Publications

2026

• PhaB-independent poly(3-hydroxybutyrate) production in the thermophilic hydrogen-oxidizing bacterium Hydrogenophilus thermoluteolus
  Kotaro Yoda, Masafumi Kameya, Hiroyuki Arai
  bioRxiv (2026)
  doi: 10.64898/2026.05.08.723683
• Metabolic diversity of microorganisms toward atypical sugar enantiomers
  Hiroaki Nishijima, Kensuke Igarashi, Wataru Kitagawa, Hiro Tabata, Shuji Nakanishi, Souichiro Kato
  bioRxiv (2026)
  doi: 10.64898/2026.01.17.700050
• The significance of sukumo (composted indigo leaves) as a microbial source for traditional Japanese indigo dyeing
  Souichiro Kato, Kensuke Igarashi, Shusei Kanie, Kyosuke Yamamoto, Wataru Kitagawa, Takashi Narihiro, Kenta Watanabe, Kenta Fujii, Isao Yumoto, Yoshiyuki Ueno
  bioRxiv (2026)
• Isolation of bacteria that catabolize abiotically synthesized tetroses via the formose reaction
  Kosei Kawasaki, Kensuke Igarashi, Hiro Tabata, Hiroaki Nishijima, Shuji Nakanishi, Souichiro Kato
  Sci. Rep. 16:734 (2026)
  doi: 10.1038/s41598-025-30247-3

2025

• Impact of acetate on CO₂ fixation pathways in thermophilic and hydrogenotrophic bacteria
  Yoko Chiba, Tomomi Sumida, Masafumi Kameya, Yuto Fukuyama, Tomoyuki Wakashima, Shigeru Shimamura, Ryoma Kamikawa, Yoshito Chikaraishi, Takuro Nunoura
  ISME Communications, 5:ycaf227 (2025)
  doi: 10.1093/ismeco/ycaf227
  Preprint (bioRxiv)
• Methanol transfer supports metabolic syntrophy between bacteria and archaea
  Yan Huang, Kensuke Igarashi, Laiyan Liu, Daisuke Mayumi, Tomomi Ujiie, Lin Fu, Min Yang, Yahai Lu, Lei Cheng, Souichiro Kato, Masaru K. Nobu
  Nature, 639:190-195 (2025)
  doi: 10.1038/s41586-024-08491-w
  プレスリリース：地下微生物はメタノールで飲みニケーション！？
• A promoter library for tuning gene expression in Cupriavidus necator under autotrophic conditions
  Wataru Kitagawa, Kensuke Igarashi, Ryo Nagasawa, Shigeyuki Kakizawa, Mizuki Horino, Kosuke Fujishima, Toshiaki Fukui, Souichiro Kato
  Front. Bioeng. Biotechnol. 13:1595440 (2025)
  doi: 10.3389/fbioe.2025.1595440
• Coelenterazine sulfotransferase from the luminous squid Watasenia scintillans
  Nowshin Farjana, Yasuo Mitani, Souichiro Kato, Shusei Kanie
  Biochem. Biophys. Res. Commun., 777:152215 (2025)
  doi: 10.1016/j.bbrc.2025.152215
• Characterization of Congregicoccus parvus gen. nov., sp. nov., a novel slow-growing ultramicrobacterium of the phylum Verrucomicrobiota
  Md. Samiul Islam, Kyosuke Yamamoto, Naoki Morita, Wataru Kitagawa, Isao Yumoto, Souichiro Kato, Ryosuke Nakai, Kensuke Igarashi
  PLoS One. 20:e0326734 (2025)
  doi: 10.1371/journal.pone.0326734
• 基礎から学ぶ微生物学（羊土社）
  石井名誉教授が監修・執筆、新井准教授と亀谷助教が分担執筆しました。
• 応用微生物学 第4版（文永堂出版）
  「嫌気呼吸」と「無機物を電子供与体とする呼吸」の項を新井准教授が、「直接CO₂利用」の項を亀谷助教が執筆しました。

2024

• Structural insights into thermophilic chaperonin complexes
  Zengwei Liao, Chai C. Gopalasingam, Masafumi Kameya, Christoph Gerle, Hideki Shigematsu, Masaharu Ishii, Takatoshi Arakawa, and Shinya Fushinobu
  Structure (2024)
  doi: 10.1016/j.str.2024.02.012
• 人工的な炭酸固定経路「THETA回路」
  亀谷将史
  現代化学 2024年4月号 8-9
  東京化学同人

