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.

Intestinal Ecology Changes in Diarrheic Père David’s Deer Revealed by Gut Microbiota and Fecal Metabolites Analysis

“…A healthy intestinal barrier is characterized by the selective permeability of nutrients, metabolites, water, and bacterial products, while processes are governed by cellular, neural, immune, and hormonal factors [ 37 ]. The gut microbiota of Père David’s deer was mostly composed of Firmicutes and Bacteroidetes, at >90% of the total community [ 2 ]. We showed that the Firmicutes to Bacteroidetes ratio (2.73) decreased in diarrheic animals when compared with healthy animals (3.47), but this was not statistically significant.…”

“…Samples were then vortexed, sonicated, and centrifuged at 12,000 rpm for 10 min at 4 °C. The supernatant was filtered through a 0.2 µm filter and then 150 μL sample was used for UPLC-MS/MS (MS/MS, QTRAP ® , AB Sciex, Framingham, MA, USA) analysis as previously [ 2 ]. Linear ion trap (LIT) and triple quadrupole (QQQ) scans were acquired on a QQQ-linear ion trap MS, equipped with an electrospray ionization (ESI).…”

“…After experiencing the extinction of wild populations in China in around 1900, 77 captive Père David’s deer overseas were reintroduced to China from 1985 to 1987, and then several reserves were established [ 1 ]. After 40 years’ effort, the population size of Père David’s deer exceeded 8000 in China in 2020 [ 1 , 2 ]. In Dafeng Reserve, there were 6119 individuals of the semi-free population and wild population in 2021 ( , accessed on 19 June 2021).…”

“…A study showed the digestive tract diseases to be the primary factor for the deaths of Père David’s deer in captivity [ 11 ]. Therefore, in addition to possible pathogen identification, several studies were conducted to reveal the gut microbiome of Père David’s deer under different conditions, such as different diets [ 2 ], captive versus wild [ 12 ], or different areas [ 11 ]. However, there are currently no detailed studies on the intestinal ecology in Père David’s deer under disease conditions, including digestive tract diseases.…”

“…Due to the convenience, noninvasiveness, and sufficient biomass for analysis, feces are the major source of samples for intestinal microecology studies, especially in wild animals [ 2 , 25 ]. Previously, it was shown that fecal metabolomic profiles are generated by functional activities in both host cells and gut microbiota, thereby reflecting gut microbiota composition and activity to a large extent [ 26 ].…”