Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets.

Abstract

The role of intestinal Prevotella species in human health is controversial, with both positive and negative associations. Strain-level diversity may contribute to discrepancies in genus and species associations with health and disease. We dissected the gut metagenomes of Italians with varying dietary habits, investigating the presence of distinct Prevotella copri strains. Fiber-rich diets were linked to P.\xa0copri types with enhanced potential for carbohydrate catabolism. P.\xa0copri strains associated with an omnivore diet had a\xa0higher prevalence of the leuB gene-involved in branched-chain amino acid biosynthesis-a risk factor for glucose intolerance and type 2 diabetes. These P.\xa0copri pangenomes were compared to existing cohorts, providing evidence of distinct gene repertoires characterizing different P.\xa0copri populations, with drug metabolism and complex carbohydrate degradation significantly associated with Western and non-Western individuals, respectively. Strain-level P.\xa0copri diversity in gut microbiomes is affected by diet and should be considered when examining host-microbe associations.