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Development of a simulator to evaluate the efficacy of an antibacterial agent to resident and resistant bacteria

Research Project

Project/Area Number 20K21875
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 90:Biomedical engineering and related fields
Research InstitutionTohoku University

Principal Investigator

Ishikawa Takuji  東北大学, 医工学研究科, 教授 (20313728)

Project Period (FY) 2020-07-30 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
Fiscal Year 2022: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2021: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2020: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Keywords腸内フローラ / シミュレーション / 可視化実験 / 大腸菌
Outline of Research at the Start

「数理モデル」は、腸内フローラのような複雑系の骨格を理解し、定量的に記述するのに最良のツールである。本研究では、「輸送現象論」を基盤とし、常在菌と耐性菌に対する抗菌薬の薬効評価を目指した腸内フローラの数理モデルを開発することを目標とする。研究対象をゼブラフィッシュと線虫とし、数理と実験を丹念に融合させることで、予測精度の高い革新的な数理モデルを構築する。

Outline of Final Research Achievements

Peristaltic movements of juvenile zebrafish were successfully measured. Visualisation of intestinal flow, drug concentrations and endogenous and resistant bacteria was also carried out. These results were published in the American Journal of Physiology, a well-established journal in the field of physiology. Mathematical modelling of the intestinal flora was also carried out, and a continuum analysis describing the macroscopic bacterial accumulation was performed. It was then clarified that the macroscopic distribution of E. coli in the gut is produced by a combination of physical and biological factors, and it was shown that the bacterial dynamics in the gut environment can be accurately described by a mathematical model. The results were published in BMC Biology, a well-established journal in the field of biology.

Academic Significance and Societal Importance of the Research Achievements

ヒトの腸内には1kgもの細菌が生息しており、腸内フローラと呼ばれる生態系を形成している。近年、腸内フローラが宿主の様々な疾患と密接に関わっていることが明らかとなり、腸内フローラの違いを利用した診断や、糞便微生物叢移植などの治療技術の革新が期待されている。こうした技術革新の核となるのは、腸内フローラを予測し、制御する技術であるが、現状では腸内フローラの形成メカニズムは解明されておらず、極めて困難と言わざるを得ない。本成果は、こうした現状を打破し、腸内フローラの形成を予測し制御するための礎となる。

Report

(5 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Research-status Report
  • 2020 Research-status Report
  • Research Products

    (28 results)

All 2024 2023 2022 2021 2020 Other

All Int'l Joint Research (2 results) Journal Article (10 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 10 results,  Open Access: 9 results) Presentation (14 results) (of which Int'l Joint Research: 9 results,  Invited: 1 results) Remarks (2 results)

  • [Int'l Joint Research] 中国医科大学(中国)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] 中国医科大学(中国)

    • Related Report
      2021 Research-status Report
  • [Journal Article] Bacterial accumulation in intestinal folds induced by physical and biological factors.2024

    • Author(s)
      Jinyou Yang, Toma Isaka, Kenji Kikuchi, Keiko Numayama-Tsuruta, Takuji Ishikawa
    • Journal Title

      BMC Biology

      Volume: 22 Issue: 1 Pages: 76-76

    • DOI

      10.1186/s12915-024-01874-5

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Glucose stockpile in the intestinal apical brush border in C. elegans2024

    • Author(s)
      Saito Takumi、Kikuchi Kenji、Ishikawa Takuji
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 706 Pages: 149762-149762

    • DOI

      10.1016/j.bbrc.2024.149762

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] High shear flow prevents bundling of bacterial flagella and induces lateral migration away from a wall2023

    • Author(s)
      Yang Jinyou、Kikuchi Kenji、Ishikawa Takuji
    • Journal Title

      Communications Physics

      Volume: 6 Issue: 1 Pages: 354-354

    • DOI

      10.1038/s42005-023-01471-y

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Reciprocating intestinal flows enhance glucose uptake in C. elegans2022

    • Author(s)
      Yuki Suzuki, Kenji Kikuchi, Keiko Numayama-Tsuruta, Takuji Ishikawa
    • Journal Title

      Scientific reports

      Volume: 12 Issue: 1 Pages: 15310-15310

    • DOI

      10.1038/s41598-022-18968-1

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Bacterial behaviors in confined diorama environments2022

    • Author(s)
      Ishikawa Takuji
    • Journal Title

      Biophysical Journal

      Volume: 121 Issue: 13 Pages: 2487-2489

    • DOI

      10.1016/j.bpj.2022.05.045

    • Related Report
      2022 Research-status Report
    • Peer Reviewed
  • [Journal Article] Impact of rheological properties on bacterial streamer formation2021

    • Author(s)
      Hiroki Kitamura, Toshihiro Omori, Takuji Ishikawa
    • Journal Title

      Journal of the Royal Society Interface

      Volume: 18 Issue: 183 Pages: 20210546-20210546

    • DOI

      10.1098/rsif.2021.0546

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Non-biodegradable objects may boost microbial growth in water bodies by harnessing bubbles2021

    • Author(s)
      Srivastava Atul、Kikuchi Kenji、Ishikawa Takuji
    • Journal Title

      Royal Society Open Science

      Volume: 8 Issue: 9 Pages: 210646-210646

    • DOI

      10.1098/rsos.210646

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Mechanical roles of anterograde and retrograde intestinal peristalses after feeding in a larval fish (Danio rerio)2020

