論文

• Hiroshi Mori, Tamotsu Kato, Hiroaki Ozawa, Mitsuo Sakamoto, Takumi Murakami, Todd D Taylor, Atsushi Toyoda, Moriya Ohkuma, Ken Kurokawa, Hiroshi Ohno. Assessment of metagenomic workflows using a newly constructed human gut microbiome mock community, DNA Research, Oxford University Press UK, Vol. 30, No. 3, pp. dsad010, May 2023.
• Taro Onuma, Toshitaka Yamauchi, Hina Kosakamoto, Hibiki Kadoguchi, Takayuki Kuraishi, Takumi Murakami, Hiroshi Mori, Masayuki Miura, Fumiaki Obata. Recognition of commensal bacterial peptidoglycans defines Drosophila gut homeostasis and lifespan, PLoS Genetics, Public Library of Science San Francisco, CA USA, Vol. 19, No. 4, pp. e1010709, Apr. 2023.
• Kana Morinaga, Hiroyuki Kusada, Sachiko Sakamoto, Takumi Murakami, Atsushi Toyoda, Hiroshi Mori, Xian-Ying Meng, Motoko Takashino, Kazutoshi Murotomi, Hideyuki Tamaki. Granulimonas faecalis gen. nov., sp. nov., and Leptogranulimonas caecicola gen. nov., sp. nov., novel lactate-producing Atopobiaceae bacteria isolated from mouse intestines, and an emended description of the family Atopobiaceae, International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 72, No. 10, pp. 005596, Oct. 2022.
• Kyosuke Yakabe, Seiichiro Higashi, Masahiro Akiyama, Hiroshi Mori, Takumi Murakami, Atsushi Toyoda, Yuta Sugiyama, Shigenobu Kishino, Kenji Okano, Akiyoshi Hirayama. Dietary-protein sources modulate host susceptibility to Clostridioides difficile infection through the gut microbiota, Cell Reports, Elsevier, Vol. 40, No. 11, Sept. 2022.
• Takumi Murakami, Nozomu Takeuchi, Hiroshi Mori, Yuu Hirose, Arwyn Edwards, Tristram Irvine-Fynn, Zhongqin Li, Satoshi Ishii, Takahiro Segawa. Metagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light-harvesting mechanisms in glacier cryoconite, Microbiome, BioMed Central London, Vol. 10, No. 1, pp. 50, Mar. 2022.
• Mitsuo Sakamoto, Nao Ikeyama, Masahiro Yuki, Takumi Murakami, Hiroshi Mori, Takao Iino, Moriya Ohkuma. Adlercreutzia hattorii sp. nov., an equol non-producing bacterium isolated from human faeces, International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 71, No. 12, pp. 005121, Dec. 2021.
• Mitsuo Sakamoto, Nao Ikeyama, Atsushi Toyoda, Takumi Murakami, Hiroshi Mori, Sho Morohoshi, Tadao Kunihiro, Takao Iino, Moriya Ohkuma. Coprobacter secundus subsp. similis subsp. nov. and Solibaculum mannosilyticum gen. nov., sp. nov., isolated from human feces, Microbiology and Immunology, Vol. 65, No. 6, pp. 245-256, June 2021.
• Mitsuo Sakamoto, Nao Ikeyama, Atsushi Toyoda, Takumi Murakami, Hiroshi Mori, Moriya Ohkuma. Complete genome sequence of Faecalibacillus intestinalis JCM 34082, isolated from feces from a healthy Japanese female, Microbiology Resource Announcements, American Society for Microbiology 1752 N St., NW, Washington, DC, Vol. 9, No. 50, pp. 10-1128, Dec. 2020.
• Nao Ikeyama, Takumi Murakami, Atsushi Toyoda, Hiroshi Mori, Takao Iino, Moriya Ohkuma, Mitsuo Sakamoto. Microbial interaction between the succinate-utilizing bacterium Phascolarctobacterium faecium and the gut commensal Bacteroides thetaiotaomicron, Microbiologyopen, Vol. 9, No. 10, pp. e1111, Oct. 2020.
• Mariko Takeuchi, Hirokazu Kuwahara, Takumi Murakami, Kazuki Takahashi, Rei Kajitani, Atsushi Toyoda, Takehiko Itoh, Moriya Ohkuma, Yuichi Hongoh. Parallel reductive genome evolution in Desulfovibrio ectosymbionts independently acquired by Trichonympha protists in the termite gut, The ISME Journal, Oxford University Press, Vol. 14, No. 9, pp. 2288-2301, Sept. 2020.
