The Vaginal Microbiome in Women Recently Experiencing BV and UTI

The vaginal microbiome (VMB) influences susceptibility to urogenital infections, yet large-scale, species-level metagenomic studies in real-world populations are rare. We analyzed shotgun metagenomic profiles and linked clinical metadata from 10,003 women across the United States who self-reported recent bacterial vaginosis (BV), urinary tract infection (UTI), both, or neither. Women reporting recent BV or UTI displayed distinct community structures, including higher prevalence of VALENCIA CST IV subtypes and significantly elevated alpha diversity compared with women who reported no prior diagnosis. Species-level Gardnerella profiling revealed that multiple Gardnerella species were enriched in BV but did not differ significantly between UTI and non-UTI groups, refining prior mechanistic hypotheses. Uropathogens such as E. coli, E. faecalis , and S. saprophyticus were detectable at higher prevalence and relative abundance in women who experienced UTI, including among participants who reported recent antibiotic use, consistent with the possibility of residual or recurrent vaginal colonization. These findings demonstrate that microbial signatures associated with recent BV and UTI remain detectable at population scale, provide a high-resolution reference for real-world vaginal metagenomics, and offer new directions for prevention strategies that consider the vaginal reservoir in recurrent urogenital infections.