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Metagenome analyses of coprolite and dental calculus for prehistoric specimens from the Japanese Archipelago

Research Project

Project/Area Number 17H03738
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Physical anthropology
Research InstitutionThe University of Tokyo (2019)
Kitasato University (2017-2018)

Principal Investigator

Hiroki Oota  東京大学, 大学院理学系研究科(理学部), 教授 (40401228)

Co-Investigator(Kenkyū-buntansha) 勝村 啓史  北里大学, 医学部, 准教授 (10649544)
植田 信太郎  東京大学, 大学院理学系研究科(理学部), 名誉教授 (20143357)
須田 亙  国立研究開発法人理化学研究所, 生命医科学研究センター, 副チームリーダー (20590847)
水野 文月  東邦大学, 医学部, 助教 (50735496)
熊谷 真彦  国立研究開発法人農業・食品産業技術総合研究機構, 高度解析センター, 研究員 (80738716)
Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥18,460,000 (Direct Cost: ¥14,200,000、Indirect Cost: ¥4,260,000)
Fiscal Year 2019: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2018: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
Fiscal Year 2017: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Keywords糞石 / 歯石 / ゲノム / DNAメタバーコーディング法 / 摂食物同定 / 狩猟採集 / 農耕牧畜 / 先史時代 / 縄文時代 / 弥生時代 / ゲノム解析 / 植物性植物 / 狩猟採取 / 古代ゲノム / 摂食物 / 腸内細菌 / 植物性食物 / 農耕 / メタゲノム / 先史日本列島人 / 食性 / メタゲノム解析 / DNAバーコーディング / 縄文人 / 弥生人 / 古人骨 / 古ゲノム解析
Outline of Final Research Achievements

The purpose of this study is to establish a technique for identifying the flora and fauna that were the target of feeding by people at that time by performing genomic analysis of coprolites and dental stones found in prehistoric sites. In this study, in order to establish this technical basis, we improved DNA extraction technology from feces by using (1) feces of captive mammals, (2) faeces of modern indigenous people who continue traditional life, and ingestion by genomic analysis. We have been optimizing food identification technology. Based on the accumulated know-how, we succeeded in identifying food by the DNA metabarcoding method by extracting DNA from (3) Japanese prehistoric coprolites and (4) historical dental stones. Regarding the fourth results, the original paper was published in the international magazine PLoS ONE.

Academic Significance and Societal Importance of the Research Achievements

これまであまり研究対象とされてこなかった糞石および歯石に着目し、過去の人々が実際に何を食べていたかを明らかにするその第一歩が達成できたことの学術的意義は大きい。わたしたちの成果からゲノム解析にもとづく食性分析により、従来の方法では分からなかった、科あるいは属レベルでの摂食対象生物の同定が可能になった。食生活は、戦後の欧米化によって劇的に変化したが、これが現代日本人の健康にどのように影響しているかを過去にまでさかのぼった定量的な研究はこれまでほぼ皆無であった。本研究で得られるゲノム配列データがその答えを与えることが期待でき、社会的意義も大きい。

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • Research Products

    (24 results)

All 2020 2019 2018 2017 Other

All Int'l Joint Research (2 results) Journal Article (6 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 6 results,  Open Access: 5 results) Presentation (15 results) (of which Int'l Joint Research: 6 results,  Invited: 7 results) Book (1 results)

  • [Int'l Joint Research] Hangzhou Normal University(中国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] コペンハーゲン大学(デンマーク)

    • Related Report
      2018 Annual Research Report
  • [Journal Article] Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan2020

    • Author(s)
      Sawafuji R, Saso A, Suda W, Hattori M, Ueda S
    • Journal Title

      PLOS ONE

      Volume: March 4 Issue: 3 Pages: 1-16

    • DOI

      10.1371/journal.pone.0226654

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 港川人のミトコンドリアDNA全塩基配列からわかること2020

    • Author(s)
      水野文月、五條堀淳
    • Journal Title

      学術の動向 特集 日本旧石器人研究の発展:沖縄の現場から

      Volume: 25 Pages: 38-41

    • NAID

      130007865037

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome2019

    • Author(s)
      Koji Ishiya、Fuzuki Mizuno、Li Wang、Shintaroh Ueda
    • Journal Title

      Bioinformatics and Biology Insights

      Volume: 13 Pages: 1-9

    • DOI

      10.1177/1177932219873884

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The prehistoric peopling of Southeast Asia2018

    • Author(s)
      Hugh McColl, Fernando Racimo, Lasse Vinner, Fabrice Demeter, Takashi Gakuhari, …, Hajime Ishida, … Eske Willerslev
    • Journal Title

      Science

      Volume: 361(6397) Issue: 6397 Pages: 88-92

    • DOI

      10.1126/science.aat3628

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A new targeted capture method using bacterial artificial chromosome (BAC) libraries as baits for sequencing relatively large genes2018

    • Author(s)
      Kae Koganebuchi, Takashi Gakuhari, Hirohiko Takeshima, Kimitoshi Sato, Kiyotaka Fujii, Toshihiro Kumabe, Satoshi Kasagi, Takehiro Sato, Atsushi Tajima, Hiroki Shibata, Motoyuki Ogawa, Hiroki Oota
    • Journal Title

      PLOS ONE

      Volume: 13 Issue: 7 Pages: 1-14

    • DOI

      10.1371/journal.pone.0200170

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Medaka Population Genome Structure and Demographic History Described via Genotyping-by-Sequencing2018

    • Author(s)
      Katsumura Takafumi、Oda Shoji、Mitani Hiroshi、Oota Hiroki
    • Journal Title

