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Constructing a Disease-Related Microbiome Atlas for Advancing Understanding of Microbial Functionality

Research Project

Project/Area Number 20K21832
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 62:Applied informatics and related fields
Research InstitutionNagoya University

Principal Investigator

Shimamura Teppei  名古屋大学, 医学系研究科, 教授 (00623943)

Project Period (FY) 2020-07-30 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2022: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2021: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Fiscal Year 2020: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
Keywordsメタゲノム / マルチオミクス解析 / ベイズモデリング / トピックモデル / 因子分解モデル / 深層生成モデル
Outline of Research at the Start

本研究課題では、最先端のオミクス計測技術とベイズ推論による最新の解析技術を駆使し、様々な疾患の原因となる細菌叢を効率的に探索するための「疾患関連細菌叢アトラス」を創出する。本研究で行うユニークなモデリング技術の開発とそれによる斬新なデータベースの構築により、細菌叢の大海原で研究者が遭難しないように「予測地図」を提供することが主たる目的である。細菌叢の機能解析への障壁を取り去り、我が国の強みを生かした研究を推進することで国際産業競争力を強化するとともに、国民のQOL、細菌叢を利用した健康・医療産業の活性化にも大きく貢献することが期待される。

Outline of Final Research Achievements

In this study, we utilize Bayesian modeling techniques, previously developed by the applicant, as the technical cornerstone to address challenges in microbiome analysis such as the management of infrequently occurring microbial species and the consideration of inter-individual variability. Targeting the human microbiota, we develop Bayesian modeling techniques aimed at elucidating the functionalities of the microbiota and its correlation with health and disease. Concurrently, we construct a suite of analytical tools enabling the analysis of microbiome data from public disease-related cohort studies, and integrate these into a comprehensive database, the 'Disease-Related Microbiome Atlas'.

Academic Significance and Societal Importance of the Research Achievements

本研究課題は、世界中に登録された公共の膨大なコホート研究の細菌叢データ(衛星地図)と最先端のベイズモデリング技術(GPS)の2つの強力なツールを駆使することによって、細菌叢の大海原で研究者が遭難しないように「予測地図」を提供することが主たる目的である。本研究の活用により、細菌叢の機能解析への障壁を取り去り、国民のQOL、細菌叢を利用した健康・医療産業の活性化にも大きく貢献することが期待される。

Report

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

    (44 results)

All 2023 2022 2021 2020

All Journal Article (23 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 22 results,  Open Access: 21 results) Presentation (20 results) (of which Int'l Joint Research: 1 results,  Invited: 20 results) Book (1 results)

  • [Journal Article] Convergent genomic diversity and novel BCAA metabolism in intrahepatic cholangiocarcinoma2023

    • Author(s)
      Kitagawa A, Osawa T,Noda M,Kobayashi Y, Aki S,Nakano Y,Saito T,Shimizu D,Komatsu H,Sugaya M,Takahashi J,...Mimori K.
    • Journal Title

      Br J Cancer

      Volume: - Issue: 12 Pages: 22068-22068

    • DOI

      10.1038/s41416-023-02256-4

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Increased flexibility of the SARS-CoV-2 RNA-binding site causes resistance to remdesivir2023

    • Author(s)
      Torii Shiho、Kim Kwang Su、Koseki Jun、Suzuki Rigel、Iwanami Shoya、Fujita Yasuhisa、Jeong Yong Dam、Ito Jumpei、Asakura Hiroyuki、Nagashima Mami、Sadamasu Kenji、Yoshimura Kazuhisa、Sato Kei、Matsuura Yoshiharu、Shimamura Teppei、Iwami Shingo、Fukuhara Takasuke、The Genotype to Phenotype Japan (G2P-Japan) Consortium
    • Journal Title

      PLOS Pathogens

      Volume: 19 Issue: 3 Pages: e1011231-e1011231

    • DOI

      10.1371/journal.ppat.1011231

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Spatial and single-cell transcriptomics decipher the cellular environment containing HLA-G+ cancer cells and SPP1+ macrophages in colorectal cancer2023

