Table 3 |
||||
|
Bacterial species identified by sequencing of cloned 16S rDNA |
||||
|
Bacterium-derived DNA identified in SF 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 = 69) |
||||
|
Bacteria previously detected in arthritis |
||||
|
Aeromonas species |
(1 UA) |
[EMBL:AF099027] |
1400 |
97.77 |
|
Burkholderia species |
(1 ReA + 1 UA) |
[EMBL:AY769903] |
1391 |
99.13 |
|
Burkholderia species |
(1 UA) |
[EMBL:AY134849] |
1388 |
99.71 |
|
Burkholderia cepacia |
(1 UA) |
[EMBL:AY946010] |
1390 |
99.89 |
|
Escherichia coli |
(1 ReA) |
[EMBL:CP000243] |
1400 |
99.14 |
|
Escherichia coli |
(2 ReA) |
[EMBL:U00096] |
1400 |
100.00 |
|
Escherichia coli |
(1 ReA + 2 UA) |
[EMBL:V00348] |
1400 |
99.50 |
|
Methylomicrobium species |
(1 UA) |
[EMBL:AF194538] |
1380 |
98.83 |
|
Propionibacterium acnes |
(5 ReA + 1 UA) |
[EMBL:AB108477] |
1386 |
99.05 |
|
Pseudomonas species |
(1 ReA) |
[EMBL:DQ213044] |
1386 |
99.06 |
|
Pseudomonas species |
(1 ReA) |
[EMBL:AY014811] |
1395 |
99.06 |
|
Pseudomonas species |
(1 UA) |
[EMBL:AM409368] |
1396 |
99.21 |
|
Paracoccus species |
(1 UA) |
[EMBL:AY745834] |
1320 |
98.92 |
|
Rhodococcus species |
(2 UA) |
[EMBL:AF420412] |
1374 |
97.29 |
|
Shigella sonnei |
(5 ReA + 5 UA) |
[EMBL:CP000038] |
1400 |
99.71 |
|
Shigella sonnei |
(1 UA) |
[EMBL:X96964] |
1389 |
99.78 |
|
Sphingomonas species |
(1 UA) |
[EMBL:AB110635] |
1341 |
99.85 |
|
Sphingomonas species |
(1 UA) |
[EMBL:AF385529] |
1341 |
100.00 |
|
Streptococcus species |
(1 UA) |
[EMBL:AF316593] |
1400 |
98.55 |
|
Streptococcus species |
(1 UA) |
[EMBL:AF385523] |
1400 |
99.28 |
|
Streptococcus mitis |
(1 ReA) |
[EMBL:AJ295848] |
1400 |
97.92 |
|
Streptococcus mitis |
(1 ReA) |
[EMBL:AJ617805] |
1322 |
98.71 |
|
Streptococcus mitis |
(1 ReA) |
[EMBL:AF003929] |
1396 |
99.36 |
|
Streptococcus mitis |
(1 ReA + 1 UA) |
[EMBL:AY518677] |
1404 |
99.86 |
|
Streptococcus pneumoniae |
(2 UA) |
[EMBL:AM157442] |
1400 |
98.64 |
|
Streptococcus thermophilus |
(2 UA) |
[EMBL:AY188354] |
1397 |
99.57 |
|
Bacteria not previously detected in arthritis but detected in human infection |
||||
|
Agrobacterium species |
(2 ReA + 1 UA) |
[EMBL:AY775177] |
1344 |
99.40 |
|
Bradyrhizobium elkanii |
(2 ReA + 4 UA) |
[EMBL:AY904749] |
1347 |
99.40 |
|
Capnocytophaga sputigena |
(1 UA) |
[EMBL:AF133536] |
1378 |
98.96 |
|
Corynebacterium durum |
(1 UA) |
[EMBL:AF537593] |
1391 |
99.58 |
|
Delftia acidovorans |
(1 ReA) |
[EMBL:AB020186] |
1309 |
97.63 |
|
Enterococcus faecium |
(1 UA) |
[EMBL:EF533988] |
1396 |
99.42 |
|
Enterobacter hormaechei |
(1 UA) |
[EMBL:AY995561] |
1400 |
99.70 |
|
Kocuria species |
(1 UA) |
[EMBL:AY864652] |
1387 |
99.85 |
|
Mycobacterium aubagnense |
(1 UA) |
[EMBL:AY859683] |
1372 |
99.27 |
|
Pantoea ananatis |
(3 ReA + 4 UA) |
[EMBL:DQ133546] |
1400 |
98.80 |
|
Photorhabdus luminescens |
(1 UA) |
[EMBL:AY444555] |
1333 |
99.85 |
|
Pseudomonas poae |
(2 UA) |
[EMBL:AJ492829] |
1386 |
98.99 |
|
Rhizobium radiobacter |
(1 UA) |
[EMBL:AJ389902] |
