The structure and diversity of strain-level variation in vaginal bacteria

The vaginal microbiome plays an important role in human health and species of bacteria have been associated with reproductive disease. Strain-level variation is also thought to be important, but the diversity, structure evolutionary history strains not as well characterized. We developed validated approach measure strain from metagenomic data based on SNPs within core genomes for six bacteria: Gardnerella vaginalis , Lactobacillus crispatus iners jensenii gasseri Atopobium vaginae . Despite inhabiting same environment, diversity varies across species. All except L. are characterized by multiple distinct groups strains. Even so, lower species, consistent a more recent colonization microbiome. Both frequency multi-strain samples related species-level which they occur, suggesting similar ecological factors influencing niche. conclude that strain-level provides both motivation means testing whether differences contribute function consequences