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.

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.

In high-altitude environments, the prevalence of high-altitude polycythemia (HAPC) ranges between 5 and 18 percent. However, there is currently no effective treatment for this condition. Therefore, disease prevention has emerged as a critical strategy against this disease. Here, we looked into the microarray profiles of GSE135109 and GSE29977, linked to either short- or long-term exposure to the Qinghai Tibet Plateau (QTP). The results revealed inhibition in the adaptive immune response during 30 days of exposure to QTP. Following a gene set enrichment analysis (GSEA) discovered that genes associated with HAPC were enriched in Cluster1, which showed a dramatic upregulation on the third day after arriving at the QTP. We then used GeneLogit to construct a logistic prediction model, which allowed us to identify 50 genes that classify HAPC patients. In these genes, LRRC18 and HCAR3 were also significantly altered following early QTP exposure, suggesting that they may serve as hub genes for HAPC development. The in-depth study of a combination of the datasets of transcriptomic changes during exposure to a high altitude and whether diseases occur after long-term exposure in Hans can give us some inspiration about genes associated with HAPC development during adaption to high altitudes.

Determining the adaptive mechanisms by which bumblebees adapt to high altitudes can help us to better understand their distribution, providing a basis for the future protection and utilization of bumblebee resources. For this study, the adaptive mechanisms of two dominant bumblebee species in the northeastern Qinghai-Tibet Plateau—Bombus kashmirensis and B. waltoni—were studied through transcriptomics methods. For each species, enrichment analysis of the differentially expressed genes and gene set enrichment analysis were carried out between samples collected at different altitudes (4000 m, 4500 m, and 5000 m). The results indicate that these bumblebees tend to up-regulate energy metabolism-related genes when facing extremely high-altitude environments. Of the enriched pathways up-regulated in higher altitudes, the pentose and glucuronate interconversions pathway presented the most severe up-regulation in multiple comparisons of different altitudes for B. kashmirensis, as well as the AMPK signaling pathway, which was found to be up-regulated in both species. Notably, limited by the extreme hypoxic conditions in this study, oxidative phosphorylation was found to be down-regulated with increasing altitude, which is uncommon in studies on bumblebee adaptation to high altitudes.

Intestinal bacteria are considered the “second genome” of the host, playing a crucial physiological role in assisting the host in degrading plant secondary compounds, nutrient absorption, immune regulation, and other aspects. To explore the effects of Stellera chamaejasme on the bacterial community of the gastrointestinal tract of plateau zokor, this study uses the 16S rRNA gene high-throughput sequencing technology, and the biodiversity and the community structure of gut bacteria in different gastrointestinal tract segments (the stomach and cecum) of plateau zokors. The results showed that at the phylum level, the dominant flora in the stomach and cecum of plateau zokors before and after ingesting Stellera chamaejasme were Firmicutes and Bacteroidetes. In plateau zokors that ingested Stellera chamaejasme, the relative abundance of Firmicutes in the stomach and cecum decreased, the relative abundance of Bacteroidetes increased, and the ratio of Firmicutes to Bacteroidetes decreased. After plateau zokors ingested Stellera chamaejasme, the ACE index demonstrated a significant reduction in the richness of the stomach bacterial community, while cecal bacterial community richness showed no significant change. Stellera chamaejasme exhibits significantly different effects on the bacterial communities in different segments of the gastrointestinal tract. Beta diversity analysis revealed that, after plateau zokors ingested Stellera chamaejasme, there were notable distinctions in the bacterial communities within both the stomach and cecum, alongside a marked reduction in the variability of the intestinal bacterial profiles across individuals. The results show that ingesting Stellera chamaejasme has a significant impact on the composition and structure of the gastrointestinal tract bacterial community in plateau zokors.