Characteristics of the bacterial community in the stomach and small intestine of Tarim red deer(Cervus elaphus yarkandensis)
The microbiota present in the stomach and small intestine of ruminants plays a vital role in nutrient digestion and metabolism. Tarim red deer, with its biological characteristics of tolerance to coarse feed and salt-alkali, may have a complex gastrointestinal microbiota contributing to its unique traits. Previous studies on Tarim red deer have mainly focused on the rumen and feces, with limited research on the microbiota of the rumen and small intestine. Therefore, to investigate the microbial composition and diversity of the stomach and small intestine of Tarim red deer. This study selected six Tarim red deer, with an equal number of males and females, all under the same feeding and management conditions. Upon slaughter, the contents of the stomach (rumen, reticulum, omasum, and abomasum) and small intestine (duodenum, jejunum, and ileum) were collected.Microbial DNA was extracted and the V3-V4 variable region of the 16S rRNA gene was sequenced. The result indicated that microbial communities in the reticulum, rumen, and omasum were significantly more abundant and diverse than those found in the small intestine (0.05<P). At the phylum level, Firmicutes and Bacteroidetes were the dominant phyla in both the stomach and small intestine. However, the relative abundance of Bacteroidetes was significantly higher in the stomach than in the small intestine, while the opposite was observed for Firmicutes(P<0.05). At the genus level, the most prevalent bacterial genera found in the stomach were Rikenellaceae RC9 gut group, Prevotella, and F082; The dominant bacterial genera in the small intestine were Clostridium sensu stricto 1, Acetitomaculum, Paeniclostridium, and Romboutsia. Bacterial communities in the stomach and small intestine are mainly enriched in Carbohydrate metabolism, Replication and repair, Translation, Membrane transport, Amino acid metabolism, Energy metabolism, Nucleotide metabolism, and Lipid metabolism.There exist correlations between the dominant bacteria and the primary metabolic pathways in various regions of the stomach and small intestine. The study revealed that Tarim red deer have developed a distinct dominant bacterial community in its stomach and intestine, which could explain its ability to tolerate coarse feed.The identification of bacterial communities in the stomach and small intestine of Tarim red deer can serve as a basis for future research on the gut microbiome and nutritional regulation of these animals.