Profiling of Vaginal Microbial Communities in Chilean Women Via Self-sampling and Full-length 16S rRNA Sequencing

Abstract The vaginal microbiota is a dynamic ecosystem that plays a crucial role in women’s health, with Lactobacillus species predominating in healthy individuals. Disruptions in this microbiota can lead to dysbiosis, increasing susceptibility to infections such as bacterial vaginosis and other reproductive health complications. While most studies on the vaginal microbiome have been conducted in North American and European populations, data from Latin America, particularly Chile, remain scarce. This study presents a comprehensive analysis of the vaginal microbiota in Chilean women using full-length 16S rRNA gene sequencing with Oxford Nanopore Technology (ONT). We implemented a self-sampling methodology and a bioinformatics pipeline to achieve species-level resolution of microbial communities. Taxonomic profiling using Emu revealed that Lactobacillus was the dominant genus in most samples, while others exhibited microbial compositions consistent with Community State Type (CST) IV, characterized by higher diversity and lower Lactobacillus abundance. Alpha and beta diversity analyses further demonstrated distinct microbial clustering patterns across CSTs, with species-level resolution providing enhanced classification accuracy. Our findings highlight the potential of long-read sequencing and self-sampling for improving vaginal microbiome studies, particularly in underrepresented populations. This research contributes valuable insights into the composition and diversity of the vaginal microbiota in Chilean women, paving the way for more precise diagnostics and targeted interventions in reproductive health. Competing Interest Statement The authors have declared no competing interest.