{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,5]],"date-time":"2026-09-05T01:42:09Z","timestamp":1788572529581,"version":"build-2803163510"},"reference-count":61,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T00:00:00Z","timestamp":1775433600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Science and Technology Projects of Shaanxi Academy of Science","award":["2024K-08"],"award-info":[{"award-number":["2024K-08"]}]},{"name":"Science and Technology Projects of Shaanxi Academy of Science","award":["2025k-26"],"award-info":[{"award-number":["2025k-26"]}]},{"name":"Shaanxi Key Research and Development Program","award":["2025NC-YBXM-120"],"award-info":[{"award-number":["2025NC-YBXM-120"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>Background: The nasopharyngeal microbiome is crucial for respiratory health in mammals, yet it remains poorly characterized in the endangered forest musk deer (Moschus berezovskii), particularly in the context of disease. Methods: We compared the bacterial (16S rRNA) and fungal (ITS2) communities in the nasopharynx of healthy (n = 6) and clinically diseased (n = 6) individuals. Results: Although alpha diversity did not differ significantly, beta diversity (PCoA) analysis revealed distinct bacterial (PERMANOVA, R2 = 0.165, p = 0.014) and fungal (R2 = 0.577, p = 0.003) community structures between groups. The diseased group exhibited a significant increase in the bacterial phylum Proteobacteria (70.97% vs. 46.27%), primarily driven by the genera Bibersteinia and Pseudomonas. Fungal communities in the diseased group were dominated by a higher relative abundance of Ascomycota and Basidiomycota, with significant enrichment of Wallemia and Aspergillus. LEfSe analysis identified Pseudomonas and multiple fungal taxa (e.g., Wallemia, Aspergillus) as biomarkers for the diseased group. PICRUSt2 prediction indicated enrichment of pathways related to carotenoid biosynthesis and sphingolipid metabolism in the diseased state, while FUNGuild analysis suggested a higher abundance of animal\/plant pathogen-related fungi. Conclusions: Symptomatic respiratory infections in forest musk deer are associated with significant dysbiosis of the nasopharyngeal microbiome, characterized by the marked enrichment of potential bacterial opportunists (e.g., Pseudomonas) and specific fungal taxa (e.g., Wallemia, Aspergillus), alongside distinct functional shifts in the microbiome. These findings provide the first integrated bacterial\u2013fungal profile of the nasopharyngeal microbiome in this endangered species, and highlight potential microbial biomarkers associated with respiratory disease.<\/jats:p>","DOI":"10.3390\/biology15070587","type":"journal-article","created":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T09:40:31Z","timestamp":1775554831000},"page":"587","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Nasopharyngeal Bacterial\u2013Fungal Dysbiosis in Respiratory-Diseased Endangered Forest Musk Deer (Moschus berezovskii)"],"prefix":"10.3390","volume":"15","author":[{"given":"Lijuan","family":"Suo","sequence":"first","affiliation":[{"name":"Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi\u2019an 710032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kun","family":"Bian","sequence":"additional","affiliation":[{"name":"Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi\u2019an 710032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3047-1474","authenticated-orcid":false,"given":"Jie","family":"Tang","sequence":"additional","affiliation":[{"name":"Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi\u2019an 710032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feiran","family":"Li","sequence":"additional","affiliation":[{"name":"Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi\u2019an 710032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6234-9713","authenticated-orcid":false,"given":"Kuo","family":"Sun","sequence":"additional","affiliation":[{"name":"Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi\u2019an 710032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7871-1641","authenticated-orcid":false,"given":"Chao","family":"Yang","sequence":"additional","affiliation":[{"name":"Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi\u2019an 710032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,4,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1038\/nrmicro.2017.14","article-title":"The microbiota of the respiratory tract: Gatekeeper to respiratory health","volume":"15","author":"Man","year":"2017","journal-title":"Nat. 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