The gut microbiome of healthy Japanese and its microbial and functional uniqueness

The human gut microbiome has profound influences on the host's health largely through its interference with various intestinal functions. As recent studies have suggested diversity in the human gut microbiome among human populations, it will be interesting to analyse how gut microbiome is corre...

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Published inDNA research Vol. 23; no. 2; pp. 125 - 133
Main Authors Nishijima, Suguru, Suda, Wataru, Oshima, Kenshiro, Kim, Seok-Won, Hirose, Yuu, Morita, Hidetoshi, Hattori, Masahira
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.04.2016
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Abstract The human gut microbiome has profound influences on the host's health largely through its interference with various intestinal functions. As recent studies have suggested diversity in the human gut microbiome among human populations, it will be interesting to analyse how gut microbiome is correlated with geographical, cultural, and traditional differences. The Japanese people are known to have several characteristic features such as eating a variety of traditional foods and exhibiting a low BMI and long life span. In this study, we analysed gut microbiomes of the Japanese by comparing the metagenomic data obtained from 106 Japanese individuals with those from 11 other nations. We found that the composition of the Japanese gut microbiome showed more abundant in the phylum Actinobacteria, in particular in the genus Bifidobacterium, than other nations. Regarding the microbial functions, those of carbohydrate metabolism were overrepresented with a concurrent decrease in those for replication and repair, and cell motility. The remarkable low prevalence of genes for methanogenesis with a significant depletion of the archaeon Methanobrevibacter smithii and enrichment of acetogenesis genes in the Japanese gut microbiome compared with others suggested a difference in the hydrogen metabolism pathway in the gut between them. It thus seems that the gut microbiome of the Japanese is considerably different from those of other populations, which cannot be simply explained by diet alone. We postulate possible existence of hitherto unknown factors contributing to the population-level diversity in human gut microbiomes.
AbstractList The human gut microbiome has profound influences on the host's health largely through its interference with various intestinal functions. As recent studies have suggested diversity in the human gut microbiome among human populations, it will be interesting to analyse how gut microbiome is correlated with geographical, cultural, and traditional differences. The Japanese people are known to have several characteristic features such as eating a variety of traditional foods and exhibiting a low BMI and long life span. In this study, we analysed gut microbiomes of the Japanese by comparing the metagenomic data obtained from 106 Japanese individuals with those from 11 other nations. We found that the composition of the Japanese gut microbiome showed more abundant in the phylum Actinobacteria, in particular in the genus Bifidobacterium , than other nations. Regarding the microbial functions, those of carbohydrate metabolism were overrepresented with a concurrent decrease in those for replication and repair, and cell motility. The remarkable low prevalence of genes for methanogenesis with a significant depletion of the archaeon Methanobrevibacter smithii and enrichment of acetogenesis genes in the Japanese gut microbiome compared with others suggested a difference in the hydrogen metabolism pathway in the gut between them. It thus seems that the gut microbiome of the Japanese is considerably different from those of other populations, which cannot be simply explained by diet alone. We postulate possible existence of hitherto unknown factors contributing to the population-level diversity in human gut microbiomes.
The human gut microbiome has profound influences on the host's health largely through its interference with various intestinal functions. As recent studies have suggested diversity in the human gut microbiome among human populations, it will be interesting to analyse how gut microbiome is correlated with geographical, cultural, and traditional differences. The Japanese people are known to have several characteristic features such as eating a variety of traditional foods and exhibiting a low BMI and long life span. In this study, we analysed gut microbiomes of the Japanese by comparing the metagenomic data obtained from 106 Japanese individuals with those from 11 other nations. We found that the composition of the Japanese gut microbiome showed more abundant in the phylum Actinobacteria, in particular in the genus Bifidobacterium, than other nations. Regarding the microbial functions, those of carbohydrate metabolism were overrepresented with a concurrent decrease in those for replication and repair, and cell motility. The remarkable low prevalence of genes for methanogenesis with a significant depletion of the archaeon Methanobrevibacter smithii and enrichment of acetogenesis genes in the Japanese gut microbiome compared with others suggested a difference in the hydrogen metabolism pathway in the gut between them. It thus seems that the gut microbiome of the Japanese is considerably different from those of other populations, which cannot be simply explained by diet alone. We postulate possible existence of hitherto unknown factors contributing to the population-level diversity in human gut microbiomes.
Author Morita, Hidetoshi
Oshima, Kenshiro
Suda, Wataru
Nishijima, Suguru
Hirose, Yuu
Hattori, Masahira
Kim, Seok-Won
Author_xml – sequence: 1
  givenname: Suguru
  surname: Nishijima
  fullname: Nishijima, Suguru
  organization: Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
– sequence: 2
  givenname: Wataru
  surname: Suda
  fullname: Suda, Wataru
  organization: Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan
– sequence: 3
  givenname: Kenshiro
  surname: Oshima
  fullname: Oshima, Kenshiro
  organization: Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
– sequence: 4
  givenname: Seok-Won
  surname: Kim
  fullname: Kim, Seok-Won
  organization: RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
– sequence: 5
  givenname: Yuu
  surname: Hirose
  fullname: Hirose, Yuu
  organization: Electronics-Inspired Interdisciplinary Research Institute, Toyohashi University of Technology, Aichi 441-8580, Japan
– sequence: 6
  givenname: Hidetoshi
  surname: Morita
  fullname: Morita, Hidetoshi
  organization: Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
– sequence: 7
  givenname: Masahira
  surname: Hattori
  fullname: Hattori, Masahira
  email: m-hattori@aoni.waseda.jp
  organization: Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan m-hattori@aoni.waseda.jp
BackLink https://www.ncbi.nlm.nih.gov/pubmed/26951067$$D View this record in MEDLINE/PubMed
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Keywords metagenome
Japanese
microbiome
gut
Language English
License The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
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SubjectTerms Actinobacteria
Adult
Asian People
Bifidobacterium
Female
Gastrointestinal Microbiome - genetics
Gastrointestinal Tract - microbiology
Geography, Medical
Humans
Male
Metagenome
Methanobrevibacter smithii
Sequence Analysis, DNA
Young Adult
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