Impact of Antiretroviral Treatment on Vaginal Microbiome Composition in People Living with HIV

Abstract Background The vaginal microbiome is a critical determinant of reproductive health and HIV transmission, yet its composition in West African populations remains poorly characterised. Antiretroviral therapy (ART) has dramatically reduced HIV-related morbidity, but its impact on the vaginal ecosystem is incompletely understood. We used PacBio long-read 16S rRNA sequencing to characterise the vaginal microbiome of five women in Lagos, Nigeria: three HIV-positive (one with only a baseline sample, two with both a baseline and a one-month follow-up after ART initiation) and two HIV-negative controls, yielding a total of seven samples. We compared microbiome composition by age, Lactobacillus diversity, pathogen prevalence, and strain consistency; assessed the effect of ART; and screened for potentially novel bacterial taxa. Results The vaginal microbiome was dominated by Lactobacillus (mean relative abundance 68.2%). Species identified included L. iners , L. crispatus , L. mulieris , and L. jensenii . HIV-positive women exhibited higher abundances of BV-associated genera ( Gardnerella , Prevotella , Atopobium , Sneathia , Mobiluncus ) and lower Lactobacillus compared to HIV-negative controls. DESeq2 analysis identified 163 differentially abundant ASVs, with 124 enriched in HIV-positive samples and 39 (all Lactobacillus ) enriched in HIV-negative controls. HIV-positive individuals showed greater strain-level variability (mean Jaccard distance 0.51) compared to HIV-negative controls (0.23). Two participants with paired samples showed divergent ART responses: one maintained high Lactobacillus abundance (~ 99%), while the other increased from 0% to 99% after one month. We detected 39 candidate novel taxa with < 97% sequence identity to known species. Conclusions HIV-positive women in Lagos harbour a vaginal microbiome with lower Lactobacillus , higher BV-associated pathogens, and greater inter-individual strain variability compared to HIV-negative controls. ART initiation may affect Lactobacillus abundance differently across individuals. These findings provide a foundation for larger longitudinal studies in West African populations. Larger cohorts with comprehensive clinical metadata are urgently needed to validate these exploratory observations and inform interventions to restore vaginal eubiosis.