar2398 |
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