Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

Abstract

Gut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteria evolve over time. Here we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples. We use this approach to study evolution in ∼30 prevalent species in the human gut. Although the patterns of between-host diversity are consistent with quasi-sexual evolution and purifying selection on long timescales, we identify new genealogical signatures that challenge standard population genetic models of these processes. On shorter timescales within hosts, we find that genetic differences only rarely arise from the invasion of distantly related strains. Instead, the resident strains more commonly acquire a smaller number of evolutionary changes, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency over ∼ 6 month timescales. By comparing these mutations with the typical between-host differences, we find evidence that sweeps are driven by introgression from other strains, rather than by new mutations. Our results suggest that gut bacteria evolve on human-relevant timescales, and highlight the feedback between short- and long-term evolution across hosts.