Comparative fecal microbiome and metabolome reveal enhanced lignocellulose-degrading potential in Cervus elaphus yarkandensis.

Abstract

Reed is rich in lignocellulose and is therefore challenging for many ruminants to use efficiently. The endangered Tarim red deer subspecies Cervus elaphus yarkandensis (TH) inhabits the Tarim Basin, where reed represents an important forage resource, whereas captive observations suggest that the closely related Cervus elaphus songaricus (TS) may exhibit poorer tolerance to reed-rich diets. Here, we compared fecal microbial composition, metagenomic functional potential, metagenome-assembled genome (MAG)-level carbohydrate-active enzyme (CAZyme) profiles, fecal enzymatic activities, in vitro reed-straw degradation capacity, and fecal and serum metabolomic profiles between TH and TS under the same reed-containing feeding conditions. Compared with TS, TH showed higher fecal microbial diversity and increased abundances of fiber-associated taxa, including Ruminococcaceae, Lachnospiraceae, and Alistipes. Shotgun metagenomics and MAG-level CAZyme analysis indicated that TH-associated microbial communities carried a broader repertoire of functions related to lignocellulose degradation and plant-polysaccharide deconstruction. Consistent with these functional profiles, TH fecal samples exhibited higher cellulase and hemicellulase activities, and TH fecal inocula showed greater reed-straw degradation capacity than TS fecal inocula in vitro. Untargeted metabolomics revealed group-specific fecal and serum metabolites related to carbohydrate fermentation, short-chain fatty-acid-related metabolism, and lipid metabolism, which were associated with TH-enriched fiber-degrading taxa and microbial functional pathways. In an exploratory mouse colonization experiment, TH-derived fecal microbiota was associated with changes in fiber-associated microbial taxa, metabolic pathways, fecal metabolites, body weight, and intestinal morphology in antibiotic-treated mice fed a reed-containing diet. Together, these results indicate that TH harbors fecal microbial and metabolic features associated with enhanced lignocellulose and reed-straw degradation capacity. These findings suggest candidate microbiome-associated pathways relevant to reed-rich forage utilization and may help identify microbial and enzymatic resources for lignocellulose bioconversion.