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Simple Summary: The gut microbiota and metabolites play a crucial role in the physiological health of the host and are influenced by various factors, including seasons. We utilized 16s sequencing and untargeted metabolomics to uncover the impact of seasonal change on the gut microbiota and metabolites of Tibetan antelopes. Overall, this study revealed differences in the gut microbiota and metabolites of Tibetan antelopes during the cold and warm seasons. These findings can provide a basis for the conservation of Tibetan antelopes. The Tibetan antelope is an endangered species suffering from poaching and habitat fragmentation. The intestinal flora and metabolites play a crucial role in the physiological homeostasis of hosts, which are influenced by various environmental factors like seasonal variation. In this particular research, our main goal was to explore the alterations in the metabolism and gut microbiota of Tibetan antelopes between the cold season (XB) and warm season (DA), using untargeted metabolomics and 16S rRNA gene-sequencing analyses. The findings indicated that Tibetan antelopes had a higher alpha-diversity of intestinal microbes during the cold season than during the warm season. Principal co-ordinate analysis revealed notable seasonal discrepancies in the function and structure of intestinal microbes in Tibetan antelopes. The relative abundance of Firmicutes was significantly increased during the cold season compared to during the warm season. Furthermore, the Tibetan antelope's primary metabolic functions of the intestinal micro-organisms were significantly higher during the cold season. The untargeted metabolomics analysis results showed a total of 532 metabolites that were significantly different between the cold season and warm season groups. These metabolites were found to be enriched in a total of 62 metabolic pathways. Among the most significant pathways of enrichment were the purine metabolism and pyrimidine metabolism. The levels of related metabolites in those pathways were remarkably higher in the warm season compared to the cold season. The comprehensive analysis of 16S rRNA and the metabolome reveals there is a significant correlation between differential microbiota and differential metabolites. Therefore, the gut microbiota changes caused by seasonal changes influenced the metabolites as well. This research reveals the function of seasonal changes in the intestinal flora and metabolites in the adaptation of Tibetan antelopes to environmental fluctuations and supplies a theoretical basis for instructing the protection management of Tibetan antelopes. [ABSTRACT FROM AUTHOR]

Simple Summary: Captivity is a common conservation method for endangered animals. However, a growing number of recent studies have shown that some animals in captivity might be in sub-health condition. The gut microbiota has been described as a complex, interactive internal system that has effects on diseases of the host with many interactions, and the occurrence of certain diseases is accompanied by changes and disorder of gut microbiota. We used16S rRNA sequencing technology and a mathematical model to find differences in gut microbiota composition and assembly processes. The results show that captivity might be unfavorable for white-lipped deer by shifting the gut microbiota composition and assembly process. White-lipped deer (Cervus albirostris) is a nationally protected wild animal species in China, as well as a unique and endangered species, according to the International Union for Conservation of Nature (IUCN) Red List. Captivity may alleviate the pressure from poaching and contribute to the repopulation and conservation of the population in the wild. The gut microbiota is described as a complex, interactive internal system that has effects on diseases of the host, with many interactions. However, the influence of captivity on the composition and assembly process of gut microbiota in white-lipped deer is unclear. This study applied high-throughput 16S rRNA sequencing technology to determine differences in the gut microbiota between captive (CW) and wild (WW) white-lipped deer. We used the null model, neutral community model, and niche width to identify whether captivity affects the composition and assembly process of gut microbiota. The results show that WW has a higher number of Firmicutes and a lower number of Bacteroidetes compared with CW at the phylum level, and it has more opportunistic pathogens and specific decomposition bacteria at the genus level. Principal coordinate analysis also indicated significant differences in the composition and function of gut microbiota in CW and WW. Moreover, the results reveal that captivity shifts the ecological assembly process of gut microbiota by raising the contribution of deterministic processes. In conclusion, our results demonstrate that captivity might potentially have an unfavorable effect on white-lipped deer by continually exerting selective pressure. [ABSTRACT FROM AUTHOR]

Simple Summary: The gut microbiota are crucial for hosts. For mammals, different gastrointestinal tract (GIT) segments have specific microbial communities, which play an essential role in the host's nutrition, metabolism, immunity, and health. Plateau zokors (Eospalax baileyi) and Gansu zokors (Eospalax cansus) are closely related species that belong to the Spalacidae family, and are common pests in agriculture, forestry, and animal husbandry in northwestern China, with a sympatric distribution area in the transition zone between the Qinghai-Tibetan Plateau and the Loess Plateau. Here, the characteristics of the microbiota communities in different GIT segments of the plateau zokor and the Gansu zokor were studied, and the microbiota communities of the two zokor species were compared. Our results provide important information for further study on the function of microbiota communities in different GIT segments and the potential use of the gut microbiota as a new method for the population management of the zokors. In this study, based on high-throughput sequencing technology, the biodiversity and the community structure of microbiota in different GIT segments (the stomach, small intestine, cecum and rectum) of plateau zokors and Gansu zokors were studied and compared. A source tracking analysis for the microbial communities of different GIT segments was carried out using the fast expectation–maximization microbial source tracking (FEAST) method. We found that, for both species, the microbial community richness and diversity of the small intestine were almost the lowest while those of the cecum were the highest among the four segments of the GIT. Beta diversity analyses revealed that the bacterial community structures of different GIT segments were significantly different. As for the comparison between species, the bacterial community compositions of the whole GIT, as well as for each segment, were all significantly different. Source tracking conducted on both zokors indicated that the soil has little effect on the bacterial community of the GIT. A fairly high percentage of rectum source for the bacterial community of the stomach indicated that both zokors may engage in coprophagy. [ABSTRACT FROM AUTHOR]