Profiling of vaginal microbial communities in Chilean women via self-sampling and nanopore sequencing

The vaginal microbiota is a dynamic ecosystem that plays a central role in women's reproductive health, with Lactobacillus species typically dominating in healthy individuals. Disruptions to this microbiota can lead to dysbiosis, increasing susceptibility to infections such as bacterial vaginosis and contributing to adverse reproductive outcomes. Despite growing global interest in vaginal microbiome research, studies in Latin American populations remain limited, particularly in Chile. In this exploratory study, we aimed to characterize the vaginal microbiota of Chilean women using a combination of self-sampling and full-length 16S rRNA gene sequencing with Oxford Nanopore Technologies (ONT). We implemented a customized bioinformatic pipeline using the Emu classifier to achieve species-level taxonomic resolution. Our analysis revealed that most participants had microbiota dominated by Lactobacillus species, while a subset exhibited diverse microbial communities consistent with Community State Type (CST) IV. Alpha and beta diversity metrics supported these classifications and demonstrated that species-level resolution enhances the ability to distinguish CSTs. These findings provide the first species-level characterization of vaginal microbiota in Chilean women and demonstrate the utility of ONT sequencing and self-sampling in underrepresented populations. This work contributes essential baseline data for the region and highlights the importance of inclusive microbial profiling in advancing personalized approaches to women's health.