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Understanding and controlling gut bacterial metabolism

Research Project

Project/Area Number 18K18153
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 62010:Life, health and medical informatics-related
Research InstitutionKyushu Institute of Technology

Principal Investigator

Maeda Kazuhiro  九州工業大学, 大学院情報工学研究院, 助教 (50631230)

Project Period (FY) 2018-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2021: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2020: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2019: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2018: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Keywordsシミュレーション / 最適化 / 大腸菌 / 腸内細菌 / システム生物学 / 窒素代謝 / C言語 / 遺伝的アルゴリズム / アンモニアトランスポーター / 細菌叢
Outline of Final Research Achievements

Abnormal gut microbiota composition is associated with the risk of various diseases. Safe and rational treatment strategies are needed to normalize it. It is essential to understand the metabolism of gut microbiota.

In this study, we have developed a technique for simulating gut microbiota metabolism. Then, we constructed a simulation model for bacterial nitrogen metabolism and showed that the uptake of ammonia as a nitrogen source significantly affects bacterial growth.

Academic Significance and Societal Importance of the Research Achievements

シミュレーションモデルを構築するための2つのソフトウェア、libRCGAとRCGAToolboxを開発した。これらはGitHubで誰でも入手可能である。さらに、それを用いて、細菌の窒素代謝に関するシミュレーションモデルを構築した。このモデルを使うことで、細胞サイズなどの生物学的パラメーターの異なる様々な細菌の窒素代謝をシミュレーションできる。今後、この研究成果に基づいて、腸内細菌の代謝の正確なシミュレーションが実現できれば、腸内細菌正常化のための食事療法の効果の予測、治療方針の合理的設計が可能になる。

Report

(5 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Research-status Report
  • 2019 Research-status Report
  • 2018 Research-status Report
  • Research Products

    (40 results)

All 2022 2021 2020 2019 2018 Other

All Int'l Joint Research (5 results) Journal Article (5 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 3 results,  Open Access: 5 results) Presentation (20 results) (of which Int'l Joint Research: 6 results,  Invited: 2 results) Remarks (10 results)

  • [Int'l Joint Research] アムステルダム自由大学(オランダ)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] アムステルダム自由大学(オランダ)

    • Related Report
      2020 Research-status Report
  • [Int'l Joint Research] アムステルダム自由大学(オランダ)

    • Related Report
      2019 Research-status Report
  • [Int'l Joint Research] アムステルダム自由大学/アムステルダム大学(オランダ)

    • Related Report
      2018 Research-status Report
  • [Int'l Joint Research] マンチェスター大学(英国)

    • Related Report
      2018 Research-status Report
  • [Journal Article] RCGAToolbox: A Real-coded Genetic Algorithm Software for Parameter Estimation of Kinetic Models2021

    • Author(s)
      Maeda Kazuhiro、Boogerd Fred C.、Kurata Hiroyuki
    • Journal Title

      IPSJ Transactions on Bioinformatics

      Volume: 14 Issue: 0 Pages: 30-35

    • DOI

      10.2197/ipsjtbio.14.30

    • NAID

      130008120842

    • ISSN
      1882-6679
    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] RCGAToolbox: A real-coded genetic algorithm software for parameter estimation of kinetic models2021

    • Author(s)
      Maeda Kazuhiro、Boogerd Fred C.、Kurata Hiroyuki
    • Journal Title

      bioRxiv

      Volume: 1 Pages: 1-1

    • DOI

      10.1101/2021.02.15.431062

    • NAID

      130008120842

    • Related Report
      2020 Research-status Report
    • Open Access / Int'l Joint Research
  • [Journal Article] 動力学パラメータ推定問題:大腸菌アンモニア輸送-同化ネットワークの事例2019

    • Author(s)
      前田 和勲
    • Journal Title

      研究報告バイオ情報学(BIO)

      Volume: 5 Pages: 1-1

    • Related Report
      2019 Research-status Report
    • Open Access
  • [Journal Article] Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network2019

