{
  "abstract": "The spatial organization of the gastrointestinal microbiome is shaped by strong physicochemical gradients along the gut, yet many region-associated microbial niches remain poorly resolved in humans. Here, we used the rhesus macaque (Macaca mulatta) as a spatially resolved primate model to profile 148 luminal and mucosal samples across the gastrointestinal tract using shotgun metagenomics, 2bRAD-M sequencing, and targeted bile acid metabolomics, complemented by comparative human datasets. Microbial communities exhibited strong spatial stratification along the gastrointestinal tract, while host species explained greater variation than anatomical location in our comparative datasets. Despite broad phylum-level similarity between humans and monkeys, substantial divergence emerged at species and functional levels. Monkey-associated Segatella copri encoded expanded carbohydrate-active enzyme (CAZyme) repertoires specialized for degradation of complex plant polysaccharides, consistent with dietary and other host-associated adaptation. Along the gastrointestinal tract, microbial load and diversity followed pronounced spatial gradients, although the low-biomass stomach retained unexpectedly high taxonomic and functional diversity. Mucosal communities largely mirrored luminal microbiota at broad taxonomic scales but exhibited distinct species-level signatures associated with niche-specific functional specialization. The monkey large intestine was further enriched in the immunomodulatory bile acid isoallo-lithocholic acid (isoalloLCA), with candidate biosynthetic genes identified in previously uncharacterized microbial lineages. Together, these findings establish a high-resolution framework of the primate gut microbiome and reveal how spatial organization and host-associated selection shape microbial metabolism and host-microbe interactions relevant to gut health.",
  "abstract_shown": true,
  "affiliations": [
    "Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China.",
    "Department of Chemistry, Faculty of Science, The University of Hong Kong, Hong Kong SAR, China.",
    "State Key Lab of Food Science and Technology, Nanchang University, Nanchang, China.",
    "Department of Oral and Maxillofacial Surgery, Nanfang Hospital, Guangzhou, China.",
    "Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.",
    "School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China.",
    "Collaborative Innovation Center of One Health, Hainan University, Haikou, China.",
    "State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China.",
    "School of Food Science and Technology, Jiangnan University, Wuxi, China.",
    "Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 12,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Shuwen Hou",
      "orcid": "0009-0004-5673-000X"
    },
    {
      "affs": [
        0
      ],
      "name": "Yuesong Jiang",
      "orcid": "0009-0007-8736-3507"
    },
    {
      "affs": [
        1
      ],
      "name": "Dengwei Zhang"
    },
    {
      "affs": [
        2
      ],
      "name": "Zhenjiang Xu"
    },
    {
      "affs": [
        1
      ],
      "name": "Yongxin Li"
    },
    {
      "affs": [
        3
      ],
      "name": "Xiqiang Liu"
    },
    {
      "affs": [
        4
      ],
      "name": "Haitao Zhang"
    },
    {
      "affs": [
        5,
        6
      ],
      "name": "Jiachao Zhang",
      "orcid": "0000-0001-8099-6749"
    },
    {
      "affs": [
        7,
        8
      ],
      "name": "Qixiao Zhai",
      "orcid": "0000-0002-0605-2675"
    },
    {
      "affs": [
        7,
        8
      ],
      "name": "Chuan Zhang"
    },
    {
      "affs": [
        4
      ],
      "name": "Xinrui Wang"
    },
    {
      "affs": [
        0,
        9
      ],
      "name": "Shi Huang",
      "orcid": "0000-0002-7529-2269"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/0dq71a8vt4f7x.bib",
  "cited_by": 0,
  "doi": "10.1080/19490976.2026.2748153",
  "fulltext_url": "https://europepmc.org/articles/PMC13682396",
  "id": "0dq71a8vt4f7x",
  "issns": [
    "1949-0976",
    "1949-0984"
  ],
  "landing_url": "https://europepmc.org/article/MED/42886573",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Gut microbiota and health"
    ]
  ],
  "openalex": "W7222452368",
  "pdf_url": "https://europepmc.org/articles/PMC13682396?pdf=render",
  "pmcid": "PMC13682396",
  "pmid": "42886573",
  "published": "2026-10-16",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/0dq71a8vt4f7x.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:46Z",
      "native_id": "MED:42886573",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42886573"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Gut microbiota and health",
      "subfield": "molecular-biology"
    }
  ],
  "title": "A high-resolution spatial model of the primate gut microbiome defines niche-specific functions and host-adapted microbial metabolism.",
  "title_text": "A high-resolution spatial model of the primate gut microbiome defines niche-specific functions and host-adapted microbial metabolism.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:46Z",
  "url": "https://research.draconitic.com/paper/0dq71a8vt4f7x",
  "venue": "Gut microbes",
  "versions": []
}