Skip to content
DraconiticResearch
Search Sources API
197,688 studies31 sourcesUpdated 5 min ago
Peer-reviewedCC BYGut microbes

A high-resolution spatial model of the primate gut microbiome defines niche-specific functions and host-adapted microbial metabolism.

  • Shuwen Hou1
  • Yuesong Jiang1
  • Dengwei Zhang2
  • Zhenjiang Xu3
  • Yongxin Li2
  • Xiqiang Liu4
  • Haitao Zhang5
  • Jiachao Zhang6,7
  • Qixiao Zhai8,9
  • Chuan Zhang8,9
  • Xinrui Wang5
  • Shi Huang1,10
10 affiliations
  1. 1Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China.
  2. 2Department of Chemistry, Faculty of Science, The University of Hong Kong, Hong Kong SAR, China.
  3. 3State Key Lab of Food Science and Technology, Nanchang University, Nanchang, China.
  4. 4Department of Oral and Maxillofacial Surgery, Nanfang Hospital, Guangzhou, China.
  5. 5Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.
  6. 6School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China.
  7. 7Collaborative Innovation Center of One Health, Hainan University, Haikou, China.
  8. 8State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China.
  9. 9School of Food Science and Technology, Jiangnan University, Wuxi, China.
  10. 10Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China.
Read full textPDFDOICite

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.

Related

  1. Colon-Specific Gut Microbiome Remodelling Is Associated with Host Metabolism in Paracetamol-Induced Liver Injury in Rats
    Zhanagul Khassenbekova, Saniya Kozhakhmetova, Dinar Tarzhanova +7
    MetabolitesPeer-reviewedCC BYFull textProteomics & metabolomicsEurope PMC
  2. Gut microbial metabolism in aging: from metabolite production to organ-specific immunometabolic effects
    Zhen Wang, Yang Liu
    Frontiers in nutritionPeer-reviewedCC BYFull textMolecular biology & gene regulationEurope PMCEurope PMCPMC
  3. Gut microbiome features associated with PIK3CA-mutated colorectal cancer: A nationwide pan-cancer genomic and microbial profiling study (MONSTAR-SCREEN)
    Shogen Boku, Shunsuke A. Sakai, Kentaro Sawada +18
    Scientific ReportsPeer-reviewedCC BY-NC-ND 4.0Full textMolecular biology & gene regulationCrossref
  4. Gut microbiome composition and oxalate-related metabolic functions in staghorn calcium oxalate stone formers: a shotgun metagenomic analysis
    Yadong Lu, Tzi Shin Toh, Lydia Lim +3
    Scientific ReportsPeer-reviewedCC BY-NC-ND 4.0Full textMolecular biology & gene regulationCrossref
  5. Acarbose differentially affects gut microbial metabolism of maltose and sucrose, distinctly modulating host metabolism
    Hayato Yoshikawa, Eunyoung Lee, Ryo Hatano +8
    iSciencePeer-reviewedCC BY 4.0Full textMolecular biology & gene regulationCell PressCrossrefEurope PMC

Cite

BibTeXRIS
BibTeX
@article{hou2026highresolution,
  title = {{A high-resolution spatial model of the primate gut microbiome defines niche-specific functions and host-adapted microbial metabolism.}},
  author = {Shuwen Hou and Yuesong Jiang and Dengwei Zhang and Zhenjiang Xu and Yongxin Li and Xiqiang Liu and Haitao Zhang and Jiachao Zhang and Qixiao Zhai and Chuan Zhang and Xinrui Wang and Shi Huang},
  journal = {Gut microbes},
  year = {2026},
  month = oct,
  doi = {10.1080/19490976.2026.2748153},
  url = {https://europepmc.org/article/MED/42886573},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - A high-resolution spatial model of the primate gut microbiome defines niche-specific functions and host-adapted microbial metabolism.
AU  - Shuwen Hou
AU  - Yuesong Jiang
AU  - Dengwei Zhang
AU  - Zhenjiang Xu
AU  - Yongxin Li
AU  - Xiqiang Liu
AU  - Haitao Zhang
AU  - Jiachao Zhang
AU  - Qixiao Zhai
AU  - Chuan Zhang
AU  - Xinrui Wang
AU  - Shi Huang
PY  - 2026
DA  - 2026/10/16
JO  - Gut microbes
DO  - 10.1080/19490976.2026.2748153
UR  - https://europepmc.org/article/MED/42886573
AB  - 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.
SN  - 1949-0976
SN  - 1949-0984
ER  -