Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque
Open accessAbstract
The gut microbiome is widely studied by fecal sampling, but the extent to which stool reflects the commensal composition at intestinal sites is poorly understood. We investigated this relationship in rhesus macaques by 16S sequencing feces and paired lumenal and mucosal samples from ten sites distal to the jejunum. Stool composition correlated highly with the colonic lumen and mucosa and moderately with the distal small intestine. The mucosal microbiota varied most based on location and was enriched in oxygen-tolerant taxa (e.g., Helicobacter and Treponema), while the lumenal microbiota showed inter-individual variation and obligate anaerobe enrichment (e.g., Firmicutes). This mucosal and lumenal community variability corresponded to functional differences, such as nutrient availability. Additionally, Helicobacter, Faecalibacterium, and Lactobacillus levels in stool were highly predictive of their abundance at most other gut sites. These results quantify the composition and biogeographic relationships between gut microbial communities in macaques and support fecal sampling for translational studies.
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Ecological conditions vary immensely along both the length of the GI tract as well as in cross-section from lumen to the mucosal brush-border.
“Ecological conditions vary immensely along both the length of the GI tract as well as in cross-section from lumen to the mucosal brush-border[173,267,308,309].”
From Enterosalivary nitrate metabolism and the microbiome: Intersection of microbial metabolism, nitric oxide and diet in cardiac and pulmonary vascular health (2017) · cites this paper as [309]
It is by no means clear that repopulation by probiotic bacteria must occur to achieve its intended effects.
“it is by no means clear that repopulation by probiotic bacteria must occur to achieve its intended effects[309,407].”
From Enterosalivary nitrate metabolism and the microbiome: Intersection of microbial metabolism, nitric oxide and diet in cardiac and pulmonary vascular health (2017) · cites this paper as [309]
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- Authors
- Yasuda, K., Oh, K., Ren, B., Tickle, T. L., Franzosa, E. A., Wachtman, L. M., Miller, A. D., Westmoreland, S. V., Mansfield, K. G., Vallender, E. J., Miller, G. M., Rowlett, J. K., Gevers, D., Huttenhower, C., & Morgan, X. C.
- Affiliations
- Broad Institute (US)
- Harvard University (US)
- Northeastern University (US)
- Corresponding author
- Morgan, Xochitl C.
- ORCID
- Venue
- Cell Host & Microbe
- Publisher
- Elsevier BV
- Published
- 2015-03
- Volume
- 17
- Issue
- 3
- Pages
- 385-391
- ISSN
- 1931-3128 (ISSN-L)
- PMC
- PMC4369771
- OpenAlex
- W2129675095
- Cited by
- 298
- References
- 41
- Citations by year
- 2026: 13 · 2025: 11 · 2024: 16 · 2023: 20 · 2022: 46 · 2021: 48 · 2020: 43 · 2019: 36 · 2018: 20 · 2017: 17 · 2016: 22 · 2015: 6
- FWCI
- 9.41
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell Host & Microbe (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (P51OD011103)
- National Human Genome Research Institute (R01HG005969, NIH R01HG005969)
- National Center for Research Resources (K26RR000168, P51RR000168)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- gut microbiota, rhesus monkeys, intestinal mucosa, fecal sampling, microbial biogeography, Helicobacter, Treponema, Faecalibacterium, Lactobacillus, Firmicutes, oxygen tolerance, interindividual variability, colonic microbiota, small intestine
- MeSH terms
- Gastrointestinal Microbiome, Animals, DNA, Bacterial, DNA, Ribosomal, Feces, Intestinal Mucosa, Macaca mulatta, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S, Cluster Analysis, Sequence Analysis, DNA
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