Genome analysis of uncultivable microbes

• Project/Area Number: 18687002
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Ecology/Environment
• Research Institution: The Institute of Physical and Chemical Research
• Principal Investigator: HONGOH Yuichi The Institute of Physical and Chemical Research, 前田バイオ工学研究室, 協力研究員 (90392117)
• Project Period (FY): 2006 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥15,600,000 (Direct Cost: ¥12,000,000、Indirect Cost: ¥3,600,000); Fiscal Year 2008: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000); Fiscal Year 2007: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000); Fiscal Year 2006: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
• Keywords: 難培養 / 微生物 / 細菌 / 共生 / ゲノム / シロアリ / 昆虫 / バイオマス / 腸内細菌 / 原生生物 / 環境 / セルロース

Research Abstract

地球上の99%以上の微生物種は培養法が不明であり、その生理・生態はほとんど未知である。本研究では、シロアリ腸内に共生する培養不能細菌の1種の少数細胞から、DNA合成酵素を使用することで全遺伝子情報を1千万倍に増幅して完全解読する手法の確立を試み、世界で初めて成功した。これにより、これまで詳細が不明であったシロアリと腸内原生生物、腸内細菌の複雑な3者共生機構を世界で初めて明らかにした。

Research Products

• [Journal Article] Genome of an endosymbiont coupling N_2-fixation to cellulolysis in protist cells in termite gut (2008)
  • Author(s): Hongoh Y., Sharma V.K., Prakash T., et al.
  • Journal Title: Science (in press)
  • Peer Reviewed
• [Journal Article] Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell (2008)
  • Author(s): Hongoh Y., Sharma V.K., Prakash T., et al.
  • Journal Title: Proceedings of the National Academy of Sciences of the United States of America 105 Pages: 5555-5560
  • Peer Reviewed
• [Journal Article] Inheritance and diversification of symbiotic trichonymphid flagellates from a common ancestor of termites and cockroach Cryptocercus (2008)
  • Author(s): Ohkuma M., Noda S., Hongoh Y., et al.
  • Journal Title: Proceedings of the Royal Society B (Biological Sciences) (in press)
  • Peer Reviewed
• [Journal Article] Identification of endosymbiotic methanogens and ectosymbiotic spirochetes of gut protists of the termite Coptotermes formosanus (2008)
  • Author(s): Inoue J., Noda S., Hongoh Y., Ui S., Ohkuma M.
  • Journal Title: Microbes and Environments 93 Pages: 94-97
  • NAID: 120006581880
  • Peer Reviewed
• [Journal Article] シロアリ腸内共生微生物群の多様性とゲノム解析 (2008)
  • Author(s): 本郷裕一, 大熊盛也
  • Journal Title: Journal of Environmental Biotechnology(環境バイオテクノロジー学会誌) 8 Pages: 29-34
• [Journal Article] ゲノムから解き明かす難培養性細菌の機能 (2008)
  • Author(s): 本郷裕一, 大熊盛也
  • Journal Title: 化学と生物(日本農芸化学会誌) (in press)
• [Journal Article] 難培養微生物のゲノム解析技術とシロアリ腸内微生物の共生機構 (2008)
  • Author(s): 大熊盛也, 本郷裕一
  • Journal Title: バイオインダストリーとサイエンス (in press)
• [Journal Article] シロアリ腸内微生物の多重共生-バイオマス資源を高効率に利用する共生 (2008)
  • Author(s): 大熊盛也, 本郷裕一, 野田悟子
  • Journal Title: 蛋白質核酸酵素 (in press)
• [Journal Article] Complete genome of the uncultures Termite Group 1 bacteria in a single host protist cell (2008)
  • Author(s): Yuichi Hongoh
  • Journal Title: Proceedings of the National Academy of Sciences of the United States of America 105 Pages: 5555-5560
  • Peer Reviewed
• [Journal Article] Inheritance and diversification of symbiotic trichonymphid flagellates from a common ancestor of termites and the cockroach Cryptocercus (2008)
  • Author(s): Moriya Ohkuma
  • Journal Title: Proceedings of the Royal Society B (in press)
  • Peer Reviewed
• [Journal Article] シロアリ腸内共生微生物群の多様性とゲノム解析 (2008)
  • Author(s): 本郷裕一
  • Journal Title: Journal of Environmental Biotechnology 8 Pages: 29-34
• [Journal Article] ゲノムから解き明かす難培養性細菌の機能 (2008)
  • Author(s): 本郷裕一
  • Journal Title: 化学と生物 (in press)
• [Journal Article] シロアリ腸内微生物の多重共生-バイオマス資源を高効率に利用する共生 (2008)
  • Author(s): 大熊盛也
  • Journal Title: 蛋白質核酸酵素 (in press)
• [Journal Article] Identification of endosymbiotic methanogens and ectosymbiotic spirochetes of gut protists of the termite Coptotermes formosanus (2008)
