The intestinal microbial composition and metabolic functions under normal physiological conditions in the donkey are crucial for health and production performance. However, compared with other animal species, limited information is currently available regarding the intestinal microbiota of donkeys. In the present study, we characterized the biogeography and potential functions of the intestinal digesta- and mucosa-associated microbiota of different segments of the intestine (jejunum, ileum, cecum, and colon) in the donkey, focusing on the differences in the microbial communities between the small and large intestine. Our results show that, Firmicutes and Bacteroidetes dominate in both the digesta- and mucosa-associated microbiota in different intestinal locations of the donkey. Starch-degrading and acid-producing (butyrate and lactate) microbiota, such as Lactobacillus and Sarcina, were more enriched in the small intestine, while the fiber- and mucin-degrading bacteria, such as Akkermansia, were more enriched in the large intestine. Furthermore, metabolic functions in membrane transport and lipid metabolism were more enriched in the small intestine, while functions for energy metabolism, metabolism of cofactors and vitamins, amino acid metabolism were more enriched in the large intestine. In addition, the microbial composition and functions in the digesta-associated microbiota among intestinal locations differed greatly, while the mucosal differences were smaller, suggesting a more stable and consistent role in the different intestinal locations. This study provides us with new information on the microbial differences between the small and large intestines of the donkey and the synergistic effects of the intestinal microbiota with host functions, which may improve our understanding the evolution of the equine digestive system and contribute to the healthy and efficient breeding of donkeys.

驴正常生理条件下的肠道微生物组成和代谢功能对于健康和生产性能至关重要。然而，与其他动物物种相比，目前有关驴肠道微生物群的信息有限。在本研究中，我们描述了驴肠道不同部分（空肠、回肠、盲肠和结肠）的消化道和粘膜相关微生物群的生物地理学和潜在功能，重点关注微生物群落的差异小肠和大肠之间。我们的结果表明，厚壁菌门和拟杆菌门在驴不同肠道位置的消化道和粘膜相关微生物群中占主导地位。淀粉降解和产酸（丁酸盐和乳酸）微生物群，例如乳酸菌和八叠球菌属，在小肠中更加富集，而纤维和粘蛋白降解细菌，例如阿克曼氏菌，在大肠中更加富集。此外，膜运输和脂质代谢的代谢功能在小肠中更为丰富，而能量代谢、辅因子和维生素代谢、氨基酸代谢的功能在大肠中更为丰富。此外，不同肠道位置的食糜相关微生物群的微生物组成和功能差异很大，而粘膜差异较小，表明不同肠道位置的作用更加稳定和一致。这项研究为我们提供了关于驴小肠和大肠之间微生物差异以及肠道微生物群与宿主功能的协同作用的新信息，这可能会提高我们对马消化系统进化的理解，并有助于健康和饮食。驴的高效养殖。