論文

• Kazuki Takakashi, Hirokazu Kuwahara, Yutaro Horikawa, Kazuki Izawa, Daiki Kato, Tatsuya Inagaki, Masahiro Yuki, Moriya Ohkuma, Yuichi Hongoh. Emergence of putative energy parasites within Clostridia revealed by genome analysis of a novel endosymbiotic clade, The ISME Journal, Oxford University Press, Vol. 17, Issue 11, Page 1895-1906, Nov. 2023.
• Jaclyn Thompson, Casey Barr, Lydia Babcock-Adams, Lina Bird, Eugenio La Cava, Arkadiy Garber, Yuichi Hongoh, Mark Liu, Kenneth H. Nealson, Akihiro Okamoto, Daniel Repeta, Shino Suzuki, Clarissa Tacto, Michelle Tashjian, Nancy Merino. Insights into the physiological and genomic characterization of three bacterial isolates from a highly alkaline, terrestrial serpentinizing system, Frontiers in Microbiology, Vol. 14, pp. e1179857, July 2023.
• Hirohito Aoki, Masahiro Yuki, Yuichi Hongoh, Yutaka YAMAGATA, Moriya Ohkuma. Agarose gel microcapsules enable easy-to-prepare, picolitre-scale, single-cell genomics, yielding high-coverage genome sequence, Scientific Reports, Vol. 12, No. 1, p. e17014, Oct. 2022.
• Kinjo Y., Bourguignon T., Hongoh Y., Lo N., Tokuda G., Ohkuma M.. Coevolution of metabolic pathways in Blattodea and their Blattabacterium endosymbionts, and comparisons with other insect-bacteria symbiose, Microbiology Spectrum, Vol. 10, no. 5, p. e0277922, Sept. 2022.
• Maneeploy Nualkul, Bundit Yuangsoi, Yuichi Hongoh, Akinori Yamada, Pinsurang Deevong. Improving the nutritional value and bioactivity of soybean meal in solid-state fermentation using Bacillus strains newly isolated from the gut of the termite Termes propinquus, FEMS Microbiology Letters, Vol. 369, Issue 1, Page fnac044, May 2022.
• Katsura Igai, Osamu Kitade, Jieyang Fu, Kazumi Omata, Takahiro Yonezawa, Moriya Ohkuma, Yuichi Hongoh. Fine-scale genetic diversity and putative ecotypes of oxymonad protists coinhabiting the hindgut of Reticulitermes speratus, Molecular Ecology, Vol. 31, Issue 4, pp. 1317-1331, Feb. 2022.
• Bourguignon T., Kinjo Y., Paula Villa-Martin, Nicholas V. Coleman, Qian Tang, Daej A. Arab, Zongqing Wang, Tokuda G., Hongoh Y., Ohkuma M., Simon Y.W. Ho, Simone Pigolotti, Lo N.. Increased mutation rate is linked to genome reduction in prokaryotes, Current Biology, Vol. 30, pp. 3848-3855, Oct. 2020.
• Merino N., Kawai M., Boyd E.S., Colman D.R., Shawn McGlynn, Nealson K., Kurokawa K., Hongoh Y.. Single-cell genomics of novel actinobacteria with the Wood-Ljungdahl pathway discovered in a serpentinizing system, Frontiers in Microbiology, vol. 11, pp. e1031, June 2020.
• Takeuchi M., Kuwahara H., Murakami T., Takahashi K., Kajitani R., Toyoda A., Itoh T., Ohkuma M., Hongoh Y. Parallel reductive genome evolution in Desulfovibrio ectosymbionts independently acquired by Trichonympha protists in the termite gut, The ISME Journal, Vol. 14, pp. 2288–2301, June 2020.
• Takumi Murakami, Syu Onouchi, Katsura Igai, Moriya Ohkuma, Yuichi Hongoh. Ectosymbiotic bacterial microbiota densely colonize the surface of thelastomatid nematodes in the gut of the wood-feeding cockroach Panesthia angustipennis, FEMS Microbiology Ecology, Vol. 95, No. 2, p. fiy238, Feb. 2019.
• Yuniar Devi Utami, Hirokazu Kuwahara, Katsura Igai, Takumi Murakami, Kaito Sugaya, Takahiro Morikawa, Yuichi Nagura, Masahiro Yuki, Pinsurang Deevong, Tetsushi Inoue, Kumiko Kihara, Nathan Lo, Akinori Yamada, Moriya Ohkuma, Yuichi Hongoh. Genome analyses of uncultured TG2/ZB3 bacteria in ‘Margulisbacteria’ specifically attached to ectosymbiotic spirochetes of protists in the termite gut, The ISME Journal, Vol. 13, No. 2, pp. 455-467, Feb. 2019.
• Eri Nishiyama, Kouichi Higashi, Hiroshi Mori, Konomi Suda, Hitomi Nakamura, Soichi Omori, Shigenori Maruyama, Yuichi Hongoh, Ken Kurokawa. The relationship between microbial community structures and environmental parameters revealed by metagenomic analysis of hot spring water in the Kirishima area, Japan, Frontiers in Bioengineering and Biotechnology, Vol. 6, p. e202, Dec. 2018.
• Takumi Murakami, Takahiro Segawa, Nozomu Takeuchi, Gonzalo Barcaza Sepúlveda, Pedro Labarca, Shiro Kohshima, Yuichi Hongoh. Metagenomic analyses highlight the symbiotic association between the glacier stonefly Andiperla willinki and its bacterial gut community, Environmental Microbiology, Vol. 20, No. 11, pp. 4170–4183, Nov. 2018.
• Yukihiro Kinjo, Thomas Bourguignon, Kwei Jun Tong, Hirokazu Kuwahara, Sang Jin Lim, Kwang Bae Yoon, Shuji Shigenobu, Yung Chul Park, Christine A. Nalepa, Yuichi Hongoh, Moriya Ohkuma, Nathan Lo, Gaku Tokuda. Parallel and gradual genome erosion in the Blattabacterium endosymbionts of Mastotermes darwiniensis and Cryptocercus wood roaches, Genome Biology and Evolution, Vol. 10, No. 6, pp. 1622-1630, June 2018.
• Yuniar Devi Utami, Hirokazu Kuwahara, Takumi Murakami, Takahiro Morikawa, Kaito Sugaya, Kumiko Kihara, Masahiro Yuki, Nathan Lo, Pinsurang Deevong, Sasitorn Hasin, Warin Boonriam, Tetsushi Inoue, Akinori Yamada, Moriya Ohkuma, Yuichi Hongoh. Phylogenetic diversity and single-cell genome analysis of "Melainabacteria", a non-photosynthetic cyanobacterial group, in the termite gut, Microbes and Envitonments, Vol. 33, No. 1, pp. 50-57, Mar. 2018.
• Masahiro Yuki, Mitsuo Sakamoto, Hirokazu Kuwahara, Yuichi Hongoh, Moriya Ohkuma. Draft genome sequence of Lactococcus sp. strain Rs-Y01, isolated from the gut of the lower termite Reticulitermes speratus, Genome Announcements, Vol. 5, No. 38, p. e00999-17, Aug. 2017.
• Kazuki Izawa, Hirokazu Kuwahara, Kaito Sugaya, Nathan Lo, Moriya Ohkuma, Yuichi Hongoh. Discovery of ectosymbiotic Endomicrobium lineages associated with protists in the gut of stolotermitid termites, Environmental Microbiology Reports, Vol. 9, No. 4, pp. 411-418, Aug. 2017.
• Ajeng Pramono, Hirokazu Kuwahara, Takehiko Itoh, Toyoda Atsushi, Akinori Yamada, Hongoh Y. Discovery and complete genome sequence of a bacteriophage from an obligate intracellular symbiont of a cellulolytic protist in the termite gut, Microbes and environments, June 2017.  公式リンク  
  