  • Author(s): Jun-Ichi Inoue
  • Journal Title: Microbes and Environments (in press)
  • Peer Reviewed
• [Journal Article] Complete genome of the uncultured"Termite Group 1"bacteria in asingle host protist cell (2008)
  • Author(s): Yuichi Hongoh
  • Journal Title: Proceedings of the National Academy of Sciences of the United States of America (in press)
  • Peer Reviewed
• [Journal Article] The motility symbiont of the termite-gut flagellate Caduceia versatilis is a member of the "Synergistes" group (2007)
  • Author(s): Hongoh Y., Sato T., Dolan M. F., et al.
  • Journal Title: Applied and Environmental Microbiology 73 Pages: 6270-6276
  • NAID: 120006581862
  • Peer Reviewed
• [Journal Article] Candidatus Symbiothrix dinenymphae : bristle-like Bacteroidales ectosymbionts of termite gut protists (2007)
  • Author(s): Hongoh Y., Sato T., Noda S., et al.
  • Journal Title: Environmental Microbiology 9 Pages: 2631-2635
  • Peer Reviewed
• [Journal Article] Evolutionary trend of phylogenetic diversity of nitrogen fixation genes in the gut community of wood-feeding termites (2007)
  • Author(s): Yamada A., Inoue T., Noda S., et al.
  • Journal Title: Molecular Ecology 16 Pages: 3768-3777
  • Peer Reviewed
• [Journal Article] The candidate phylum 'Termite Group 1' of bacteria : phylogenetic diversity, distribution, and endosymbiont members of various gut flagellated protists (2007)
  • Author(s): Ohkuma M., Sato T., Noda S.
  • Journal Title: FEMS Microbiology Ecology 60 Pages: 467-476
  • Peer Reviewed
• [Journal Article] Coevolutionary history of a triplex symbiotic system of termites, their gut protists, and bacterial endosymbionts of the protists (2007)
  • Author(s): Noda S., Kitade O., Inoue T., et al.
  • Journal Title: Molecular Ecology 16 Pages: 1257-1266
  • Peer Reviewed
• [Journal Article] The candidate phylum‘Termite Group 1'of bacteria: phylogenetic diversity, distribution, and endosymbiont members of various gut flagellated protists (2007)
  • Author(s): Moriya Ohkuma
  • Journal Title: FEMS Microbiology Ecology 60 Pages: 467-476
  • Peer Reviewed
• [Journal Article] Evolutionary trend of phylogenetic diversity of nitrogen fixation genes in the gut community of wood-feeding termites (2007)
  • Author(s): Akinori Yamada
  • Journal Title: Molecular Ecology 16 Pages: 3768-3777
  • Peer Reviewed
• [Journal Article] Candidatus Symbiothrix dinenymphae: bristle-like Bacteroidales ectosy mbionts of termite gut protists (2007)
  • Author(s): Yuichi Hongoh
  • Journal Title: Environmental Microbiology 9 Pages: 2631-2635
  • Peer Reviewed
• [Journal Article] The motility symbiont of the termite-gut flagellate Caduceia versatilis is a member of the"Synergistes"group (2007)
  • Author(s): Yuichi Hongoh
  • Journal Title: Applied and Environmental Microbiology 73 Pages: 6270-6276
  • NAID: 120006581862
  • Peer Reviewed
• [Journal Article] Coevolutionary history of a triplex symbiotic system of termites, their gut protists, and bacterial endosymbionts of the protists (2007)
  • Author(s): Satoko Noda
  • Journal Title: Molecular Ecology (in press)
• [Journal Article] The candidate phylum "Termite Group 1" of bacteria : phylogenetic diversity, distribution, and endosymbiont members of various gut flagellated protists (2007)
  • Author(s): Moriya Ohkuma
  • Journal Title: FEMS Microbiology Ecology (in press)
• [Journal Article] Phylogenetic diversity, localization, and cell morphologies of members of the candidate phylum TG3 and a subphylum in the phylum Fibrobacteres, recently discovered bacterial groups dominant in termite guts (2006)
  • Author(s): Hongoh Y., Deevong P., Hattori S., et al.
