Evolution of genome and metagenome association in primates

• Project/Area Number: 16K18630
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Physical anthropology
• Research Institution: Kyoto University
• Principal Investigator: Hayakawa Takashi 京都大学, 霊長類研究所, 特定助教 (00758493)
• Research Collaborator: Hirata Satoshi
• Project Period (FY): 2016-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2018: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2017: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2016: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: 霊長類 / ゲノム / メタゲノム / 腸内細菌叢 / 口腔細菌叢 / 共進化 / チンパンジー / 動物福祉 / 次世代シークエンサー / 細菌叢 / ゲノム多様性 / 腸内細菌

Outline of Final Research Achievements

This study aimed to elucidate the genome and metagenome association in captive and wild primates. Fecal samples of about 50 captive chimpanzees in Kyoto University were collected and subject to 16S rRNA sequencing analysis for symbiont gut bacteria. Relationship between individual background (especially genomic polymorphisms) and 16S diversity was analyzed. Fecal and oral bacterial samples of many primate species in Japan Monkey Centre and some field areas were collected for analysis of metagenomic profile in terms of species specificity and phylogenetic constraint.

Academic Significance and Societal Importance of the Research Achievements

ゲノムとメタゲノムは哺乳類をはじめとする多細胞生物の生命活動の根幹を支えるが、その両者の連関についての理解はまだ乏しい。そうした視点で研究を進めることは、基礎的な進化生物学の理解につながるとともに、ヒトに最も近縁なチンパンジーを対象としたことで、ヒト自身のゲノム、メタゲノム進化の背景を探る契機となった。また、メタゲノムの確立は後天的要素が大きいものなので、飼育下動物の福祉にも貢献する知見である。

