Diet leaves a genetic signature in a keystone member of the gut microbiota

Dietary switch from a low-fat and high-fiber diet to a Western-style high-fat and high-sugar diet is a common cause of microbiota imbalances underlying a variety of pathological conditions (i.e. dysbiosis). Although the effects of such dietary changes on microbiota composition and functions are well documented, their putative impact in gut bacterial evolution remains unexplored. Here we followed the emergence of mutations in Bacteroides thetaiotaomicron, a prevalent fiber-degrading microbiota member, upon colonization of the murine gut under different dietary regimens. B. thetaiotaomicron evolved rapidly to the gut and Western-style diet selected for mutations that promote the degradation of mucin-derived glycans. Periodic changes in diet led to fluctuations in the frequency of such mutations and were associated with metabolic shifts, resulting in the maintenance of higher intra-species genetic diversity compared to constant dietary regimens. Finally, our results suggest that B. thetaiotaomicron genetic diversity can be a biomarker for dietary differences among individuals.