View Program - 2022 Population, Evolutionary, and Quantitative Genetics Conference

The human gut microbiome is a complex ecological community composed of a large number of microbial species which are genetically diverse both within and between hosts. These gut microbes experience selective pressures across multiple timescales, from evolution within individual hosts occurring in a matter of months to longer-term processes occurring over many host generations. But despite the considerable effects of the gut microbiome on human health, our understanding of the evolution of these populations—particularly over timescales greatly exceeding individual hosts’ lifetimes—remains limited. Here, we leverage linkage disequilibrium statistics, which measure correlations between sites, to assess evidence for both positive and negative selection across hosts among a broad cohort of species inhabiting the human gut microbiome. With this approach, we find signatures of both purifying selection and adaptation in several gut microbial species. Our findings highlight the heterogeneity of evolutionary outcomes across species, as well as the critical role played by recombination in driving adaptation in these populations.

Signatures of positive and negative selection in the human gut microbiome