Diet-specific genetic signature underlies evolution in a keystone member of the gut microbiota

A common cause of microbiota imbalances with negative consequences for host health (dysbiosis) is the switch from a diet low in fat and rich in plant fibres to a western style diet rich in saturated fat and simple sugars. Although ecological changes affecting microbiota composition and activity due to these dietary changes are well documented, potential evolutionary implications remained unexplored. We measured emergence of de novo mutations in Bacteroides thetaiotaomicron (B. theta), a prevalent member of the microbiota, during gut colonization under different dietary regimens. B. theta adapted quickly to the mouse gut. Western style diet selected for mutations with advantages in degrading mucin-derived glycans, which fluctuate in response to diet shifts and corresponding metabolomics changes. Overall, we showed that fluctuating dietary regimen lead to the maintenance of a higher genetic diversity than stable regimens and genetic diversity in B. theta is a powerful biomarker of dietary differences among individuals.