    • Author(s)
      Ozato Y, Mimori K(28番目),他26名
    • Journal Title

      Cell Reports

      Volume: 42 Issue: 1 Pages: 111929-111929

    • DOI

      10.1016/j.celrep.2022.111929

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Bayesian statistical method for detecting structural and topological diversity in polymorphic proteins2022

    • Author(s)
      Hayashi Shuto、Koseki Jun、Shimamura Teppei
    • Journal Title

      Computational and Structural Biotechnology Journal

      Volume: 20 Pages: 6519-6525

    • DOI

      10.1016/j.csbj.2022.11.038

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Smoking enhances the expression of angiotensin‐converting enzyme 2 involved in the efficiency of severe acute respiratory syndrome coronavirus 2 infection2022

    • Author(s)
      Suzuki Rigel、Ono Yuki、Noshita Koji、Kim Kwang Su、Ito Hayato、Morioka Yuhei、Tamura Tomokazu、Okuzaki Daisuke、Tagawa Tetsuzo、Takenaka Tomoyoshi、Yoshizumi Tomoharu、Shimamura Teppei、Iwami Shingo、Fukuhara Takasuke
    • Journal Title

      Microbiology and Immunology

      Volume: 67 Issue: 1 Pages: 22-31

    • DOI

      10.1111/1348-0421.13034

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Detecting time-evolving phenotypic components of adverse reactions against BNT162b2 SARS-CoV-2 vaccine via non-negative tensor factorization2022

    • Author(s)
      Ikeda Kei、Nakada Taka-Aki、Kageyama Takahiro、Tanaka Shigeru、Yoshida Naoki、Ishikawa Tetsuo、Goshima Yuki、Otaki Natsuko、Iwami Shingo、Shimamura Teppei、Taniguchi Toshibumi、Igari Hidetoshi、Hanaoka Hideki、Yokote Koutaro、Tsuyuzaki Koki、Nakajima Hiroshi、Kawakami Eiryo
    • Journal Title

      iScience

      Volume: 25 Issue: 10 Pages: 105237-105237

    • DOI

      10.1016/j.isci.2022.105237

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Metabolic remodeling of pyrimidine synthesis pathway and serine synthesis pathway in human glioblastoma2022

    • Author(s)
      Nakamizo Akira、Miyamatsu Yuichiro、Hirose Haruka、Amano Toshiyuki、Matsuo Satoshi、Fujiwara Minako、Shimamura Teppei、Yoshimoto Koji
    • Journal Title

      Scientific Reports

      Volume: 12 Issue: 1 Pages: 16277-16277

    • DOI

      10.1038/s41598-022-20613-w

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Metabolome and transcriptome analysis on muscle of sporadic inclusion body myositis.2022

    • Author(s)
      Murakami, A., Noda, S., Kazuta, T., Hirano, S., Kimura, S., Nakanishi, H., Matsuo, K., Tsujikawa, K., Iida, M., Koike, H., Sakamoto, K., Hara, Y., Kuru, S., Kadomatsu, K., Shimamura, T., Ogi, T., Katsuno, M.
    • Journal Title

      Ann Clin Transl Neurol.

      Volume: 9 Issue: 10 Pages: 1602-1615

    • DOI

      10.1002/acn3.51657

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] An analysis modality for vascular structures combining tissue-clearing technology and topological data analysis2022

    • Author(s)
      Takahashi K, Abe K, Kubota SI, Fukatsu N, Morishita Y, Yoshimatsu Y, Satoshi Hirakawa, Yoshiaki Kubota, Tetsuro Watabe, Shogo Ehata, Hiroki R. Ueda, Teppei Shimamura, Kohei Miyazono
    • Journal Title

      Nature Communiactions

      Volume: 13 Issue: 1 Pages: 5239-5239

    • DOI

      10.1038/s41467-022-32848-2

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A bifurcation concept for B-lymphoid/plasmacytoid dendritic cells with largely fluctuating transcriptome dynamics.2022

    • Author(s)
      Nagaharu K, Kojima Y, Hirose H, Minoura K, Hinohara K, Minami H, Kageyama Y, Sugimoto Y, Masuya M, Nii S, Seki M, Suzuki Y, Tawara I, Shimamura T, Katayama N, Nishikawa H, Ohishi K.
    • Journal Title

      Cell Rep.

