PR002777 (Project)

Description:Ruminants thrive in diverse ecosystems by leveraging their rumen microbiome to ferment fibrous plants. However, the spatial biogeography of the rumen microbiome and genetic diversity of ventral rumen among the ruminants remain unknown. Here, we present a multi-omics integrating region-resolved microbiome across eleven ruminal sacs, metabolomics, and single-cell RNA sequencing, ATAC-seq, and bulk RNA-seq of ventral epithelium of roe deer, sika deer and sheep. Our results reveal species-specific rumen microbial compositions and metabolic capacities that contribute to differences in short-chain fatty acids and vitamin B production. We uncover functional divergence, genomic specialization and metabolic changes across distinct ruminal sacs microbiome. Single-cell profiling reveals changes of immune responses and structural remodeling in ventral rumen. We demonstrate that vitamin B12 promotes epithelial growth, and four novel genes that enhance stem cell differentiation. Our results highlight variation in microbial ecology and epithelial architecture among three ruminant species, offering insights to improve livestock productivity.