    • Author(s)
      Kenji Kikuchi, Hyontack Noh, Keiko Numayama-Tsuruta, Takuji Ishikawa
    • Journal Title

      American Journal of Physiology - Gastrointestinal and Liver Physiology

      Volume: - Issue: 6 Pages: G1013-G1021

    • DOI

      10.1152/ajpgi.00165.2019

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] How do Caenorhabditis elegans worms survive in highly viscous habitats?2020

    • Author(s)
      Yuki Suzuki, Kenji Kikuchi, Keiko Numayama-Tsuruta, Takuji Ishikawa
    • Journal Title

      Journal of Experimental Biology

      Volume: 223 Pages: 1-10

    • DOI

      10.1242/jeb.224691

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Bacterial biomechanics?From individual behaviors to biofilm and the gut flora2020

    • Author(s)
      Ishikawa Takuji、Omori Toshihiro、Kikuchi Kenji
    • Journal Title

      APL Bioengineering

      Volume: 4 Issue: 4 Pages: 041504-041504

    • DOI

      10.1063/5.0026953

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Intestinal folds accumulate bacteria through physical and biological factors2023

    • Author(s)
      J. Yang, T. Isaka,K. Kikuchi, K. Numayama-Tsuruta,T. Ishikawa
    • Organizer
      76th Annual Meeting of the APS Division of Fluid Dynamics
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Stagnation Phenomenon of Motile E. Coli in a Folding Wall2023

    • Author(s)
      Toma Isaka, Kenji Kikuchi, Keiko Numayama-Tsuruta and Takuji Ishikawa
    • Organizer
      AP-Biomech 2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Transdermal Transport through Intercellular Gaps of Liposomes in Suspensions2023

    • Author(s)
      Jiawei Huang, Kenji Kikuchi, Keiko Numayama-Tsuruta and Takuji Ishikawa
    • Organizer
      AP-Biomech 2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Nutrient delivery pathway tracing and drug efficacy evaluation by fluorescent glucose2023

    • Author(s)
      Jiawei HUANG, Kenji KIKUCHI, Keiko NUMAYAMA, Takuji ISHIKAWA
    • Organizer
      第51回可視化情報シンポジウム
    • Related Report
      2023 Annual Research Report
  • [Presentation] ゼブラフィッシュ腸蠕動に伴う腸内細菌分布の可視化計測2023

    • Author(s)
      菊永祐太,菊地謙次,沼山恵子,石川拓司
    • Organizer
      第51回可視化情報シンポジウム
    • Related Report
      2023 Annual Research Report
  • [Presentation] 窪みを有する壁面近傍における大腸菌滞留性の解明2023

    • Author(s)
      井坂斗真,菊地謙次,沼山 恵子,石川 拓司
    • Organizer
      日本流体力学会年会2023
    • Related Report
      2023 Annual Research Report
  • [Presentation] Microbial transport of E.coli in the gut of a zebrafish larva2022

    • Author(s)
      Yuta Kikunaga,Kenji Kikuchi, Keiko Numayama-Tsuruta, Takuji Ishikawa
    • Organizer
      9th World Congress of Biomechanics
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] Visualization of microbial transport in the gut of a zebrafish larva2022

    • Author(s)
      Yuta Kikunaga, Kenji Kikuchi, Keiko Numayama-Tsuruta and Takuji Ishikawa
    • Organizer
      PSFVIP13
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] SIMULATION OF A PACKED SUSPENSION OF MICROSWIMMERS2022

    • Author(s)
      Yu Kogure,Toshihiro Omori and Takuji Ishikawa
    • Organizer
      PSFVIP13
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] Mass transport in induced by a packed lattice of squirmers2022

    • Author(s)
      Yu Kogure,Toshihiro Omori,Takuji Ishikawa
    • Organizer
      9th World Congress of Biomechanics
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] Mass Transport in a Packed Suspension of Swimming Microorganisms2021

    • Author(s)
      Y. Kogure, T. Omori, T. Ishikawa
    • Organizer
      18th International Conference on Flow Dynamics
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Mass transport in an aggregation of swimming microorganisms2021

    • Author(s)
      Yu Kogure, Toshihiro Omori, Takuji Ishikawa
    • Organizer
      The 11th Asian-Pacific Conference on Biomechanics
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] 微生物濃厚懸濁液中の物質拡散シミュレーション2021

    • Author(s)
      小暮悠, 大森俊宏, 石川拓司
    • Organizer
      第35回数値流体力学シンポジウム CFD35
    • Related Report
      2021 Research-status Report
  • [Presentation] Biomechanics can provide a new perspective on microbiology2020

    • Author(s)
      Takuji Ishikawa
    • Organizer
      Webinar in Sharif University of Technology
    • Related Report
      2020 Research-status Report
    • Invited
  • [Remarks] Biological Flow Studies Laboratory

    • URL

      http://www.bfsl.mech.tohoku.ac.jp/

    • Related Report
      2022 Research-status Report 2020 Research-status Report
  • [Remarks] Biological Flow Studies Laboratory

    • URL

      http://www.bfsl.mech.tohoku.ac.jp/index_jp.html

    • Related Report
      2021 Research-status Report

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Published: 2020-08-03   Modified: 2025-01-30  

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