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Post-Koch Ecosystem revealed by Functional informatics

Planned Research

Project AreaPost-Koch Ecology: The next-era microbial ecology that elucidates the super-terrestrial organism system
Project/Area Number 19H05688
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionThe University of Tokyo

Principal Investigator

Matsui Motomu  東京大学, 大学院新領域創成科学研究科, 特任助教 (10803728)

Co-Investigator(Kenkyū-buntansha) 岩崎 渉  東京大学, 大学院新領域創成科学研究科, 教授 (50545019)
Project Period (FY) 2019-06-28 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥90,740,000 (Direct Cost: ¥69,800,000、Indirect Cost: ¥20,940,000)
Fiscal Year 2023: ¥16,770,000 (Direct Cost: ¥12,900,000、Indirect Cost: ¥3,870,000)
Fiscal Year 2022: ¥16,770,000 (Direct Cost: ¥12,900,000、Indirect Cost: ¥3,870,000)
Fiscal Year 2021: ¥16,770,000 (Direct Cost: ¥12,900,000、Indirect Cost: ¥3,870,000)
Fiscal Year 2020: ¥16,770,000 (Direct Cost: ¥12,900,000、Indirect Cost: ¥3,870,000)
Fiscal Year 2019: ¥23,660,000 (Direct Cost: ¥18,200,000、Indirect Cost: ¥5,460,000)
Keywordsバイオインフォマティクス / 微生物ダークマター / ポストコッホ生態系 / データベース / 機能インフォマティクス / ネットワーク解析 / 微生物生態 / メタゲノム解析 / ネットワーク / ポストコッホ生態 / 微生物生態学 / 窒素循環 / 微生物形態 / 微生物相互作用
Outline of Research at the Start

本研究計画ではまず、生態学と情報学の新たな複合領域である「機能インフォマティクス」を創成する。本領域が収集する情報は(i) 環境コンテキストと微生物メタゲノム、(ii) 微生物機能情報に紐づけられた個々の種のゲノム情報、(iii) メタボロームと代謝パスウェイ遺伝子の共起関係、のように従来の解析に用いられる情報よりも圧倒的に多様かつ多量である。そこで、高次元・大規模な環境コンテキスト情報から「微生物が発現する機能と環境の相関」を明らかにするための新規情報処理技術を開発する。次に、集積された情報に本技術を適用し、領域が設定するモデル圃場の「ポストコッホ機能生態系モデル」を創成する。

Outline of Final Research Achievements

By obtaining dense time-series NGS data and diverse environmental context data from crop rotation plots, we finally constructed a novel Post-Koch functional ecosystem model. The model revealed that the ecosystem is highly robust to environmental perturbation and that appropriate fertilizer application is important for maintaining soil ecosystem stability. Several factors such as competition among closely related species, offensiveness against plasmid phage, and strong convergence pressure on the trait template were also revealed to support this robustness. Many other important findings were also obtained, including the relationship between carbon fixation, nitrogen metabolism, and fertilizer application, the differentiation between Generalist and Specialist strategies, and more than 200 novel species genomes.

Academic Significance and Societal Importance of the Research Achievements

モデル圃場から4年もの長期にわたって取得した、緻密な時系列アンプリコンシーケンスデータ、大規模ショットガンメタゲノムデータ、詳細な土壌性状データは微生物生態学において類を見ない規模かつ多様なメタデータを含むものであり、今後、当該分野におけるモデルデータとして広く活用されることが期待される。また、Graph Splitting法やNeTaGFT法、逆相関ネットワーク解析法といった我々が開発した新規ネットワーク解析手法は、汎用的な情報解析技術としても新規性があるため、生物学に限らず分野外の幅広い分野において転用されていくことが期待される。

Report

(6 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • Research Products

    (40 results)

All 2024 2023 2022 2021 2020 2019 Other

All Journal Article (15 results) (of which Peer Reviewed: 14 results,  Open Access: 14 results) Presentation (24 results) (of which Invited: 8 results) Remarks (1 results)

  • [Journal Article] NeTaGFT: A similarity network‐based method for trait analysis2023

    • Author(s)
      Matsumoto Hirotaka、Matsui Motomu
    • Journal Title

      Methods in Ecology and Evolution

      Volume: 15 Issue: 1 Pages: 153-163

    • DOI

      10.1111/2041-210x.14251

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Seq2Phase: language model-based accurate prediction of client proteins in liquid-liquid phase separation2023

    • Author(s)
      Miyata Kazuki、Iwasaki Wataru
    • Journal Title

      Bioinformatics Advances

      Volume: 4 Issue: 1

    • DOI

      10.1093/bioadv/vbad189

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] AlphaCutter: Efficient removal of non‐globular regions from predicted protein structures2023

    • Author(s)
      Tam Chunlai、Iwasaki Wataru
    • Journal Title

      PROTEOMICS

      Volume: 23 Issue: 16 Pages: 2300176-2300176

    • DOI

      10.1002/pmic.202300176

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Machine learning enables prediction of metabolic system evolution in bacteria2023

