Abstract

The vaginal microbiota plays a critical role in maintaining reproductive health. Although Lactobacillus species often dominate the vaginal environment in healthy individuals, recent studies have shown that healthy microbiota compositions can also include Lactobacillus-depleted states, as described by the Community State Types (CSTs) framework. However, disruptions in the microbiota composition, such as those caused by sexually transmitted infections (STIs), can lead to increased diversity and instability, compromising host protection. This study investigates the association between vaginal microbiota composition and the prevalence of STIs in a cohort of incarcerated women in Chile. Using metataxonomic approaches targeting 16S and 18S rRNA genes, we characterized prokaryotic and eukaryotic components of the vaginal microbiota across healthy, dysbiotic, and pathogen-dominated subjects. Alpha diversity analysis using the Shannon index indicated that Lactobacillus-dominant communities were associated with lower microbial diversity correlates with reduced variability. Whereas communities dominated by pathogens including Trichomonas vaginalis, Gardnerella vaginalis, Treponema pallidum, and HIV, tended to exhibit higher diversity. The pathogen-dominated group displayed an increased prevalence of opportunistic microorganisms and reduced Lactobacillus abundance, which may reflect an imbalance in the microbial ecosystem, often interpreted as reduced stability. This study provides novel insights into the intricate dynamics between normal and altered vaginal microbiomes and their association with STIs. Understanding these community-level patterns and associations is crucial for designing targeted interventions aimed at restoring microbial balance and preventing infections. © The Author(s) 2025.