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Metagenome analysis of polymicrobial diseases and its application to clinical fields

Research Project

Project/Area Number 23310144
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Applied genomics
Research InstitutionUniversity of Miyazaki

Principal Investigator

HAYASHI Tetsuya  宮崎大学, フロンティア科学実験総合センター, 教授 (10173014)

Co-Investigator(Kenkyū-buntansha) MISAWA Naoaki  宮崎大学, 産業動物防疫リサーチセンター, 教授 (20229678)
Co-Investigator(Renkei-kenkyūsha) OOKA Tadasuke  宮崎大学, 医学部, 助教 (50363594)
Research Collaborator GOTOH Yasuhiro  宮崎大学, 医学部, 助教 (20558358)
ITOH Takehiko  東京工業大学, 生命理工学研究科, 教授 (90501106)
TANIGUCHI Takako  宮崎大学, 産業動物防疫リサーチセンター, 特任助教 (50500097)
YAMAZAKI Wataru  宮崎大学, 農学部, 准教授 (70393262)
Project Period (FY) 2011-04-01 – 2014-03-31
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥20,410,000 (Direct Cost: ¥15,700,000、Indirect Cost: ¥4,710,000)
Fiscal Year 2013: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Fiscal Year 2012: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
Fiscal Year 2011: ¥7,800,000 (Direct Cost: ¥6,000,000、Indirect Cost: ¥1,800,000)
Keywordsゲノム解析 / polymicrobial disease / メタゲノム解析 / ウシ趾乳頭腫症 / 比較ゲノム / 難培養細菌 / 次世代シーケンサー / polymicrobial diseases / 次世代代シーケンサー
Research Abstract

Papillomatous digital dermatitis (PDD) is caused by multiple bacteria including non-cultivable species, and is one of the polymicrobial diseases, a new category of infectious diseases. In this project, we developed a protocol for DNA extraction and a genome sequence assembler, both suitable for metagenome analysis of PDD. By using them, we obtained high quality reference metagenome sequences that can be used to reconstitute the genomes of major causative agents of PDD. As for Treponema phagedenis, a uniquely cultivable PDD-related species, we determined the complete genome sequences of one PDD-derived strain and one human-derived standard strain and, in addition, the high quality draft sequences of 5 PDD-derived strains. By comparing these genomes, we revealed unique mechanisms of evolution and diversification of this microbe via explosive amplification of IS and MITE elements, multiple phage infections, and extensive genome rearrangements mediated by these mobile genetic elements.

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • Research Products

    (35 results)

All 2014 2013 2012 2011 Other

All Journal Article (9 results) (of which Peer Reviewed: 9 results) Presentation (21 results) (of which Invited: 1 results) Book (5 results)

  • [Journal Article] A PCR-RFLP assay for the detection and differentiation of Campylobacter jejuni, C. coli, C. fetus, C. hyointestinalis, C. lari, C. helveticus and C. upsaliensis2014

    • Author(s)
      K. Kamei, M. Asakura, S. Somroop, A. Hinenoya, A. Nagita, N. Misawa, M. Matsuda, S. Nakagawa, S. Yamasaki
    • Journal Title

      J. Med. Microbiol

      Volume: not available Issue: 5 Pages: 659-666

    • DOI

      10.1099/jmm.0.071498-0

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Detection of diverse aquatic microbes in blood and organs of drowning victims : First metagenomic approach using high- throughput 454-pyrosequencing2012

    • Author(s)
      E. Kakizaki, Y. Ogura, S. Kozawa, S. Nishida, T. Uchiyama, T. Hayashi, N. Yukawa
    • Journal Title

      Forensic Sci. Int

      Volume: 220 Pages: 135-146

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Culture-negative brain abscess with Streptococcus intermedius infection with diagnosis established by direct nucleotide sequence analysis of the 16S ribosomal RNA gene2012

    • Author(s)
      N. Saito, A. Hida, Y. Koide, T. Ooka, Y. Ichikawa, J. Shimizu, A. Mukasa, H. Nakatomi, S. Hatakeyama, T. Hayashi, S. Tsuji
    • Journal Title

