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Evaluating and designing microbial ecosystems using metabolic networks: theory and its applications

Research Project

Project/Area Number 17H04703
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypeSingle-year Grants
Research Field Life / Health / Medical informatics
Research InstitutionKyushu Institute of Technology

Principal Investigator

Takemoto Kazuhiro  九州工業大学, 大学院情報工学研究院, 准教授 (40512356)

Project Period (FY) 2017-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥20,670,000 (Direct Cost: ¥15,900,000、Indirect Cost: ¥4,770,000)
Fiscal Year 2020: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Fiscal Year 2019: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2018: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000)
Fiscal Year 2017: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Keywordsネットワーク科学 / 微生物生態系 / 代謝ネットワーク / 数理生物学 / 環境変動 / 環境 / 生態系 / ネットワーク理論
Outline of Final Research Achievements

Understanding microbial community structure is important in medical and environmental sciences. Remarkable development of high-throughput sequencing techniques have provided snapshots of taxonomic compositions in microbial communities across diverse ecosystems; however, uniderstanding of the structure is fall behind due to a lack of reliable methods. Thus, we developed a novel method for estimating microbial community structure using metabolic network analysis: Estimator of COmmunity Structure based on MetabOlic networkS (ECOSMOS). we applied ECOSMOS to human gut microbiome and Erath microbiome data and revealed how micribial community strcture altered with respect to disease and environemntal changes. Our method and findings open new possibilities for medical diagnosis and enviromnetal assessment based on microbiome data.

Academic Significance and Societal Importance of the Research Achievements

ヒトの腸内や土壌のような様々な環境で微生物は生態系を形成している。微生物の生態系構造を理解することは医療・環境分野で極めて重要である。遺伝子配列を決定する技術が飛躍的に進歩したものの、そのような生態系構造の理解は既存手法の限界のため進んでいない。そこで本研究では、微生物の生体分子ネットワークを利用することで微生物の生態系構造を明らかにする計算手法を開発した。この手法を様々な事例に適用し、疾病や環境変動によって微生物生態系がどのように応答するのかを定量的に評価することができるようになった。提案手法や研究成果は微生物叢に基づく病気の治療、環境影響評価や環境浄化支援に広く役立てることができる。

Report

(5 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • Research Products

    (37 results)

All 2021 2020 2019 2018 2017 Other

All Journal Article (12 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 12 results,  Open Access: 10 results) Presentation (21 results) (of which Int'l Joint Research: 9 results,  Invited: 4 results) Book (1 results) Remarks (3 results)

  • [Journal Article] Diversity of Dominant Soil Bacteria Increases with Warming Velocity at the Global Scale2021

    • Author(s)
      Kanzaki Yoshiaki、Takemoto Kazuhiro
    • Journal Title

      Diversity

      Volume: 13 Issue: 3 Pages: 120-120

    • DOI

      10.3390/d13030120

    • NAID

      120006997074

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The brain-derived neurotrophic factor Val66Met polymorphism increases segregation of structural correlation networks in healthy adult brains2020

    • Author(s)
      Ueda Issei、Takemoto Kazuhiro、Watanabe Keita、Sugimoto Koichiro、Ikenouchi Atsuko、Kakeda Shingo、Katsuki Asuka、Yoshimura Reiji、Korogi Yukunori
    • Journal Title

      PeerJ

      Volume: 8 Pages: e9632-e9632

    • DOI

      10.7717/peerj.9632

    • NAID

      120006997075

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Revisiting the hypothesis of an energetic barrier to genome complexity between eukaryotes and prokaryotes2020

    • Author(s)
      Chiyomaru K, Takemoto K
    • Journal Title

      Royal Society Open Science

      Volume: 7 Issue: 2 Pages: 191859-191859

    • DOI

      10.1098/rsos.191859

    • NAID

      120006997082

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Difficulty in inferring microbial community structure based on co-occurrence network approaches2019

    • Author(s)
      Hirano H, Takemoto K
    • Journal Title

      BMC Bioinformatics

      Volume: 20 Issue: 1

    • DOI

      10.1186/s12859-019-2915-1

    • NAID

      120006649510

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] MAPLE 2.3.0: an improved system for evaluating the functionomes of genomes and metagenomes2018

