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Background  Bacterial vaginosis (BV) is the most common vaginal syndrome among women in their reproductive years. It is associated with an increased risk of acquiring sexually transmitted infections and complications like preterm labor. BV is characterized by a high recurrence rate for which biofilms frequently found on vaginal epithelial cells may be a reason.    Results  Here, we report a controlled randomized clinical trial that tested the safety and effectiveness of a newly developed pessary containing an amphoteric tenside (WO3191) to disrupt biofilms after metronidazole treatment of BV. Pessaries containing lactic acid were provided to the control group, and microbial community composition was determined via Illumina sequencing of the V1-V2 region of the 16S rRNA gene. The most common community state type (CST) in healthy women was characterized by  Lactobacillus crispatus.  In BV, diversity was high with communities dominated by either  Lactobacillus iners, Prevotella bivia ,  Sneathia amnii , or  Prevotella amnii.  Women with BV and proven biofilms had an increased abundance of  Sneathia sanguinegens  and a decreased abundance of  Gardnerella vaginalis.  Following metronidazole treatment, clinical symptoms cleared, Nugent score shifted to Lactobacillus dominance, biofilms disappeared, and diversity (Shannon index) was reduced in most women. Most of the patients responding to therapy exhibited a  L. iners  CST. Treatment with WO 3191 reduced biofilms but did not prevent recurrence. Women with high diversity after antibiotic treatment were more likely to develop recurrence.    Conclusions  Stabilizing the low diversity healthy flora by promoting growth of health-associated  Lactobacillus  sp. such as  L. crispatus  may be beneficial for long-term female health.    Trial registration  ClinicalTrials.gov  NCT02687789Electronic supplementary material  The online version of this article (doi:10.1186/s40168-017-0326-y) contains supplementary material, which is available to authorized users.

Treatment of biofilms in bacterial vaginosis by an amphoteric tenside pessary-clinical study and microbiota analysis