The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates
Open accessAbstract
The human gastrointestinal tract (GI tract) harbors a complex community of microbes. The microbiota composition varies between different locations in the GI tract, but most studies focus on the fecal microbiota, and that inhabiting the colonic mucosa. Consequently, little is known about the microbiota at other parts of the GI tract, which is especially true for the small intestine because of its limited accessibility. Here we deduce an ecological model of the microbiota composition and function in the small intestine, using complementing culture-independent approaches. Phylogenetic microarray analyses demonstrated that microbiota compositions that are typically found in effluent samples from ileostomists (subjects without a colon) can also be encountered in the small intestine of healthy individuals. Phylogenetic mapping of small intestinal metagenome of three different ileostomy effluent samples from a single individual indicated that Streptococcus sp., Escherichia coli, Clostridium sp. and high G+C organisms are most abundant in the small intestine. The compositions of these populations fluctuated in time and correlated to the short-chain fatty acids profiles that were determined in parallel. Comparative functional analysis with fecal metagenomes identified functions that are overrepresented in the small intestine, including simple carbohydrate transport phosphotransferase systems (PTS), central metabolism and biotin production. Moreover, metatranscriptome analysis supported high level in-situ expression of PTS and carbohydrate metabolic genes, especially those belonging to Streptococcus sp. Overall, our findings suggest that rapid uptake and fermentation of available carbohydrates contribute to maintaining the microbiota in the human small intestine.
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The small intestine contains a very different abundance and composition of bacteria, with much more dynamic variation compared with the colon.
“the small intestine contains a very different abundance and composition of bacteria, with much more dynamic variation compared with the colon.3”
From The gut microbiota and host health: a new clinical frontier (2016) · cites this paper as [3]
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- Authors
- Zoetendal, E. G., Raes, J., van den Bogert, B., Arumugam, M., Booijink, C. C. G. M., Troost, F. J., Bork, P., Wels, M., de Vos, W. M., & Kleerebezem, M.
- Affiliations
- TiFN (NL)
- Vrije Universiteit Brussel (BE)
- TI Food and Nutrition , Wageningen , The Netherlands
- European Molecular Biology Laboratory (DE)
- Maastricht University Medical Centre (NL)
- European Molecular Biology Laboratory , Heidelberg , Germany
- Radboud University Medical Center (NL)
- Corresponding author
- Zoetendal, Erwin G
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-01-19
- Volume
- 6
- Issue
- 7
- Pages
- 1415-1426
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- PMC
- PMC3379644
- OpenAlex
- W2110491379
- Cited by
- 722
- References
- 60
- Citations by year
- 2026: 24 · 2025: 39 · 2024: 60 · 2023: 61 · 2022: 66 · 2021: 73 · 2020: 76 · 2019: 54 · 2018: 58 · 2017: 47 · 2016: 38 · 2015: 44 · 2014: 33 · 2013: 32 · 2012: 15
- FWCI
- 15.93
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- The ISME Journal (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Socio-Environmental Systems Modeling (acceptedVersion)
- Research Publications (Maastricht University) (submittedVersion, other-oa)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Radboud Repository (Radboud University) (submittedVersion)
- VUBIR (Vrije Universiteit Brussel) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Funders
- Radboud Universiteit
- Universiteit Maastricht
- Wageningen University and Research
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Keywords
- small intestinal microbiota, carbohydrate fermentation, phosphotransferase system, Streptococcus, Escherichia coli, Clostridium, short-chain fatty acids, metagenomics, metatranscriptomics, biotin production, central carbon metabolism
- MeSH terms
- Adult, Clostridium, Colon, Escherichia coli, Female, Fermentation, Humans, Ileostomy, Intestine, Small, Male, Phylogeny, Streptococcus, Ecosystem, Carbohydrate Metabolism, Metagenome
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