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

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*