Gut Microbiota Divergence Between Wild Alpine Musk Deer and Ex-Situ Conserved Forest Musk Deer: Insights for Ex-Situ Conservation and Reintroduction Strategies

The gut microbial ecosystem is structured by the gut microbiota residing in animal hosts. It plays a critical role in modulating core host physiological functions, covering food digestion, nutrient absorption, energy metabolism and immune regulation. In this study, we performed 16S rDNA high-throughput sequencing to characterize the gut microbiota of wild alpine musk deer (Moschus chrysogaster, AMD) and ex situ conserved forest musk deer (Moschus berezovskii, FMD). We then inferred the putative functional profiles based on known taxon–function relationships. Our analyses revealed no significant difference in gut microbiota alpha diversity between wild AMD and ex situ conserved FMD. However, significant divergence in gut microbiota beta diversity was detected between the two species. The family Muribaculaceae and its unclassified affiliated genus as well as the genus Monoglobus and Pseudomonas were significantly more abundant in wild AMD than in ex situ conserved FMD. By contrast, the genera Prevotellaceae_UCG_004, Alistipes, Christensenellaceae_R-7_group, Akkermansia and the family Oscillospiraceae were significantly more abundant in ex situ conserved FMD than in wild AMD. Furthermore, the Firmicutes/Bacteroidetes ratio was numerically higher in FMD than in AMD. Together, these results indicate that the gut microbiota differences between the two musk deer species are consistent with the dietary factors differences. These findings further suggest that the formulated concentrate diet fed to FMD was lower in fiber and higher in digestible energy than the natural diet of AMD. These dietary factors may partly underlie the observed microbiota differences. Accordingly, we recommend adjusting the feeding regime and husbandry practices for FMD to better match the native food plants consumed by AMD. Such adjustment represents an evidence-based strategy for improving the health of FMD populations.