• Kuwahara H., Yuki M., Izawa K., Ohkuma M., Hongoh Y.. Genome of ‘Ca. Desulfovibrio trichonymphae’, an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut, The ISME Journal, Vol. 11, No. 3, pp. 766–776, Mar. 2017.
• Takumi Murakami, Takahiro Segawa, Roman Dial, Nozomu Takeuchi, Shiro Kohshima, Yuichi Hongoh. Bacterial microbiota associated with the glacier ice worm is dominated by both worm-specific and glacier-derived facultative lineage, Vol. 32, No. 1, pp. 32-39, Mar. 2017.
• Takahiro Yonezawa, Takahiro Segawa, Hiroshi Mori, Paula F. campos, Yuichi Hongoh, Hideki Endo, Ayumi Akiyoshi, Naoki Kohno, Shin Nishida, Jiaqi Wu, Haofei Jin, Jun Adachi, Hirohisa Kishino, Ken Kurokawa, Yoshifumi Nogi, Hideyuki Tanabe, Harutaka Mukoyama, Kunio Yoshida, Armand Rasoamiaramanana, Satoshi Yamagishi, Yoshihiro Hayashi, Akira Yoshida, Hiroko Koike, Fumihito Akishinonomiya, Eske Willerslev, Masami Hasegawa. Phylogenomics and morphology of extinct paleognaths reveal the origin and evolution of the ratites, Current Biology, Vol. 27, No. 1, pp. 68-77, Jan. 2017.
• Katsuo Mogi, Chikako Shirataki, Kumiko Kihara, Hirokazu Kuwahara, Yuichi Hongoh, Takatoki Yamamoto. Trapping and isolation of single prokaryotic cells in a micro-chamber array using dielectrophoresisaryotic cells in a micro-chamber array using dielectrophoresis, RSC Advances, Vol. 6, pp. 11300 - 113006, Nov. 2016.
• Kazuki Izawa, Hirokazu Kuwahara, Kumiko Kihara, Masahiro Yuki, Nathan Lo, Takehiko Itoh, Moriya Ohkuma, Yuichi Hongoh. Comparison of Intracellular "Ca. Endomicrobium Trichonymphae" Genomovars Illuminates the Requirement and Decay of Defense Systems against Foreign DNA, Genome biology and evolution, Oxford University Press, Vol. 8, No. 10, 3099-3107, Oct. 2016.
• Kazuki Izawa, Hirokazu Kuwahara, Kumiko Kihara, Masahiro Yuki, Nathan Lo, Moriya Ohkuma, Yuichi Hongoh. Comparison of intracellular “Ca. Endomicrobium trichonymphae” genomovars illuminates the requirement and decay of defense systems against foreign DNA, Genome Biology and Evolution, Oxford Academic, Vol. 8, No. 10, pp. 3099-3107, Sept. 2016.
• Katsura Igai, Manabu Itakura, Suguru Nishijima, Hiroto Tsurumaru, Wataru Suda, Takumi Tsutaya, Eriko Tomitsuka, Kiyoshi Tadokoro, Jun Baba, Shingo Odani, Kazumi Natsuhara, Ayako Morita, Minoru Yoneda, Andrew R. Greenhill1, Paul F. Horwood, Jun-Ichi Inoue, Moriya Ohkuma, Yuichi Hongoh, Taro Yamamoto, Peter Siba, Masahira Hattori, Kiwamu Minamisawa, Masahiro Umezaki. Nitrogen fixation and nifH diversity in human gut microbiota, Scientific Reports, Springer Nature, 6, 31942, Aug. 2016.
• Hao Zheng, Carsten Dietrich, Yuichi Hongoh, Andreas Brune. Restriction-modification systems as mobile genetic elements in the evolution of an intracellular symbiont, Molecular Biology and Evolution, Vol. 33, No. 3, pp. 721-725, Mar. 2016.
• Masahiro Yuki, Hirokazu Kuwahara, Masaki Shintani, Kazuki Izawa, Tomoyuki Sato, David Starns, Yuichi Hongoh, Moriya Ohkuma. Dominant ectosymbiotic bacteria of cellulolytic protists in the termite gut also have the potential to digest lignocellulose, Environmental Microbiology, 17, 12, 4942-4953, Dec. 2015.
• Moriya Ohkuma, Satoko Noda, Satoshi Hattori, Toshiya Iida, Masahiro Yuki, David Starns, Jun-Ichi Inoue, Alistair C. Darby, Yuichi Hongoh. Acetogenesis from H2 plus CO2 and nitrogen fixation by an endosymbiotic spirochete of a termite-gut cellulolytic protist., Proceedings of the National Academy of Sciences of the United States of America, 12, 33, 10224-30, Aug. 2015.
• Ajeng K. Pramono, Mitsuo Sakamoto, Takao Iino, Yuichi Hongoh, Moriya Ohkuma. Dysgonomonas termitidis sp. nov., isolated from the gut of the subterranean termite Reticulitermes speratus, International Journal of Systematic and Evolutionary Microbiology, 65, 2, 681-685, Feb. 2015.
• Kaoru Kawafune, Yuichi Hongoh, Takashi Hamaji, Tomoaki Sakamoto, Tetsuya Kurata, Shunsuke Hirooka, Shin-ya Miyagishima, Hisayoshi Nozaki. Two different rickettsial bacteria invading Volvox carteri, PLoS One., 10, 2, e0116192, Feb. 2015.
• Jun-Ichi Inoue, Kenshiro Ohshima, Wataru Suda, Mitsuo Sakamoto, Takao Iino, Satoko Noda, Yuichi Hongoh, Masahira Hattori, Moriya Ohkuma. Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes, Microbes and Environments, 30, 1, 44-50, Jan. 2015.
• Takumi Murakami, Takahiro Segawa, Dylan Bodington, Roman Dial, Nozomu Takeuchi, Shiro Kohshima, Yuichi Hongoh. Census of bacterial microbiota associated with the glacier ice worm Mesenchytraeus solifugus, FEMS Microbiology Ecology, 91, 3, fiv003, Jan. 2015.
• Guichard, P., Hachet, V., Majubu, N., Neves, A., Demurtas, D., Olieric, N., Fluckiger, I., Yamada, A., Kihara, K., Steinmetz, M., Yuichi Hongoh, Goenczy, P.. Native architecture of the centriole proximal region reveals features underlying its 9-fold radial symmetry, FEBS EMBO 2014 Conference, FEBS JOURNAL, WILEY-BLACKWELL, Vol. 281, pp. 256-256, Sept. 2014.
• Toshiaki Kudo, Tomomi Nakahara, Xiaochi Zhang, Shigeto Taniyama, Osamu Arakawa, Shinji Murase, Hideaki Nakata, Kenshiro Ohshima, Wataru Suda, Keiko KItamura, Toshiya Iida, Yumi Oshida, Tetsushi Inoue, Yuichi Hongoh, Masahira Hattori, Moriya Ohkuma. Draft genome sequences of Geomicrobium sp. strains JCM 19037,JCM 19038, JCM 19039, and JCM 19055, isolated from aquatic samples, Genome Announcements, vol. 2, no. 3, e00622-14, June 2014.
