TABLE 1.
Bacterial targets, primers, and PCR conditions for each bacterium-specific PCR assay
| Target (GenBank accession no.) | Primera | Sequence | Annealing temp (°C) | Cycle no. |
|---|---|---|---|---|
| Atopobium sp. (AY738657, AY738658) | Atop-442F | 5′-GCAGGGACGAGGCCGCAA-3′ | 55 | 40 |
| Atop-1017R | 5′-GTGTTTCCACTGCTTCACCTAA-3′ | |||
| BVAB1 (AY724739) | BVAB1-1019F | 5′-GTATATTTTCTACGGAACACAGG-3′ | 55 | 40 |
| BVAB1-1280R | 5′-TTTGCTCCGGATCGCTCCTT-3′ | |||
| BVAB2 (AY724740) | BVAB2-619F | 5′-TTAACCTTGGGGTTCATTACAA-3′ | 55 | 40 |
| BVAB2-1024R | 5′-AATTCAGTCTCCTGAATCGTCAGA-3′ | |||
| BVAB3 (AY724741) | BVAB3-999F | 5′-CTTGAWCGATGTAGAGATACATAA-3′ | 55 | 40 |
| BVAB3-1278R | 5′-TGCTTCGCCTCGCGACGTC-3′ | |||
| BVAB-TM7 (AY738690) | TM7-641F | 5′-AACTGCTTGGCTCGAGATTATC-3′ | 53 | 45 |
| TM7-1020R | 5′-TCTCCTTTCGGAGAAATTCTAGG-3′ | |||
| Eggerthella-like uncultured bacterium | Egger-621F | 5′-AACCTCGAGCCGGGTTCC-3′ | 55 | 40 |
| (AY738656) | Egger-859R | 5′-TCGGCACGGAAGATGTAATCT-3′ | ||
| G. vaginalis (AY738665-AY738668; AY738695) | G.vag 644F | 5′-GGGCGGGCTAGAGTGCA-3′ | 62 | 40 |
| G.vag 851R | 5′-GAACCCGTGGAATGGGCC-3′ | |||
| L. crispatus (AY738663, AY738664) | L.crisp-452F | 5′-GATAGAGGTAGTAACTGGCCTTTA-3′ | 54 | 45 |
| L.crisp-1023R | 5′-CTTTGTATCTCTACAAATGGCACTA-3′ | |||
| L. iners (AY738669) | L.iners-453F | 5′-ACAGGGGTAGTAACTGACCTTTG-3′ | 55 | 40 |
| L.iners-1022R | 5′-ATCTAATCTCTTAGACTGGCTATG-3′ | |||
| Leptotrichia/Sneathia spp. (AY724742, | Lepto-395F | 5′-CAATTCTGTGTGTGTGAAGAAG-3′ | 55 | 40 |
| AY738659) | Lepto-646R | 5′-ACAGTTTTGTAGGCAAGCCTAT-3′ | ||
| Megasphaera phylotype 1 (AY738672) | MegaE-456F | 5′-GATGCCAACAGTATCCGTCCG-3′ | 55 | 40 |
| MegaE-667R | 5′-CCTCTCCGACACTCAAGTTCGA-3′ | |||
| Megasphaera phylotype 2 (AY738697) | MegaM-453F | 5′-AAGGTGGTAAATAGCCATCATGAG-3′ | 57 | 40 |
| MegaM-666R | 5′-CTCTCCGACACTCAAGTCTTC-3′ | |||
| M. curtisii (EF428974) | M.curt-440F | 5′-TTCTCGCGAAAAAGGCACAG-3′ | 57 | 40 |
| M.curt-1026R | 5′-CTGGCCCATCTCTGGAACCA-3′ | |||
| M. mulieris (AY738684) | Mobil-577F | 5′-GCTCGTAGGTGGTTCGTCGC-3′ | 62 | 40 |
| M.mulie-1026R | 5′-CCACACCATCTCTGGCATG-3′ | |||
| Peptoniphilus lacrimalis (AY738692) | P.lacri-999F | 5′-AAGAGACGAACTTAGAGATAAGTTTT-3′ | 55 | 40 |
| Pepton-1184R | 5′-CACCTTCCTCCGATTTATCATC-3′ | |||
| Peptoniphilus sp. (AY738691) | Pepton-1003F | 5′-GACCGGTATAGAGATATACCCT-3′ | 55 | 40 |
| Pepton-1184R | 5′-CACCTTCCTCCGATTTATCATC-3′ | |||
| Prevotella G1 (AY738676, AY738677) | PrevG1-468F | 5′-GTCCCTTATTGCATGTACCATAC-3′ | 55 | 40 |
| PrevG1-857R | 5′-GCCGCTAACACTAGGTGCTA-3′ |
a
Numbers on primers refer to the corresponding E. coli 16S rRNA gene base position of the first nucleotide.