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

Abstract

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.