      Intern. Med

      Volume: 51(2) Pages: 211-216

    • NAID

      130002062067

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Culture-negative Brain Abscess with <i>Streptococcus intermedius</i> Infection with Diagnosis Established by Direct Nucleotide Sequence Analysis of the 16S Ribosomal RNA Gene2012

    • Author(s)
      N.Saito, et al
    • Journal Title

      Internal Medicine

      Volume: 51 Issue: 2 Pages: 211-216

    • DOI

      10.2169/internalmedicine.51.6419

    • NAID

      130002062067

    • ISSN
      0918-2918, 1349-7235
    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Bile acid is a host factor that regulates the composition of the cecal microbiota in rats2011

    • Author(s)
      K.B. Islam, S. Fukiya, M. Hagio, N. Fujii, S. Ishizuka, T. Ooka, Y. Ogura, T. Hayashi, A. Yokota
    • Journal Title

      Gastroenterology

      Volume: 141(5) Pages: 1773-1781

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Characterisation of the Porphyromonas gingivalis conjugative transposon CTnPg1 : determination of the integration site and the genes essential for conjugal transfer2011

    • Author(s)
      M. Naito, K. Sato, M. Shoji, H. Yukitake, Y. Ogura, T. Hayashi, K. Nakayama
    • Journal Title

      Microbiology

      Volume: 157 Pages: 2022-2032

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Bile Acid is a Host Factor that Regulates the Composition of the Cecal Microbiota in Rats2011

    • Author(s)
      Islam KBMS, Fukiya S, Hagio M, Fujii N, Ishizuka S, Ooka T, Ogura Y, Hayashi T, Yokota A
    • Journal Title

      Gastroenterology

      Volume: VOL. 141 Issue: 5 Pages: 1773-1781

    • DOI

      10.1053/j.gastro.2011.07.046

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Characterisation of the Porphyromonas gingivalis conjugative transposon CTnPg1 : determination of the integration site and the genes essential for conjugal transfer2011

    • Author(s)
      M.Naito, et al
    • Journal Title

      Microbiology

      Volume: 157 Issue: 7 Pages: 2022-2032

    • DOI

      10.1099/mic.0.047803-0

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Detection of diverse aquatic microbes in blood and organs of drowning victims : First metagenomic approach using high-throughput 454-pyrosequencing

    • Author(s)
      E.Kakizaki, et al
    • Journal Title

      Forensic Sci.Int.

      Volume: (in press)

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] 難培養菌群によるpolymicrobial diseaseへのゲノムからのアプローチ2014

    • Author(s)
      後藤恭宏, 林哲也
    • Organizer
      第87回日本細菌学会総会
    • Place of Presentation
      東京
    • Related Report
      2013 Final Research Report
  • [Presentation] 牛趾皮膚炎病変部の治療前後における細菌叢の比較解析2014

    • Author(s)
      山崎渉, 谷口喬子, 後藤恭宏, 林哲也, 三澤尚明
    • Organizer
      第87回日本細菌学会総会
    • Place of Presentation
      東京
    • Related Report
      2013 Final Research Report
  • [Presentation] ウシとヒト由来Treponema phagedenis のゲノム比較2014

    • Author(s)
      後藤恭宏, 山崎和子, 小椋義俊, 大岡唯祐, 桂啓介,矢 野貴久, 大島健志朗, 服部正平, 三澤尚明, 林哲也
    • Organizer
      第8回日本ゲノム微生物学会年会
    • Place of Presentation
      東京
    • Related Report
      2013 Final Research Report
  • [Presentation] ウシとヒト由来Treponema phagedenisのゲノム比較2014

    • Author(s)
      後藤恭宏,山崎和子,小椋義俊,大岡唯祐,桂啓介,矢野貴久,大島健志朗,服部正平,三澤尚明,林哲也
    • Organizer
      第8回日本ゲノム微生物学会年会
    • Place of Presentation
      東京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] 難培養菌群によるpolymicrobial diseaseへのゲノムからのアプローチ2014