• Toshiaki Kudo, Ayumi Kawauchi, Tomomi Nakahara, Xiaochi Zhang, Shigeto Taniyama, Tomohiro Takatani, Osamu Arakawa, Kenshiro Ohshima, Wataru Suda, Keiko KItamura, Toshiya Iida, Takao Iino, Tetsushi Inoue, Yuichi Hongoh, Masahira Hattori, Moriya Ohkuma. Draft genome sequences of Vibrio sp. strains isolated from tetrodotoxin-bearing scavenging gastropod., Genome Announcements, vol. 2, no. 3, pp. e00623-14, June 2014.
• Toshiaki Kudo, Kazuaki Sakamoto, Masashi Akinaga, Ayumi Kawauchi, Tomomi Nakahara, Xiaochi Zhang, Akinori Yamada, Kenshiro Ohshima, Wataru Suda, Hirokazu Kuwahara, Nobuyuki Nakamura, Yuichi Nogi, Keiko KItamura, Masahiro Yuki, Toshiya Iida, Shigeharu Moriya, Tetsushi Inoue, Yuichi Hongoh, Masahira Hattori, Moriya Ohkuma. Draft genome sequences of cyclodextrin-producing alkaliphilic Bacillus strains JCM 19045, JCM 19046, and JCM 19047, vol. 2, no. 2, pp. e00211-14, Mar. 2014.
• Suda K., Ueno Y., Yoshizaki M., Hitomi Nakamura, Eri Nishiyama, Yoshino K., Hongoh Y., Kawachi K., Omori S., keita Yamada, Yoshida N., Maruyama S.. Origin of methane in serpentinite-hosted hydrothermal system: the CH4-H2-H2O hydrogen isotope systematics of the Happo hot spring., Earth and Planetary Science Letters, 2014.
• Nakabachi, A., Ishida, K., Yuichi Hongoh, Ohkuma, M., Miyagishima, S.-Y.. Aphid gene of bacterial origin encodes a protein transported to an obligate endosymbiont, Current Biology, Vol. 24, No. 14, pp. R640-R641, 2014.
• Paul Guichard, Virginie Hachet, Norbert Majubu, Aitana Neves, Davide Demurtas, Natacha Olieric, Isabelle Fluckiger, Akinori Yamada, Kumiko Kihara, Nishida Yuichiro, Shigeharu Moriya, Michel O. Steinmetz, Yuichi Hongoh, Pierre Gönczy. Native architecture of the centriole proximal region reveals novel features underlying their 9-fold radial symmetry., Current Biology, Volume 23, 17, Page 1620-1628, Sept. 2013.
• Satoshi Hattori, Yuichi Hongoh, Takashi Itoh, Pinsurang Deevong, Savitr Trakulnaleamsai, Napavarn Noparatnaraporn, Toshiaki Kudo, Moriya Ohkuma. Sporomusa intestinalis sp. nov., a homoacetogenic bacterium isolated from the gut of a higher termite, Termes comis (Termitinae), Journal of General and Applied Microbiology, Vol. 59, No. 4, p. 321-324, Sept. 2013.
• Haruyo Yamaguchi, Takeshi Nakayama, Hongoh Yuichi, Masanobu Kawachi, Isao Inouye. Molecular diversity of endosymbiotic Nephroselmis (Nephroselmidophyceae) in Hatena arenicola (Katablepharidophycota)., Journal of Plant Research, Aug. 2013.
• Atsushi Nakabachi, Reiko Ueoka, Kenshirou Oshima, Roberta Teta, Alfonso Mangoni, Mihaela Gurgui, Neil J. Oldham, Gerhild van Echten-Deckert, Keiko Okamura, Kohei Yamamoto, Hiromitsu Inoue, Moriya Ohkuma, Yuichi Hongoh, Shin-ya Miyagishima, Shouhei Hattori, Jörn Piel, Takema Fukatsu. Defensive bacteriome symbiont with a drastically reduced genome., Current Biology, Volume 23, 15, Page 1478-1484, Aug. 2013.
• Zheng H., Bodington D., Zhang C., Miyanaga K., Tanji Y., Hongoh Y.*, Xing X.-H.. Comprehensive phylogenetic diversity of [FeFe]-hydrogenase genes in termite gut microbiota., Microbes and Environments, 2013.
• Sato T., Hirokazu Kuwahara, Fujita K., Satoko Noda, Kihara K., Yamada A., Ohkuma M., Hongoh Y.. Intranuclear verrucomicrobial symbionts and evidence of lateral gene transfer to the host protist in the termite gut., The ISME Journal, 2013.
• Kaoru Kawafune, Yuichi Hongoh, Hisayoshi Nozaki. A rickettsial endosymbiont inhabiting the cytoplasm of Volvox carteri (Volvocales, Chlorophyceae)., Phycologia, 2013.
• Nakabachi A., Naruo Nikoh, Oshima K., Inoue H., Ohkuma M., Hongoh Y., Miyagishima S., Hattori M., Fukatsu T.. Horizontal gene acquisition of Liberibacter plant pathogens from a bacteriome-confined endosymbiont of their psyllid vector., PLoS ONE, 2013.
• 本郷裕一. ゲノムから解き明かす難培養微生物の機能, 日本乳酸菌学会誌 = Journal of Japan Society for Lactic Acid Bacteria, Vol. 23, No. 3, pp. 167-168, Nov. 2012.
• Kaoru Kawafune, Yuichi Hongoh, Takashi Hamaji, Hisayoshi Nozaki. Molecular identification of rickettsial endosymbionts in the non-phagotrophic volvovalean green algae., PLoS ONE, 7, e31749, Feb. 2012.
• Kawafune, K., Yuichi Hongoh, Hamaji, T., Nozaki, H.. MOLECULAR IDENTIFICATION OF RICKETTSIACEAN ENDOSYMBIONTS IN THE VOLVOCALEANS, CARTERIA CERASIFORMIS AND PLEODORINA JAPONICA (CHLOROPHYTA), JOURNAL OF PHYCOLOGY, WILEY-BLACKWELL, Vol. 47, pp. S13-S14, Sept. 2011.
• Bodington Dylan, 瀬川 高弘, 本郷裕一, 幸島 司郎. ヒマラヤの氷河上細菌群集の高度変化：16S rRNA遺伝子に基づく解析, 雪氷研究大会講演要旨集, 公益社団法人 日本雪氷学会／日本雪工学会, Vol. 2010, pp. 199-199, 2010.
• Satoko Noda, Yuichi Hongoh, Tomoyuki Sato, Moriya Ohkuma. Complex coevolutionary history of symbiotic Bacteroidales bacteria of various protists in the gut of termites, BMC Evolutionary Biology, 9, e158, July 2009.
• Tomoyuki Sato, Yuichi Hongoh, Satoko Noda, Satoshi Hattori, Sadaharu Ui, Moriya Ohkuma. Candidatus Desulfovibrio trichonymphae, a novel intracellular symbiont of the flagellate Trichonympha agilis in termite gut, Environmental Microbiology, Wiley Interscience, 11, 1007-1015, Apr. 2009.
• Moriya Ohkuma, Satoko Noda, Yuichi Hongoh, Christine C. Nalepa, Tetsushi Inoue. Inheritance and diversification of symbiotic trichonymphid flagellates from a common ancestor of termites and cockroach Cryptocercus, Proceedings of the Royal Society B, 276, 239-245, Jan. 2009.