1300 |
99.67 |
|
Staphylococcus pasteuri |
(1 UA) |
[EMBL:AJ717376] |
1411 |
99.86 |
|
Bacteria not previously detected in humans |
||||
|
Aquabacterium commune |
(1 UA) |
[EMBL:AF035054] |
1416 |
99.70 |
|
Aminobacter aminovorans |
(1 UA) |
[EMBL:AJ011759] |
1344 |
98.72 |
|
Bacillus niacini |
(1 UA) |
[EMBL:AB021194] |
1400 |
99.14 |
|
Bradyrhizobium japonicum |
(1 UA) |
[EMBL:AB072418] |
1200 |
97.81 |
|
Diaphorobacter species |
(1 ReA) |
[EMBL:DQ294626] |
1387 |
99.78 |
|
Pelomonas saccharophila |
(1 ReA) |
[EMBL:AB021407] |
1381 |
99.42 |
|
Paenibacillus species |
(1 ReA) |
[EMBL:AM162345] |
1385 |
99.35 |
|
Sphingomonas faeni |
(1 ReA) |
[EMBL:AJ429239] |
1340 |
97.82 |
|
Uncultured bacteria |
||||
|
Bacteroidetes bacterium |
(2 UA + 1 ReA) |
[EMBL:AY395022] |
1394 |
96.11* |
|
Bacteroidetes bacterium |
(1 ReA) |
[EMBL:DQ195837] |
1300 |
98.39 |
|
β Proteobacterium |
(2 ReA + 2 UA) |
[EMBL:AY162033] |
1396 |
99.57 |
|
γ Proteobacterium |
(4 ReA + 6 UA) |
[EMBL:AY162042] |
1399 |
99.00 |
|
γ Proteobacterium |
(1 ReA + 4 UA) |
[EMBL:AY162068] |
1400 |
99.50 |
|
swine manure bacterium |
(1 ReA) |
[EMBL:AY167969 ] |
1395 |
99.21 |
|
Uncultured α proteobacterium |
(1 ReA) |
[EMBL:AF445680] |
1342 |
97.00 |
|
Uncultured Bacteroidetes bacterium |
(2 ReA) |
[EMBL:AY921801] |
1384 |
97.04 |
|
Uncultured bacterium |
(2 UA) |
[EMBL:AY958813] |
1388 |
99.88 |
|
Uncultured β proteobacterium |
(1 ReA + 1 UA) |
[EMBL:AF445700] |
1372 |
99.78 |
|
Uncultured β proteobacterium |
(1 UA) |
[EMBL:DQ316806] |
1391 |
97.46 |
|
Uncultured candidate division OP10 bacterium |
(2 UA) |
[EMBL:AF418946] |
1362 |
90.29* |
|
Uncultured Firmicutes bacterium |
(1 UA) |
[EMBL:EF071401] |
1400 |
99.57 |
|
Uncultured γ Proteobacterium |
(1 UA) |
[EMBL:AF324537] |
1396 |
99.96 |
|
Uncultured γ Proteobacterium |
(1 ReA) |
[EMBL:AJ318146] |
1400 |
97.63 |
|
Uncultured γ Proteobacterium |
(1 ReA) |
[EMBL:AY770720] |
1393 |
96.91* |
|
Uncultured Methylococcaceae bacterium |
(1 ReA) |
[EMBL:EF019533] |
1398 |
97.55 |
|
Uncultured organism |
(2 UA) |
[EMBL:DQ395839] |
1392 |
99.85 |
|
Uncultured soil bacterium |
(1 ReA) |
[EMBL:DQ297948] |
1340 |
99.85 |
|
Uncultured Streptococcus species |
(1 UA) |
[EMBL:AY256519] |
1400 |
99.21 |
|
Uncultured Veillonella species |
(2 UA) |
[EMBL:AM157449] |
1400 |
99.37 |
|
Bacteria identified in control group (RA and OA patients; n = 10) |
||||
|
Bacteria previously detected in arthritis (in joint) |
||||
|
Acinetobacter junii |
(1 OA) |
[EMBL:AB101444] |
1387 |
99.28 |
|
Bacillus cereus |
(1 OA) |
[EMBL:AB247137] |
1399 |
98.36 |
|
Rothia mucilaginosa |
(1 OA) |
[EMBL:DQ409140] |
1375 |
98.69 |
|
Staphylococcus cohnii |
(1 RA) |
[EMBL:AJ717378] |
1399 |
99.57 |
|
Bacteria not previously detected in arthritis but detected in human infection |
||||
|
Escherichia coli O157 |
(1 OA) |
[EMBL:AE005174] |
1394 |
97.56 |
|
Bacteria not previously detected in humans |
||||
|
Sphingobacterium thalpophilum |
(1 RA) |
[EMBL:AJ43817] |
1388 |
94.02* |
