Altitude‐Associated Divergence of the Gut Microbiome in Endangered Forest Musk Deer: Evidence From Integrated Metagenomics, Metabolomics, and Culturomics

ABSTRACT

High‐altitude environments expose mammals and their gut symbionts to multifaceted stressors—hypoxia, cold, and intense UV radiation. Whether gut microbial communities undergo compositional restructuring in response to these stressors, and whether such restructuring carries translational value for captive conservation, remain unresolved questions. Here, we integrated deep shotgun metagenomics (≥ 15 Gb per sample), untargeted fecal metabolomics, and culturomics in 75 captive forest musk deer ( Moschus berezovskii Flerov, 1929) housed at high altitude (~3900 m) and low altitude (~1450 m) facilities under uniform husbandry. Neutral community modeling showed a greater contribution of deterministic processes at high altitude (only 34.3% of species conformed to neutral expectations vs. 89.3% at low altitude), consistent with stronger environmental filtering. At high altitude, we observed enrichment of a functionally coherent guild of short‐chain fatty acid (SCFA)‐producing bacteria—centered on Flavonifractor plautii , Intestinimonas butyriciproducens , and Enterococcus faecium —that formed antagonistic co‐occurrence networks with opportunistic pathogens including Clostridioides difficile and Campylobacter species, mirroring SCFA enrichment in phylogenetically diverse high‐altitude mammals. Fecal metabolomics revealed coordinated shifts in urolithin biosynthesis, branch‐specific regulation of the tryptophan–kynurenine pathway, and energy metabolism remodeling, all robustly predicted by microbiome composition via neural network modeling. Culturomics yielded seven safety‐validated isolates with confirmed gastrointestinal stress tolerance and broad‐spectrum pathogen‐antagonistic activity in vitro. These findings provide an actionable framework for altitude‐informed facility siting, fecal microbiota transplantation (FMT) donor selection, host‐derived probiotic development, and non‐invasive health surveillance in captive endangered species, and are broadly transferable to other taxa facing microbiome‐associated disease pressure in captivity.