• Yuichi Hongoh, Vineet K. Sharma, Tulika Prakash, Satoko Noda, Hidehiro Toh, Todd D. Taylor, Toshiaki Kudo, Yoshiyuki Sakaki, Toyoda Atsushi, Masahira Hattori, Moriya Ohkuma. Genome of an endosymbiont coupling N2 fixation to cellulolysis within protist cells in termite gut, Science, 322, 1108-1109, Nov. 2008.
• Yuichi Hongoh, Vineet K. Sharma, Tulika Prakash, Satoko Noda, Todd D. Taylor, Toshiaki Kudo, yoshiyuki sakaki, Toyoda Atsushi, Masahira Hattori, Moriya Ohkuma. Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell, Proceedings of the National Academy of Sciences of the United States of America, 105, 5555-5560, Apr. 2008.
• Jun-Ichi Inoue, Satoko Noda, Yuichi Hongoh, Sadaharu Ui, Moriya Ohkuma. Identification of endosymbiotic methanogens and ectosymbiotic spirochetes of gut protists of the termite Coptotermes formosanus, Microbes and Environments, 93, 94-97, Jan. 2008.
• Yuichi Hongoh, Tomoyuki Sato, Satoko Noda, Sadaharu Ui, Toshiaki Kudo, Moriya Ohkuma. Candidatus Symbiothrix dinenymphae: bristle-like Bacteroidales ectosymbionts of termite gut protists, Environmental Microbiology, Wiley Interscience, 9, 2631-2635, Oct. 2007.
• Yuichi Hongoh, Tomoyuki Sato, Michael F. Dolan, Satoko Noda, Moriya Ohkuma. The motility symbiont of the termite-gut flagellate Caduceia versatilis is a member of the “Synergistes” group, Applied and Environmental Microbiology, 73, 6270-6276, Oct. 2007.
• Akinori Yamada, Tetsushi Inoue, Satoko Noda, Yuichi Hongoh, Moriya Ohkuma. Evolutionary trend of phylogenetic diversity of nitrogen fixation genes in the gut community of wood-feeding termites, Molecular Ecology, 16, 3768-3777, Sept. 2007.
• Moriya Ohkuma, Tomoyuki Sato, Satoko Noda, Sadaharu Ui, Toshiaki Kudo, Yuichi Hongoh. The candidate phylum ‘Termite Group 1’ of bacteria: phylogenetic diversity, distribution, and endosymbiont members of various gut flagellated protists, FEMS Microbiology Ecology, 60, 467-476, June 2007.
• Satoko Noda, Osamu Kitade, Tetsushi Inoue, Miho Kawai, Kanuka M., Hiroshima K., Yuichi Hongoh, Constantino R., Uys V., Zhong J., Toshiaki Kudo, Moriya Ohkuma. Coevolutionary history of a triplex symbiotic system of termites, their gut protists, and bacterial endosymbionts of the protists, Molecular Ecology, 16, 1257-1266, Mar. 2007.
• Yuichi Hongoh, Pinsurang Deevong, Satoshi Hattori, Tetsushi Inoue, Satoko Noda, Napavarn Noparatnaraporn, Toshiaki Kudo, Moriya Ohkuma. 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, Applied and Environmental Microbiology, 72, 6780-6788, Oct. 2006.
• Tetsushi Inoue, Yoko Takematsu, Akinori Yamada, Yuichi Hongoh, Johjima Toru, Shigeharu Moriya, Yupaporn Sornnuwat, Charunee Vongkaluang, Moriya Ohkuma, Toshiaki Kudo. Diversity and abundance of termites along an altitudinal gradients in Khao Kitchagoot National Park, Thailand, Journal of Tropical Ecology, 22, 609-612, Sept. 2006.
• Pinsurang Deevong, Yuichi Hongoh, Tetsushi Inoue, Savitr Trakulnaleamsai, Toshiaki Kudo, Napavarn Noparatnaraporn, Moriya Ohkuma. Effect of temporal preservation on molecular study of complex microbial community in the gut of the termite Microcerotermes sp., Microbes and Environments, 21, 78-85, Apr. 2006.
• Yuichi Hongoh, Lukkaew Ekpornprasit, Tetsushi Inoue, Shigeharu Moriya, Savitr Trakulnaleamsai, Moriya Ohkuma, Napavarn Noparatnaraporn, Toshiaki Kudo. Intracolony variation of bacterial gut microbiota in the fungus-growing termite Macrotermes gilvus, Molecular Ecology, 15, 505-516, Feb. 2006.
• Satoko Noda, Tetsushi Inoue, Yuichi Hongoh, Miho Kawai, Christine A. Nalepa, Charunee Vongkaluang, Toshiaki Kudo, Moriya Ohkuma. Identification and characterization of ectosymbionts of distinct lineages in Bacteroidales attached to flagellated protists in the gut of termites and a wood-feeding cockroach, Environmental Microbiology, 8, 11-20, Jan. 2006.
• Hideaki Nakajima, Yuichi Hongoh, Satoko Noda, Yasuhiko Yoshida, Ron Usami, Toshiaki Kudo, Moriya Ohkuma. Phylogenetic and morphological diversity of Bacteroidales members associated with gut wall of termites, Bioscience, Biotechnology and Biochemistry, 70, 211-218, Jan. 2006.
• Yuichi Hongoh, Pinsurang Deevong, Tetsushi Inoue, Savitr Trakulnaleamsai, Moriya Ohkuma, Charunee Vongkaluang, Noparatnaraporn, Toshiaki Kudo. Intra- and interspecific comparisons of bacterial diversity and community structure support coevolution of gut microbiota and termite host, Applied and Environmental Microbiology, 71, 11, 6590-6599, Nov. 2005.
• Hideaki Nakajima, Yuichi Hongoh, Ron Usami, Toshiaki Kudo, Moriya Ohkuma. Spatial distribution of bacterial phylotypes in the gut of the termite Reticulitermes speratus and bacterial community on the gut epithelium, FEMS Microbiology Ecology, 54, 2, 247-255, Oct. 2005.
• Taksawan Thongaram, Yuichi Hongoh, Saori Kosono, Moriya Ohkuma, Savitr Trakulnaleamsai, Napavarn Noparatnaraporn, Toshiaki Kudo. Comparison of bacterial communities in the alkaline gut segment among various species of higher termites, Extremophile, 9, 3, 229-238, June 2005.
• Tetsushi Inoue, Yuichi Hongoh, Chirasak Klanglaew, Yoko Takematsu, Charunee Vongkaluang, Moriya Ohkuma, Toshiaki Kudo. Plasticity and specificity of termite nest structure (Isoptera), Sociobiology, 45, 3, 671-678, 2005.

