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

摘要: The structure and function of the gut microbiome are shaped by a combination ecological evolutionary forces. While dynamics community have been extensively studied, much less is known about how strains bacteria evolve over time. Here we show that with model-based analysis existing shotgun metagenomic data, can gain new insights into within across hosts. We find long-term evolution hosts consistent quasi-sexual purifying selection, relatively weak geographic in many prevalent species. However, our quantitative approach also reveals between-host genealogical signatures cannot be explained standard population genetic models. By comparing samples from same host ~6 month timescales, within-host differences rarely arise invasion as distantly related those other Instead, more commonly observe small number changes resident strains, which nucleotide variants or gene gains losses rapidly sweep to high frequency host. these mutations typical differences, evidence sweeps driven introgression species rather than de novo mutations. These data suggest on human relevant highlight feedback between short-term longer-term