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However, their functional roles in shaping microbial network structure and niche differentiation remain unexplored in most animal species, especially endangered primates. Here, we compared the NAS and INT microbiomes of golden snub-nosed monkeys (Rhinopithecus roxellana) using full-length 16S rRNA amplicon sequencing and metagenomics, focusing on taxonomic composition, functional profiles (KEGG, CAZy, PHI), and microbial co-occurrence networks. Results: Our results indicate that microbial community structure and diversity (Shannon evenness) differ significantly between the two niches. Taxonomically, both sequencing approaches consistently show that, at the relative-abundance level, NAS is dominated by genera such as Dolosigranulum and Vibrio, whereas the INT is characterized by Campylobacter, Helicobacter, and Aerococcus. Notably, metagenomic analysis indicates a relatively high abundance of potential pathogens, including Helicobacter pylori and Chlamydia psittaci. LEfSe analysis shows Dolosigranulum and Campylobacter are key microbial markers for the NAS and INT niches, respectively. KEGG pathway analysis reveals that the NAS microbiome is enriched in valine\/leucine\/isoleucine degradation and glutathione metabolism, while the INT microbiome is enriched in amino sugar and nucleotide sugar metabolism and ribosome pathways. At the CAZy level, all 29 differentially abundant families (e.g., GH13_29, GH103, AA3_2) were enriched in the NAS. Distinct pathogen\u2013host interaction profiles further reflect niche-specific adaptations. Exploratory Spearman-based co-occurrence networks (in which no genus\u2013CAZy edge survived Benjamini\u2013Hochberg (FDR) correction) linked core commensals to KEGG pathways and CAZy families (e.g., GT35, GH0). In the INT, Campylobacter and Helicobacter form high-connectivity modules associated with pathways such as those involving the two-component system and ABC transporters. Conclusions: The nasopharyngeal and rectal microbiomes in golden snub-nosed monkeys differ not only taxonomically but also functionally, exhibiting clear spatially specialized functional differentiation. Given the small sample size (n = 8), these findings provide preliminary evidence for niche-specific microbial and functional partitioning and suggest that the nasopharynx may harbor a relatively high abundance of potential zoonotic pathogens. This study provides a basis for further exploration with a larger sample size.<\/jats:p>","DOI":"10.3390\/biology15171530","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T16:21:21Z","timestamp":1788452481000},"page":"1530","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Spatially Specialized Nasopharynx\u2013Rectal Microbiomes in Golden Snub-Nosed Monkeys (Rhinopithecus roxellana)"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3047-1474","authenticated-orcid":false,"given":"Jie","family":"Tang","sequence":"first","affiliation":[{"name":"Shaanxi Provincial Field Observation & Research Station for Golden Monkey, Giant Panda and Biodiversity, Shaanxi Institute of Zoology, Xi\u2019an 710032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nianlong","family":"Li","sequence":"additional","affiliation":[{"name":"Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi\u2019an 710069, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenhui","family":"Zhou","sequence":"additional","affiliation":[{"name":"Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi\u2019an 710069, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruliang","family":"Pan","sequence":"additional","affiliation":[{"name":"Shaanxi Provincial Field Observation & Research Station for Golden Monkey, Giant Panda and Biodiversity, Shaanxi Institute of Zoology, Xi\u2019an 710032, China"},{"name":"International Centre of Biodiversity and Primate Conservation, Dali University, Dali 671000, China"},{"name":"School of Human Sciences, University of Western Australia, Perth, WA 6009, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lijuan","family":"Suo","sequence":"additional","affiliation":[{"name":"Shaanxi Provincial Field Observation & Research Station for Golden Monkey, Giant Panda and Biodiversity, Shaanxi Institute of Zoology, Xi\u2019an 710032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baoguo","family":"Li","sequence":"additional","affiliation":[{"name":"Shaanxi Provincial Field Observation & Research Station for Golden Monkey, Giant Panda and Biodiversity, Shaanxi Institute of Zoology, Xi\u2019an 710032, China"},{"name":"Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi\u2019an 710069, China"},{"name":"College of Life Science, Yan\u2019an University, Yan\u2019an 716000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8132-3626","authenticated-orcid":false,"given":"Haitao","family":"Zhao","sequence":"additional","affiliation":[{"name":"Shaanxi Provincial Field Observation & Research Station for Golden Monkey, Giant Panda and Biodiversity, Shaanxi Institute of Zoology, Xi\u2019an 710032, China"},{"name":"Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi\u2019an 710069, China"},{"name":"The School of Technology, Beijing Forestry University, Beijing 100091, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"3229","DOI":"10.1073\/pnas.1218525110","article-title":"Animals in a bacterial world, a new imperative for the life sciences","volume":"110","author":"Hadfield","year":"2013","journal-title":"Proc. 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