著書

• 本郷裕一. マトリョーシカ型共生が支えるシロアリの繁栄, つむぐ, 新曜社, pp. 113-117, Nov. 2016.
• 本郷裕一. 昆虫における共生の総論, 共生微生物, 化学同人, pp. 60-74, Oct. 2016.
• 本郷裕一. 腸内微生物の生態, シリーズ 現代の生態学 第11巻『微生物生態学』, 共立出版, Mar. 2011.
• Yuichi Hongoh. Complete genome of an uncultured endosymbiont coupling nitrogen fixation to cellulolysis within protist cells in termite gut, Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats, Wiley-Blackwell, 2011.
• Yuichi Hongoh, Moriya Ohkuma. Termite gut flagellates and their methanogenic and eubacterial symbionts, (Endo)symbiotic Methanogenic Archaea (Microbiology Monographs 19, Oct. 2010.
• 本郷裕一, 大熊盛也. 統計学的微生物群集構造の解析, 難培養微生物研究の 最新技術 II—ゲノム解析を中心とした最前線と将来展望—, シーエムシー出版, June 2009.
• 本郷裕一, 大熊盛也. Single Cellのゲノム解析, 難培養微生物研究の 最新技術 II—ゲノム解析を中心とした最前線と将来展望—, シーエムシー出版, June 2009.

