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Development of new method for environmental impact assessment by combination of genomics and mathematical statistics

Research Project

Project/Area Number 26550053
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Environmental impact assessment
Research InstitutionJapan Agency for Marine-Earth Science and Technology

Principal Investigator

TAKAMI Hideto  国立研究開発法人海洋研究開発機構, 海底資源研究開発センター, 上席研究員 (70359165)

Co-Investigator(Kenkyū-buntansha) TAKEMOTO Kazuhiro  九州工業大学, 情報工学研究院, 准教授 (40512356)
Project Period (FY) 2014-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2015: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2014: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Keywords環境メタゲノム / 生理代謝機能 / 環境影響評価 / 機能モジュール / MAPLEシステム / Q値 / 存在度 / KEGG / 生理代謝
Outline of Final Research Achievements

Objective of this study is to develop a new method for environmental impact assessment based on the metagenomic data of microbial communities obtained from the targeted environments by combination of genomics and mathematical statistics. First of all, we quantified the metabolic and physiological potential based on completion ratio of the KEGG functional modules.
Module completion ratio is easy-to-understand measure to evaluate functional potential but when the genes used for a module are shared with the other modules, the MCR does not necessarily reflect the working probability. Thus, we proposed the use of the Q-value for determining the significance of module completion. We also developed calculation method for abundance of each complete module to evaluate functional robustness. Since we could clarify the difference in functional potential between different sites using these methods, it is expected that our method is sufficiently applicable to actual environmental impact assessment.

Report

(3 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • Research Products

    (10 results)

All 2016 2015 2014

All Journal Article (1 results) (of which Peer Reviewed: 1 results,  Open Access: 1 results,  Acknowledgement Compliant: 1 results) Presentation (9 results) (of which Int'l Joint Research: 2 results,  Invited: 1 results)

  • [Journal Article] Functional classification of uncultured “Candidatus Caldiarchaeum subterraneum” using the MAPLE system2015

    • Author(s)
      Hideto Takami, Wataru Arai, Kazuhiro Takemoto, Ikuo Uchiyama, Takeaki Taniguchi
    • Journal Title

      PLoS ONE

      Volume: 10 Issue: 7 Pages: e0132994-e0132994

    • DOI

      10.1371/journal.pone.0132994

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] MAPLE 2.1による生理・代謝機能ポテンシャルの比較ゲノム解析2016

    • Author(s)
      荒井渉、谷口丈晃、竹本和広、守屋勇樹、五斗進、高見英人
    • Organizer
      第10回日本ゲノム微生物学会年会
    • Place of Presentation
      東工大 大岡山キャンパス (東京都・目黒区)
    • Year and Date
      2016-03-05
    • Related Report
      2015 Annual Research Report
  • [Presentation] Functional classification of uncultured“Ca. Caldiarchaeum subterraneum”using the Maple system2015

    • Author(s)
      Hideto Takami, Wataru Arai, Kazuhiro Takemoto, Ikuo Uchiyama, Takeaki Taniguchi
    • Organizer
      日本微生物生態学会 第30回大会
    • Place of Presentation
      土浦亀城プラザ (茨城県・土浦市)
    • Year and Date
      2015-10-19
    • Related Report
      2015 Annual Research Report
  • [Presentation] MAPLE 2.1による生理・代謝機能ポテンシャルの比較メタゲノム解析2015

    • Author(s)
      荒井渉、谷口丈晃、竹本和広、守屋勇樹、五斗進、高見英人
    • Organizer
      日本微生物生態学会 第30回大会
    • Place of Presentation
      土浦亀城プラザ (茨城県・土浦市)
    • Year and Date
      2015-10-19
    • Related Report
      2015 Annual Research Report
  • [Presentation] Metagenomic characterization of carbon fixation pathways in deep subseafloor microbial communities2015

    • Author(s)
      Hideto Takami, Wataru Arai, Yoshihiro Takaki, Toyoda Atsushi, Takeaki Taniguchi, Shinro Nishi,Taishi Tsubouchi, Mikihiko Kaewai, Fumio Inagaki
    • Organizer
      15th International Symposium on Microbial Ecology
    • Place of Presentation
      Seoul (韓国)
    • Year and Date
      2015-08-25
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] MAPLE system for evaluation of metabolic and physiological potential harbored in genome and metagenome2015

    • Author(s)
      Wataru Arai, Takeaki Taniguchi, Yuki Moriya, Susumu Goto, Hideto Takami
    • Organizer
      15th International Symposium on Microbial Ecology
    • Place of Presentation
      Seoul (韓国)
    • Year and Date
      2015-08-25
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] MAPLEシステムによるアーキアの機能分類と未培養アーキア“Ca. Caldiarchaeum subterraneum”の生理・代謝ポテンシャル解析2015

    • Author(s)
      高見英人、荒井渉、竹本和広、内山郁夫、谷口丈晃
    • Organizer
      日本アーキア研究会 第28回講演会
    • Place of Presentation
      愛媛大学 (愛媛県・松山市)
    • Year and Date
      2015-07-23
    • Related Report
      2015 Annual Research Report
  • [Presentation] MAPLEステムによる未培養アーキア”Ca. Caldiarchaeum subterraneum” の生理・代謝ポテンシャル解析2015

    • Author(s)
      高見英人
    • Organizer
      日本農芸化学会 2015年度大会
    • Place of Presentation
      岡山大学(岡山県岡山市)
    • Year and Date
      2015-03-28
    • Related Report
      2014 Research-status Report
  • [Presentation] 未培養アーキアのMAPLEシステムを用いた比較機能解析2015

    • Author(s)
      高見英人
    • Organizer
      第9回日本ゲノム微生物学会 年会
    • Place of Presentation
      神戸大学(兵庫県神戸市)
    • Year and Date
      2015-03-08
    • Related Report
      2014 Research-status Report
  • [Presentation] メタゲノム解析から見た海底下生態系の機能ポテンシャル2014

    • Author(s)
      高見英人
    • Organizer
      環境微生物系学会合同学会 2014
    • Place of Presentation
      アクトシティ浜松(静岡県浜松市)
    • Year and Date
      2014-10-22
    • Related Report
      2014 Research-status Report
    • Invited

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Published: 2014-04-04   Modified: 2017-05-10  

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