Microbiome mining: machine learning for discovery of genetic dark matter, metabolic pathways, and ecological processes from metagenomes

• Project/Area Number: 18H03367
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Review Section: Basic Section 63010:Environmental dynamic analysis-related
• Research Institution: National Institute of Advanced Industrial Science and Technology
• Principal Investigator: NOBU Masaru Konishi 国立研究開発法人産業技術総合研究所, 生命工学領域, 主任研究員 (40805644)
• Project Period (FY): 2018-04-01 – 2023-03-31
• Project Status: Completed (Fiscal Year 2022)
• Budget Amount: ¥17,420,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥4,020,000); Fiscal Year 2022: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2021: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2020: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000); Fiscal Year 2019: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000); Fiscal Year 2018: ¥8,190,000 (Direct Cost: ¥6,300,000、Indirect Cost: ¥1,890,000)
• Keywords: Metagenomics / Bioinformatics / Methanogenesis / Archaea / Genomics / Bacteria / Metabolism / Evolution / メタゲノム解析 / 環境ゲノム解析 / 遺伝子解析 / 微生物代謝 / 微生物 / 代謝 / ゲノム / メタゲノム / 遺伝子 / ゲノム解析 / 機械学習 / Machine Learning / Machine learning / Syntrophy

Outline of Final Research Achievements

The basis for all of life's various biochemical capabilities is encoded in the genome and genes stored within each cell. However, more than half of the genes are unknown genes whose functions have not yet been identified, and we have only captured a small fraction of life's hidden capabilities. By unraveling the new functions of these unknown genes, we have discovered unknown biological phenomena that drive material-cycling processes in various ecosystems, and have also succeeded in elucidating the evolution of life in both ancient and modern times, which has been overlooked.

Academic Significance and Societal Importance of the Research Achievements

持続的な社会実現において地球上の様々な生態プロセスを理解し、社会の自然環境への影響を最小限にする必要がある。地球上の多様な生態系の物質循環、社会から自然界への廃棄物の流れ、どちらの中心にも微生物の特異的な能力による生化学反応がある。しかし、現代のデータサイエンスが駆動する学術界では、生命の研究は進めば進むほど未知な領域が拡大していく。本研究ではこの膨大な未知微生物・未知遺伝子データの解読を軸に、地球や社会にとって有用な微生物機能を発掘する手法の開発に貢献し、さらにこれまで見落とされてきた進化の道筋の解明にも成功した。

Research Products

• [Journal Article] The origin and evolution of methanogenesis and<i>Archaea</i>are intertwined (2023)
  • Author(s): Mei Ran、Kaneko Masanori、Imachi Hiroyuki、Nobu Masaru K
  • Journal Title: PNAS Nexus Volume: 2 Issue: 2 Pages: 1-10
  • DOI: 10.1093/pnasnexus/pgad023
  • Peer Reviewed / Open Access
• [Journal Article] Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds (2021)
  • Author(s): Kurth Julia M.、Nobu Masaru K.、Tamaki Hideyuki、de Jonge Nadieh、Berger Stefanie、Jetten Mike S. M.、Yamamoto Kyosuke、Mayumi Daisuke、Sakata Susumu、Bai Liping、Cheng Lei、Nielsen Jeppe Lund、Kamagata Yoichi、Wagner Tristan、Welte Cornelia U.
  • Journal Title: The ISME Journal Volume: 15 Issue: 12 Pages: 3549-3565
  • DOI: 10.1038/s41396-021-01025-6
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Deep Sequencing Uncovers Caste-Associated Diversity of Symbionts in the Social Ant Camponotus japonicus (2020)
  • Author(s): Koto Akiko、Nobu Masaru Konishi、Miyazaki Ryo
  • Journal Title: mBio Volume: 11 Issue: 2
  • DOI: 10.1128/mbio.00408-20
  • Peer Reviewed
• [Journal Article] A hydrogen-dependent geochemical analogue of primordial carbon and energy metabolism (2020)
  • Author(s): Preiner Martina、Igarashi Kensuke、Muchowska Kamila B.、Yu Mingquan、Varma Sreejith J.、Kleinermanns Karl、Nobu Masaru K.、Kamagata Yoichi、T?ys?z Harun、Moran Joseph、Martin William F.
  • Journal Title: Nature Ecology & Evolution Volume: 4 Issue: 4 Pages: 534-542
  • DOI: 10.1038/s41559-020-1125-6
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Isolation of an archaeon at the prokaryote-eukaryote interface (2020)
  • Author(s): Imachi Hiroyuki、Nobu Masaru K.、Nakahara Nozomi、Morono Yuki、Ogawara Miyuki、Takaki Yoshihiro、Takano Yoshinori、Uematsu Katsuyuki、Ikuta Tetsuro、Ito Motoo、Matsui Yohei、Miyazaki Masayuki、Murata Kazuyoshi、Saito Yumi、Sakai Sanae、Song Chihong、Tasumi Eiji、Yamanaka Yuko、Yamaguchi Takashi、Kamagata Yoich
  • Journal Title: Nature Volume: 577 Issue: 7791 Pages: 519-525
  • DOI: 10.1038/s41586-019-1916-6
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Community analysis of gut microbiota in hornets, the largest eusocial wasps, Vespa mandarinia and V. simillima (2019)
  • Author(s): Suenami Shota、Konishi Nobu Masaru、Miyazaki Ryo
  • Journal Title: Scientific Reports Volume: 9 Issue: 1
  • DOI: 10.1038/s41598-019-46388-1
  • Peer Reviewed