  • Journal Title: Applied and Environmental Microbiology 72 Pages: 6780-6788
  • Peer Reviewed
• [Journal Article] Effect of temporal preservation on molecular study of complex microbial community in the gut of the termite Microcerotermes sp. (2006)
  • Author(s): Deevong P., Hongoh Y., Inoue T., et al.
  • Journal Title: Microbes and Environments 21 Pages: 78-85
  • Peer Reviewed
• [Journal Article] Diversity and abundance of termites along an altitudinal gradients in Khao Kitchagoot National Park, Thailand (2006)
  • Author(s): Inoue T., Takematsu Y., Yamada A., et al.
  • Journal Title: Journal of Tropical Ecology 22 Pages: 609-612
  • Peer Reviewed
• [Journal Article] Effect of temporal preservation on molecular study of complex microbial community in the gut of the termite Microcerotermes sp. (2006)
  • Author(s): Pinsurang Deevong
  • Journal Title: Microbes and Environments 21 Pages: 78-85
• [Journal Article] Diversity and abundance of termites along an altitudinal gradients in Khao Kitchagoot National Park, Thailand. (2006)
  • Author(s): Tetsushi Inoue
  • Journal Title: Journal of Tropical Ecology 22 Pages: 609-612
• [Journal Article] Phylogenetic diversity, localization, and cell morphologies of members of the candidate phylum TG3 and a subphylum in the phylum Fibrobacteres, recently discovered bacterial groups dominant in termite guts (2006)
  • Author(s): Yuichi Hongoh
  • Journal Title: Applied and Environmental Microbiology 72 Pages: 6780-6788
• [Presentation] シロアリ腸内原生生物に細胞内共生するAlphaproteobacteria新属細菌の検出と分子系統解析 (2008)
  • Author(s): 佐藤朋之
  • Organizer: 第24回日本微生物生態学会(予定)
  • Place of Presentation: 北大
• [Presentation] シロアリ腸内共生系研究の最前線-ゲノムから解き明かす培養不能微生物群の実体- (2008)
  • Author(s): 本郷裕一
  • Organizer: 産業技術総合研究所公開セミナー
  • Place of Presentation: 産総研、つくば
• [Presentation] Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell (2008)
  • Author(s): Hongoh Y.
  • Organizer: 12th International Society for Microbial Ecology (ISME-12)
  • Place of Presentation: Cairns, Australia
• [Presentation] Simultaneous association of Desulfovibrio and Termite Group 1 of bacteria with a single flagellate cell in termite guts (2008)
  • Author(s): Sato T.
