A metabolomic-based evaluation of the role of commensal microbiota throughout the gastrointestinal tract in mice

Yuri Yamamoto, Yumiko Nakanishi, Shinnosuke Murakami, Wanping Aw, Tomoya Tsukimi, Ryoko Nozu, Masami Ueno, Kyoji Hioki, Kenji Nakahigashi, Akiyoshi Hirayama, Masahiro Sugimoto, Tomoyoshi Soga, Mamoru Ito, Masaru Tomita, Shinji Fukuda

Research output: Contribution to journalArticlepeer-review

18 Citations (Scopus)


Commensal microbiota colonize the surface of our bodies. The inside of the gastrointestinal tract is one such surface that provides a habitat for them. The gastrointestinal tract is a long organ system comprising of various parts, and each part possesses various functions. It has been reported that the composition of intestinal luminal metabolites between the small and large intestine are different; however, comprehensive metabolomic and commensal microbiota profiles specific to each part of the gastrointestinal lumen remain obscure. In this study, by using capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS)-based metabolome and 16S rRNA gene-based microbiome analyses of specific pathogen-free (SPF) and germ-free (GF) murine gastrointestinal luminal profiles, we observed the different roles of commensal microbiota in each part of the gastrointestinal tract involved in carbohydrate metabolism and nutrient production. We found that the concentrations of most amino acids in the SPF small intestine were higher than those in the GF small intestine. Furthermore, sugar alcohols such as mannitol and sorbitol accumulated only in the GF large intestine, but not in the SPF large intestine. On the other hand, pentoses, such as arabinose and xylose, gradually accumulated from the cecum to the colon only in SPF mice, but were undetected in GF mice. Correlation network analysis between the gastrointestinal microbes and metabolites showed that niacin metabolism might be correlated to Methylobacteriaceae. Collectively, commensal microbiota partially affects the gastrointestinal luminal metabolite composition based on their metabolic dynamics, in cooperation with host digestion and absorption.

Original languageEnglish
Article number101
Issue number4
Publication statusPublished - 2018 Dec


  • Gastrointestinal tract
  • Metabolome
  • Metagenome
  • Microbiota

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)
  • Virology


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