Rapid genetic diversification of B. thetaiotaomicron in germ-free mice
Studying the within-host evolution of gut commensals is an essential step for understanding the role of microbiome in health and disease. It can provide insights into the mechanisms underlying the development of various gastrointestinal disorders, metabolic conditions, autoimmune diseases, and other health disorders. Additionally, this kind of research can further drive the development of personalized therapies, such as strain-level or gene specific interventions for improving health outcomes. Here, we reported high standing genetic variation within days upon colonization of mice with B. thetaiotaomicron and discovered genes that can accumulate persistent and highly prevalent genetic polymorphisms across a mouse population. We also discovered several haplotypes in phase-variable loci. Altogether, our findings underscore the rapid pace of genetic diversification in the gut and the potential role of phase variation in it.