      G3: GENES, GENOMES, GENETICS

      Volume: 9 Issue: 1 Pages: 217-228

    • DOI

      10.1534/g3.118.200779

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] メタゲノム解析の基礎2019

    • Author(s)
      熊谷真彦
    • Organizer
      第214 回農林交流センターワークショップ「NGSデータ解析シンポジウム」
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] ミトコンドリアDNAからみた居家以岩陰遺跡出土人骨の遺伝的系統2019

    • Author(s)
      植田信太郎、水野文月
    • Organizer
      日本考古学協会第85回総会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 港川人骨のミトコンドリアDNA全塩基配列からわかること2019

    • Author(s)
      水野文月、五條堀淳
    • Organizer
      日本旧石器人研究の発展:沖縄の現場から
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] The Jomon genome and migration of anatomical modern humans to East Asia2019

    • Author(s)
      H. Oota
    • Organizer
      Transeurasian millets and beans, language and genes
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 遺伝人類学からみた東アジア・日本列島への人類の拡散2018

    • Author(s)
      太田博樹
    • Organizer
      日本旧石器学会第16回大会シンポジウム「日本列島への人類拡散と後期旧石器時代の成立を考える」
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] A new targeted-capture method using bacteria artificial chromosome (BAC) as baits exclusively developed for sequencing relatively large loci of ancient DNA2018

    • Author(s)
      K. Koganebuchi, T. Gakuhari, H. Takeshima, S. Kasagi, T. Sato, A. Tajima, H. Shibata, M. Ogawa, H. Oota
    • Organizer
      The Society for Molecular Biology and Evolution, Annual Meeting
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] The Transition to Farming in Eneolithic (Copper Age) Ukraine was Largely Driven by Population Replacement2018

    • Author(s)
      R.W. Schmidt, D. Fernandes, J. Karsten, T. Harper, G. Madden, S. Ledogar, M. Sokhatsky, H. Oota, R. Pinhasi
    • Organizer
      The Society for Molecular Biology and Evolution, Annual Meeting
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Whole genome analysis of the Jomon remain reveals deep lineage of East Eurasian populations2018

    • Author(s)
      T. Gakuhari, M. Sikora, S. Rasmussen, M. Allentoft, T. Sato, T. Kornrliussen, M. Yonda, H. Ishida, Y. Yamada, H. Shibata, S. Nakagome, E. Willerslev, H. Oota
    • Organizer
      The Society for Molecular Biology and Evolution, Annual Meeting
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Complex human histories of Northeast Asia revealed by correlaions between genes, language, and music2018

    • Author(s)
      H. Matsumae, P.E. Savage, B. Bickel, T.E. Currie, T. Sato, A. Tajima, M. Stoneking, K.K. Shimizu, M. Gillan, S. Brown, H. Oota
    • Organizer
      The Society for Molecular Biology and Evolution, Annual Meeting
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Human population history in the southwestern coastal region of Sea of Okhotsk, inferred from ancient genome analysis2018

    • Author(s)
      T. Sato, N. Adachi, R. Kimura, M. Yoneda, H. Oota, A. Tajima, A. Toyoda, H. Matsumae, K. Koganebuchi, K.K. Shimizu, T. Hanihara, A. Weber, H. Kato, H. Ishida
    • Organizer
      The Society for Molecular Biology and Evolution, Annual Meeting
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A trial for reconstructing human population history in the Japanese archipelago~through the simulation besed on genome-wide deta and ancient DNA analyses2017

    • Author(s)
      H. Oota
    • Organizer
      The Genome Evolution at Mishima
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 古代ゲノム学の現状とキャッチアップにむけての試行2017

    • Author(s)
      太田博樹
    • Organizer
      日本進化日本進化学会第19回大会 シンポジウム「比較ゲノムから幹細胞人類学へ:ヒト表現型進化のゲノム基盤解明に向けた新たな取り組み」
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Ukrainian Eneolithic (3500BCE) Trypillian agropastoralists and their genetic association with Neolithic farmers from Sourthern Europe and the Near East2017

    • Author(s)
      R.W.Schmidt, D. Fernandes. K. Wakabayashi, K. Koganebuchi, T. Gakuhari, J. Karsten, K. Kubehl, G. Madden, M. Sokhatsky, H. Oota, R. Pinhasi
    • Organizer
      The Society for Experimental Biology conference
    • Related Report
      2017 Annual Research Report
  • [Presentation] ヴァティーバ洞窟遺跡出土人骨のDNA分析~初期牧畜農耕民の集団構造推定に向けて2017

    • Author(s)
      若林賢、ライアン シュミット W.,覚張隆史、小金渕佳江、ジョーダン カーステン、ミハイオ ソハトスキー、小川元之、太田博樹
    • Organizer
      第71回日本人類学会大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 古代ゲノム解析への応用に向けたBACダブルキャプチャー法の検討2017

    • Author(s)
      小金渕佳江、覚張隆史、武島弘彦、笠木聡、佐藤丈寛、田嶋敦、柴田弘紀、小川元之、太田博樹
    • Organizer
      第71回日本人類学会大会
    • Related Report
      2017 Annual Research Report
  • [Book] アフロ・ユーラシアの考古植物学2019

    • Author(s)
      熊谷 真彦、庄田 慎矢、水野 文月、王 瀝
    • Total Pages
      262
    • Publisher
      クバプロ
    • ISBN
      9784878051616
    • Related Report
      2019 Annual Research Report

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Published: 2017-04-28   Modified: 2021-02-19  

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