Seasonal Variation in Gut Microbiota Composition: Comparative Analysis of Siberian Musk Deer (Moschus moschiferus) and Forest Musk Deer (Moschus berezovskii)

Abstract Background: Musk deer is famous for its secretion of musk, but due to various factors that the musk deer population has dropped sharply and it is difficult to expand herd sizes.In light of the rapid development of animal husbandry and scientific technology, as well as the urgent need for wildlife conservation, research on the gut microbiota of musk deer is warranted. The gut microbiota is a complex ecosystem that is regulated by many factors, such as dietary, environmental, host factors, and seasonal changes. Results: We studied the gut microbiota in Siberian and Forest musk deer using high-throughput sequencing of the V3–V4 region of the 16S rRNA gene. Fecal samples were collected during two seasons to determine associations between community diversity, composition, and seasonal factors. The results showed that the Firmicutes and Bacteroidetes were the predominant phyla in Siberian and Forest musk deer , their relative abundance was significantly different with species and seasonal factors. The Siberian musk deer population sampled in this study had a wider feeding range and no dietary limitations. Affected by the type of food sources and the feed intake , the microbial α-diversity is higher in summer than winter. Conclusions: The gut bacterial composition of these two musk deer is significantly different, and the abundance between core bacteria is affected by seasonal factors. This study is the first to analyze the composition of the gut microflora in Siberian musk deer, and these results provide a foundation for improving feeding for musk deer populations and further studies investigating the environmental impact of musk deer.