Abstract
The vaginal mycobiome, though a minor component of the cervicovaginal ecosystem, plays a crucial role in reproductive health and disease. However, its composition and interactions with bacterial communities remain poorly understood, particularly among Hispanic women, who experience disproportionately high rates of Human papillomavirus (HPV) infection and cervical cancer. We characterized the vaginal mycobiota across reproductive stages and examined its associations with cervical disease, HPV status, and bacterial community state types (CSTs) in 86 Hispanic participants from Puerto Rico using ITS1 amplicon sequencing. Amplicon sequence variants were inferred with QIIME2/DADA2 and taxonomically classified using the UNITE database, with diversity and discriminant taxa analyses applied to explore clinical and microbial associations. We detected 173 fungal Species Hypotheses, dominated by Candida albicans, Agaricomycetes sp., Scopuloides dimorpha, and Hortaea werneckii. While fungal composition did not differ significantly by reproductive stage, non-pregnant individuals exhibited greater inter-individual variability. Alpha diversity was reduced in high-grade squamous intraepithelial lesions compared with low-grade or normal cytology, and Candida parapsilosis prevalence was elevated in low-grade lesions. CST III, characterized by Lactobacillus iners dominance, showed greater dispersion variance than other CSTs. Collectively, these findings reveal a diverse vaginal mycobiome with stage- and disease-specific features, and a notable contribution of environmental fungi that may influence cervical pathogenesis. This work provides foundational insight into cervicovaginal fungal ecology in a high-risk Hispanic population and highlights the importance of integrating bacteriome-mycobiome analyses in women's health research.