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.

Habitat connectivity is indispensable for the survival of species that occupy a small habitat area and have isolated habitat patches from each other. At present, the development of human economy squeezes the living space of wildlife and interferes and hinders the dispersal of species. The Przewalski’s gazelle (Procapra przewalskii) is one of the most endangered ungulates, which has experienced a significant reduction in population and severe habitat shrinkage. Although the population of this species has recovered to a certain extent, human infrastructure severely hinders the gene flow between several patches of this species. Therefore, we used the maximum entropy (MaxEnt) model to simulate the habitat suitability of the Przewalski’s gazelle. In addition, we combined habitat suitability and ecological characteristics of the species to obtain eight habitat patches. Finally, we used the least-cost path (LCP) and circuit theory based on the resistance model to simulate the landscape network of this species. The results showed that habitat patches and connectivity in the east of the Qinghai Lake were crucial to the communication between populations of the Przewalski gazelle, and our study provided important reference for the distribution of important habitats and the construction of corridor between patches. Our study aimed to provide habitat networks and maintain landscape connectivity for achieving the fundamental goal of protecting and revitalizing populations of the Przewalski’s gazelle.

Maintaining a healthy status is crucial for the successful captive breeding of endangered alpine musk deer (Moschus chrysogaster, AMD), and captive breeding programs are beneficial to the ex-situ conservation and wild population recovery of this species. Meanwhile, the gut microbiota is essential for host health, survival, and environmental adaptation. However, changes in feeding environment and food can affect the composition and function of gut microbiota in musk deer, ultimately impacting their health and adaptation. Therefore, regulating the health status of wild and captive AMD through a non-invasive method that targets gut microbiota is a promising approach. Here, 16S rRNA gene sequencing was employed to reveal the composition and functional variations between wild (N = 23) and captive (N = 25) AMD populations. The results indicated that the gut microbiota of wild AMD exhibited significantly higher alpha diversity (P < 0.001) and greater abundance of the phylum Firmicutes, as well as several dominant genera, including UCG-005, Christensenellaceae R7 group, Monoglobus, Ruminococcus, and Roseburia (P < 0.05), compared to captive AMD. These findings suggest that the wild AMD may possess more effective nutrient absorption and utilization, a more stable intestinal microecology, and better adaption to the complex natural environment. The captive individuals displayed higher metabolic functions with an increased abundance of the phylum Bacteroidetes and certain dominant genera, including Bacteroides, Rikenellaceae RC9 gut group, NK4A214 group, and Alistipes (P < 0.05), which contributed to the metabolic activities of various nutrients. Furthermore, captive AMD showed a higher level of 11 potential opportunistic pathogens and a greater enrichment of disease-related functions compared to wild AMD, indicating that wild musk deer have a lower risk of intestinal diseases and more stable intestinal structure in comparison to captive populations. These findings can serve as a valuable theoretical foundation for promoting the healthy breeding of musk deer and as a guide for evaluating the health of wild-released and reintroduced musk deer in the future. Key points: • Wild and captive AMD exhibit contrasting gut microbial diversity and certain functions. • With higher diversity, certain bacteria aid wild AMD’s adaptation to complex habitats. • Higher potential pathogens and functions increase disease risk in captive AMD.

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.

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.

The gut microbiota in animals is a dynamic ecosystem influenced by both the host itself and the environment it inhabits. It is known that short-term captivity can significantly impact the gut microbiota of plateau zokors, leading to substantial inter-individual variation. However, the specific changes in the assembly process of the gut microbiota in plateau zokors during captivity remain unclear. In this study, we conducted a comparative analysis on the assembly process of the gut microbiota in 22 male plateau zokors from the same location in Qinglin Township, Datong County, Qinghai Province, before (W) and after (L) laboratory rearing. We performed a single-factor correlation network analysis on the top 50 genera with relative abundance in each group. The results revealed that captivity increased the complexity of the gut microbiota in plateau zokors, indicating a higher number of interactions between different microbial species. However, this increase in complexity was accompanied by a decrease in stability, suggesting a higher degree of variability and potential disruption in the microbial community. According to the results of the neutral community model, the gut microbiota of plateau zokors in the W had a higher Nm value (Nm = 48,135) compared to the L (Nm = 39,671), indicating that species dispersal of the gut microbiota was greater in the wild than in captivity. In the wild, the modified stochasticity ratio (MST) was less than 0.5, suggesting that deterministic processes dominated. However, after 15 days of laboratory rearing, the MST became greater than 0.5, indicating a shift toward stochastic processes, and this difference was highly significant (p < 0.001). This differs from research related to aboveground animals. This study provides theoretical support for the application of gut microbiota in subterranean endangered species.