    • Author(s)
      Arai Wataru、Taniguchi Takeaki、Goto Susumu、Moriya Yuki、Uehara Hideya、Takemoto Kazuhiro、Ogata Hiroyuki、Takami Hideto
    • Journal Title

      Bioscience, Biotechnology, and Biochemistry

      Volume: 82 Issue: 9 Pages: 1515-1517

    • DOI

      10.1080/09168451.2018.1476122

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A network biology-based approach to evaluating the effect of environmental contaminants on human interactome and diseases2018

    • Author(s)
      Iida, M. and Takemoto, K.
    • Journal Title

      Ecotoxicology and Environmental Safety

      Volume: 160 Pages: 316-327

    • DOI

      10.1016/j.ecoenv.2018.05.065

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Decomposing the effects of ocean environments on predator-prey body-size relationships in food webs2018

    • Author(s)
      Dobashi, T., Iida, M. and Takemoto K.
    • Journal Title

      Royal Society Open Science

      Volume: 5 Issue: 7

    • DOI

      10.1098/rsos.180707

    • NAID

      120006649507

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Network resilience of mutualistic ecosystems and environmental changes: an empirical study2018

    • Author(s)
      Nagaishi Ellie、Takemoto Kazuhiro
    • Journal Title

      Royal Society Open Science

      Volume: 5 Issue: 9 Pages: 180706-180706

    • DOI

      10.1098/rsos.180706

    • NAID

      120006649509

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Brain structural connectivity and neuroticism in healthy adults2018

    • Author(s)
      Ueda, I., Kakeda, S., Watanabe, K., Sugimoto, K., Igata, N., Moriya, J., Takemoto, K., Katsuki, A., Yoshimura, R., Abe, O. and Korogi, Y.
    • Journal Title

      Scientific Reports

      Volume: 8 Issue: 1

    • DOI

      10.1038/s41598-018-34846-1

    • NAID

      120006649508

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework2018

    • Author(s)
      J. Song, F. Li, K. Takemoto, G. HaHaffari, T. Akutsu, K-C. Chou, and G. I. Webb
    • Journal Title

      Journal of Theoretical Biology

      Volume: 443 Pages: 125-137

    • DOI

      10.1016/j.jtbi.2018.01.023

    • NAID

      120007026466

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding.2018

    • Author(s)
      Uemura E, Niwa T, Minami S, Takemoto K, Fukuchi S, Machida K, Imataka H, Ueda T, Ota M, Taguchi H.
    • Journal Title

      Sci Rep.

      Volume: 8 Issue: 1 Pages: 678-678

    • DOI

      10.1038/s41598-017-18977-5

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Limitations of a metabolic network-based reverse ecology method for inferring host-pathogen interactions.2017

    • Author(s)
      Takemoto, K. and Aie, K.
    • Journal Title

      BMC Bioinformatics

      Volume: 18 Issue: 1 Pages: 278-278

    • DOI

      10.1186/s12859-017-1696-7

    • NAID

      120006649515

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] 環境変動と土壌マイクロバイオームの関係についての全球規模解析2020

    • Author(s)
      神崎祥昭, 竹本和広
    • Organizer
      2020年日本バイオインフォマティクス学会年会・第9回生命医薬情報学連合大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] COVID-19伝播速度における気候の役割:地理空間データ分析2020

    • Author(s)
      竹本和広, 千代丸勝美
    • Organizer
      2020年日本バイオインフォマティクス学会年会・第9回生命医薬情報学連合大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 微生物群集構造の推定:共起ネットワーク分析と代謝ネットワーク解析2020

    • Author(s)
      竹本和広
    • Organizer
      第320回京都大学生態学研究セミナー
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Simple iterative method for generating targeted universal adversarial perturbations2020

    • Author(s)
      Hirano H, Takemoto K
    • Organizer
      25th International Symposium on Artificial Life and Robotics (AROB 25th 2020)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Are co-occurrence network approaches really useful for inferring microbial community structure?2019

    • Author(s)
      Hirano H, Takemoto K
    • Organizer
      Conference on Complex Systems (CCS) 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A metabolic network-based reverse ecology method indicates that gut microbial communities are fragile in diseased patients2019

