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Table 4 Bacterial species identified by sequencing of cloned 16S rDNA

From: Analysis of bacterial DNA in synovial tissue of Tunisian patients with reactive and undifferentiated arthritis by broad-range PCR, cloning and sequencing

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 bacteria d (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*
  1. 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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Arthritis Research & Therapy

ISSN: 1478-6362

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