Associations Between Vaginal Microbiota and Sexual Activity in Kenyan Adolescent Girls: A Focus on Lactobacillus and Limosilactobacillus Species

Background: The vaginal microbiota is a key component of genital and reproductive health. Sexual activity can influence the dominant microbes present, shifting away from colonization with key protective bacteria. This study characterized the relationship between vaginal Lactobacillus and Limosilactobacillus species and history of sexual activity. Methods: This cross-sectional study used data collected at the baseline visit for the Kenya Girls Study cohort of adolescent girls and young women (AGYW) aged 16–18 in Thika, Kenya. Bacterial composition was determined from vaginal swabs using 16S rRNA gene sequencing. Participants were classified as sexually active based on self-report and biological markers (incident STI, Y chromosome detection, spermatozoa on Gram stain, or pregnancy). Microbial diversity was evaluated using Shannon diversity indices and Bray-Curtis distances. Poisson regression with robust standard errors was used to estimate associations between sexual activity and detection of specific Lactobacillus and Limosilactobacillus species. A compositional LASSO model incorporating relative abundance data was used to describe odds of sexual activity, and an additional analysis assessed correlates of Limosilactobacillus species detection. Results: We included 142 AGYW, 65.5% who had never had sex and 34.5% who were classified as sexually active. The most common species detected by relative abundance was Lactobacillus crispatus/gallinarum. Beta diversity analysis using Bray-Curtis distances revealed significant differences in community composition between groups (PERMANOVA p = 0.009, R² = 0.0332, while Lactobacillus iners was more often detected in the sexually active group [PR unweighted 1.36 (1.02-1.83) p= 0.039, PR weighted 1.49 (0.87-2.55) p = 0.148], and detection of Lactobacillus jensenii/mulieris was also associated with sexual activity [PR unweighted 2.44 (1.12-5.29) p=0.024, PR weighted 3.09 (1.27–7.52) p = 0.014]. A compositional LASSO model showed that odds of belonging to the sexually active group increased with higher relative abundance of L. iners (OR 1.022) and decreased with higher abundance of L. crispatus/gallinarum (OR 0.978). Limosilactobacillus detection was positively associated with detections of L. crispatus/gallinarum, L. iners, and L. gasseri/paragasseri. Conclusion: This study found that sexual activity among AGYW in Kenya was associated with increased detection of L. iners. Understanding functional roles of diverse Lactobacilli could inform interventions to promote an optimal vaginal microbiome.