Forest musk deer (Moschus berezovskii Flerov), a critically endangered ruminant species, faces extinction risks, with captive populations further threatened by prevalent digestive and immune disorders. This study utilized comparative metagenomic sequencing to assess intestinal microbiota structure and functional profiles between wild populations in Chongqing and Hunan and captive individuals. Wild populations exhibited a Pseudomonadota-dominated gut microbiota (significantly more abundant than in captive counterparts), enriched with lignin-degrading genera Novosphingobium and Acinetobacter. In contrast, the captive group demonstrated increased abundances of Bacillota/Bacteroidota, alongside abnormal proliferation of Escherichia and Clostridium. Both alpha and beta diversity analyses confirmed significant compositional divergences among the three groups, with wild populations maintaining higher diversity than captive populations. Notably, while substantial disparities in microbial abundance existed between wild populations (attributed to habitat vegetation differences), core microbial diversity and carbohydrate metabolic functions exhibited convergence. Functional analyses marked divergences in metabolic pathways: Captive microbiota showed enrichment in translation and glycan metabolism pathways, whereas wild populations displayed pronounced enrichment in immune regulation and environmental sensing pathways. These findings establish a theoretical foundation for optimizing wild population conservation strategies and developing science-based captive management protocols.

Global climate change exerts profound impacts on biodiversity and species distributions, potentially leading to habitat contraction and species extinction. As an endemic near‐threatened species designated under China's National Class II Protected Wildlife, the tufted deer ( Elaphodus cephalophus ) lacks comprehensive predictions regarding its future distribution under climate change. This study employs an optimized MaxEnt model integrated with 19 climatic variables and environmental factors (topography, vegetation, and anthropogenic disturbances) to systematically predict the species' potential habitat distribution across China. Through parameter screening of 248 combinations using the Kuenm package, the optimal model configuration achieved exceptional predictive accuracy (AUC = 0.977 ± 0.002). Key findings include: (1) Current suitable habitats span 145.98 × 10 ⁴ km ² , predominantly clustered in the Sichuan‐Guizhou‐Yunnan mountainous regions and the Qinling‐Daba‐Wuling ranges; (2) Annual precipitation, elevation, slope, temperature annual range, NDVI, and temperature seasonality emerged as the variables that performed best in predicting habitat suitability for tufted deer; (3) Projected habitat areas under future climate scenarios will contract by 21.8%–28.4%, with shrinkage concentrated in eastern low‐elevation zones and expansion toward the eastern Qinghai‐Tibet Plateau; (4) Habitat centroids exhibit significant westward shifts, reaching 141.8 km under SSP585 (2090s). This study provided theoretical foundations for conserving E. cephalophus genetic resources and climate‐adaptive management, emphasizing the urgency to prioritize ecological corridor construction in western Sichuan‐southeastern Tibet.

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.

Global climate change exerts profound impacts on biodiversity and species distribution, potentially leading to habitat contraction and species extinction. As an endemic vulnerable species listed under China’s National Class II Protected Animals, the tufted deer (Elaphodus cephalophus) lacks comprehensive predictions regarding its future distribution under climate change. This study employs an optimized MaxEnt model integrated with 19 climatic variables and environmental factors (topography, vegetation, and anthropogenic disturbances) to systematically predict the species’ potential habitat distribution across China. Through parameter screening of 248 combinations using the Kuenm package, the optimal model configuration (FC=QH, RM=2.5) achieved exceptional predictive accuracy (AUC = 0.977 ± 0.002). Key findings include: (1) Current suitable habitats span 145.98×104 km², predominantly clustered in the Sichuan-Guizhou-Yunnan mountainous regions and the Qinling-Daba-Wuling ranges; (2) Annual precipitation (Bio12, 33.2%), elevation (18.7%), slope (14.5%), temperature annual range (Bio7, 9.2%), NDVI (7.9%), and temperature seasonality (Bio4, 7.5%) emerged as critical limiting factors; (3) Projected habitat areas under future climate scenarios will contract by 21.8%-28.4%, with shrinkage concentrated in eastern low-elevation zones and expansion toward the eastern Qinghai-Tibet Plateau; (4) Habitat centroids exhibit significant westward shifts, reaching 141.8 km under SSP585 (2090s). This study provides theoretical foundations for conserving Elaphodus cephalophus genetic resources and climate-adaptive management, emphasizing the urgency to prioritize ecological corridor construction in western Sichuan-southeastern Tibet.