Research Products

• [Journal Article] Next-Generation Sequencing in Primate Molecular Ecology (2018)
  • Author(s): HAYAKAWA Takashi
  • Journal Title: Primate Research Volume: 34 Issue: 1 Pages: 65-78
  • DOI: 10.2354/psj.34.004
  • NAID: 130007437735
  • ISSN: 0912-4047, 1880-2117
  • Year and Date: 2018-06-20
  • Peer Reviewed
• [Journal Article] Improving the standards for gut microbiome analysis of fecal samples: insights from the field biology of Japanese macaques on Yakushima Island (2018)
  • Author(s): Hayakawa Takashi、Sawada Akiko、Tanabe Akifumi S.、Fukuda Shinji、Kishida Takushi、Kurihara Yosuke、Matsushima Kei、Liu Jie、Akomo-Okoue Etienne-Francois、Gravena Waleska、Kashima Makoto、Suzuki Mariko、Kadowaki Kohmei、Suzumura Takafumi、Inoue Eiji、Sugiura Hideki、Hanya Goro、Agata Kiyokazu
  • Journal Title: Primates Volume: 59 Issue: 5 Pages: 423-436
  • DOI: 10.1007/s10329-018-0671-x
  • NAID: 40021661058
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Adaptation and conservation insights from the koala genome (2018)
  • Author(s): Rebecca N. Johnson et al.
  • Journal Title: Nature Genetics Volume: 50 Issue: 8 Pages: 1102-1111
  • DOI: 10.1038/s41588-018-0153-5
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] First report of foregut microbial community in proboscis monkeys: are diverse forests a reservoir for diverse microbiomes? (2018)
  • Author(s): Hayakawa Takashi、Nathan Senthilvel K. S. S.、Stark Danica J.、Saldivar Diana A. Ramirez、Sipangkui Rosa、Goossens Benoit、Tuuga Augustine、Clauss Marcus、Sawada Akiko、Fukuda Shinji、Imai Hiroo、Matsuda Ikki
  • Journal Title: Environmental Microbiology Reports Volume: 10 Issue: 6 Pages: 655-662
  • DOI: 10.1111/1758-2229.12677
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Functional decline of sweet taste sensitivity of colobine monkeys. (2018)
  • Author(s): Nishi E, Suzuki-Hashido N, Hayakawa T, Tsuji Y, Suryobroto B, Imai H
  • Journal Title: Primates Volume: 59 Issue: 6 Pages: 523-530
  • DOI: 10.1007/s10329-018-0679-2
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Evolution of vomeronasal receptor 1 ( V1R ) genes in the common marmoset ( Callithrix jacchus ) (2018)
  • Author(s): Moriya-Ito Keiko、Hayakawa Takashi、Suzuki Hikoyu、Hagino-Yamagishi Kimiko、Nikaido Masato
  • Journal Title: Gene Volume: 642 Pages: 343-353
  • DOI: 10.1016/j.gene.2017.11.048
  • Peer Reviewed
• [Journal Article] Morphometric and Genetic Determination of Age Class and Sex for Fecal Pellets of Sika Deer (Cervus nippon) (2017)
  • Author(s): Hanya Goro、Naito Senri、Namioka Erina、Ueda Yosuke、Sato Yo、Pastrana Josue Alejandro、He Tianmeng、Yan Xiaochan、Saito Miho、Costa Raquel Filomena Pereira、Allanic Morgane、Honda Takeaki、Kurihara Yosuke、Yumoto Takakazu、Hayakawa Takashi
  • Journal Title: Mammal Study Volume: 42 Issue: 4 Pages: 1-8
  • DOI: 10.3106/041.042.0406
  • NAID: 210000182462
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Direct estimation of de novo mutation rates in a chimpanzee parent-offspring trio by ultra-deep whole genome sequencing (2017)
  • Author(s): Tatsumoto Shoji、Go Yasuhiro、Fukuta Kentaro、Noguchi Hideki、Hayakawa Takashi、Tomonaga Masaki、Hirai Hirohisa、Matsuzawa Tetsuro、Agata Kiyokazu、Fujiyama Asao
  • Journal Title: Scientific Reports Volume: 7 Issue: 1 Pages: 13561-13561
  • DOI: 10.1038/s41598-017-13919-7
  • NAID: 120006358802
  • Peer Reviewed / Open Access
• [Journal Article] Functional characterization of the TAS2R38 bitter taste receptor for phenylthiocarbamide in colobine monkeys. (2017)
  • Author(s): L. H. P. Purba, K. A. Widayati, K. Tsutsui, N. Suzuki-Hashido, T. Hayakawa, S. Nila, B. Suryobroto, H. Imai.
  • Journal Title: Biology Letters Volume: 13 Issue: 1 Pages: 20160834-20160834
  • DOI: 10.1098/rsbl.2016.0834
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Variation in ligand responses of the bitter taste receptors TAS2R1 and TAS2R4 among New World monkeys. (2016)
  • Author(s): K. Tsutsui, M. Otoh, K. Sakurai, N. Suzuki-Hashido, T. Hayakawa, T. Misaka, Y. Ishimaru, F. Aureli, A. D. Melin, *S. Kawamura, *H. Imai.
  • Journal Title: BMC Evolutionary Biology Volume: 16 Issue: 1 Pages: 208-208
  • DOI: 10.1186/s12862-016-0783-0
  • NAID: 120006223634
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] Natural gum feeding to captive marmosets: diet preference and gut microbiome (2019)
  • Author(s): Takashi Hayakawa et al.
  • Organizer: 第63回プリマーテス研究会
• [Presentation] Life slowly, life in the dark: insight from slow loris genome (2019)
  • Author(s): Takashi Hayakawa, Shoji Tatsumoto, Takushi Kishida, Hikoyu Suzuki, Hiroe Ishikawa, Masato Nikaido, Yasuhiro Go
  • Organizer: The 11 International Symposium on Primatology and Wildlife Science
  • Int'l Joint Research
• [Presentation] ドゥクラングール乳児の腸内細菌叢の適応 (2018)
  • Author(s): 早川卓志、澤田晶子、川口芳矢、鈴木健大、小林智男、福田真嗣、松田一希
  • Organizer: 第34回日本霊長類学会大会
• [Presentation] 霊長類の苦味受容体遺伝子ファミリー進化の再検討 (2018)
  • Author(s): 早川卓志、橋戸南美
  • Organizer: 日本進化学会第20回大会
• [Presentation] 同所的に生息する野生グエノン3種における全遺伝子配列の比較解析 (2017)
  • Author(s): 早川卓志, 田代靖子, 橋本千絵, 五百部裕, 今井啓雄
  • Organizer: 第61回プリマーテス研究会
  • Place of Presentation: 公益財団法人日本モンキーセンター
  • Year and Date: 2017-01-28
• [Presentation] 大型類人猿情報ネットワークGAINを活用した生物学研究 (2017)
  • Author(s): 早川卓志
  • Organizer: 第26回 サル疾病ワークショップ
  • Invited
• [Presentation] Microbiome adaptation and flexibility to the captive environments in lessor slow loris (2017)
  • Author(s): Takashi Hayakawa, Kei Matsushima, Wataru Yano, Yumi Yamanashi, Daisuke Shimizu, Yumiko Terao, Fumihiko Okumura, Mari Hirosawa, Yui Fujimori, Naoki Okabe, Sayaka Tsuchida, Kazunari Ushida
  • Organizer: The 8th International Symposium on Primatology and Wildlife Science
  • Int'l Joint Research
• [Presentation] 動物園でのキュレーターのミッション ～基礎研究から動物福祉まで～ (2017)
  • Author(s): 早川卓志
  • Organizer: 第20回SAGAシンポジウム
• [Presentation] Genetic background of the gustationin a specialized arboreal folivore, koala (2017)
  • Author(s): Takashi Hayakawa, Don Colgan, Rebecca N. Johnson, Katherine Belov
  • Organizer: The 62nd Primates Conference
  • Int'l Joint Research
• [Book] 霊長類図鑑―サルを知ることはヒトを知ること (2018)
  • Author(s): 日本モンキーセンター（編）
  • Total Pages: 155
  • Publisher: 京都通信社
  • ISBN: 4903473619
• [Patent(Industrial Property Rights)] 菌叢バランス調節組成物及びその応用 (2018)
  • Inventor(s): 松島慶、他
  • Industrial Property Rights Holder: 公益財団法人日本モンキーセンター、他
  • Industrial Property Rights Type: 特許
  • Filing Date: 2018