• Toshitaka Yamauchi, Ayano Oi, Hina Kosakamoto, Yoriko Akuzawa-Tokita, Takumi Murakami, Hiroshi Mori, Masayuki Miura, Fumiaki Obata. Gut bacterial species distinctively impact host purine metabolites during aging in Drosophila, Iscience, Elsevier, Vol. 23, No. 9, Sept. 2020.
• Nao Ikeyama, Atsushi Toyoda, Sho Morohoshi, Tadao Kunihiro, Takumi Murakami, Hiroshi Mori, Takao Iino, Moriya Ohkuma, Mitsuo Sakamoto. Amedibacterium intestinale gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium dolichum Moore et al. 1976 (Approved Lists 1980) as Amedibacillus dolichus gen. nov., comb. nov, International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 70, No. 6, pp. 3656-3664, Aug. 2020.
• Hina Kosakamoto, Toshitaka Yamauchi, Yoriko Akuzawa-Tokita, Kei Nishimura, Tomoyoshi Soga, Takumi Murakami, Hiroshi Mori, Kyosuke Yamamoto, Ryo Miyazaki, Akiko Koto. Local necrotic cells trigger systemic immune activation via gut microbiome dysbiosis in Drosophila, Cell Reports, Elsevier, Vol. 32, No. 3, July 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.
• Mitsuo Sakamoto, Nao Ikeyama, Atsushi Toyoda, Takumi Murakami, Hiroshi Mori, Takao Iino, Moriya Ohkuma. Dialister hominis sp. nov., isolated from human faeces, International journal of systematic and evolutionary microbiology, Microbiology Society, Vol. 70, No. 1, pp. 589-595, Feb. 2020.
• 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.
• Mitsuo Sakamoto, Nao Ikeyama, Takumi Murakami, Hiroshi Mori, Masahiro Yuki, Moriya Ohkuma. Comparative genomics of Parolsenella catena and Libanicoccus massiliensis: Reclassification of Libanicoccus massiliensis as Parolsenella massiliensis comb. nov., International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 69, No. 4, pp. 1123-1129, Feb. 2019.
• Takumi Murakami, Shu 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, Oxford University Press, Vol. 95, No. 2, pp. fiy238, Feb. 2019.
• 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.
• Takumi Murakami, Hiroshi Mori, Viktoria A Shcherbakova, Yoshitaka Yoshimura, Takahiro Segawa. Draft genome sequence of Clostridium tagluense strain A121T, isolated from a permafrost core in the Canadian High Arctic, Microbiology Resource Announcements, American Society for Microbiology 1752 N St., NW, Washington, DC, Vol. 8, No. 5, pp. 10-1128, Jan. 2019.
• 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.
• 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.
• 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.
• 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.

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)

• 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.
• 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.

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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.

学位論文

• 氷河無脊椎動物に共生する細菌叢の網羅的群集構造・機能遺伝子解析,  要約,  博士(理学),  東京工業大学,  2017/03/26,   
• 氷河無脊椎動物に共生する細菌叢の網羅的群集構造・機能遺伝子解析,  審査の要旨,  博士(理学),  東京工業大学,  2017/03/26,   
• 氷河無脊椎動物に共生する細菌叢の網羅的群集構造・機能遺伝子解析,  論文要旨,  博士(理学),  東京工業大学,  2017/03/26,   
• 氷河無脊椎動物に共生する細菌叢の網羅的群集構造・機能遺伝子解析,  本文,  博士(理学),  東京工業大学,  2017/03/26, 

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