Search

Gut microbiota plays an essential role in regulating human health. How host environment drives microbial evolution was studied in some bacterial species, however, some studies concluded long-term purifying selection while others demonstrated evidence of adaptation. To address this problem, we broadly investigated the within-person evolution of 64 gut commensal species in healthy subjects. We found that most (24 of 27) species with sufficient genetic variation underwent recent adaptation, evidenced by parallel evolution (PE). This finding was supported by three lines of evidence on PE mutations (significantly more than expected, significantly higher dN/dS, significant enrichment of truncations). Moreover, signal transduction pathways underwent the strongest and most widespread positive selection. One striking example is an HTH-type transcriptional regulator (msmR) regulating carbohydrate transportation that underwent widespread PE in six species across 28 people, potentially driven by host diet changes. We resolved the previous debate of gut microbiota evolution showing widespread within-host adaptation, and identified adaptive mutations to guide precise microbiome manipulations.