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

ABSTRACT 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. IMPORTANCE Variation in dietary carbohydrate composition shapes the resource environment available to the gut microbiota and can influence microbial community structure and stability. In this study, we show that isocaloric diets with a reduced number of different dietary carbohydrate sources (with total carbohydrate levels constant) significantly altered the structure of gut microbial communities in mice. A reduction in the variety of carbohydrate sources led to decreased microbial diversity and taxonomic redundancy within key microbial groups. These occurred without notable effects on host physiology, although our current study did not focus on long-term host consequences. Our findings suggest that mixtures of structurally distinct carbohydrate sources help sustain the diversity of host-associated microbiomes, in line with ecological theory predicting that reduced resource heterogeneity narrows microbial niches and increases competitive exclusion. These results also shed light into the context of human health, where simplified diets have become increasingly more common.