Gut biogeography of the bacterial microbiota
Open accessAbstract
Animals assemble and maintain a diverse but host-specific gut microbial community. In addition to characteristic microbial compositions along the longitudinal axis of the intestines, discrete bacterial communities form in microhabitats, such as the gut lumen, colonic mucus layers and colonic crypts. In this Review, we examine how the spatial distribution of symbiotic bacteria among physical niches in the gut affects the development and maintenance of a resilient microbial ecosystem. We consider novel hypotheses for how nutrient selection, immune activation and other mechanisms control the biogeography of bacteria in the gut, and we discuss the relevance of this spatial heterogeneity to health and disease.
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Enterobacteriaceae are typically dominant in the upper GI tract and may become enriched with the faster stool transit time that occurs during diarrhea.
“Enterobacteriaceae are typically dominant in the upper GI tract and may become enriched with the faster stool transit time that occurs during diarrhea (Donaldson et al., 2016)”
From Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers (2021) · cites this paper as Donaldson et al., 2016
The taxonomic composition of the gut microbiota changes throughout the gastrointestinal tract according to nutrient availability, mucus structure, pH and oxygen availability.
“The taxonomic composition of the gut microbiota changes throughout the gastrointestinal tract, according to nutrient availability, mucus structure, pH and oxygen availability [1–6].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [1]
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- Authors
- Donaldson, G. P., Lee, S. M., & Mazmanian, S. K.
- Affiliations
- California Institute of Technology (US)
- Corresponding author
- Mazmanian, Sarkis K.
- Venue
- Nature Reviews Microbiology
- Published
- 2015-10-26
- Volume
- 14
- Issue
- 1
- Pages
- 20-32
- ISSN
- 1740-1526 (ISSN-L)
- 1740-1534
- PMC
- PMC4837114
- OpenAlex
- W1902150932
- Cited by
- 2,535
- References
- 135
- Citations by year
- 2026: 205 · 2025: 205 · 2024: 307 · 2023: 292 · 2022: 280 · 2021: 317 · 2020: 287 · 2019: 206 · 2018: 207 · 2017: 135 · 2016: 90 · 2015: 2
- FWCI
- 14.02
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Reviews Microbiology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Funders
- National Institute of Mental Health (R01MH100556, MH100556)
- National Institute of General Medical Sciences (GM099535, R01GM099535)
- National Institute of Diabetes and Digestive and Kidney Diseases (DK 078938, R01DK078938, R56DK078938)
- National Institute of Neurological Disorders and Stroke (R01NS085910)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- gut microbiota, microbial biogeography, colonic mucus, colonic crypts, gut lumen, microbial community assembly, immune activation, nutrient selection, host-microbe interactions
- MeSH terms
- Gastrointestinal Microbiome, Animals, Humans, Symbiosis, Ecosystem, Gastrointestinal Tract, Host-Pathogen Interactions
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