Table 1.

Species of bacteria and archaea tested in PCRs using amplimer 63f and 1387f to amplify 16S rRNA genes

StrainaWoese groupingPCR amplificationb
Chlamydia psittacic Planctomyces and relatives+
Synechocystis sp. strain PCC 6803Cyanobacteria and chloroplasts+
Synechococcus sp. strain WH 7803Cyanobacteria and chloroplasts+
Synechococcus sp. strain PCC 7942Cyanobacteria and chloroplasts+
Nostoc sp.Cyanobacteria and chloroplasts+
Anabaena sp. strain PCC 7120c Cyanobacteria and chloroplasts+
Runella sp. Flexibacter-Cytophaga-Bacteroidesphylum+
Prevotella oris Flexibacter-Cytophaga-Bacteroides phylum+
Prevotella veroralis Flexibacter-Cytophaga-Bacteroides phylum+
Prevotella buccalis Flexibacter-Cytophaga-Bacteroidesphylum+
Prevotella intermedia Flexibacter-Cytophaga-Bacteroides phylum+
Cytophaga ochracea Flexibacter-Cytophaga-Bacteroidesphylum+
Rhodobacter sphaeroides α-Proteobacteria+
Alcaligenes eutrophus JMP222β-Proteobacteria+
Myxococcus xanthus NCIMB 9412c δ-Proteobacteria+
Desulfovibrio desulfuricansc δ-Proteobacteria+
Desulfovibrio salexigensc δ-Proteobacteria+
Desulfovibrio sapovorans δ-Proteobacteria+
Desulfobacter postgatei δ-Proteobacteria+
Desulfobulbus propionicusc δ-Proteobacteria+
Wolinella succinogenes ATCC 29543ɛ-Proteobacteria+
Fusobacterium nucleatumc ɛ-Proteobacteria+
Campylobacter concisus ATCC 33237ɛ-Proteobacteria+
Campylobacter sputorum subsp. sputorum ATCC 35980ɛ-Proteobacteria+
Campylobacter rectus ATCC 33238ɛ-Proteobacteria+
Campylobacter curvus ATCC 35224ɛ-Proteobacteria+
Campylobacter showae ATCC 51146ɛ-Proteobacteria+
Escherichia coliHB101c γ-Proteobacteria+
Acinetobacter calcoaceticus AC8250γ-Proteobacteria+
Pseudomonas putida UWC1c γ-Proteobacteria+
Klebsiella pneumoniae γ-Proteobacteria+
Eubacterium nodatum ATCC 33099c Clostridia and relatives+
Eubacterium brachy ATCC 33089Clostridia and relatives+
Eubacterium timidum ATCC 33092, ATCC 33093Clostridia and relatives+
Eubacterium tardumSC68,c SC88PClostridia and relatives+
Eubacterium exiguum ATCC 700122Clostridia and relatives+
Eubacterium minutum ATCC 700079, ATCC 700080Clostridia and relatives+
Eubacterium saburreumATCC 33271, ATCC 33318, ATCC 33319, ATCC 43850Clostridia and relatives+
Pseudoramibacter alactolyticus DSM 3980 (= ATCC 23263)Clostridia and relatives+
Ruminococcus torquesATCC 27756Clostridia and relatives+
Veillonella atypica ATCC 17744Clostridia and relatives+
Veillonella dispar ATCC 17748Clostridia and relatives+
Veillonella parvula ATCC 10790Clostridia and relatives+
Veillonella caviae ATCC 33540Clostridia and relatives+
Veillonella criceti ATCC 17747Clostridia and relatives+
Veillonella rodentium ATCC 17743Clostridia and relatives+
Veillonella ratti ATCC 17746Clostridia and relatives+
Eubacterium lentum NCTC 11813,c ATCC 25559Gram positive, high G+C+
Micrococcus luteus Gram positive, high G+C+
Actinomyces naeslundii genosp. 1 ATCC 12104Gram positive, high G+C+
Actinomyces naeslundii genosp. 2 WVU 627Gram positive, high G+C+
Actinomyces israelii ATCC 12102, ATCC 10048, MTU 01003, MTU 01004Gram positive, high G+C+
Actinomyces gerencseriae ATCC 23860Gram positive, high G+C+
Actinomyces odontolyticus ATCC 17929Gram positive, high G+C+
Actinomyces meyeri ATCC 35568Gram positive, high G+C+
Actinomyces georgiae ATCC 49285Gram positive, high G+C+
Actinomyces viscosusATCC 15987Gram positive, high G+C+
Propionibacterium acnes ATCC 11827Gram positive, high G+C+
Bacillus cereus NCTC 7464 Bacillus-Lactobacillus-Streptococcussubdivision+
Bacillus popilliae NRRL B2309Mc Bacillus-Lactobacillus-Streptococcussubdivision+
Peptostreptococcus anaerobius Bacillus-Lactobacillus-Streptococcussubdivision+
Lactobacillus delbrueckii subsp.delbrueckii ATCC 9649 Bacillus-Lactobacillus-Streptococcussubdivision+
Lactobacillus coryniformis subsp.torquens ATCC 25600 Bacillus-Lactobacillus-Streptococcussubdivision+
Streptococcus salivarius ATCC 7073 Bacillus-Lactobacillus-Streptococcussubdivision+
Streptococcus sanguis ATCC 10556 Bacillus-Lactobacillus-Streptococcussubdivision+
Eubacterium saphenum ATCC 49989Gram positive, low G+C+
Leptospira inadai ATCC 43289 Spirochaeta-Treponema-Borreliasubdivision+d
Leptospira kirschneri ATCC 23469 Spirochaeta-Treponema-Borreliasubdivision+d
Leptospira wolbachii ATCC 43284 Spirochaeta-Treponema-Borreliasubdivision+d
Treponema denticola ATCC 35405, ATCC 33520 Spirochaeta-Treponema-Borreliasubdivision+
Treponema vincentii ATCC 35580 Spirochaeta-Treponema-Borrelia subdivision+
Treponema pallidum subsp. pallidum Nichols strain Spirochaeta-Treponema-Borrelia subdivision+
Treponema phagedenis biovar Kazan ATCC 27087, biovar Reiter Spirochaeta-Treponema-Borrelia subdivision+
Treponema socranskii subsp. socranskii ATCC 35536 Spirochaeta-Treponema-Borrelia subdivision+
Treponema mediumG7201 Spirochaeta-Treponema-Borrelia subdivision+
Methanosarcina frisius Euryarchaeota,Methanosarcinale
Halobacterium halobium NCMB 2090 Euryarchaeota, extreme halophile
  • a Strains not identified as originating from specific culture collections were well-characterized strains from culture collections held by participating laboratories.

  • b +, positive reaction, i.e., a single amplicon of the correct predicted size (ca. 1,300 bp); −, no PCR product.

  • c The PCR product of this strain was sequenced to ensure that it represented the 16S rRNA gene from the organism.

  • d The 16S rRNA gene from thisLeptospira species was successfully amplified; however, the resulting amount was approximately 90% less than the signal generated an amplification of the 16S rRNA gene of E. coli.