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.

The forest musk deer (Moschus berezovskii) is a national Class I protected wild animal in China, and the IUCN Red list classifies it as globally endangered. It has significant value in traditional Chinese medicine and spices. However, wild M. berezovskii has faced a severe population decline due to human hunting, habitat loss, and fragmentation. Thus, studying its population size and distribution pattern is of great importance to develop effective conservation measures. Here, we determined the optimal MaxEnt model and used stratified sampling and the fecal pile counting method to predict the population size and potential habitat distribution of wild M. berezovskii in Chongqing using 133 species distribution points and 28 environmental variables. The results were as follows: (1) When the optimal model parameters were RM = 3.5 and FC = LQHPT, it had high model prediction accuracy (AUC = 0.909 ± 0.010, TSS = 0.663). (2) Under various climatic, topographic, vegetation, and anthropogenic disturbance scenarios, M. berezovskii was primarily distributed in northern, eastern, southwestern regions of Chongqing, covering an area of approximately 5562.80 km². (3) The key environmental factors affecting the potential habitat distribution of M. berezovskii were elevation (36.5%), normalized difference vegetation index (NDVI, 16.6%), slope (11.8%), and land-use type (7.6%), whereas climate and anthropogenic disturbance factors had relatively little influence. (4) A population estimation for M. berezovskii identified approximately 928 ± 109 individuals in Chongqing. We recommend prioritizing the preservation of high-altitude habitats and native vegetation to mitigate human interference and minimize road damage. In summary, our results can enhance the understanding of M. berezovskii distribution and provide a basis for effective conservation and management initiatives.

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.