Development of prediction methods for intestinal phage-bacteria associations from metagenomic data by hierarchical Bayesian model

• Project/Area Number: 16K16144
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Life / Health / Medical informatics
• Research Institution: The University of Tokyo
• Principal Investigator: Kimura Yasumasa 東京大学, 医科学研究所, 特任助教 (30632913)
• Project Period (FY): 2016-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000); Fiscal Year 2017: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2016: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: 細菌・ファージ感染関係 / メタゲノム / ウイルス分類 / プロファージ / CRISPR / 腸内ウイルス / ウイルス / 細菌 / ゲノム / モデル化

Outline of Final Research Achievements

The intestine contains commensal viruses, the majority of which are unidentified bacteriophages (phages). This study revealed many genomes of unknown phages by reconstructing them from metagenomic sequence reads. To understand infectious hosts of the unknown phages, I developed prediction methods of phage-bacteria infectious association based on the phage genomic sequence remaining in the host bacterial genome. After validating the prediction methods, I analyzed the infectious associations of intestinal bacteria / phage in healthy humans and obtained knowledge on symbiotic relationship between phage and bacteria.

Research Products

• [Journal Article] Generation of tumor antigen-specific murine CD8+ T cells with enhanced anti-tumor activity via highly efficient CRISPR/Cas9 genome editing (2018)
  • Author(s): Ouchi Y, Patil A, Tamura Y, Nishimasu H, Negishi A, Paul SK, Takemura N, Satoh T, Kimura Y, Kurachi M, Nureki O, Nakai K, Kiyono H, Uematsu S.
  • Journal Title: International Immunology Volume: 30 Issue: 4 Pages: 141-154
  • DOI: 10.1093/intimm/dxy006
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] L, Bannai E, Yoshikawa N, Kimura Y, Satoh T, Uematsu S, Tanaka H, Yamamoto K. Intestinal microbiota link lymphopenia to murine autoimmunity via PD-1(+)CXCR5(-/dim) B-helper T cell induction. (2017)
  • Author(s): Eri T, Kawahata K, Kanzaki T, Imamura M, Michishita K, Akahira L, Bannai E, Yoshikawa N, Kimura Y, Satoh T, Uematsu S, Tanaka H, Yamamoto K.
  • Journal Title: Scientific Reports Volume: 7 Issue: 1 Pages: 1-17
  • DOI: 10.1038/srep46037
  • Peer Reviewed / Open Access / Int'l Joint Research