Host factors associated with vaginal microbiome structure in pregnancy: results from the ECHO cohorts

AbstractUsing pooled vaginal microbiota data from pregnancy cohorts (N = 683 participants) in the Environmental Influences on Child Health Outcomes (ECHO) Program, we analyzed vaginal 16S rRNA gene amplicon sequences to identify clinical and demographic host factors that associate with vaginal microbiota structure in pregnancy bothwithinandacrossdiverse cohorts. Using PERMANOVA models, we assessed factors associated with vaginal community structure in pregnancy and examined whether host factors were conserved across populations and tested the independent and combined effects of host factors on vaginal community state types (CSTs) using multinomial logistic regression models. Demographic and social factors explained a larger amount of variation in the vaginal microbiome in pregnancy than clinical factors. After adjustment, only lower education remained a robust predictor ofL. inersdominant and Diverse CSTs (OR = 8.44, 95% CI = 4.06–17.6 and OR = 4.18, 95% CI = 1.88–9.26, respectively). In random forest models, we identified specific taxonomic features of host factors, particularly urogenital pathogens associated with pregnancy complications (Aerococcus christenseniiandGardnerella vaginalis) among other facultative anaerobes and key markers of community instability (L. iners). Sociodemographic factors were robustly associated with vaginal microbiota structure in pregnancy and should be considered as sources of variation in human microbiome studies.