Differential analysis of gut microbiota between captive and wild forest musk deer (Moschus berezovskii) based on 16S rRNA sequencing

Forest musk deer ( Moschus berezovskii ) is a globally endangered species, and its conservation has long been a matter of concern. Wild populations are scarce, while artificially captive populations are also constrained by health issues such as digestive system diseases. To reveal the differences in gut microbiota between captive and wild forest musk deer from different geographical regions, fecal samples were collected from captive individuals in Nanyang, Henan (HN) and Gaoping, Shanxi (SX), as well as wild individuals in Baotianman, Henan (YS), with 5 samples per group. High-throughput 16S rRNA sequencing was employed to analyze the microbial community structure and function. The sequencing revealed Firmicutes, Bacteroidota, and Proteobacteria as the dominant phyla across all three groups, with Actinobacteriota exhibiting a significantly higher abundance in the YS wild group (11.13%) than in the HN (1.29%) captive and SX (6.12%) captive groups. There were no significant differences in α -diversity among the groups. However, β -diversity analysis (PCoA and NMDS) indicated a clear separation in microbial community structure between captive and wild groups, with some individuals in the SX captive group clustering with the wild group. LEfSe analysis identified 36 differential biomarkers: the YS wild group was enriched in genera including Bacillus , Arthrobacter , and Microbacterium , whereas the HN captive group was enriched in Bacteroides , Clostridium , and Eubacterium , while the SX captive group was enriched in Skermanella (genus) and Cytophagales (order). Functional prediction analysis revealed that the gut microbiota of the wild group was significantly enriched in the pathways of xenobiotics biodegradation and metabolism as well as lipid metabolism, whereas the captive groups showed higher activity in the translation and nucleotide metabolism pathways. This study reveals the impacts of rearing methods and geographical factors on the gut microbial community structure and function of forest musk deer. These findings can serve as a theoretical foundation for promoting healthy breeding of captive populations and as a reference for evaluating the health status of wild populations.