TABLE 1.

Bacterial targets, primers, and PCR conditions for each bacterium-specific PCR assay

Target (GenBank accession no.)PrimeraSequenceAnnealing temp (°C)Cycle no.
Atopobium sp. (AY738657 , AY738658 )Atop-442F5′-GCAGGGACGAGGCCGCAA-3′5540
Atop-1017R5′-GTGTTTCCACTGCTTCACCTAA-3′
BVAB1 (AY724739 )BVAB1-1019F5′-GTATATTTTCTACGGAACACAGG-3′5540
BVAB1-1280R5′-TTTGCTCCGGATCGCTCCTT-3′
BVAB2 (AY724740 )BVAB2-619F5′-TTAACCTTGGGGTTCATTACAA-3′5540
BVAB2-1024R5′-AATTCAGTCTCCTGAATCGTCAGA-3′
BVAB3 (AY724741 )BVAB3-999F5′-CTTGAWCGATGTAGAGATACATAA-3′5540
BVAB3-1278R5′-TGCTTCGCCTCGCGACGTC-3′
BVAB-TM7 (AY738690 )TM7-641F5′-AACTGCTTGGCTCGAGATTATC-3′5345
TM7-1020R5′-TCTCCTTTCGGAGAAATTCTAGG-3′
Eggerthella-like uncultured bacteriumEgger-621F5′-AACCTCGAGCCGGGTTCC-3′5540
    (AY738656)Egger-859R5′-TCGGCACGGAAGATGTAATCT-3′
G. vaginalis (AY738665 -AY738668 ; AY738695 )G.vag 644F5′-GGGCGGGCTAGAGTGCA-3′6240
G.vag 851R5′-GAACCCGTGGAATGGGCC-3′
L. crispatus (AY738663 , AY738664 )L.crisp-452F5′-GATAGAGGTAGTAACTGGCCTTTA-3′5445
L.crisp-1023R5′-CTTTGTATCTCTACAAATGGCACTA-3′
L. iners (AY738669 )L.iners-453F5′-ACAGGGGTAGTAACTGACCTTTG-3′5540
L.iners-1022R5′-ATCTAATCTCTTAGACTGGCTATG-3′
Leptotrichia/Sneathia spp. (AY724742 ,Lepto-395F5′-CAATTCTGTGTGTGTGAAGAAG-3′5540
    AY738659 )Lepto-646R5′-ACAGTTTTGTAGGCAAGCCTAT-3′
Megasphaera phylotype 1 (AY738672 )MegaE-456F5′-GATGCCAACAGTATCCGTCCG-3′5540
MegaE-667R5′-CCTCTCCGACACTCAAGTTCGA-3′
Megasphaera phylotype 2 (AY738697 )MegaM-453F5′-AAGGTGGTAAATAGCCATCATGAG-3′5740
MegaM-666R5′-CTCTCCGACACTCAAGTCTTC-3′
M. curtisii (EF428974)M.curt-440F5′-TTCTCGCGAAAAAGGCACAG-3′5740
M.curt-1026R5′-CTGGCCCATCTCTGGAACCA-3′
M. mulieris (AY738684 )Mobil-577F5′-GCTCGTAGGTGGTTCGTCGC-3′6240
M.mulie-1026R5′-CCACACCATCTCTGGCATG-3′
Peptoniphilus lacrimalis (AY738692 )P.lacri-999F5′-AAGAGACGAACTTAGAGATAAGTTTT-3′5540
Pepton-1184R5′-CACCTTCCTCCGATTTATCATC-3′
Peptoniphilus sp. (AY738691 )Pepton-1003F5′-GACCGGTATAGAGATATACCCT-3′5540
Pepton-1184R5′-CACCTTCCTCCGATTTATCATC-3′
Prevotella G1 (AY738676 , AY738677 )PrevG1-468F5′-GTCCCTTATTGCATGTACCATAC-3′5540
PrevG1-857R5′-GCCGCTAACACTAGGTGCTA-3′
  • a Numbers on primers refer to the corresponding E. coli 16S rRNA gene base position of the first nucleotide.