Impacts of Captive Domestication and Geographical Divergence on the Gut Microbiome of Endangered Forest Musk Deer

Forest musk deer (Moschus berezovskii), one of the world's most endangered ruminants, faces extinction risks, with captive populations additionally threatened by prevalent diseases including digestive and immune disorders. This study employed comparative metagenomic sequencing to analyze intestinal microbiota structure and function between wild populations in Chongqing and Hunan and captive individuals. Wild musk deer exhibited a Pseudomonadota-dominated gut microbiota (significantly higher than captive), enriched in lignin-degrading genera Novosphingobium and Acinetobacter. In contrast, captive groups showed increased abundances of Firmicutes/Bacteroidota, with abnormal proliferation of Escherichia and Clostridium. Alpha and beta diversity analyses revealed significant differences in gut microbial community composition among the three groups, with wild cohorts exhibiting higher diversity than captive groups. Although substantial disparities in microbial abundance existed between the two wild populations due to differential vegetation in their habitats, convergence was observed in core microbial diversity and carbohydrate metabolic functions. Functional analyses have revealed significant divergences in metabolic pathways，Captive deer microbiota was enriched in translation and glycan metabolism pathways, while wild populations exhibited superior enrichment in immune regulation and environmental sensing pathways. This research provides a theoretical foundation for optimizing wild conservation strategies and developing scientifically informed feeding regimens for captive Moschus berezovskii.