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Cited by 30Gut microbiota and healthMetabolomics and Mass Spectrometry StudiesAnimal Nutrition and Physiology

A Metabolomic-Based Evaluation of the Role of Commensal Microbiota throughout the Gastrointestinal Tract in Mice

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Yamamoto, Yuri, Nakanishi, Yumiko, Murakami, Shinnosuke, Aw, Wanping, Tsukimi, Tomoya, Nozu, Ryoko, Ueno, Masami, Hioki, Kyoji +7 more·2018·Microorganisms
DOI 10.3390/microorganisms6040101PMC PMC6313407
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Abstract

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.

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  • GF animals have lower concentrations of most gastrointestinal luminal amino acids than SPF mice.

    “have lower concentrations of most gastrointestinal luminal amino acids than SPF mice (Yamamoto et al., 2018)”

    From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Yamamoto et al., 2018

    Results §3.4 and the Discussion report different distributions of luminal amino acids: concentrations were relatively higher in the upper gastrointestinal tract of SPF mice, while GF mice showed the opposite pattern. They do not establish that GF mice had lower concentrations of most amino acids across the gastrointestinal tract as a whole. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

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Authors
Yamamoto, Y., Nakanishi, Y., Murakami, S., Aw, W., Tsukimi, T., Nozu, R., Ueno, M., Hioki, K., Nakahigashi, K., Hirayama, A., Sugimoto, M., Soga, T., Ito, M., Tomita, M., & Fukuda, S.
Affiliations
  • Keio University (JP)
  • Central Institute for Experimental Animals (JP)
  • Tokyo Medical University (JP)
  • University of Tsukuba (JP)
Corresponding author
Fukuda, Shinji
ORCID
Venue
Microorganisms
Publisher
MDPI AG
Published
2018-09-29
Volume
6
Issue
4
Pages
101
ISSN
2076-2607 (ISSN-L)
DOI
10.3390/microorganisms6040101
PMC
PMC6313407
OpenAlex
W2895348834
Cited by
30
References
3
Citations by year
2026: 2 · 2025: 1 · 2024: 3 · 2023: 6 · 2022: 6 · 2021: 2 · 2020: 6 · 2019: 3 · 2018: 1
FWCI
1.07
Type
journal article
Language
en
Open access
Licence
Locations
  • Microorganisms (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Japan Society for the Promotion of Science (15H01522, 16H04901, 17H05654, 18H04805)
  • Japan Science and Technology Agency (JPMJPR1537)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
  • Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Nutrition and Physiology
Keywords
commensal microbiota, gastrointestinal tract, germ-free mice, small intestine, large intestine, carbohydrate metabolism, sugar alcohols, pentoses, amino acids, niacin metabolism, Methylobacteriaceae, host-microbe interactions

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