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Table 3 Bacterial species identified by sequencing of cloned 16S rDNA

From: Broad-range PCR, cloning and sequencing of the full 16S rRNA gene for detection of bacterial DNA in synovial fluid samples of Tunisian patients with reactive and undifferentiated arthritis

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
Burkholderiaspecies (1 ReA + 1 UA) [EMBL:AY769903] 1391 99.13
Burkholderiaspecies (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
Methylomicrobiumspecies (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
Agrobacteriumspecies (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
Kocuriaspecies (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
Diaphorobacterspecies (1 ReA) [EMBL:DQ294626] 1387 99.78
Pelomonas saccharophila (1 ReA) [EMBL:AB021407] 1381 99.42
Paenibacillusspecies (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 bacteria d (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
Aranicolaspecies (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*
  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 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.
  2. Bacterial species detected only in SF samples and not in ST samples from our previous study [15], are indicated in bold.
  3. OA = osteoarthritis; RA = rheumatoid arthritis; ReA = reactive arthritis; SF = synovial fluid; UA = undifferentiated arthritis.