Sub-communities of the vaginal ecosystem in pregnant and non-pregnant women

Diverse and non- Lactobacillus -dominated vaginal microbial communities are associated with adverse health outcomes such as preterm birth and acquisition of sexually transmitted infections. Despite the importance of recognizing and understanding the key risk-associated features of these communities, their heterogeneous structure and properties remain ill-defined. Clustering approaches have been commonly used to characterize vaginal communities, but they lack sensitivity and robustness in resolving community substructures and revealing transitions between potential sub-communities. We used a highly resolved approach based on mixed membership topic models with multi-domain longitudinal data from cohorts of pregnant and non-pregnant study participants to identify several non- Lactobacillus -dominated sub-communities common to both cohorts regardless of reproductive status. These sub-communities correlated with clusters in metabolite concentrations. In non-pregnant individuals, we identified non- Lactobacillus -dominated sub-communities that were more common during menses but did not predict an increased likelihood of other non- Lactobacillus -dominated communities during the rest of the menstrual cycle. The menstrual cycle was a strong driver of transitions between sub-communities and was correlated with changes in levels of cytokines and metabolites, such as elevated TNF-α concentrations at the time of ovulation, and elevated kynurenine concentrations during menses, respectively. In pregnant individuals, some metabolite clusters were predictive of temporal instability in vaginal microbiota structure. Overall, our analyses based on mixed membership models revealed new substructures of the vaginal ecosystems which may have potentially important clinical or biological associations. ### Competing Interest Statement J.R. is the cofounder of LUCA Biologics, a biotechnology company focusing on translating microbiome research into live biotherapeutics drugs for women's health. All remaining authors have no disclosures to declare.