    • Author(s)
      後藤恭宏,林哲也
    • Organizer
      第87回日本細菌学会総会
    • Place of Presentation
      東京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] 牛趾皮膚炎病変部の治療前後における細菌叢の比較解析2014

    • Author(s)
      山崎渉, 谷口喬子, 後藤恭宏, 林哲也, 三澤尚明
    • Organizer
      第87回日本細菌学会総会
    • Place of Presentation
      東京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] 細菌のゲノム解析とその臨床応用 ~次世代シーケンサの時代を迎えて~2013

    • Author(s)
      林哲也
    • Organizer
      第61回日本化学療法学会西日本支部総会
    • Place of Presentation
      大阪市
    • Related Report
      2013 Annual Research Report 2013 Final Research Report
  • [Presentation] 趾皮膚炎罹患牛の歩様と病態の関係2013

    • Author(s)
      千葉香菜子, 眞鍋弘行, 山本匠, 花田直子, 三澤尚明, 佐藤繁, 岡田啓司
    • Organizer
      第156回日本獣医学会学術集会
    • Place of Presentation
      岐阜市
    • Related Report
      2013 Annual Research Report 2013 Final Research Report
  • [Presentation] Polymicrobial disease であるウシ趾乳頭腫症から分離されたTreponema phagedenis のゲノムおよびヒト由来株とのゲノム比較解析2013

    • Author(s)
      後藤恭宏, 山崎和子, 小椋義俊, 大岡唯祐,桂啓介, 矢野貴久, 大島健志朗, 服部正平,三澤尚明, 林哲也
    • Organizer
      第66回日本細菌学会九州支部総会
    • Place of Presentation
      長崎市
    • Related Report
      2013 Final Research Report
  • [Presentation] ウシ趾乳頭腫症由来株Treponema phagedenis とヒト由来株の比較ゲノム解析2013

    • Author(s)
      後藤恭宏, 山崎和子, 小椋義俊, 大岡唯祐,矢野貴久, 大島健志朗, 服部正平, 三澤尚明, 林哲也
    • Organizer
      第86回日本細菌学会総会
    • Place of Presentation
      千葉市
    • Related Report
      2013 Final Research Report
  • [Presentation] ウシ趾乳頭腫症病変部から分離されたTreponema phagedenisのゲノム解析2013

    • Author(s)
      後藤恭宏, 山崎和子, 小椋義俊, 大岡唯祐,矢野貴久, 大島健志朗, 服部正平, 三澤尚明,林哲也
    • Organizer
      第7回日本ゲノム微生物学会年会
    • Place of Presentation
      滋賀県長浜市
    • Related Report
      2013 Final Research Report
  • [Presentation] Polymicrobial diseaseであるウシ趾乳頭腫症から分離されたTreponema phagedenisのゲノムおよびヒト由来株とのゲノム比較解析2013

    • Author(s)
      後藤恭宏, 山崎和子, 小椋義俊, 大岡唯祐, 桂啓介, 矢野貴久, 大島健志朗, 服部正平, 三澤尚明, 林哲也
    • Organizer
      第66回日本細菌学会九州支部総会
    • Place of Presentation
      長崎市
    • Related Report
      2013 Annual Research Report
  • [Presentation] ウシ趾乳頭腫症由来株Treponema phagedenisとヒト由来株の比較ゲノム解析2013

    • Author(s)
      後藤恭宏, 山崎和子, 小椋義俊, 大岡唯祐, 矢野貴久, 大島健志朗, 服部正平, 三澤尚明, 林哲也
    • Organizer
      第86回日本細菌学会総会
    • Place of Presentation
      千葉市
    • Related Report
      2012 Annual Research Report
  • [Presentation] ウシ趾乳頭腫症病変部から分離されたTreponema phagedenisのゲノム解析2013

    • Author(s)
      後藤恭宏, 山崎和子, 小椋義俊, 大岡唯祐, 矢野貴久, 大島健志朗, 服部正平, 三澤尚明, 林哲也
    • Organizer
      第7回日本ゲノム微生物学会年会
    • Place of Presentation
      長浜市
    • Related Report
      2012 Annual Research Report
  • [Presentation] ゲノム解析技術の急速な進化がもたらすゲノム研究の新たな展・開2012