    • Author(s)
      Konno Naoki、Iwasaki Wataru
    • Journal Title

      Science Advances

      Volume: 9 Issue: 2

    • DOI

      10.1126/sciadv.adc9130

    • Related Report
      2023 Annual Research Report 2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] バイオインフォマティクスでポストコッホ生態系を解き明かす2022

    • Author(s)
      松井 求
    • Journal Title

      Japanese Society of Microbial Ecology

      Volume: 37 Issue: 1 Pages: 37-39

    • DOI

      10.20709/jsmeja.37.1_37

    • ISSN
      2424-1989
    • Year and Date
      2022-03-01
    • Related Report
      2021 Annual Research Report
    • Open Access
  • [Journal Article] Nondestructive microbial discrimination using single-cell Raman spectra and random forest machine learning algorithm2022

    • Author(s)
      Kanno Nanako、Kato Shingo、Ohkuma Moriya、Matsui Motomu、Iwasaki Wataru、Shigeto Shinsuke
    • Journal Title

      STAR Protocols

      Volume: 3 Issue: 4 Pages: 101812-101812

    • DOI

      10.1016/j.xpro.2022.101812

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Lifestyle Evolution Analysis by Binary-State Speciation and Extinction (BiSSE) Model2022

    • Author(s)
      Suzuki Takao K.、Matsui Motomu、Sriswasdi Sira、Iwasaki Wataru
    • Journal Title

      Methods in Molecular Biology

      Volume: 2569 Pages: 327-342

    • DOI

      10.1007/978-1-0716-2691-7_16

    • ISBN
      9781071626900, 9781071626917
    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Unexpected absence of ribosomal protein genes from metagenome-assembled genomes2022

    • Author(s)
      Mise Kazumori、Iwasaki Wataru
    • Journal Title

      ISME Communications

      Volume: 2 Issue: 1 Pages: 118-118

    • DOI

      10.1038/s43705-022-00204-6

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Mirage 2.0: fast and memory-efficient reconstruction of gene-content evolution considering heterogeneous evolutionary patterns among gene families2022

    • Author(s)
      Tsukasa Fukunaga、Wataru Iwasaki
    • Journal Title

      Bioinformatics

      Volume: 38 Issue: 16 Pages: 4039-4041

    • DOI

      10.1093/bioinformatics/btac433

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Inverse Potts model improves accuracy of phylogenetic profiling2022

    • Author(s)
      Fukunaga Tsukasa、Iwasaki Wataru
    • Journal Title

      Bioinformatics

      Volume: 38 Issue: 7 Pages: 1794-1800

    • DOI

      10.1093/bioinformatics/btac034

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Deep distributed computing to reconstruct extremely large lineage trees2022

    • Author(s)
      Konno Naoki、Kijima Yusuke、Watano Keito、Ishiguro Soh、Ono Keiichiro、Tanaka Mamoru、Mori Hideto、Masuyama Nanami、Pratt Dexter、Ideker Trey、Iwasaki Wataru、Yachie Nozomu
    • Journal Title

      Nature Biotechnology

      Volume: 40 Issue: 4 Pages: 566-575

    • DOI

      10.1038/s41587-021-01111-2

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Machine learning-assisted single-cell Raman fingerprinting for in situ and nondestructive classification of prokaryotes2021

    • Author(s)
      Nanako Kanno、Shingo Kato、Moriya Ohkuma、Motomu Matsui、Wataru Iwasaki、Shinsuke Shigeto
    • Journal Title

      iScience

      Volume: 24 Issue: 9 Pages: 102975-102975

    • DOI

      10.1016/j.isci.2021.102975

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Frontier of Inferring Phylogenies2021

    • Author(s)
      松井 求
    • Journal Title

      JSBi Bioinformatics Review

      Volume: 2 Issue: 1 Pages: 30-57

    • DOI

      10.11234/jsbibr.2021.7

    • NAID

      130008101617

    • ISSN
      2435-7022
    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families2021

    • Author(s)
      Fukunaga Tsukasa、Iwasaki Wataru
    • Journal Title

      Bioinformatics Advances

      Volume: 1 Issue: 1

    • DOI

      10.1093/bioadv/vbab014

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Graph Splitting: A Graph-Based Approach for Superfamily-Scale Phylogenetic Tree Reconstruction2019

    • Author(s)
      Matsui Motomu、Iwasaki Wataru
    • Journal Title

      Systematic Biology

      Volume: 69 Pages: 265-279

    • DOI

      10.1093/sysbio/syz049

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Reconstructing Phylogenetic Reconstruction2024

    • Author(s)
      Motomu Matsui
    • Organizer
      DATA SCIENCE FOR GENOME DYNAMICS
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] バイオインフォマティクスが駆動する微生物科学2023

    • Author(s)
      松井求
    • Organizer
      微生物科学イノベーション特論II
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 分子系統学の進化可能性を考える2023

    • Author(s)
      松井求
    • Organizer
      Intelligence and Cultural Evolution Theoryワークショップ
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Tree of Lifeは完成できるか?2023

