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 composition of gut microbiota is closely related to health and nutrition of livestock. Research on the interaction between gut microbiota in livestock and grazing management strategies is unfortunately sparse. By studying the compositions of gut microbiota in sheep and goats in a single, mixed grazing population under the control of herdsman, as well as those of free-range camels in the same area of Qaidam Basin, we found that the composition of gut microbiota between sheep and goats showed no significant difference. However, there were significant differences between mixed group and camels at α- and β-diversities. We speculate that grazing management can shape gut microbial diversity indirectly. Mixed grazing under the control of herdsman lead to similarities in the diversity of gut microbiota among different species and limit their diversities of gut microbiota, which is not conducive to healthy growth of the host. On the contrary, free-range grazing is better for the diversity of gut microbiota. In order to sustainably manage populations of livestock, gut microbiota analysis may prove to be an important indicator for evaluating the merits of different grazing management strategies. Our results lay a foundation to improve the health of livestock and grazing management.

The gut microbiota is integral to the health and adaptability of wild herbivores. Interactions with soil microbiota can shape the composition and function of the gut microbiota, thereby influencing the hosts’ adaptive strategies. As a result, soil microbiota plays a pivotal role in enabling wild herbivores to thrive in extreme environments. However, the influence of soil microbiota from distinct regions on host’s gut microbiota has often been overlooked. We conducted the first comprehensive analysis of the composition and diversity of gut and soil microbiota in goitered gazelles across six regions in the Qaidam Basin, utilizing source tracking and ecological assembly process analyses. Significant differences were observed in the composition and diversity of soil and gut microbiota among the six groups. Source tracking analysis revealed that soil microbiota in the GangciGC (GC) group contributed the highest proportion to fecal microbiota (8.94%), while the Huaitoutala (HTTL) group contributed the lowest proportion (1.80%). The GC group also exhibited the lowest α-diversity in gut microbiota. The observed differences in gut microbial composition and diversity among goitered gazelles from six regions in the Qaidam Basin were closely tied to their adaptive strategies. Ecological assembly process analysis indicated that the gut microbiota were primarily influenced by stochastic processes, whereas deterministic processes dominated most soil microbial groups. Both the differences and commonalities in gut and soil microbiota play essential roles in enabling these gazelles to adapt to diverse environments. Notably, the utilization pattern of soil microbiota by gut microbiota did not align with regional trends in gut microbial α-diversity. This discrepancy may be attributed to variations in environmental pressures and the gut’s filtering capacity, allowing gazelles to selectively acquire microbiota from soil to maintain homeostasis. This study highlights the significant regional variation in gut and soil microbiota diversity among goitered gazelle populations in the Qaidam Basin and underscores the critical role of soil-derived microbiota in their environmental adaptation.

Gut microbiota plays a vital role in host resilience but may be disrupted under environmental antibiotic pressure. The goitered gazelle (Gazella subgutturosa), a keystone ungulate in the Qaidam Basin, is crucial for ecosystem stability. We aimed to investigate how this species responds to antibiotic pressure through gut microbial adaptation. Using 16S rRNA sequencing and weighted gene co-expression network analysis (WGCNA) on fecal and soil samples from six regions, we identified 18 microbial modules, of which three were strongly associated with antibiotics (|r| ≥ 0.75, p < 0.05). Gut microbial α-diversity was lowest in the antibiotic-rich, vegetation-poor TGL region and highest in XRH, where diverse vegetation appeared to buffer antibiotic impact. Antibiotic pressure can reshape gut microbial communities, exerting both adaptive benefits and adverse effects. High-quality habitats may alleviate the negative impacts of antibiotic pressure.

The Qaidam Basin on the Qinghai–Tibet Plateau is an extreme arid environment, posing severe survival challenges. The goitered gazelle (Gazella subgutturosa) is a keystone species in this fragile ecosystem, yet the ecological role of its gut microbiota and its associations with environmental drivers remain poorly understood. We collected fecal samples from gazelles across seven regions of the basin. Metagenomic sequencing was employed to characterize the gut microbiome. Statistical analyses (Mantel tests, multiple regression on matrices, co-occurrence networks) were used to link microbial composition and function with key environmental factors. The gut microbiota was dominated by fiber-degrading phyla (Firmicutes, Bacteroidota) and enriched in metabolic pathways, aligning with a high-fiber diet. Regarding environmental drivers of gut microbial composition variations, isothermality and soil organic carbon were significant predictors, likely via vegetation and environmental inoculation. Regarding environmental drivers of gut microbial function variations, winter solar radiation was uniquely associated with metabolic function without altering microbial composition, suggesting a functional plasticity—the capacity to shift metabolic profiles independently of taxonomic turnover—in response to environmental variation. The gut microbiota of the goitered gazelle exhibits a stable core composition alongside environmentally responsive functional modules. This suggests the microbiome may serve as a significant mediator of host resilience, highlighting adaptation as a dynamic interplay between host, microbiome, and environment. These insights are crucial for microbiome-assisted conservation.

This study focused on the links between soil physicochemical properties and the gut microbiota of goitered gazelles (Gazella subgutturosa) in the hyper-arid Qaidam Basin. By integrating 16S rRNA gene sequencing, soil physicochemical analysis (11 soil indicators), and microbial source tracking (FEAST) on samples of feces (n = 58), soil (n = 35), and water (n = 35) collected from six typical regions. We systematically revealed the mechanisms by which soil properties influence the gut microbiome of wildlife in an arid desert ecosystem based on source tracking and Multiple Regression on distance Matrices (MRM) analysis. The results showed that soil total phosphorus (TP) was significantly positively correlated with the α-diversity of gut microbiota (coefficient = 0.4/0.23/0.332; p < 0.05), while soil organic carbon (SOC) was significantly negatively correlated (coefficient = −0.44/−0.436; p < 0.05), indicating that soil nutrients indirectly predict host microbial diversity by regulating vegetation productivity and forage quality. β-diversity analysis further demonstrated that spatial heterogeneity in soil pH (coefficient = 0.3083; p < 0.05) and TP (coefficient = 0.227; p < 0.05) significantly drove the structural differentiation of gut microbial communities. Source-tracking results based on FEAST revealed significant regional differences in the proportional contribution of environmental microorganisms to the gut microbiota, with individuals in resource-poor habitats (ALK region) exhibiting higher input from soil microbes (8.0672% ± 6.9291%; p < 0.05). In conclusion, this study clarifies the ecological mechanism by which soil physicochemical properties regulate the diversity and composition of herbivore gut microbiota through a “soil–plant–food–gut microbiota” cascading pathway, providing important empirical evidence for understanding animal–microbe–environment interactions and adaptive evolution in extreme environments.