国際会議発表 (査読有り)

• Yuniar Devi Utami, Hirokazu Kuwahara, Katsura Igai, Takumi Murakami, Takahiro Morikawa, Kaito Sugaya, Masahiro Yuki, Akinori Yamada, Moriya Ohkuma, Yuichi Hongoh. Genome analyses of uncultured ZB3/TG2 bacteria (“Margulisbacteria”) attached to ectosymbiotic spirochetes of protist cells in the termite gut, The 17th International Symposium on Microbial Ecology, Aug. 2018.

国際会議発表 (査読なし・不明)

• Yuichi Hongoh. Multi-layered symbiotic system in the termite gut, The 8th Global Network Forum on Infection and Immunity: Microbiome, Jan. 2020.
• Yuichi Hongoh. Multi-layered symbiotic system in the termite gut, International Symposium: Ecology and Evolution of Termite Gut Microbes, Dec. 2019.
• Yuichi Hongoh. Multi-layered symbiotic system in the termite gut, North Carolina State University Entomology Seminar, Sept. 2019.
• Yuichi Hongoh. Genomics of uncultivable bacteria deciphers the multilayered symbiotic system in the termite gut, OIST seminar, Nov. 2018.
• Yuichi Hongoh. Multilayered-symbiotic system in the termite gut, 華中師範大学セミナー, Oct. 2018.
• Yuichi Hongoh. Genomics of uncultivable bacteria deciphers multilayered symbiotic system in the termite gut, 2018 World Life Science Conference, Oct. 2018.
• Yuichi Hongoh. Multi-layered symbiotic system in the termite gut, The 46th Naito Conference, Oct. 2018.
• Yuichi Hongoh. Genomics of uncultivable bacteria deciphers multilayered symbiotic system in the termite gut, Max Planck Institute "International Workshop on Insect Gut Microbiology", Aug. 2018.
• Yuichi Hongoh. Single-cell genomics deciphers the termite gut ecosystem, 第91回日本細菌学会総会 国際シンポジウム「Frontiers in Bacterial Genomics」, Mar. 2018.
• Takumi Murakami, Takahiro Segawa, Nozomu Takeuchi, Pedro Labarca, Gonzalo Barcaza Sepúlveda, Shiro Kohshima, Yuichi Hongoh. Analyses on the community structure and metagenome of the bacterial consortium from the gut of glacier stonefly, International Symposium on Cryosphere and Biosphere 2018, Mar. 2018.
• Ajeng Pramono, Hirokazu Kuwahara, Takehiko Itoh, Toyoda Atsushi, Moriya Ohkuma, Akinori Yamada, Yuichi Hongoh. Bacteriophage from an obligate intracellular symbiont of a cellulolytic protist in the termite gut, Prorhinotermes japonicus (Isoptera: family Rhinotermitidae), The 5th International Conference on Biological Science, Sept. 2017.
• Takumi Murakami, Takahiro Segawa, Nozomu Takeuchi, Pedro Labarca, Gonzalo Barcaza Sepúlveda, Shiro Kohshima, Yuichi Hongoh. Analyses of bacterial community structures associated with glacier-adapted invertebrates, The 7th International Conference on Polar & Alpine Microbiology, Sept. 2017.
• Yuichi Hongoh. Single cell genomics deciphers the complex symbiotic system in the termite gut microbiota, The 11th International Workshop on Advanced Genomics, May 2015.
• Yuichi Hongoh. Genomics of single bacterial species in termite gut, 109th General Meeting of American Society for Microbiology (ASM), May 2009.  公式リンク  
  
• Yuichi Hongoh. Genome analysis to unveil the symbiotic roles of gut bacteria in termite gut, International Symposium for Subsurface Microbiology (ISSM), Nov. 2008.

国内会議発表 (査読なし・不明)

