Prediction and control of multi-species systems: 10000-microbiome experiments

• Project/Area Number: 20K20586
• Research Category: Grant-in-Aid for Challenging Research (Pioneering)
• Allocation Type: Multi-year Fund
• Review Section: Medium-sized Section 45:Biology at organismal to population levels and anthropology, and related fields
• Research Institution: Kyoto University
• Principal Investigator: Toju Hirokazu 京都大学, 生命科学研究科, 教授 (60585024)
• Project Period (FY): 2020-07-30 – 2024-03-31
• Project Status: Completed (Fiscal Year 2023)
• Budget Amount: ¥25,870,000 (Direct Cost: ¥19,900,000、Indirect Cost: ¥5,970,000); Fiscal Year 2022: ¥8,710,000 (Direct Cost: ¥6,700,000、Indirect Cost: ¥2,010,000); Fiscal Year 2021: ¥7,930,000 (Direct Cost: ¥6,100,000、Indirect Cost: ¥1,830,000); Fiscal Year 2020: ¥9,230,000 (Direct Cost: ¥7,100,000、Indirect Cost: ¥2,130,000)
• Keywords: 時系列 / 微生物叢 / 生態系 / 時系列動態 / 生物群集 / 微生物 / 生物間相互作用 / 群集動態 / 代替安定性 / 群集の安定性

Outline of Research at the Start

微生物学・ゲノム科学・分析化学・生態学・数学を融合し、微生物群集（微生物叢）の動態を予測・制御する科学的アプローチを確立する。
多数の種で構成されるシステムの制御は、これまで不可能とされてきた。しかし、これまでの予備研究で開発した技術を応用すれば、生物叢動態の予測と制御に関する基盤技術を世界に先駆けて構築できると期待される。生物叢の動態をほぼリアルタイムに予測する分析システムと時系列分析に関する理論生態学・数学を融合し、生物群集や生態系を科学的に制御できる研究対象へと昇華させる。

Outline of Final Research Achievements

DNA metabarcoding data of time-series samples obtained from experimental microbial co-culture systems and aquatic microflora were analyzed to provide insight into the diversity of their dynamics. First, shotgun genomic analysis was used to elucidate the genetic repertoire of each bacterial species comprising the community. We then estimated the degree of competition for the same resources among bacterial species present in the same time-series sample (among MAGs). We calculated the degree of genetic overlap between pairs on a round-robin basis within a community and took the average of these values as an indicator for the degree of overlap in the basic niche. We found that the degree of niche overlap estimated from the degree of gene overlap was higher prior to major changes in community structure.

Academic Significance and Societal Importance of the Research Achievements

従来の群集生態学においては、前者は、代替安定状態（alternative stable states）という概念を中心に発展し、後者はカオス時系列動態として理論的に発展してきた。しかし、種多様な生物群集の時系列データ自体がこれまでほとんど存在してこなかったため、この２つの捉え方を整理して実証研究と理論研究をフィードバックさせるような取り組みは例がなかった。本研究プロジェクトにおいて得られた大規模生物群集時系列データによって、この２つの理論的枠組の間で整理を行うことが可能となった

Research Products

• [Int'l Joint Research] Vrije Universiteit Amsterdam(オランダ)
• [Int'l Joint Research] アムステルダム自由大学(オランダ)
• [Journal Article] Deterministic and stochastic processes generating alternative states of microbiomes (2024)
  • Author(s): Hayashi Ibuki、Fujita Hiroaki、Toju Hirokazu
  • Journal Title: ISME Communications Volume: 4 Issue: 1
  • DOI: 10.1093/ismeco/ycae007
  • Peer Reviewed / Open Access
• [Journal Article] Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics (2023)
  • Author(s): Fujita Hiroaki、Ushio Masayuki、Suzuki Kenta、Abe Masato S.、Yamamichi Masato、Okazaki Yusuke、Canarini Alberto、Hayashi Ibuki、Fukushima Keitaro、Fukuda Shinji、Kiers E. Toby、Toju Hirokazu
  • Journal Title: Frontiers in Microbiology Volume: 14 Pages: 1261137-1261137
  • DOI: 10.3389/fmicb.2023.1261137
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Facilitative interaction networks in experimental microbial community dynamics (2023)
  • Author(s): Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi Y, Yusuke Okazaki, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H (
  • Journal Title: Frontiers in Microbiology Volume: 14 Pages: 153952-153952
  • DOI: 10.3389/fmicb.2023.1153952
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics (2023)
  • Author(s): Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi Y, Iwayama K, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H
  • Journal Title: Microbiome Volume: 11 Issue: 1 Pages: 63-63
  • DOI: 10.1186/s40168-023-01474-5
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Core species and interactions prominent in fish-associated microbiome dynamics (2023)
  • Author(s): Yajima D, Fujita H, Hayashi I, Shima G, Suzuki K, Toju H
  • Journal Title: Microbiome Volume: 11 Issue: 1 Pages: 53-53
  • DOI: 10.1186/s40168-023-01498-x
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] 多種生物システムの動態理解に向けたゲノム科学と群集生態学の融合 (2022)
  • Author(s): 東樹宏和
  • Organizer: ERATO共生進化機構先端セミナー.
  • Invited
• [Presentation] 多様な生態系をみつめることで多種システムの共通駆動原理に到達できるか？ (2022)
  • Author(s): 東樹宏和
  • Organizer: 第69回日本生態学会
• [Presentation] 異分野融合で解き明かす生物間相互作用と生態系動態 (2021)
  • Author(s): 東樹宏和
  • Organizer: 高遠分子細胞生物学シンポジウム
  • Invited
• [Presentation] 食物網、共生ネットワーク、そして生態系の再生へ (2021)
  • Author(s): 東樹宏和
  • Organizer: 日本生態学会第68回全国大会シンポジウム
• [Presentation] Does informatics of microbiomes revolutionize agriculture? (2020)
  • Author(s): Hirokazu Toju
  • Organizer: Keynote lecture. The Joint Meeting of The eDNA Society & The Society of Population Ecology
  • Int'l Joint Research / Invited
• [Presentation] Microbiome design for optimizing multi-species biological functions (2020)
  • Author(s): Hirokazu Toju
  • Organizer: Workshop "New Trends and Fundamental Technologies for Microbial Ecosystems. The 44th Annual Meeting of the Molecular Biology Society of Japan
  • Int'l Joint Research / Invited
• [Remarks] 魚の健康において鍵となる「コア微生物叢」 -ウナギ養殖水槽内の細菌叢動態-
  • URL: https://www.kyoto-u.ac.jp/ja/research-news/2023-03-30-3
• [Remarks] 微生物生態系の崩壊は予測できる -医療・工業・農業における微生物叢制御の基盤情報学-
  • URL: https://www.kyoto-u.ac.jp/ja/research-news/2023-03-30-2