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Understanding metabolic systems for human gut microbiome

Research Project

Project/Area Number 25710016
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypePartial Multi-year Fund
Research Field Genome biology
Research InstitutionTokyo Institute of Technology

Principal Investigator

Yamada Takuji  東京工業大学, 生命理工学研究科, 講師 (10437262)

Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥25,870,000 (Direct Cost: ¥19,900,000、Indirect Cost: ¥5,970,000)
Fiscal Year 2015: ¥7,410,000 (Direct Cost: ¥5,700,000、Indirect Cost: ¥1,710,000)
Fiscal Year 2014: ¥7,410,000 (Direct Cost: ¥5,700,000、Indirect Cost: ¥1,710,000)
Fiscal Year 2013: ¥11,050,000 (Direct Cost: ¥8,500,000、Indirect Cost: ¥2,550,000)
Keywordsバイオインフォマティクス / メタゲノミクス / ヒト腸内細菌 / データベース / 腸内細菌 / メタゲノム / 代謝ネットワーク
Outline of Final Research Achievements

Human gut harbors millions of microbiome, and their functional ability have wide diversity. Most of related works are based on KEGG database for their functional annotation, however, most of functional modules are not well known.
Here we developed the database for gut microbiome, called as “enteropathway”, allows researchers uncover functionality of gut microbiome more clearly. For example, we suggested few modules have high diversity across 1000 individuals, showing the diverse metabolic potential. In addition, these novel defined modules are under represented in Obesity patients comparing with healthy individuals.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (11 results)

All 2016 2015 2014 Other

All Int'l Joint Research (1 results) Journal Article (3 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 3 results,  Open Access: 2 results) Presentation (7 results) (of which Int'l Joint Research: 2 results,  Invited: 7 results)

  • [Int'l Joint Research] European Molecular Biology Laboratory(Germany)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.2016

    • Author(s)
      Moriya, Y., Yamada, T., Okuda, S., Nakagawa, Z., Kotera, M., Tokimatsu, T., Kanehisa, M. & Goto, S.
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: 56 Issue: 3 Pages: 510-516

    • DOI

      10.1021/acs.jcim.5b00216

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data.2015

    • Author(s)
      Uchiyama T, Irie M, Mori H, Kurokawa K, Yamada T.
    • Journal Title

      PLoS One.

      Volume: 10 Issue: 5 Pages: e0126967-e0126967

    • DOI

      10.1371/journal.pone.0126967

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe.2015

    • Author(s)
      Wang T, Mori H, Zhang C, Kurokawa K, Xing X, Yamada T
    • Journal Title

      BMC Bioinformatics

      Volume: 16 Issue: 1 Pages: 96-96

    • DOI

      10.1186/s12859-015-0499-y

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Metabolic pathway database for Human gut microbiome2015

    • Author(s)
      Takuji Yamada
    • Organizer
      第67回日本生物工学会大会
    • Place of Presentation
      城山観光ホテル(鹿児島)
    • Year and Date
      2015-10-26
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Fecal metagenomic analysis of colorectal cancer cohort2015

    • Author(s)
      Takuji Yamada
    • Organizer
      第74回日本癌学会学術総会
    • Place of Presentation
      名古屋国際会議場
    • Year and Date
      2015-10-08
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ヒト腸内細菌代謝機能データベースの構築2015

    • Author(s)
      Takuji Yamada
    • Organizer
      第15回日本抗加齢医学会総会
    • Place of Presentation
      福岡国際会議場
    • Year and Date
      2015-05-29
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Metabolic pathway database for human microbiome2014

    • Author(s)
      山田拓司
    • Organizer
      第5回アジアトピックカンファレンス
    • Place of Presentation
      神戸ポートピアホテル 神戸
    • Year and Date
      2014-10-21
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Metabolic pathway database for human microbiome2014

    • Author(s)
      山田拓司
    • Organizer
      1st international Symposium on Mucosal Immunity and Vaccine Development 2014
    • Place of Presentation
      The University of Tokyo 東京
    • Year and Date
      2014-10-21
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] ヒト腸内細菌叢代謝データベースの構築2014

    • Author(s)
      山田拓司
    • Organizer
      第17回日本臨床腸内微生物学会
    • Place of Presentation
      東京慈恵会医科大学 東京
    • Year and Date
      2014-10-04
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 腸内細菌代謝反応データベースの構築2014

    • Author(s)
      山田拓司
    • Organizer
      第46回日本動脈硬化学会総会・学術集会
    • Place of Presentation
      京王プラザホテル 東京
    • Year and Date
      2014-07-10
    • Related Report
      2014 Annual Research Report
    • Invited

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Published: 2013-05-21   Modified: 2019-07-29  

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