• 村上匠, 瀬川高弘, 森宙史, 本郷裕一, 竹内望. 氷河微生物群集「クリオコナイト」の形成過程をメタゲノムデータから解き明かす, 第18回日本ゲノム微生物学会年会, Mar. 2024.
• Kazuki Takahashi, Hirokazu Kuwahara, Yuutarou Horikawa, Kazuki Izawa, Tatsuya Inagaki, Masahiro Yuki, Moriya Ohkuma, Yuichi Hongoh. Discovery and evolution of obligately-intracellular parasites belonging to the class Clostridia, 日本微生物生態学会第36回大会, Nov. 2023.
• 金子真之, 大森樹生, 猪飼桂, 間渕貴子, 西原 亜理沙, 木原久美子, 吉村剛, 大熊盛也, 本郷裕一. シロアリ腸内原生生物細胞内共生メタン菌の生態とゲノム解析, 日本共生生物学会第７回大会, Nov. 2023.
• 板垣優大, 高橋一樹, 雪真弘, 清水美智留, 村上匠, 大熊盛也, 本郷裕一. シロアリ腸内で優占するBetaproteobacteria綱細菌の1細胞ゲノム解析, 日本微生物生態学会第36回大会, Nov. 2023.
• 齋藤崇登, 室岡聡, 猪飼桂, 高橋一樹, 佐藤朋之, 村上匠, 大熊盛也, 本郷裕一. 他細菌種に特異的に付着共生するAlphaproteobacteria の形態とゲノム解析, 日本微生物生態学会第36回大会, Nov. 2023.
• 村上匠, 瀬川高弘, 森宙史, 本郷裕一, 竹内望. 様々な地域の氷河を対象とした細菌群集メタゲノム解析, 日本微生物生態学会第36回大会, Nov. 2023.
• 大須賀奨, 高橋一樹, 猪飼桂, 雪真弘, 清水美智留, 桑原宏和, 村上匠, 大熊盛也, 本郷裕一. シロアリ腸内原生生物に細胞内共生するPlanctomycetota 門細菌の発見とゲノム解析, 日本微生物生態学会第36回大会, Nov. 2023.
• Fu Jieyang, Liu Yiting, 猪飼桂, 桑原宏和, 木原久美子, 村上匠, 大熊盛也, 本郷 裕一. シロアリ腸内原生生物Mixotricha paradoxa と2種の細胞表面付着共生細菌の共生機構の解析, 日本微生物生態学会第36回大会, Nov. 2023.
• 杉山奈緒, 高橋一樹, 関謙二郎, 堀川雄太郎, 佐藤朋之, 桑原宏和, 村上匠, 大熊盛也, 本郷裕一. シロアリ腸内原生生物細胞共生Mycoplasmatota 門細菌の生態とゲノム解析, 日本微生物生態学会第36回大会, Nov. 2023.
• 髙橋一樹, 桑原宏和, 堀川雄太郎, 伊澤和輝, 加藤大貴, 稲垣辰哉, 雪真弘, 大熊盛也, 本郷裕一. 細胞内寄生性クロストリディア綱細菌の発見と寄生体進化プロセスの解明, 第21回微生物研究会, Oct. 2023.
• 本郷裕一. ゲノミクスで解き明かす未培養微生物間細胞共生系の実態, 大隅基礎科学創成財団・微生物機能探求コンソーシアム・グループ3（相互作用）定例会, June 2023.
• Kazuki Takahashi, Hirokazu Kuwahara, Yuutarou Horikawa, Kazuki Izawa, Tatsuya Inagaki, Masahiro Yuki, Moriya Ohkuma, Yuichi Hongoh. Parasitic lifestyle and genome evolution of novel endosymbiotic clostridia of the protists inhabiting the termite gut, 第96回日本細菌学会総会, Mar. 2023.
• 田守正樹, 竹花康弘, 山田章, 佐久間敦丈, 二階堂雅人, 猪飼桂, 本郷裕一. 組換えソフニン候補タンパク質はナマコの真皮を軟化させる,, 日本動物学会 第93回 早稲田大会, Sept. 2022.
• 本郷裕一. めくるめくシロアリ腸内複雑共生系〜虫屋の目で見る微生物多様性〜, 第14回微生物生態マラソンセミナー, Aug. 2022.
• 猪飼桂, 北出理, Fu Jieyang, 尾又 一実, 米澤 隆弘, 大熊盛也, 本郷裕一. シロアリ腸内共生原生生物群集におけるエコタイプ・シミュレーション解析, 日本微生物生態学会第34回大会, Oct. 2021.
• 本郷裕一. シロアリ腸内に共生する非光合成シアノバクテリアとその近縁系統群のゲノム解析, ラン藻ゲノム交流会2019, June 2019.
• ウタミ ユニア デビ, 桑原宏和, 村上匠, 猪飼桂, 守川貴裕, 菅谷快斗, 雪真弘, 山田明徳, 大熊盛也, 本郷裕一. Genome analyses of non-photosynthetic cyanobacteria associated with protist cells in the termite gut, 第12回日本ゲノム微生物学会年会, Mar. 2018.
• 名倉有一, 桑原宏和, 原田 真実, 豊田敦, 大熊盛也, 本郷裕一. シロアリ腸内原生生物の核内に共生する未培養Verrucomicrobia門細菌の多様性とゲノム解析, 第12回日本ゲノム微生物学会年会, Mar. 2018.
• 村上匠, 瀬川高弘, 竹内望, ラバルサペドロ, Sepúlveda Gonzalo Barcaza, 幸島司郎, 本郷裕一. 氷河に生息するカワゲラの腸内細菌叢メタゲノム解析, 第12回日本ゲノム微生物学会年会, Mar. 2018.
• 金城幸宏, ブルギニョン トーマス, 本郷裕一, ロウネーサン, 徳田岳. ムカシシロアリおよびキゴキブリの細胞内共生細菌ゲノムの平行退縮進化, 日本蚕糸学会第88回大会, Mar. 2018.
• 川舩 かおる, 桑原宏和, 坂本智昭, 倉田哲也, 廣岡俊亮, 宮城島進也, 野崎久義, 本郷裕一. 光合成生物の細胞質内に共生するリケッチアのゲノム解析, 第1回日本共生生物学会大会, Nov. 2017.
• 小野内思有, 村上匠, 大熊盛也, 本郷裕一. 食材性オオゴキブリ腸内線虫の体表に共生する細菌群集, 第1回日本共生生物学会大会, Nov. 2017.
• 坪井亜里沙, 本郷裕一, 守屋繁春. Total RNA Seqを用いたアマゾン流域のネグロ川における微生物群集構造と発現遺伝子の解析, 第1回日本共生生物学会大会, Nov. 2017.
• 本郷裕一. シロアリはなぜ木だけを食べて生きられるのか, 名古屋大学理学部セミナー, Sept. 2017.
• 村上匠, 瀬川高弘, 竹内望, ラバルサペドロ, セプルベーダ ゴンサロ バルサーサ, 幸島司郎, 本郷裕一. パタゴニアに生息する氷河カワゲラの網羅的腸内細菌叢解析, 環境微生物系学会合同大会2017, Aug. 2017.
• 本郷裕一. 1細胞ゲノムとメタゲノムから読み解くシロアリ腸内多重共生系, 平成28年度EIIRISプロジェクト研究成果報告会－バイオ情報技術の社会応用－, Mar. 2017.
• 本郷裕一. シロアリと腸内微生物の多重共生機構, 奈良先端科学技術大学院大学セミナー, Feb. 2017.
• 村上匠, 瀬川高弘, 竹内望, Roman Dial, Pedro Labarca, Gonzalo B. Sepulveda, 幸島司郎, 本郷裕一. 氷河に特化した無脊椎動物の共生細菌群集構造解析, 日本微生物生態学会第31回大会, Oct. 2016.
• Yuichi Hongoh. Tripartite symbiosis within a protist cell in the termite gut, Meetings of Biology of Symbiosis, Oct. 2016.
• Yuniar Devi Utami, Hirokazu Kuwahara, Kaito Sugaya, Masahiro Yuki, Moriya Ohkuma, Yuichi Hongoh. Uncovering rare candidate bacterial phylum TG2 in the termite gut, 日本微生物生態学会第31回大会, Oct. 2016.
• 伊澤和輝, 名倉有一, Nathan Lo, 大熊盛也, 本郷裕一. シロアリ腸内原生生物の細胞表面に共生する新規Endomicrobium属細菌, 日本微生物生態学会第31回大会, Oct. 2016.
• 桑原宏和, 雪真弘, 伊澤和輝, 大熊盛也, 本郷裕一. シロアリ腸内原生生物に共生するDesulfovibrio属細菌のゲノム解析による3者間共生システムの解明, 日本微生物生態学会第31回大会, Oct. 2016.
• 本郷裕一. シロアリ腸内多重共生系の進化, 日本進化学会第18回大会, Aug. 2016.
• 伊澤和輝, 麥島雄太, 桑原宏和, 河合幹彦, 木原久美子, Nathan Lo, 雪真弘, 伊藤武彦, 大熊盛也, 本郷裕一. 対ファージ防衛機構が示すEndomicrobium属細胞内共生細菌の適応進化, 第18回日本進化学会大会, Aug. 2016.
• 本郷裕一. シロアリと絶対共生する腸内微生物群集の進化と機能, 第27回日本生体防御学会総会, July 2016.
• 本郷裕一. ゲノムから読み解くシロアリ腸内難培養微生物群集の多重共生機構, 第89回日本細菌学会総会, Mar. 2016.
• 猪飼 桂, 板倉 学, 西嶋 傑, 鶴丸 博人, 須田亙, 蔦谷 匠, 冨塚 江利子, 田所 聖志, 馬場 淳, 小谷 真吾, 夏原 和美, 森田 彩子, 米田穰, 井上潤一, 大熊盛也, 本郷裕一, 山本 太郎, シーバ ピーター, 服部正平, 南澤 究, 梅崎 昌裕. ヒト腸内微生物叢における窒素固定活性とnifH遺伝子の多様性, 日本微生物生態学会第30回大会, Oct. 2015.