      Volume: 40 Issue: 9 Pages: 111260-111260

    • DOI

      10.1016/j.celrep.2022.111260

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] UVB-Induced Skin Autoinflammation Due to Nlrp1b Mutation and Its Inhibition by Anti-IL-1β Antibody2022

    • Author(s)
      Murase Yuya、Takeichi Takuya、Koseki Jun、Miyasaka Yuki、Muro Yoshinao、Ohno Tamio、Shimamura Teppei、Akiyama Masashi
    • Journal Title

      Frontiers in Immunology

      Volume: 13 Pages: 876390-876390

    • DOI

      10.3389/fimmu.2022.876390

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Exome sequencing of Japanese schizophrenia multiplex families supports the involvement of calcium ion channels2022

    • Author(s)
      Toyama Miho、Takasaki Yuto、Branko Aleksic、Kimura Hiroki、Kato Hidekazu、Nawa Yoshihiro、Kushima Itaru、Ishizuka Kanako、Shimamura Teppei、Ogi Tomoo、Ozaki Norio
    • Journal Title

      PLOS ONE

      Volume: 17(5) Issue: 5 Pages: e0268321-e0268321

    • DOI

      10.1371/journal.pone.0268321

    • Related Report
      2022 Annual Research Report 2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A mixture-of-experts deep generative model for integrated analysis of single-cell multiomics data2021

    • Author(s)
      Minoura Kodai、Abe Ko、Nam Hyunha、Nishikawa Hiroyoshi、Shimamura Teppei
    • Journal Title

      Cell Reports Methods

      Volume: 1(5) Issue: 5 Pages: 100071-100071

    • DOI

      10.1016/j.crmeth.2021.100071

    • Related Report
      2021 Research-status Report
  • [Journal Article] Depletion of central memory CD8+ T cells might impede the antitumor therapeutic effect of Mogamulizumab2021

    • Author(s)
      Maeda Yuka、Wada Hisashi、Sugiyama Daisuke、Saito Takuro、Irie Takuma、Itahashi Kota、Minoura Kodai、Suzuki Susumu、Kojima Takashi、Kakimi Kazuhiro、Nakajima Jun、Funakoshi Takeru、Iida Shinsuke、Oka Mikio、Shimamura Teppei、Doi Toshihiko、Doki Yuichiro、Nakayama Eiichi、Ueda Ryuzo、Nishikawa Hiroyoshi
    • Journal Title

      Nature Communications

      Volume: 12(1) Issue: 1 Pages: 7280-7280

    • DOI

      10.1038/s41467-021-27574-0

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Hierarchical non-negative matrix factorization using clinical information for microbial communities2021

    • Author(s)
      Abe Ko、Hirayama Masaaki、Ohno Kinji、Shimamura Teppei
    • Journal Title

      BMC Genomics

      Volume: 22 Issue: 1 Pages: 104-104

    • DOI

      10.1186/s12864-021-07401-y

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] CYBERTRACK2.0: zero-inflated model-based cell clustering and population tracking method for longitudinal mass cytometry data2020

    • Author(s)
      Minoura K*, Abe K*, Maeda Y, Nishikawa H, Shimamura T§
    • Journal Title

      Bioinformatics

      Volume: - Issue: 11 Pages: 873-873

    • DOI

      10.1093/bioinformatics/btaa873

    • Related Report
      2021 Research-status Report 2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Short-Chain Fatty Acid-Producing Gut Microbiota Is Decreased in Parkinson’s Disease but Not in Rapid-Eye-Movement Sleep Behavior Disorder2020

