Gut microbiota forms a unique microecosystem and performs various irreplaceable metabolic functions for ruminants. The gut microbiota is important for host health and provides new insight into endangered species conservation. Forest musk deer (FMD) and alpine musk deer (AMD) are typical small ruminants, globally endangered due to excessive hunting and habitat loss. Although nearly 60 years of captive musk deer breeding has reduced the hunting pressure in the wild, fatal gastrointestinal diseases restrict the growth of captive populations. In this study, 16S rRNA high-throughput sequencing revealed the differences in gut microbiota between FMD and AMD based on 166 fecal samples. The alpha diversity was higher in FMD than in AMD, probably helping FMD adapt to different and wider habitats. The ß-diversity was higher between adult FMD and AMD than juveniles and in winter than late spring. The phylum Firmicutes and the genera Christensenellaceae R7 group, Ruminococcus, Prevotellaceae UCG-004, and Monoglobus were significantly higher in abundance in FMD than in AMD. However, the phylum Bacteroidetes and genera Bacteroides, UCG-005, Rikenellaceae RC9 gut group, and Alistipes were significantly higher in AMD than FMD. The expression of metabolic functions was higher in AMD than in FMD, a beneficial pattern for AMD to maintain higher energy and substance metabolism. Captive AMD may be at higher risk of intestinal diseases than FMD, with higher relative abundances of most opportunistic pathogens and the expression of disease-related functions. These results provide valuable data for breeding healthy captive musk deer and assessing their adaptability in the wild. Key points: • Alpha diversity of gut microbiota was higher in FMD than that in AMD • Expression of metabolic and disease-related functions was higher in AMD than in FMD

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 endangered species conservation, fecal samples are a vital non-invasive tool for gut microbiota analysis. Yet, the influence of external exposure time o

Przewalski’s gazelle (Procapra przewalskii) is an endangered ungulate endemic to the Qinghai–Tibet Plateau, with a small population size and exposure to multiple ecological pressures. Its gut microbiota may play a crucial role in host environmental adaptation. To investigate the functional divergence of gut microbial communities, we performed high-throughput metagenomic sequencing on 105 wild fecal samples collected from 10 geographic regions around Qinghai Lake. The results revealed significant regional differentiation in key functional modules related to metabolism, antibiotic resistance mechanisms, and virulence-associated pathways. All populations showed enrichment in core metabolic pathways such as carbohydrate and amino acid metabolism, with carbohydrate-active enzymes dominated by glycoside hydrolases (GHs) and glycosyltransferases (GTs), exhibiting overall functional conservation. Although populations shared many antibiotic- and virulence-related reference genetic markers, the marker composition associated with distinct resistance mechanisms and pathogenic processes exhibited clear population-specific patterns, suggesting differential microbial responses to local environmental pressures. Correlation network analysis further identified core taxa (e.g., Arthrobacter and Oscillospiraceae/Bacteroidales lineages) as key genera linking community structure with core metabolic, resistance-related, and virulence-associated marker functions. Overall, the gut microbiota of Przewalski’s gazelle exhibits a complex spatially structured functional differentiation, reflecting host–microbiome co-adaptation under region-specific ecological pressures. These findings provide critical methodological and theoretical support for microecological health assessment and regionally informed conservation management of this endangered species.