Profiling of disease factors in human microbiome

• Project/Area Number: 26700029
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Partial Multi-year Fund
• Research Field: Life / Health / Medical informatics
• Research Institution: Niigata University
• Principal Investigator: Okuda Shujiro 新潟大学, 医歯学系, 准教授 (00512310)
• Project Period (FY): 2014-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥24,570,000 (Direct Cost: ¥18,900,000、Indirect Cost: ¥5,670,000); Fiscal Year 2017: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000); Fiscal Year 2016: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000); Fiscal Year 2015: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000); Fiscal Year 2014: ¥8,190,000 (Direct Cost: ¥6,300,000、Indirect Cost: ¥1,890,000)
• Keywords: 腸内細菌 / マイクロバイオーム / メタゲノム / 種間相互作用 / 共生細菌叢

Outline of Final Research Achievements

An important factor in promoting the research of human microbiome including gut microbiome is to estimate what interaction between bacteria are needed and how bacterial community are built. We have developed the fundamental method that is necessary for that purpose. We infer the interaction points on the metabolic pathways which are likely to be responsible for the interaction among bacteria and also developed a method to estimate the bacterial interaction network based on these interaction points. This makes it possible to analyze and visualize the relationships between bacteria in complex microbiome systems.

Research Products

• [Journal Article] Genomic landscape of colorectal cancer in Japan: Clinical implications of comprehensive genomic sequencing for precision medicine. (2016)
  • Author(s): Nagahashi M, Wakai T, Shimada Y, Ichikawa H, Kameyama H, Kobayashi T, Sakata J, Sato N, Kitagawa Y, Uetake H, Yoshida K, Oki E, Kudo S, Izutsu H, Komada K, Nakada M, Tse J, Russelｌ M, Heyer J, Powers W, Sun R, Ring J. E, Takabe K, Protopopov A, Ling Y, Okuda S, Lyle S.
  • Journal Title: Genome Medicine Volume: 8 Issue: 1 Pages: 136-136
  • DOI: 10.1186/s13073-016-0387-8
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Large-scale analysis of evolutionary histories of phosphorylation motifs in the human genome. (2015)
  • Author(s): Hisayoshi Yoshizaki and Shujiro Okuda
  • Journal Title: GigaScience Volume: 4 Issue: 1 Pages: 21-21
  • DOI: 10.1186/s13742-015-0057-6
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] Genome-wide analysis of single nucleotide variants on phosphorylation motifs. (2018)
  • Author(s): Yoshizaki, H., Ling Y., Kohno, M., Okuda, S.
  • Organizer: ASBMB2018
  • Int'l Joint Research
• [Presentation] Inference of microbial interactions from human gut meta genome data. (2017)
  • Author(s): Watanabe, Y., Ling, Y. and Okuda, S.
  • Organizer: ISMB/ECCB2017
  • Int'l Joint Research
• [Presentation] ヒト腸内細菌の代謝反応データベース構築 (2016)
  • Author(s): 佃直紀、山本希、東光一、入江満、五斗進、奥田修二郎、守屋勇樹、森宙史、黒川顕、山田拓司
  • Organizer: 第10回日本ゲノム微生物学会年会
  • Place of Presentation: 東京工業大学（東京都目黒区）
  • Year and Date: 2016-03-04
• [Presentation] Characterization of a large-scale phosphorylation motifs in human proteome. (2016)
  • Author(s): Ling, Y., Yoshizaki, H. and Okuda, S.
  • Organizer: HUPO2016
  • Place of Presentation: Taipei (Taiwan)
  • Int'l Joint Research
• [Presentation] Proteome-wide human phosphomotif analysis. (2016)
  • Author(s): Okuda, S., Ling, Y., and Yoshizaki, H.
  • Organizer: ISMB2016
  • Place of Presentation: Florida (USA)
  • Int'l Joint Research
• [Presentation] ヒトゲノム上のリン酸化モチーフ解析 (2015)
  • Author(s): 吉崎尚良、奥田修二郎、河野美幸
  • Organizer: 第38回日本分子生物学会年会
  • Place of Presentation: 神戸ポートアイランド（兵庫県神戸市）
  • Year and Date: 2015-12-01
• [Presentation] Evolutionary histories of phospho-motifs in the human genome. (2015)
  • Author(s): Shujiro Okuda and Hisayoshi Yoshizaki
  • Organizer: ISMB2015
  • Place of Presentation: Conventio Centre Dublin, Dublin, Ireland
  • Year and Date: 2015-07-11
  • Int'l Joint Research
• [Presentation] Large-scale analysis of the evolutionary history of phosphorylation motifs. (2014)
  • Author(s): Shujiro Okuda, and Hisayoshi Yoshizaki
  • Organizer: ASCB/IFCB2014
  • Place of Presentation: Pennsylvania Convention Center, Philadelphia, USA
  • Year and Date: 2014-12-09
• [Presentation] A web tool to infer metagenomic contents from16S rRNA sequences. (2014)
  • Author(s): Shujiro Okuda, and Yu Watanabe
  • Organizer: ISME2014
  • Place of Presentation: Coex Convention Center, Seoul, Korea
  • Year and Date: 2014-08-28
• [Presentation] Characterizatoin of protein phosphorylation in the context of evolution. (2014)
  • Author(s): Shujiro Okuda, and Hisayoshi Yoshizaki
  • Organizer: ISMB2014
  • Place of Presentation: Hynes Convention Center, Boston, USA
  • Year and Date: 2014-07-13