PCR was used to survey bacterial vaginosis flora before and after metronidazole treatment. The species composition for pretreatment patients was variable. Lactobacillus iners was prominent in all patients posttreatment. Atopobium vaginae concentrations were highest for patients who failed or responded incompletely to treatment and lowest for patients who were cured.Bacterial vaginosis (BV) is the most common cause of vaginal irritation and is associated with adverse pregnancy outcomes (4, 13) and an increased risk of human immunodeficiency virus infection (14,15). BV results when the normal, predominantly Lactobacillus vaginal flora shifts to one dominated by Gardnerella vaginalis, Mycoplasma hominis, and a variety of anaerobic organisms. However, no specific pathogen has been identified, and the cause of BV is unknown (6). Metronidazole is the most commonly prescribed antibiotic for treatment of BV, but failure and recurrence rates are high (7). Recent cultivation-independent analyses of PCR-amplified 16S rRNA gene sequences reveal that there are bacterial genera associated with BV that were not previously recognized, including a metronidozole-resistant anaerobe, Atopobium vaginae (8,9,17,19). We examined the species composition of the vaginal flora of BV patients before and 1 month after metronidazole treatment by using PCR assays directed toward a broad range of bacterial genera and a quantitative PCR assay targeting A. vaginae.Clinical assessments of BV were made just prior to treatment and at 4 weeks posttreatment. All six BV patients in the study met all Amsel criteria (2) and had Nugent scores of Ն4 (12). Treatment was a 0.75% topical metronidazole gel applied once daily for 5 days. The study was approved by the Louisiana State University Health Sciences Center institutional review board, and informed consent was obtained from each participant. Vaginal swabs were collected prior to treatment and 30 days posttreatment by using a standard protocol and were stored frozen. To isolate DNA, swabs were agitated in 0.5 ml of molecular-biology-grade water, suspensions were centrifuged, and nucleic acids were isolated from pellets by using an AquaPure genomic DNA kit (Bio-Rad, Hercules, CA). Primers for quantitative PCR assays of A. vaginae 16S rRNA genes were designed using Primrose (3); primers were 5Ј-GTTAGG TCAGGAGTTAAATCTG-3Ј and 5Ј-TCATGGCCCAGAC C-3Ј. Real-time amplifications were performed on an iCycler (Bio-Rad) using iQ-SYBR Green Supermix (Bio-Rad). Thermal cycling consisted of 95°C for 2.5 min, followed by 40 cycles of 95°C for 30 s, 62°C for 30 s, and 72°C for 30 s; 10 ng of template DNA was used in each amplification. PCR amplification of vaginal DNA using primers targeting conserved regions of the16S rRNA gene were used to generate clone libraries with a TOPO