Fecal microbiota reveal adaptation of herbivores to the extreme environment of the Qinghai–Tibet Plateau

Abstract Background Gut microbiota is pivotal in regulating hosts' biological processes and maintaining homeostasis, but knowledge about its role in wild herbivores in extreme environments remains limited. Methods Gut bacteria and fungi were sequenced in ruminant (Chiru and Yak) and nonruminant (Kiang) herbivores on the Qinghai–Tibet Plateau, and their community structure, co‐occurrence networks, functions, and assembly mechanisms were investigated using multivariate ecological and statistical methods. Results Kiang had lower gut microbial diversity than Chiru and Yak. Bacterial host‐specific exclusivity was greater than that of fungi. In addition to the evidence of glycan biosynthesis and carbohydrate metabolism, Chiru had a high Firmicutes/Bacteroidetes ratio and low animal pathogen abundance, suggesting better adaptation to the plateau's harsh environment. Additionally, members of gut microbiota tended to co‐occur rather than co‐exclude in all herbivores. Different network complexity and stability patterns were observed between bacterial and fungal communities. Furthermore, gut bacterial assembly was primarily controlled by stochastic dispersal limitation and drift, whereas fungal assembly was primarily controlled by deterministic homogeneous selection except in Chiru. Conclusions On the Qinghai–Tibet Plateau, Chiru and Yak exhibit more diverse gut microbiota and more diverse metabolic functions than Kiang, and gut bacteria are more divergent than gut fungi in these herbivores.