    • Author(s)
      Maeda Kazuhiro、Westerhoff Hans V.、Kurata Hiroyuki、Boogerd Fred C.
    • Journal Title

      npj Systems Biology and Applications

      Volume: 5 Issue: 1 Pages: 1-1

    • DOI

      10.1038/s41540-019-0091-6

    • NAID

      120006778226

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] libRCGA: a C library for real-coded genetic algorithms for rapid parameter estimation of kinetic models2018

    • Author(s)
      Maeda Kazuhiro、Boogerd Fred C.、Kurata Hiroyuki
    • Journal Title

      IPSJ Transactions on Bioinformatics

      Volume: 11 Issue: 0 Pages: 31-40

    • DOI

      10.2197/ipsjtbio.11.31

    • NAID

      130007483197

    • ISSN
      1882-6679
    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] RCGAToolbox: 動力学モデルのパラメーター推定 のための実数値遺伝的アルゴリズムソフトウェア2022

    • Author(s)
      前田和勲、Fred C. Boogerd、倉田博之
    • Organizer
      第69回 情報処理学会 バイオ情報学研究会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 動力学シミュレーションを使った生化学システムの理解と設計2021

    • Author(s)
      前田和勲
    • Organizer
      第2回分子サイバネティクス・第46回分子ロボティクス定例研究会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] RCGAToolboxを使った遺伝子回路の自動設計2021

    • Author(s)
      前田和勲、倉田博之
    • Organizer
      IIBMP2021
    • Related Report
      2021 Annual Research Report
  • [Presentation] RCGAToolbox: A real-coded genetic algorithm software for parameter estimation of kinetic models2021

    • Author(s)
      Kazuhiro Maeda, Fred C. Boogerd, Hiroyuki Kurata
    • Organizer
      ISMB/ECCB 2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] RCGAToolbox: 生化学システムの動力学パラメータ推定のためのツールボックス2020

    • Author(s)
      前田和勲、倉田博之
    • Organizer
      IIBMP2020
    • Related Report
      2020 Research-status Report
  • [Presentation] 大腸菌アンモニア輸送-同化ネットワークの定量的動力学モデルの構築2019

    • Author(s)
      前田和勲
    • Organizer
      第71回日本生物工学会大会
    • Related Report
      2019 Research-status Report
  • [Presentation] 制約付き最適化に基づくパラメータ推定を用いた大腸菌アンモニア輸送-同化の動力学モデリング2019

    • Author(s)
      前田和勲
    • Organizer
      IBMP2019
    • Related Report
      2019 Research-status Report
  • [Presentation] 動力学パラメータ推定問題:大腸菌アンモニア同化-輸送ネットワークの事例2019

    • Author(s)
      前田和勲
    • Organizer
      第59回 情報処理学会 バイオ情報学研究会
    • Related Report
      2019 Research-status Report
  • [Presentation] The ‘rubber band method’ of ranking network mechanisms rather than claimi the single best: E. coli's active ammonium transport is 130 times better than the passive transport network2019

    • Author(s)
      前田和勲
    • Organizer
      ICSB2019
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Ranking E. coli’s ammonium transport and assimilation networks2019

    • Author(s)
      Fred C. Boogerd
    • Organizer
      AIMMS Meeting
    • Related Report
      2019 Research-status Report
  • [Presentation] Ranking E. coli’s ammonium transport and assimilation networks by how they fit diverse experiments2019

    • Author(s)
      前田和勲
    • Organizer
      BioSB 2019
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Ranking E. coli’s ammonium transport and assimilation netwoks by how they fit diverse experiments2019

    • Author(s)
      Kazuhiro Maeda, Hans V. Westerhoff, Hiroyuki Kurata, and Fred C. Boogerd
    • Organizer
      AMSA Meeting
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] 生物シミュレーションモデルのパラメータ推定問題2019

    • Author(s)
      前田和勲
    • Organizer
      創価大学
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Ranking E. coli’s ammonium transport and assimilation network by how they fit diverse experiments2019

    • Author(s)
      Kazuhiro Maeda, Hans V. Westerhoff, Hiroyuki Kurata, and Fred C. Boogerd
    • Organizer
      AIMMS Meeting
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Ranking E. coli’s ammonium transport and assimilation networks by how they fit diverse experiments2019

