Metagenomic Sequencing Reveals that High-Grain Feeding Alters the Composition and Metabolism of Cecal Microbiota and Induces Cecal Mucosal Injury in Sheep

The cecum serves as an additional fermentation site for ruminants, but it lacks buffering capacity and has a relatively simple epithelial structure compared to the rumen. The role of high-grain (HG) diets in manipulating the rumen microbiome has been well elucidated, yet the microbial response to such diets in the cecum and the subsequent microbe-host interactions remain largely unexplored. Here, we describe the modification of the cecal microbiome and host epithelial gene expression based on data from 20 sheep grouped to feed an HG diet for 7, 14, and 28 days. Our data indicate that the alteration of cecal microbial fermentation was manifested by a decrease in luminal pH and an increase in acetate and butyrate concentrations following the diet change to HG. We further demonstrate that the alteration of the microbiome was driven by microbes that are likely acetate producers (e.g., Blautia spp. and Akkermansia spp.) and butyrate producers (e.g., Anaerostipes spp. and Roseburia spp.). Moreover, the core microbiota in the cecal microbiome was predominantly maintained after HG diet feeding, while the specific populations of the cecal microbiomes adaptively varied at the species and genomic levels time dependently. Association analysis suggests that the perturbations of the cecal microbiome under the HG diet were closely linked to the variations in the two key enzymes that catalyze the conversion of pyruvate to acetyl-CoA and urease enzymes that hydrolyze urea into ammonia, alongside mucosal inflammatory responses. Overall, our findings here provide novel insights into understanding microbiome-host interactions in the hindgut of ruminants. IMPORTANCE High-grain (HG) diets are known to alter the rumen microbiome. However, the responses of the hindgut microbiota and its epithelial function need further investigation in ruminants. Using 20 sheep as the experimental model, we found that the microbial fermentation pattern of the cecum changed after switching to the HG diet. The taxa of the acetate and butyrate producers increased with the feeding time. Moreover, enzymes engaged in carbon and nitrogen metabolisms of the cecal microbiome are altered. The expression of epithelial genes related to volatile fatty acid (VFA) absorption and metabolism, cytokines, and tight junction proteins, alongside light microscopy visualization of epithelial tissue, suggested that the HG diet may induce cecal mucosal inflammatory responses. Our findings reveal cecal microbial and metabolic perturbations in response to HG diets in sheep and provide a new reference for the research on hindgut microbial homeostasis and host health in ruminants.