  • Organizer: 12th International Society for Microbial Ecology (ISME-12)
  • Place of Presentation: Cairns, Australia
• [Presentation] シロアリ腸内共生系ゲノミクス解析 (2008)
  • Author(s): 本郷裕一
  • Organizer: 日本農芸化学会2008年度大会 公開シンポジウム「微生物による地球炭素循環と環境バイオテクノロジー」
  • Place of Presentation: 名城大、名古屋
• [Presentation] 培養不能シロアリ腸内細菌のゲノム全長取得と解析 (2008)
  • Author(s): 本郷裕一
  • Organizer: 第81回日本細菌学会総会(公開シンポジウム「ゲノム微生物学の新展開」)
  • Place of Presentation: 京都
• [Presentation] 偽遺伝子が明らかにしたシロアリ腸内共生未培養新門細菌の適応進化 (2008)
  • Author(s): 本郷裕一
  • Organizer: 第2回日本ゲノム微生物学会
  • Place of Presentation: 阪大
• [Presentation] シロアリ腸内原生生物細胞内共生細菌の全ゲノム解析 (2007)
  • Author(s): 本郷 裕一
  • Organizer: 第23回日本微生物生態学会
  • Place of Presentation: 愛媛大
  • Year and Date: 2007-09-18
• [Presentation] 培養不能シロアリ腸内細菌のゲノム全長取得と解析 (2007)
  • Author(s): 本郷 裕一
  • Organizer: 第81回日本細菌学会総会
  • Place of Presentation: 京都国際会館
  • Year and Date: 2007-03-26
• [Presentation] 偽遺伝子が明らかにしたシロアリ腸内共生未培養新門細菌の適応進化 (2007)
  • Author(s): 本郷 裕一
  • Organizer: 日本ゲノム微生物学会第二回年会
  • Place of Presentation: 大阪大
  • Year and Date: 2007-03-06
• [Presentation] 培養できない細菌のゲノム完全長取得による機能推定の試み (2007)
  • Author(s): 本郷裕一
  • Organizer: 理研公開セミナー
  • Place of Presentation: 和光
• [Presentation] Complete genome of un uncultured bacterial symbiont in the termite gut (2007)
  • Author(s): Hongohy Y.
  • Organizer: 応用ゲノム国際会議
  • Place of Presentation: 東京
• [Presentation] シロアリ腸内原生生物細胞内共生細菌の全ゲノム解析 (2007)
  • Author(s): 本郷裕一
  • Organizer: 第23回日本微生物生態学会(公開シンポジウム「微生物生態学における環境ゲノムミクス」)
  • Place of Presentation: 愛媛大
• [Presentation] Toward understanding the function of highly structured symbiotic microbial community in the gut of termites (2007)
  • Author(s): Ohkuma M.
  • Organizer: ISME-Asia
  • Place of Presentation: 愛媛大
• [Presentation] 培養不能細菌のゲノム全長解析 (2007)
  • Author(s): 本郷裕一
  • Organizer: 第6回微生物研究会(公開シンポジウム「微生物の潜在能力を探る」)
  • Place of Presentation: 理研、和光
• [Presentation] シロアリ腸内原生生物とその細胞内共生細菌の共進化 (2007)
  • Author(s): 大熊盛也
  • Organizer: 日本進化原生生物学研究会
  • Place of Presentation: JANSTEC、横浜
• [Presentation] シロアリに共生する難培養性腸内細菌の全ゲノム配列の決定と解析 (2007)
  • Author(s): 本郷裕一
  • Organizer: 日本ゲノム微生物学会第一回年会
  • Place of Presentation: かずさ
• [Presentation] Complete genome of an uncultured bacterial symbiont in the termite gut (2007)
  • Author(s): Yuichi Hongoh
  • Organizer: The 7th International Workshop on advanced genomics
  • Place of Presentation: 東京インターナショナルフォーラム
• [Presentation] Culture- independent characterization of the novel candidate phylum TG3 in domain Bacteria (2006)
  • Author(s): Hongoh Y.
  • Organizer: 11^<th> International Society for Microbial Ecology (ISME-11)
  • Place of Presentation: Vienna, Austria
• [Remarks] 理研プレスリリース(2008.4.1)「シロアリ腸内微生物のゲノム解読に世界で初めて成功」
  • URL: http://www.riken.go.jp/r-world/info/release/press/2008/080401/index.html