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Bacterial vaginosis (BV) increases transmission of HIV, enhances the risk ofpreterm labour, and its associated malodour impacts the quality of life formany women. Clinical diagnosis primarily relies on microscopy to presumptivelydetect a loss of lactobacilli and acquisition of anaerobes. This diagnosticdoes not reflect the microbiota composition accurately as lactobacilli canassume different morphotypes, and assigning BV associated morphotypes tospecific organisms is challenging. Using an untargeted metabolomics approach weidentify novel biomarkers for BV in a cohort of 131 Rwandan women, anddemonstrate that metabolic products in the vagina are strongly associated withbacterial diversity. Metabolites associated with high diversity and clinical BVinclude 2-hydroxyisovalerate and gamma-hydroxybutyrate (GHB), but not theanaerobic end-product succinate. Low diversity, and high relative abundance oflactobacilli, is characterized by lactate and amino acids. Biomarkersassociated with diversity and BV are independent of pregnancy status, and werevalidated in a blinded replication cohort from Tanzania (n=45), in which wepredicted clinical BV with 91% accuracy. Correlations between the metabolomeand microbiota identified Gardnerella vaginalis as a putative producer of GHB,and we demonstrate production by this species in vitro. This work provides adeeper understanding of the relationship between the vaginal microbiota andbiomarkers of vaginal health and dysbiosis.

A multi-platform metabolomics approach identifies novel biomarkers associated with bacterial diversity in the human vagina