Liu Huilin, Xiao Lu, Liu Zhiqiang, Deng You, Zhu Jinpeng, Yang Chengzhong, Liu Qing, Tian Di, Cui Xiaojuan, Peng Jianjun
School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China.
Animal Biology Key Laboratory of Chongqing Education Commission of China, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China.
Animals (Basel). 2025 Jul 2;15(13):1954. doi: 10.3390/ani15131954.
Forest musk deer ( 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 and . In contrast, the captive group demonstrated increased abundances of Bacillota/Bacteroidota, alongside abnormal proliferation of and . 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.
林麝（弗勒洛夫氏）是一种极度濒危的反刍动物，面临灭绝风险，圈养种群还受到普遍存在的消化和免疫紊乱的进一步威胁。本研究利用比较宏基因组测序来评估重庆和湖南野生种群与圈养个体之间的肠道微生物群结构和功能概况。野生种群的肠道微生物群以假单胞菌门为主（比圈养种群明显更丰富），富含木质素降解属和。相比之下，圈养组的芽孢杆菌门/拟杆菌门丰度增加，同时和异常增殖。α和β多样性分析均证实三组之间存在显著的组成差异，野生种群的多样性高于圈养种群。值得注意的是，虽然野生种群之间微生物丰度存在很大差异（归因于栖息地植被差异），但核心微生物多样性和碳水化合物代谢功能表现出趋同。功能分析表明代谢途径存在差异：圈养微生物群在翻译和聚糖代谢途径中富集，而野生种群在免疫调节和环境感知途径中显著富集。这些发现为优化野生种群保护策略和制定科学的圈养管理方案奠定了理论基础。
