High-altitude adaptation of the gut microbiome in endangered forest musk deer: evidence from integrated metagenomics, metabolomics, and culturomics
High-altitude environments impose multifaceted selective pressures--hypoxia, cold, and intense UV irradiance--on mammals and their symbiotic gut microbiota. Whether gut microbial communities undergo adaptive restructuring in response to these pressures, and whether such restructuring carries translational value for captive conservation management of endangered species, remain fundamental yet unresolved questions in evolutionary conservation biology. Here, we integrated deep shotgun metagenomics (>=15 Gb per sample), untargeted fecal metabolomics, and culturomics-based strain recovery to characterize the gut microbiome-metabolome axis in 75 captive forest musk deer (Moschus berezovskii Flerov, 1929) housed at high-altitude (ca.3,900 m) and low-altitude (ca.1,450 m) breeding facilities under uniform husbandry. Neutral community modeling revealed that the high-altitude gut microbiome is governed by significantly stronger deterministic ecological selection (only 34.3% of species conformed to neutral expectations vs. 89.3% at low altitude), consistent with adaptive environmental filtering. This selective regime enriched 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, a pattern convergent with SCFA-enrichment reported in phylogenetically diverse high-altitude mammals. Concurrently, fecal metabolomics revealed coordinated shifts in urolithin biosynthesis, tryptophan-kynurenine pathway branch-specific regulation, and energy metabolism remodeling, all robustly predicted by microbiome composition via neural network modeling. Culturomics-based phenotypic screening yielded seven probiotic candidates with confirmed gastrointestinal stress tolerance and broad-spectrum pathogen-antagonistic activity in vitro. These findings yield a directly actionable, practical framework for altitude-informed facility siting, fecal microbiota transplant donor selection, host-derived probiotic development, and non-invasive health surveillance in captive endangered species. These findings illustrate how evolutionary analysis of host-microbiome adaptation to altitude can be translated into evidence-based conservation strategies, and this evolutionary framework is broadly transferable to other endangered taxa facing microbiome-associated disease pressure in captivity.