|
Uncultured bacteria |
||||
|
Uncultured bacterium |
(1 OA) |
[EMBL:DQ800655] |
1394 |
97.99 |
|
Uncultured bacterium |
(1 RA) |
[EMBL:AY958855] |
1388 |
99.78 |
|
Uncultured bacterium |
(1 RA) |
[EMBL:AY958896] |
1380 |
99.57 |
|
Uncultured bacterium |
(1 RA + 1 OA) |
[EMBL:DQ818800] |
1398 |
99.57 |
|
Common bacteriad (n = 20) |
||||
|
Bacteria previously detected in arthritis |
||||
|
Achromobacter xylosoxidans |
(1 ReA + 2 UA+ 1 OA) |
[EMBL:AF439314] |
1389 |
99.50 |
|
Alcaligenes faecalis |
(2 ReA + 6 UA + 2 OA + 1 RA) |
[EMBL:AY548384] |
1395 |
99.70 |
|
Comamonas testosterone |
(1 ReA + 4 UA +1 OA + 3 RA) |
[EMBL:AB007996] |
1390 |
99.35 |
|
Comamonas testosterone |
(2 ReA + 3 UA + 1 OA) |
[EMBL:M11224] |
1390 |
98.05 |
|
Escherichia species |
(3 ReA + 5 UA + 1 OA + 1 RA) |
[EMBL:DQ337503] |
1400 |
99.86 |
|
Flavobacterium mizutaii |
(4 ReA + 6 UA + 2 OA + 1 RA) |
[EMBL:AJ438175] |
1385 |
94.00* |
|
Shigella species |
(5 ReA + 8 UA + 3 OA + 2 RA) |
[EMBL:DQ337523] |
1399 |
99.70 |
|
Stenotrophomonas maltophilia |
(5 ReA + 8 UA + 3 OA + 1 RA) |
[EMBL:AJ293470] |
1396 |
99.75 |
|
Stenotrophomonas maltophilia |
(5 ReA + 8 UA + 3 OA + 1 RA) |
[EMBL:AB294557] |
1396 |
99.86 |
|
Bacteria not previously detected in arthritis but detected in human infection |
||||
|
Aranicola species |
(4 ReA + 3 UA + 1 RA) |
[EMBL:AM398227] |
1400 |
99.64 |
|
Ralstonia species |
(3 ReA + 7 UA + 1 OA) |
[EMBL:AB045276] |
1387 |
99.86 |
|
Bacteria not previously detected in humans |
||||
|
Paenibacillus humicus |
(4 ReA + 6 UA +1 OA + 1 RA) |
[EMBL:AM411528] |
1399 |
98.60 |
|
Uncultured bacteria |
||||
|
Uncultured bacterium |
(4 ReA + 4 UA + 1 OA) |
[EMBL:DQ818781] |
1394 |
98.90 |
|
Uncultured bacterium |
(5 ReA + 4 UA + 2 OA + 2 RA) |
[EMBL:AY838480] |
1389 |
94.00* |
|
Uncultured bacterium |
(2 ReA + 3 UA + 1 OA + 2 RA) |
[EMBL:AB076874] |
1389 |
94.00* |
|
Uncultured bacterium |
(1 ReA +1 OA) |
[EMBL:AY838458] |
1382 |
99.64 |
|
Uncultured bacterium |
(1 UA + 1 OA) |
[EMBL:DQ824599] |
1398 |
99.57 |
|
Uncultured β proteobacterium |
(4 ReA + 6 UA + 1 OA + 1 RA) |
[EMBL:DQ366010] |
1384 |
99.71 |
|
Uncultured Flavobacterium species |
(3 ReA + 5 UA + 1 OA + 2 RA) |
[EMBL:DQ366085] |
1300 |
97.20 |
|
Uncultured Sphingobacterium species |
(1 ReA + 3 UA + 1 OA + 2 RA) |
[EMBL:AB076874] |
1389 |
94.16* |
|
|
||||
|
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 EMBL 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 highlight instances where the % similarity is below 97%. dThe 'Common bacteria' row shows the bacteria identified in ReA, UA, RA, and OA patients. Bacterial species detected only in SF samples and not in ST samples from our previous study [15], are indicated in bold. OA = osteoarthritis; RA = rheumatoid arthritis; ReA = reactive arthritis; SF = synovial fluid; UA = undifferentiated arthritis. |
||||
|
Siala et al. Arthritis Research & Therapy 2009 11:R102 doi:10.1186/ar2748 |
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