Decreased carbohydrate sources reduce microbial diversity and taxonomic redundancy in the murine gut

Changes in dietary composition, particularly in carbohydrate diversity, alter the resource environment of the gut microbiome, with downstream effects on community assembly and diversity. However, the extent to which reducing the number of distinct dietary carbohydrates, independent of total carbohydrate intake, shapes microbiota structure remains unclear. This study investigated how reducing the number of dietary carbohydrates, but not total carbohydrate intake, shapes gut microbial diversity in C57BL/6 mice. Over 8 weeks, mice consumed isocaloric diets varying solely in carbohydrate complexity ( n = 8, 6, or 3 different carbohydrate types) but matched for total carbohydrate content. Using 16S rRNA amplicon sequencing, we found that reducing carbohydrate sources led to significant declines in microbial diversity and taxonomic redundancy among important bacterial groups, such as unclassified Lachnospiraceae, Ruminococcaceae, and Muribaculaceae, despite no immediate changes in host physiology. Concurrently, Akkermansia increased under low-complexity diets, independent of the taxonomic redundancy of other species. These changes suggest that loss of diverse sources within a single major nutrient source for microbes (i.e., carbohydrates) narrows microbial niches, which could subsequently disrupt metabolic interactions and functional stability of the gut ecosystem. In the context of modern, industrialized diets often characterized by reduced diversity and structural complexity of carbohydrates, these findings emphasize the importance of diverse nutrient sources in maintaining gut microbial diversity. While short-term host effects were minimal, the microbial shifts observed could presage long-term consequences for gut resilience and disease susceptibility.