Bacterial vaginosis (BV) is associated with HIV acquisition and adverse pregnancy outcomes. Recurrence after metronidazole treatment is high. HIV-negative, non-pregnant Rwandan BV patients were randomized to four groups (n = 17/group) after seven-day oral metronidazole treatment: behavioral counseling only (control), or counseling plus intermittent use of oral metronidazole, Ecologic Femi+ vaginal capsule (containing multiple Lactobacillus and one Bifidobacterium species), or Gynophilus LP vaginal tablet (L. rhamnosus 35) for two months. Vaginal microbiota assessments at all visits included Gram stain Nugent scoring and 16S rRNA gene qPCR and HiSeq sequencing. All interventions were safe. BV (Nugent 7-10) incidence was 10.18 per person-year at risk in the control group, and lower in the metronidazole (1.41/person-year; p = 0.004), Ecologic Femi+ (3.58/person-year; p = 0.043), and Gynophilus LP groups (5.36/person-year; p = 0.220). In mixed effects models adjusted for hormonal contraception/pregnancy, sexual risk-taking, and age, metronidazole and Ecologic Femi+ users, each compared to controls, had higher Lactobacillus and lower BV-anaerobes estimated concentrations and/ or relative abundances, and were less likely to have a dysbiotic vaginal microbiota type by sequencing. Inter-individual variability was high and effects disappeared soon after intervention cessation. Lactobacilli-based vaginal probiotics warrant further evaluation because, in contrast to antibiotics, they are not expected to negatively affect gut microbiota or cause antimicrobial resistance.Most women have a vaginal microbiota (VMB) that consists predominantly of lactobacilli 1 . The most common type of vaginal dysbiosis is bacterial vaginosis (BV), characterized by a decrease in lactobacilli and increase in fastidious anaerobes 2 . Other types of bacterial dysbiosis, vulvovaginal candidiasis, and Trichomonas vaginalis (TV) are also common. These conditions are associated with vaginal inflammation, thereby increasing the risk of HIV acquisition 3 . BV is also associated with pelvic inflammatory disease, infertility, and adverse pregnancy outcomes 2 .The majority of women seeking care for vaginal symptoms receive antibiotic or antifungal treatment empirically or syndromically without any diagnostic testing 4 . In some specialized clinics, women might be offered www.nature.com/scientificreports www.nature.com/scientificreports/ limited diagnostic testing, such as vaginal pH determination and/or wet mount microscopy. In research settings, BV is typically diagnosed by the Amsel criteria or Nugent scoring 5,6 , with the latter currently being considered the gold standard: Gram-stained vaginal smears are scored based on microscopic visualization of three bacterial morphotypes with a score of 0-3 considered normal, 4-6 intermediate, and 7-10 BV regardless of symptoms. In the last 15 years, molecular methods have become more widely available, and have been applied to the VMB, although mostly in descriptive studies to date 1 .Evidence is mounting that 'm...