    • Author(s)
      Takemoto K
    • Organizer
      Conference on Complex Systems (CCS) 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Revisiting the energetics of the prokaryote-eukaryote divide2019

    • Author(s)
      Chiyomaru K, Takemoto K
    • Organizer
      Conference on Complex Systems (CCS) 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 原核生物-真核生物間のエネルギー障壁の統計解析2019

    • Author(s)
      千代丸勝美, 竹本和広
    • Organizer
      日本生体エネルギー研究会第45回討論会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Universal Adversarial Perturbationを用いた医療画像診断用ディープニューラルネットワークの信頼性評価2019

    • Author(s)
      平野北斗, 三奈木啓成, 竹本和広
    • Organizer
      第22回情報論的学習理論ワークショップ(IBIS 2019)
    • Related Report
      2019 Annual Research Report
  • [Presentation] 転移学習された画像分類モデルのUniversal Adversarial Perturbationに対する脆弱性:病理画像診断を例にして2019

    • Author(s)
      三奈木啓成, 平野北斗, 竹本和広
    • Organizer
      第22回情報論的学習理論ワークショップ(IBIS 2019)
    • Related Report
      2019 Annual Research Report
  • [Presentation] Is metabolic network-based reverse ecology method really useful for inferring host-pathogen interactions?2018

    • Author(s)
      Takemoto, K. and Aie K.
    • Organizer
      The 2018 edition of the annual International Conference and School of Network Science 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Resilience of plant-animal mutualistic networks is associated with environmental changes.2018

    • Author(s)
      Nagaishi, E. and Takemoto, K.
    • Organizer
      The 2018 edition of the annual International Conference and School of Network Science 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ネットワーク科学で展開する統合生物学:生物学的階層をつなぐ2018

    • Author(s)
      竹本和広
    • Organizer
      ネットワーク科学セミナー
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 環境汚染物質とヒト疾患の関連性評価2018

    • Author(s)
      飯田緑, 竹本和広
    • Organizer
      第24回日本環境毒性学会研究発表会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Exosomes may increase habitat variability in mammals2018

    • Author(s)
      Takemoto, K. and Imoto, M.
    • Organizer
      Conference on Complex Systems 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Effects of ocean environments on predator-prey body-size relationships in marine food-web networks2018

    • Author(s)
      Dobashi, T., Iida, M. and Takemoto, K.
    • Organizer
      Conference on Complex Systems 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 理論とデータをつなぐネットワーク生態学:ネットワークのマクロ生態学研究を例にして2018

    • Author(s)
      竹本和広
    • Organizer
      第66回日本生態学会大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 何が代謝ネットワークの進化を促進したのか2017

    • Author(s)
      竹本和広
    • Organizer
      生命の起源および進化学会第42回講演会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 代謝ネットワークを用いた微生物生態系構造の推定2017

    • Author(s)
      竹本和広
    • Organizer
      環境微生物系学会合同大会2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] Estimating microbial community structure using metabolic networks2017

    • Author(s)
      Takemoto, K.
    • Organizer
      7th Congress of European Microbiologists (FEMS 2017)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 竹本和広2017

    • Author(s)
      複雑ネットワーク生物学:理論と応用
    • Organizer
      第6回生命医薬情報学連合大会
    • Related Report
      2017 Annual Research Report
  • [Book] Encyclopedia of Bioinformatics and Computational Biology2018

    • Author(s)
      Ranganathan, S., Nakai, K., Schonbach C. and Gribskov, M. (eds.)
    • Total Pages
      3284
    • Publisher
      Elsevier
    • ISBN
      9780128114148
    • Related Report
      2018 Annual Research Report
  • [Remarks] ECOSMOSソフトウェア

    • URL

      http://takemoto08.bio.kyutech.ac.jp/ecosmos-lite/

    • Related Report
      2020 Annual Research Report
  • [Remarks] 研究室ホームページ

    • URL

      https://sites.google.com/view/takemotolab

    • Related Report
      2020 Annual Research Report
  • [Remarks] 業績リスト

    • URL

      https://sites.google.com/site/kztakemoto/publication

    • Related Report
      2019 Annual Research Report 2018 Annual Research Report 2017 Annual Research Report

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Published: 2017-04-28   Modified: 2022-01-27  

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