    • Author(s)
      Kazuhiro Maeda, Hans V. Westerhoff, Hiroyuki Kurata, and Fred C. Boogerd
    • Organizer
      BioSB 2019
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] 大腸菌アンモニア輸送-同化システムのシミュレーション2019

    • Author(s)
      Kazuhiro Maeda, Hans V. Westerhoff, Hiroyuki Kurata, and Fred C. Boogerd
    • Organizer
      定量生物学の会 第9回年会
    • Related Report
      2018 Research-status Report
  • [Presentation] 制約付き最適化を使った動力学パラメータ推定手法の提案と大腸菌アンモニア同化-輸送ネットワークへの応用2018

    • Author(s)
      Kazuhiro Maeda, Hans V. Westerhoff, Hiroyuki Kurata, and Fred C. Boogerd
    • Organizer
      生命科学系フロンティアミーティング
    • Related Report
      2018 Research-status Report
  • [Presentation] libRCGA: 動力学モデルの高速なパラメータ推定のための遺伝的アルゴリズムライブラリ2018

    • Author(s)
      前田和勲、Fred C. Boogerd、倉田博之
    • Organizer
      第55回 情報処理学会 バイオ情報学研究会
    • Related Report
      2018 Research-status Report
  • [Presentation] 大腸菌AmtBはアンモニアの能動輸送体か?それとも受動輸送体か?2018

    • Author(s)
      Kazuhiro Maeda, Hans V. Westerhoff, Hiroyuki Kurata, and Fred C. Boogerd
    • Organizer
      The 41th Annual Meeting of the Molecular Biology Society of Japan
    • Related Report
      2018 Research-status Report
  • [Presentation] ネガティブフィードバック構造に基づく生物振動子の頑健性と調節可能性の解析2018

    • Author(s)
      前田和勲、倉田博之
    • Organizer
      IIBMP2018
    • Related Report
      2018 Research-status Report
  • [Remarks] Kazuhiro Maeda - SysMod - Poster - ISMB/ECCB 2021

    • URL

      https://www.youtube.com/watch?v=oooDjwyCipQ&ab_channel=ISCB

    • Related Report
      2021 Annual Research Report
  • [Remarks] RCGAToolboxのビデオチュートリアル

    • URL

      https://www.youtube.com/playlist?list=PLOpE8E-aX1H8qqWvf1YSoN2nA6O-2wfYA

    • Related Report
      2021 Annual Research Report
  • [Remarks] RCGAToolbox (GitHub)

    • URL

      https://github.com/kmaeda16/RCGAToolbox

    • Related Report
      2021 Annual Research Report
  • [Remarks] 研究成果ダウンロードサイト

    • URL

      https://github.com/kmaeda16/RCGAToolbox

    • Related Report
      2020 Research-status Report
  • [Remarks] 研究成果に関するウェブサイト

    • URL

      https://www.biorxiv.org/content/10.1101/2021.02.15.431062v1

    • Related Report
      2020 Research-status Report
  • [Remarks] 研究者ウェブサイト

    • URL

      https://sites.google.com/view/kazuhiro-maeda/%E3%83%9B%E3%83%BC%E3%83%A0

    • Related Report
      2019 Research-status Report
  • [Remarks] 研究成果に関するウェブサイト

    • URL

      http://www.ccr.kyutech.ac.jp/ttacademy/news/entry-4435.html

    • Related Report
      2019 Research-status Report
  • [Remarks] 研究成果に関するウェブサイト

    • URL

      https://www.aimms.vu.nl/en/news-events/news-archive/2019/apr-jun/ranking-e-colis-ammonium-transport-and-assimilation-networks.aspx

    • Related Report
      2019 Research-status Report
  • [Remarks] 九州工業大学 若手研究者フロンティア研究アカデミー

    • URL

      http://www.ccr.kyutech.ac.jp/ttacademy/news/entry-4435.html

    • Related Report
      2018 Research-status Report
  • [Remarks] 研究代表者ウェブサイト

    • URL

      http://kurata21.bio.kyutech.ac.jp/maeda/

    • Related Report
      2018 Research-status Report

URL: 

Published: 2018-04-23   Modified: 2023-01-30  

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