The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates.

E.G. Zoetendal, J. Raes, B. van den Bogert, M. Arumugam, C.C. Booijink, F.J. Troost, P. Bork, M. Wels, W.M. de Vos, M. Kleerebezem

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

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.
Original languageEnglish
Pages (from-to)1415-1426
Number of pages12
JournalThe ISME Journal: multidisciplinary journal of microbial ecology
Volume6
Issue number7
DOIs
Publication statusPublished - Jul 2012

Keywords

  • ecological model
  • function
  • microbiota
  • phylogeny
  • small intestine
  • HUMAN GASTROINTESTINAL-TRACT
  • FRAGMENT-LENGTH-POLYMORPHISM
  • GUT MICROBIOME
  • BACTERIAL DIVERSITY
  • MICROARRAY ANALYSIS
  • SEQUENCE DATA
  • HUMAN ILEAL
  • SAMPLES
  • TWINS
  • MUCOSA

Cite this

Zoetendal, E. G., Raes, J., van den Bogert, B., Arumugam, M., Booijink, C. C., Troost, F. J., Bork, P., Wels, M., de Vos, W. M., & Kleerebezem, M. (2012). The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. The ISME Journal: multidisciplinary journal of microbial ecology, 6(7), 1415-1426. https://doi.org/10.1038/ismej.2011.212