    • Author(s)
      林哲也
    • Organizer
      日本科学哲学会第45回(2012年)大会
    • Place of Presentation
      宮崎市
    • Related Report
      2013 Final Research Report
  • [Presentation] ウシ趾乳頭腫症由来Treponema phagedenis のゲノム特性と比較ゲノム解析2012

    • Author(s)
      後藤恭宏, 山崎和子, 小椋義俊, 大岡唯祐, 矢野貴久, 大島健志朗, 服部正平, 三澤尚明, 林哲也
    • Organizer
      第85回日本細菌学会総会
    • Place of Presentation
      長崎
    • Related Report
      2013 Final Research Report
  • [Presentation] ゲノム解析技術の急速な進化がもたらすゲノム研究の新たな展開2012

    • Author(s)
      林哲也
    • Organizer
      日本科学哲学会第45回(2012年)大会
    • Place of Presentation
      宮崎市
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] ウシ趾乳頭腫症由来Treponema phagedenisのゲノム特性と比較ゲノム解析2012

    • Author(s)
      後藤恭宏, 他
    • Organizer
      第85回日本細菌学会総会
    • Place of Presentation
      長崎
    • Related Report
      2011 Annual Research Report
  • [Presentation] Genome sequence analysis of Treponema phagedenis isolated from bovine papillomatous digital dermatitis (PDD)2011

    • Author(s)
      Y.Gotoh, et al
    • Organizer
      IUMS 2011(第84回日本細菌学会総会)
    • Place of Presentation
      Sapporo
    • Year and Date
      2011-09-07
    • Related Report
      2011 Annual Research Report
  • [Presentation] 家兎における牛の趾乳頭腫症病変モデル作出の試み2011

    • Author(s)
      福田圭祐, 後藤恭宏, 林哲也, 谷口喬子, 山崎渉, 吉谷一紀, 三澤尚明
    • Organizer
      第152回日本獣医学科学術集会
    • Place of Presentation
      堺市
    • Related Report
      2013 Final Research Report 2011 Annual Research Report
  • [Presentation] Genome sequence analysis of Treponema phagedenis isolated from bovine papillomatous digital dermatitis (PDD)2011

    • Author(s)
      Y.Gotoh, K. Yamazaki, Y. Ogura, T. Ooka, T. Yano, K. Oshima, M. Hattori, N. Misawa, T. Hayashi
    • Organizer
      第84回日本細菌学会総会
    • Place of Presentation
      Sapporo
    • Related Report
      2013 Final Research Report
  • [Book] 第4章 新規ゲノム配列決定編細菌ゲノム. 細胞工学別冊 次世代シークエンサー 目的別アドバンストメソッド2012

    • Author(s)
      小椋義俊, 林哲也
    • Publisher
      秀潤社
    • Related Report
      2013 Final Research Report
  • [Book] 細胞工学別冊 次世代シークエンサー 目的別アドバンストメソッド2012

    • Author(s)
      小椋義俊, 林哲也
    • Total Pages
      252
    • Publisher
      秀潤社
    • Related Report
      2012 Annual Research Report
  • [Book] 6.1 病原菌と常在菌の境界(第6 章腸内共生系の破綻と疾病)2011

    • Author(s)
      小椋義俊, 林哲也
    • Publisher
      丸善出版
    • Related Report
      2013 Final Research Report
  • [Book] 動物の感染症第三版2011

    • Author(s)
      三澤尚明
    • Total Pages
      131
    • Publisher
      近代出版
    • Related Report
      2013 Final Research Report 2011 Annual Research Report
  • [Book] 腸内共生系のバイオサイエンス2011

    • Author(s)
      小椋義俊, 林哲也
    • Total Pages
      292
    • Publisher
      丸善出版
    • Related Report
      2011 Annual Research Report

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Published: 2011-04-06   Modified: 2019-07-29  

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