Integrative metagenomic, metabolomic and single-cell transcriptomic analyses uncover cellular and microbial mechanisms of rumen development in early-life yaks
We employed rumen metagenomics and metabolomics together with single-cell RNA sequencing (scRNA-seq) of rumen epithelium to investigate how the rumen microbiome-metabolite landscape aligns with epithelial functional programming during yak postnatal development. Metagenomics revealed pronounced age-dependent microbial succession and functional reconfiguration, including structured shifts in carbohydrate-active enzyme repertoires consistent with changing polysaccharide-deconstruction strategies. Metabolomics showed clear age-wise separation of global profiles, M6 was enriched for amino acid-and lipid-associated metabolites and lipid-related signaling pathways, whereas M12 showed greater prominence of membrane lipid remodeling (glycerophospholipid metabolism; biosynthesis of unsaturated fatty acids) together with riboflavin-related redox metabolism. Single-nucleus transcriptomics resolved major rumen-resident cell types and multiple epithelial states, and M12 epithelium exhibited strengthened barrier/junction features and upregulated transport and acid-base regulatory genes relevant to SCFA handling, including SLC16A1, SLC16A7, SLC9A1, and SLC4A4. Together, these data support coordinated maturation of microbial functions, luminal metabolic outputs, and epithelial homeostatic programs ac