    • Author(s)
      松井求
    • Organizer
      IIBMP2023
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 環境微生物研究におけるバイオインフォマティクス活用法2023

    • Author(s)
      松井求
    • Organizer
      アグリバイオ
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 未培養微生物研究におけるバイオインフォマティクスの役割2022

    • Author(s)
      松井求
    • Organizer
      日本生物工学会バイオインフォマティクス相談部会第五回講演会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 機能インフォマティクスが解き明かすポストコッホ生態系2022

    • Author(s)
      松井求、岩崎渉
    • Organizer
      新学術領域「ポストコッホ生態」第4回領域会議
    • Related Report
      2022 Annual Research Report
  • [Presentation] Bac2Feature:系統情報を利用した微生物の形質推定パイプライン2022

    • Author(s)
      藤吉真生、鈴木誉保、松井求、岩崎渉
    • Organizer
      第24回日本進化学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] シン・近隣結合法:PANJEP法が問い直す系統解析の常識2022

    • Author(s)
      松井求、岩崎渉
    • Organizer
      第24回日本進化学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 系統樹推定の常識を問い直す2022

    • Author(s)
      松井求
    • Organizer
      国立遺伝学研究所研究集会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] ポストコッホ機能生態学が目指すもの2022

    • Author(s)
      松井求
    • Organizer
      ポストコッホ生態研究集会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 微生物群集は普遍的に極めて安定な形質組成を持つ2022

    • Author(s)
      鈴木誉保、松井求、森ヶ崎進、大津厳生、土肥裕希、林久喜、高谷直樹、岩崎渉
    • Organizer
      第60回日本生物物理学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] ポストコッホ生態学が解き明かす輪作に呼応した微生物動態2022

    • Author(s)
      松井求、明石基洋、鈴木誉保、藤吉真生、土肥裕希、森ヶ崎進、林久喜、高谷直樹、岩崎渉
    • Organizer
      第35回日本微生物生態学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Bac2Feature による微生物群集の表現型解析2022

    • Author(s)
      藤吉真生、鈴木誉保、松井求、岩崎渉
    • Organizer
      第35回日本微生物生態学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Trait-based アプローチでせまる 細菌の群集構造とその安定性2022

    • Author(s)
      鈴木誉保、松井求、森ヶ崎進、大津厳生、土肥裕希、河野祐介、林久喜、高谷直樹、岩崎渉
    • Organizer
      第35回日本微生物生態学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 施肥条件の異なる農地土壌の時系列ショットガンメタゲノム解析2021

    • Author(s)
      Motohiro Akashi, Motomu Matsui, Susumu Morigasaki, Hisayoshi Hayashi, Naoki Takaya, and Wataru Iwasaki
    • Organizer
      日本微生物生態学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] バイオインフォマティクスが解き明かすポストコッホ生態系2021

    • Author(s)
      Motomu Matsui
    • Organizer
      IIBMP2021
    • Related Report
      2021 Annual Research Report
  • [Presentation] アラインメントで問い直す系統樹推定の常識:GS法とNJ法2021

    • Author(s)
      Motomu Matsui
    • Organizer
      第23回日本進化学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 機能インフォマティクスが解き明かすポストコッホ生態系2021

    • Author(s)
      Motomu Matsui and Wataru Iwasaki
    • Organizer
      新学術領域「ポストコッホ生態」第3回領域会議
    • Related Report
      2021 Annual Research Report
  • [Presentation] Nondestructive prokaryotic species discrimination using single-cell Raman spectroscopy and machine learning2021

    • Author(s)
      Nanako Kanno, Shingo Kato, Motomu Matsui and Shinsuke Shigeto
    • Organizer
      日本農芸化学会
    • Related Report
      2020 Annual Research Report
  • [Presentation] ウイルスの初期進化と高速進化を解き明かす2020

    • Author(s)
      Motomu Matsui
    • Organizer
      第43回日本分子生物学会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Graph Splitting: A Graph-Based Approach for Superfamily-Scale Phylogenetic Tree Reconstruction2020

    • Author(s)
      Motomu Matsui and Wataru Iwasaki
    • Organizer
      IIBMP2020
    • Related Report
      2020 Annual Research Report
  • [Presentation] 機能インフォマティクスが解き明かすポストコッホ生態系2020

    • Author(s)
      Motomu Matsui and Wataru Iwasaki
    • Organizer
      新学術領域「ポストコッホ生態」第2回領域会議
    • Related Report
      2020 Annual Research Report
  • [Presentation] グラフに基づく新たな系統解析手法で隠れた遠距離進化を発掘する2019

    • Author(s)
      Motomu Matsui and Wataru Iwasaki
    • Organizer
      第21回日本進化学会
    • Related Report
      2019 Annual Research Report
  • [Remarks] Graph Splitting portal

    • URL

      http://gs.bs.s.u-tokyo.ac.jp/

    • Related Report
      2019 Annual Research Report

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Published: 2019-07-04   Modified: 2025-01-30  

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