Comparative study of the function and structure of the gut microbiota in Siberian musk deer and Forest musk deer

Musk deer are famous for their secretion of musk; however, the scale of artificial breeding of musk deer is limited. Considering the lack of a comprehensive understanding of the gut microbiota, there is a need to study the gut microbiota of Siberian musk deer (SMD). Quantitative PCR analysis and high-throughput sequencing were used to show the differences in gut microbial communities and functions between SMD and forest musk deer (FMD). The relative abundance of Firmicutes was significantly higher in SMD than in FMD, with a corresponding decrease in Bacteroidetes, and showed significant seasonal variation. The gut microbiome of FMD has enriched activity for carbohydrate metabolism, while in SMD, amino acids and energy metabolism was higher. The key enzymatic reactions were related to pyruvate metabolism in SMD; however, in FMD, enzymes that digest cellulose (EC:3.2.1.21, EC:3.2.1.4.) were more abundant, and these were related to the living environment and feeding habits. This indicates that FMD and SMD have significant differences in their microbial communities and functions. Furthermore, antibiotic resistances were identified and significantly different in gut microbes of SMD and FMD. For SMD, seasonal variations alter microbial communities and function. The key enzymes of the short-chain fatty acids (EC:1.3.1.44, EC:6.4.1.2) were significantly different, with higher relative abundance in winter-a mechanism of natural selection and environmental adaptation. This study is the first to analyze the composition of the gut microbiota of SMD and can be used to develop or modify conservation and husbandry strategies for musk deer, to improve their productivity. KEY POINTS: • Significant differences in microbial communities and their function between FMD and SMD. • The energy metabolism and the relative abundance of Firmicutes were significantly higher in SMD. • Seasonal variations alter microbial function in SMD, carbohydrate metabolism was higher in summer.