    • Author(s)
      Nishiwaki Hiroshi、Hamaguchi Tomonari、Ito Mikako、Ishida Tomohiro、Maeda Tetsuya、Kashihara Kenichi、Tsuboi Yoshio、Ueyama Jun、Shimamura Teppei、Mori Hiroshi、Kurokawa Ken、Katsuno Masahisa、Hirayama Masaaki、Ohno Kinji
    • Journal Title

      mSystems

      Volume: 5 Issue: 6

    • DOI

      10.1128/msystems.00797-20

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Model-based clustering for flow and mass cytometry data with clinical information2020

    • Author(s)
      Abe K, Minoura K, Maeda Y, Nishikawa H, Shimamura T§
    • Journal Title

      BMC Bioinformatics

      Volume: 21(Suppl 13) Issue: S13 Pages: 393-393

    • DOI

      10.1186/s12859-020-03671-7

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] ARHGAP10, which encodes Rho GTPase-activating protein 10, is a novel gene for schizophrenia risk2020

    • Author(s)
      Mariko Sekiguchi, Akiko Kodama,... Emiko Shishido,... Daisuke Mori, Norio Ozaki
    • Journal Title

      Translational psychiatry

      Volume: 10 Issue: 1 Pages: 1-15

    • DOI

      10.1038/s41398-020-00917-z

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Integrated multiomics analysis of hepatoblastoma unravels its heterogeneity and provides novel druggable targets.2020

    • Author(s)
      Sekiguchi M, Seki M, Kawai T, Yoshida K, Yoshida M, Isobe T, Hoshino N, Shirai R, Tanaka M, Souzaki R, Watanabe K, Arakawa Y, Nannya Y, Suzuki H, Fujii Y, Kataoka K, Shiraishi Y, Chiba K, Tanaka H, Shimamura T, Sato Y, Sato-Otsubo A, Kimura S, Kubota Y, Hiwatari M, et al
    • Journal Title

      NPJ Precis Oncol.

      Volume: Jul 7;4:20. Issue: 1 Pages: 20-20

    • DOI

      10.1038/s41698-020-0125-y

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Meta‐Analysis of Gut Dysbiosis in Parkinson's Disease2020

    • Author(s)
      Nishiwaki Hiroshi、Ito Mikako、Ishida Tomohiro、Hamaguchi Tomonari、Maeda Tetsuya、Kashihara Kenichi、Tsuboi Yoshio、Ueyama Jun、Shimamura Teppei、Mori Hiroshi、Kurokawa Ken、Katsuno Masahisa、Hirayama Masaaki、Ohno Kinji
    • Journal Title

      Movement Disorders

      Volume: 35 Issue: 9 Pages: 1626-1635

    • DOI

      10.1002/mds.28119

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] EXOSC9 depletion attenuates P-body formation, stress resistance, and tumorigenicity of cancer cells.2020

    • Author(s)
      Yoshino S, Matsui Y, Fukui Y, Seki M, Yamaguchi K, Kanamori A, Saitoh Y, Shimamura T, Suzuki Y, Furukawa Y, Kaneko S, Seiki M, Murakami Y, Inoue JI, Sakamoto T.
    • Journal Title

      Sci Rep

      Volume: 10 Issue: 1 Pages: 9275-9275

    • DOI

      10.1038/s41598-020-66455-2

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells2020

    • Author(s)
      Higashijima Y, Matsui Y, Shimamura T, Nakaki R, Nagai N, Tsutsumi S, Abe Y, Link VM, Osaka M, Yoshida M, Watanabe R, Tanaka T, Taguchi A, Miura M, Ruan X, Li G, Inoue T, Nangaku M, Kimura H, Furukawa T, Aburatani H, Wada Y, Ruan Y, Glass CK, Kanki Y
    • Journal Title

      The EMBO Journal

      Volume: 39 Issue: 7 Pages: 1-1

    • DOI

      10.15252/embj.2019103949

    • NAID

      120006902140

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 深層生成モデルで読み解く生命システムの動作原理2023

    • Author(s)
      島村 徹平
    • Organizer
      第7回理論免疫学ワークショップ
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 深層学習による生体内微小環境の新次元俯瞰2022

