Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analysis Reveals Impact of Microbiota on Clinical Variables

Background: Bacterial vaginosis (BV) is a common condition that is associated with numerous adverse health outcomes and is characterized by poorly understood changes in the vaginal microbiota. We sought to describe the composition and diversity of the vaginal bacterial biota in women with BV using deep sequencing of the 16S rRNA gene coupled with species-level taxonomic identification. We investigated the associations between the presence of individual bacterial species and the clinical diagnostic variables for BV. Methodology/Principal Findings: Broad-range 16S rRNA gene PCR and pyrosequencing was performed on vaginal swabs from 220 women with and without BV. BV was assessed by Amsel’s clinical criteria and confirmed by Gram stain. Taxonomic classification was performed using phylogenetic placement tools resulting in 99% of query sequence reads being assigned to the species-level. Women with BV had heterogeneous vaginal bacterial communities that were usually not dominated by a single taxon. In the absence of BV, vaginal bacterial communities were dominated by either Lactobacillus crispatus or Lactobacillus iners. Leptotrichia amnionii and Eggerthella sp. were the only two BV-associated bacteria significantly associated with each of the four Amsel clinical variables. Co-occurrence analysis revealed the presence of several sub-groups of BV-associated bacteria suggesting metabolic co-dependencies. Several taxa exhibited race-dependent prevalence when we analyzed in separate groups by BV status. Conclusions/Significance: The human vaginal bacterial biota is heterogeneous and marked by greater species richness and diversity in women with BV; no species is universally present. Different bacterial species have different associations with the four clinical variables used to diagnose BV, which may account for discrepancies between Amsel and Nugent (Gram stain) diagnostic criteria. Greater abundance of several BV-associated bacteria in Black women without BV may contribute their increased risk for BV. Tools developed in this project can be used to study microbial ecology in diverse settings at high resolution.