The gut microbiome: connecting spatial organization to function
Open accessAbstract
The first rudimentary evidence that the human body harbors a microbiota hinted at the complexity of host-associated microbial ecosystems. Now, almost 400 years later, a renaissance in the study of microbiota spatial organization, driven by coincident revolutions in imaging and sequencing technologies, is revealing functional relationships between biogeography and health, particularly in the vertebrate gut. In this Review, we present our current understanding of principles governing the localization of intestinal bacteria, and spatial relationships between bacteria and their hosts. We further discuss important emerging directions that will enable progressing from the inherently descriptive nature of localization and -omics technologies to provide functional, quantitative, and mechanistic insight into this complex ecosystem.
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Stool samples are not representative of the microbiome of more proximal regions of the large intestine.
“However, these samples are not representative of the microbiome of more proximal regions of the large intestine, and the nonuniform localization and spatial organization of the gut microbiota along the gastrointestinal tract require further evaluation in terms of the functional implications for microbial xenobiotic metabolism (Tropini et al., 2017).”
From Gut reactions: Breaking down xenobiotic–microbiome interactions (2019) · cites this paper as Tropini et al., 2017
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- Authors
- Tropini, C., Earle, K. A., Huang, K. C., & Sonnenburg, J. L.
- Affiliations
- Stanford Medicine (US)
- Stanford University (US)
- Corresponding author
- Huang, Kerwyn Casey
- Sonnenburg, Justin L.
- Venue
- Cell Host & Microbe
- Publisher
- Elsevier BV
- Published
- 2017-04
- Volume
- 21
- Issue
- 4
- Pages
- 433-442
- ISSN
- 1931-3128 (ISSN-L)
- PMC
- PMC5576359
- OpenAlex
- W2606802599
- Cited by
- 685
- References
- 107
- Citations by year
- 2026: 71 · 2025: 86 · 2024: 79 · 2023: 80 · 2022: 84 · 2021: 99 · 2020: 84 · 2019: 54 · 2018: 36 · 2017: 11
- FWCI
- 4.76
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell Host & Microbe (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- NSF CAREER Award (MCB-1149328)
- James S. McDonnell Studying Complex Systems Postdoctoral Fellowship (R01-DK101674, R01-DK085025)
- National Institutes of Health NIDDK
- 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 › Medicine › Gastroenterology › Gastrointestinal motility and disorders
- Keywords
- gut microbiota, host-microbe interactions
- MeSH terms
- Gastrointestinal Microbiome, Animals, Bacteria, Humans, Ecosystem, Bacterial Physiological Phenomena, Gastrointestinal Tract, Microbiota
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