    • Author(s)
      島村 徹平
    • Organizer
      第45回日本分子生物学会年会ワークショップ
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 深層学習で細胞社会を読み解く2022

    • Author(s)
      島村 徹平
    • Organizer
      第45回日本分子生物学会年会フォーラム
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 深層学習による生体内微小環境の新次元俯瞰2022

    • Author(s)
      島村 徹平
    • Organizer
      LINK-Jセミナー
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 深層学習による生体内微小環境の新次元俯瞰2022

    • Author(s)
      島村 徹平
    • Organizer
      第95回日本生化学会大会企画シンポジウム
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 深層学習による生体内微小環境の新次元俯瞰2022

    • Author(s)
      島村 徹平
    • Organizer
      第60回日本癌治療学会学術集会会長企画シンポジウム
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Estimating fluctuations in cell state dynamics and predicting fate bifurcations under influenza infection using deep learning2022

    • Author(s)
      島村 徹平
    • Organizer
      第20回あわじ感染と免疫国際フォーラム
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] A new modality for elucidating tumor microenvironment using deep learning2022

    • Author(s)
      島村 徹平
    • Organizer
      第81回日本癌学会学術総会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 細胞間コミュニケーションを読み解くためのデータ科学2022

    • Author(s)
      島村徹平
    • Organizer
      第6回理論免疫学ワークショップ
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] データから読み解く生命医科学2022

    • Author(s)
      島村徹平
    • Organizer
      脳神経内科医のためのバイオインフォマティクス・ハンズオン 2021
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] Deep learning to decipher cell dynamics and cell-cell interactions2021

    • Author(s)
      島村徹平
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] 一細胞マルチモーダル情報をデータとモデルから読み解く2021

    • Author(s)
      島村徹平
    • Organizer
      産業技術研究所人工知能研究センター第51回AIセミナー
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] 細胞間コミュニケーションを読み解く深層学習2021

    • Author(s)
      島村徹平
    • Organizer
      第94回日本生化学会大会
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] Modeling cell population dynamics and cell-to-cell communication from single-cell multi-omics data2021

    • Author(s)
      島村徹平
    • Organizer
      第80回日本癌学会学術総会
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] データとモデルが駆動する生命科学2021

    • Author(s)
      島村徹平
    • Organizer
      第32回高遠・分子細胞生物学シンポジウム
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] シングルセルオミクス解析のためのAI技術の最新動向2021

    • Author(s)
      島村徹平
    • Organizer
      第39回内分泌代謝学サマーセミナー
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] 細胞集団のダイナミクスを捉えるためのベイズモデリング2021

    • Author(s)
      島村徹平
    • Organizer
      第5回理論免疫学ワークショップ
    • Related Report
      2020 Research-status Report
    • Invited
  • [Presentation] がん研究における一細胞解析のためのモデリング・AI 技術の最新動向2020

    • Author(s)
      島村徹平
    • Organizer
      第79回日本癌学会学術総会
    • Related Report
      2020 Research-status Report
    • Invited
  • [Presentation] 臓器連関トランスオミクス解析のためのベイズモデリング2020

    • Author(s)
      島村徹平
    • Organizer
      第93回日本生化学会大会
    • Related Report
      2020 Research-status Report
    • Invited
  • [Presentation] 今こそ知りたい!行列因子分解~ゼロから始めるマルチオミクス解析~2020

    • Author(s)
      島村徹平
    • Organizer
      代謝統合オミクス若手技術セミナー
    • Related Report
      2020 Research-status Report
    • Invited
  • [Book] 実験医学別冊最強のステップUPシリーズ 空間オミクス解析スタートアップ実践ガイド、空間トランスクリプトームに基づく細胞間相互作用ネットワークの解析技術2022

    • Author(s)
      小嶋泰弘、島村徹平
    • Total Pages
      244
    • Publisher
      羊土社
    • ISBN
      9784758122610
    • Related Report
      2022 Annual Research Report

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Published: 2020-08-03   Modified: 2024-01-30  

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