Effect of Different Dietary Regimes on the Gut Microbiota and Fecal Metabolites of Père David’s Deer

Abstract

Simple SummaryPère David’s deer is native to the middle and lower reaches of the Yangtze River and the Yellow River in China. However, the wild population became extinct in China around 1900. In 1986, 39 Père David’s deer were reintroduced into Dafeng. Up until now, its wild population has reached 2658, with a total of 6119 in 2021. At present, due to the continuous increase in the population, the repeated grazing on the same plants by the Père David’s deer has affected the re-growth of plants, which has led to insufficient natural food. Therefore, feeding supplement with silage is necessary. As a key nutritional factor, diet is the most important for the gut microbiota and metabolites of wild animals. In order to determine the effect of different dietary patterns on the nutrition and health of Père David’s deer in Dafeng Reserve in spring, we conducted a comprehensive analysis of Père David’s deer feces by UPLC-MS/MS and 16S rRNA gene sequencing to reveal its intestinal chemical environment and the differences in the fecal microbiome. Altogether, our data explored the significant changes in the gut microbiota and metabolic pathways during the transition from full silage to a combination diet with silage and plant in spring. These data provided important information to make more reasonable measures for Père David’s deer’s protection.A deep understanding of the effect of seasonal dietary changes on the nutrition and health of Père David’s deer in Dafeng Reserve will contribute greatly to Père David’s deer’s protection. In this reserve, there were three seasonal dietary regimes: feeding on naturally occurring plants (PLANT diet), silage (SILAGE diet), and a combination of natural plants and silage (COMB diet). To some extent, the COMB diet reflects the seasonal transition from silage to the all-natural plant diet, especially in early spring. However, little is known regarding the gut microbiota changes and metabolic consequences under the COMB diet. Based on 16S rRNA sequencing and ultra-high performance liquid chromatography combined with tandem mass spectrometry, the gut microbiota and fecal metabolites of Père David’s deer under these three diets were compared. Results showed the alpha diversity of the gut microbiota was significantly lower under the COMB diet compared to either the SILAGE or PLANT diets. Although no significant changes were observed in the core phyla, Firmicutes and Bacteroidetes, among the three dietary regimes, a significant lower abundance of several other phyla (Spirochaetes, Melainabacteria, Proteobacteria, and Verrucobacteria) was observed in the COMB diet compared to the SILAGE diet. A greater number of fecal metabolite differences was identified between the COMB and SILAGE or COMB and PLANT diets than between the SILAGE and PLANT diets, suggesting that the COMB diet had more of an effect on the metabolism of Père David’s deer. The integrated pathway analysis showed that several metabolic pathways were significantly affected by the different dietary regimes, such as tryptophan metabolism, vitamin metabolism, and the platelet activation pathways. These metabolic changes reflect the responses and adaptations of Père David’s deer to different diets. Taken overall, our data reveal the difference in the gut microbiota and metabolic pathways of Père David’s deer under three dietary regimes in Dafeng Reserve, which provides important information for Père David’s deer conservation.