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: 延 優 国立研究開発法人産業技術総合研究所, 生命工学領域, 研究員 (40805644)
• Project Period (FY): 2018-04-01 – 2023-03-31
• Project Status: Granted (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: Genomics / Metagenomics / Bacteria / Archaea / 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 Annual Research Achievements

Through synthesis of machine-learning and phylogenetic analyses, plastics xenobiotics degrading genes in soil bacteria were identified and their evolutionary history/origin was predicted. Through comparison with bacteria living in engineering environments, their evolutionary trends were found to be nearly opposite - one depending on ancient inheritances and the other recent innovations. As a parallel project, combining phylogenetic, genomic, and thermodynamic analyses, a novel recently evolved metabolism in methanogenic archaea was discovered.

Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

There have been major setbacks due to COVID-19, but progress is being made at a satisfactory pace.

Strategy for Future Research Activity

In the coming year, further analyses will be performed to identify novel genes evolved recently, presumably to degrade xenobiotic compounds. Through machine learning-facilitated data mining, we will search for operons of novel genes phylogenetically restricted to specific lineages and environmentally restricted to environments exposed to xenobiotic pollutants. The results will also be used to identify lineages that tend to make evolutionary breakthroughs in pollutant remediation.

Research Products

• [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 Pages: 3549-3565
  • DOI: 10.1038/s41396-021-01025-6
• [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
  • 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 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 H., Nobu M. K., Nakahara N., Morono Y., Ogawara M., Takaki Y., Takano Y., Uematsu K., Ikuta T., Ito M., Matsui Y., Miyazaki M., Murata K., Saito Y., Sakai S., Song C., Tasumi E., Yamanaka Y., Yamaguchi T., Kamagata Y., Tamaki H., Takai K.
  • Journal Title: Nature Volume: 577 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
  • DOI: 10.1038/s41598-019-46388-1
  • Peer Reviewed