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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.
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Arthritis Research & Therapy

ISSN: 1478-6362

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