その他の論文・著書など

• 本郷裕一. 「材食を可能とするシロアリ腸内多重共生機構の解明, アグリバイオ, ニューサイエンス社, Vol. 4, No. 4, pp. 317-322, Apr. 2020.
• 本郷裕一. 「材食を可能とするシロアリ腸内多重共生機構の解明, 昆虫と自然, ニューサイエンス社, Vol. 54, No. 2, pp. 35-38, Feb. 2019.
• Yuichi Hongoh, Moriya Ohkuma. Termite gut flagellates and their methanogenic and eubacterial symbionts, (Endo)symbiotic Methanogenic Archaea Second Edition, Springer, Volume 19, pp. 55-80, Nov. 2018.
• 本郷裕一. ゲノム解析によるシロアリ腸内原生生物共生細菌の役割の解明, しろあり（公益社団法人日本しろあり対策協会 機関誌）, Vol. 169, pp. 12-26, Jan. 2018.
• 本郷裕一. 環境微生物学研究に革命をもたらしたシングルセル解析, 実験医学別冊「シングルセル解析プロトコール」, pp. 40-46, Oct. 2017.
• 本郷裕一. 難培養性微生物の1細胞ゲノム解析, 化学療法の領域, Vol. 33, pp. 90-99, June 2017.
• 本郷裕一. マトリョーシカ型共生が支えるシロアリの繁栄, JT生命誌ジャーナル, JT生命誌研究館, 86, Sept. 2015.
• Yuichi Hongoh. Who digests the lignocellulose?, Environmental Microbiology, Vol. 16, No. 9, pp. 2644-2645, 2014.
• 本郷裕一. 難培養微生物種のゲノム解析による機能解明と遺伝子資源化 , 日本乳酸菌学会誌, Japan Society for Lactic Acid Bacteria, Vol. 24, No. 3, pp. 167-173, 2013.
• Yuichi Hongoh, Toyoda, A.. Whole-genome sequencing of unculturable bacterium using whole-genome amplification., Methods in molecular biology (Clifton, N.J.), Vol. 733, pp. 25-33, 2011.
• 本郷裕一. シロアリ腸内原生生物と原核生物の細胞共生, 原生動物学雑誌, 日本原生生物学会, Vol. 44, No. 2, pp. 115-129, 2011.
• 本郷裕一. 難培養性細菌種のゲノム完全長配列取得による機能解明, 土と微生物, Vol. 64, No. 2, pp. 77-80, Oct. 2010.
• Yuichi Hongoh. Diversity and genomes of uncultured microbial symbionts in the termite gut, Bioscience, Biotechnology, and Biochemistry, 74, 1145-1151, June 2010.
• 本郷裕一. Single-cell genomicsへの展望, 日本ゲノム微生物学会ニュース レター, 1, 3-4, Dec. 2009.
• 大熊盛也, 本郷裕一. シロアリ腸内微生物の多重共生, 生物の科学 遺伝, 63, 110-113, July 2009.
• 本郷裕一. 培養できない微生物の機能を探る, 生物工学会誌, 87, 342, July 2009.
• 大熊盛也, 本郷裕一. 動物と窒素固定細菌の共生は成立するか？, 化学と生物, 47, 307-309, May 2009.
• 大熊盛也, 本郷裕一. 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, バイオインダストリー, 25, 81-88, Dec. 2008.
• 本郷裕一, 大熊盛也. ゲノムから解き明かす難培養性細菌の機能, 化学と生物, 46, 742-743, Nov. 2008.
• 大熊盛也, 本郷裕一, 野田悟子. 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, 蛋白質核酸酵素, 53, 1841-1849, Nov. 2008.
• 本郷裕一, 大熊盛也. シロアリ腸内共生微生物群の多様性とゲノム解析, 環境バイオテクノロジー学会誌, 8, 29-34, June 2008.

学位論文

• Studies on nitrogen recycling by fungal endosymbionts of plant hoppers and origin of their symbiosis,  Thesis,  The University of Tokyo,  2000/03/--, 

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