A unified catalog of 14,062 microbial species reference genomes provides new insight into the gut microbiota in high-altitude mammals.

BACKGROUND: The gut microbiota is essential for host health and survival. The understanding of the diversity, stability, and functional traits of mammalian gut microbiota, as well as the evolutionary patterns of the host-gut microbiota holobiont in non-human mammals remains limited. Here, we conducted a comprehensive analysis of the gut microbiota in non-human mammals. RESULT: We used 1,412 samples from large herbivores living in the Qinghai-Tibetan Plateau (QTP), recovered 14,062 high-confidence species-level genome bins (SGBs), of which more than 88% represent potentially novel species. We found that recurring lineage-specific bacterial gain-loss events along the host phylogeny might drive the shaping of the gut microbiota in these QTP mammals. Functional characteristics of host-specific SGBs showed host-specific functional enrichment, but few cases of convergence in at least two hosts. Our analyses further revealed that both co-phylogeny and host-swap events are frequent between mammalian hosts and their individual gut symbionts at QTP ecosystem. The genome-wide evolutionary analyses of 60 genera, comprising 376 core microbial species occurring within at least two animal hosts, discovered that co-phylogeny or host-swap signals might be impacted by phylogenetic inertia, but not by selective constraints. CONCLUSIONS: Our results showed that animals living in harsh environments are promising sources for the discovery of novel biological functions of gut residing microbes. The results of this study provide insight into the diversity and functionality of the gut microbiota in large herbivores living at QTP as well as the diverse evolutionary patterns of host-gut microbiota interaction over evolutionary times. Video Abstract.