Background Forest musk deer is an endangered species globally. The death of captive forest musk deer can be caused by certain respiratory system diseases. Acute respiratory distress syndrome (ARDS) is a huge threat to the life of forest muck deer that breed in our department. Methods Lung histopathologic analysis was conducted by hematoxylin and eosin (HE) staining. The lung gene changes triggered by ARDS were examined by RNA sequencing and related bioinformatics analysis in forest musk deer. The potential functions of unigenes were investigated by NR, SwissProt KOG, GO, and KEGG annotation analyses. Vital biological processes or pathways in ARDS were examined by GO and KEGG enrichment analyses. Results A total of 3265 unigenes were differentially expressed (|log2fold-change|> 2 and adjusted P value < 0.01) in lung tissues of 3 forest musk deer with ARDS compared with normal lung tissues of the non-ARDS group. These differentially expressed unigenes (DEGs) played crucial roles in immunity and defense responses to pathogens. Moreover, we identified the DEGs related to one or more of the following biological processes: lung development, immunity, and bacterial/viral/fungal infection. And six DEGs that might be involved in lung injury caused by immune dysregulation or viral/fungal infection were identified. Conclusion ARDS-mediated lung gene alterations were identified in forest musk deer. Moreover, multiple genes involved in lung development and lung defense responses to bacteria/viruses/fungi in ARDS were filtered out in forest musk deer.

Pneumonia can seriously threaten the life of forest musk deer (FMD, an endangered species). To gain a comprehensive understanding of pneumonia pathogenesis in FMD, iTRAQ-based proteomics analysis was performed in diseased (Pne group) lung tissues of FMD that died of pneumonia and normal lung tissues (Ctrl group) of FMD that died from fighting against each other. Results showed that 355 proteins were differentially expressed (fold change ≥ 1.2 and adjusted P-value &lt; 0.05) in Pne vs. Ctrl. GO/KEGG annotation and enrichment analyses showed that dysregulated proteins might play vital roles in bacterial infection and immunity. Given the close association between bacterial infection and pneumonia, 32 dysregulated proteins related to Staphylococcus aureus infection, bacterial invasion of epithelial cells, and pathogenic Escherichia coli infection were screened out. Among these 32 proteins, 13 proteins were mapped to the bovine genome. Given the close phylogenetic relationships of FMD and bovine, the protein-protein interaction networks of the above-mentioned 13 proteins were constructed by the String database. Based on the node degree analysis, 5 potential key proteins related to pneumonia-related bacterial infection in FMD were filtered out. Moreover, 85 dysregulated proteins related to the immune system process were identified given the tight connection between immune dysregulation and pneumonia pathogenesis. Additionally, 12 proteins that might function as crucial players in pneumonia-related immune response in FMD were screened out using the same experimental strategies described above. In conclusion, some vital proteins, biological processes, and pathways in pneumonia development were identified in FMD.

Breeding captive forest musk deer is an important way to obtain musk resources, but it also causes changes in the ecological environment of the breeding site. This study compared the changes in soil bacterial communities inside and outside the captive breeding site and tried to find out its influencing factors. High-throughput sequencing analysis and other methods were used to analyze the changes in the bacterial community structure in the natural soil and forest surrounding the musk deer site after 4 years of captivity. The results showed that the main dominant phyla in the captive soil samples were Proteobacteria, Acidobacteria and Chloroflexi. In order, Sphingomonadales (8.7%), Acidobacteriales (9.9%) and Solibacterales (6.1%) were dominant in the captive soil, while Rhizobiales (11.3%) and Gaiellales (6.2%) were found in non-captive soil. The main soil-specific microorganisms under captive conditions were Burkholderiales, Pseudomonadales and Sphingomadales. These microorganisms mainly gather at the order level and can be used as indicator microorganisms. A canonical correspondence analysis (CCA) showed that the microbial diversity in captivity soil was significantly affected by the contents of organic matter, available phosphorus and total nitrogen. These results will provide a basis for the healthy breeding of animals and shed light on the protection of the ecological environment in the Bashan Mountains of Qinling.