2023

• Unlocking Microalgal Host —Exploring Dark-Growing Microalgae Transformation for Sustainable High-Value Phytochemical Production
  Surumpa Jareonsin, Kanjana Mahanil, Kittiya Phinyo, Sirasit Srinuanpan, Jeeraporn Pekkoh, Masafumi Kameya, Hiroyuki Arai, Masaharu Ishii, Ruttaporn, Chundet, Pachara Sattayawat, and Chayakorn Pumas
  Front. Bioeng. Biotechnol. 11 (2023)
  doi: 10.3389/fbioe.2023.1296216
• 独立栄養細菌の炭酸固定経路と基本的性質
  亀谷将史、新井博之、石井正治
  独立栄養細菌によるCO₂資源化技術 (ISBN 978-4-7813-1756-4) 3-15
  シーエムシー出版
  Preprint
• 合成生物学による新規独立栄養生物・炭酸固定経路の創出
  亀谷将史、千葉洋子
  独立栄養細菌によるCO₂資源化技術 (ISBN 978-4-7813-1756-4) 35-46
  シーエムシー出版
  Preprint
• 水素細菌マイクロコンパートメントによるCO₂の濃縮・固定機構
  新井博之、石井正治
  独立栄養細菌によるCO₂資源化技術 (ISBN 978-4-7813-1756-4) 53-59
  シーエムシー出版
• 極限環境から分離された好熱性水素細菌の代謝解析
  亀谷将史、新井博之、石井正治
  極限環境微生物の先端科学と社会実装最前線 (ISBN 978-4-86043-848-7) 287-298
  エヌ・ティー・エス出版
  Preprint

2022

• Regulation of the high-specificity Rubisco genes by the third CbbR-type regulator in a hydrogen-oxidizing bacterium Hydrogenovibrio marinus
  Koichi Toyoda, Yoichi Yoshizawa, Masaharu Ishii, and Hiroyuki Arai
  J. Biosci. Bioeng., 134:496-500 (2022)
  doi: 10.1016/j.jbiosc.2022.09.003
• Simple transformation of the filamentous thermophilic cyanobacterium Leptolyngbya sp. KC45
  Kanjana Mahanil, Pachara Sattayawat, Jeeraporn Pekkoh, Masafumi Kameya, MasaharuIshii, and Chayakorn Pumas
  Algal Res., 66:102758 (2022)
  doi: 10.1016/j.algal.2022.102758
• Reversible glutamate coordination to high-valent nickel protects the active site of a [NiFe] hydrogenase from oxygen
  Kulka-Peschke, C. J., Schulz, A.-C., Lorent, C., Rippers, Y., Wahlefeld, S., Preissler, J., Schulz, C., Wiemann, C., Bernitzky, C. C. M., Karafoulidi-Retsou, C., Wrathall, S. L. D., Procacci, B., Matsuura, H., Greetham, G. M., Teutloff, C., Lauterbach, L., Higuchi, Y., Ishii, M., Hunt, N. T., Lenz, O., Zebger, I. and Horch, M.
  J. Am. Chem. Soc. 144:17022-17032 (2022)
  doi: 10.1021/jacs.2c06400

2020

• Complete genome sequence of an acetic acid bacterium Acetobacter aceti NBRC 14818
  Hiroyuki Arai, Masafumi Kameya, and Masaharu Ishii
  Microbiol. Res. Announc., 9:e01039-20 (2020)
  doi: 10.1128/MRA.01039-20
• Importance of electron flow in microbiological metabolism
  Masafumi Kameya, Hiroyuki Arai, and Masaharu Ishii
  Electron-Based Bioscience and Biotechnology (ISBN 978-981-15-4762-1) 13-32.
  doi: 10.1007/978-981-15-4763-8_2
• 効率的な生物炭酸固定経路を探る
  石井正治、亀谷将史、新井博之
  脱石油に向けたCO₂資源化技術―化学・生物プロセスを中心に― (ISBN 978-4-7813-1510-2) 310-330
  シーエムシー出版
• 水素細菌の代謝特性と低炭素社会実現に向けての展開
  亀谷将史、新井博之、石井正治
  極限環境生物学会誌 18, 30-38 (2020)
  Journal
  Preprint

2019

• Complete genome sequence of a mesophilic obligately chemolithoautotrophic hydrogen-oxidizing bacterium, Hydrogenovibrio marinus MH-110
  Hiroyuki Arai and Masaharu Ishii
  Microbiol. Resour. Announc., 8, e01132-19 (2019)
  doi: 10.1128/MRA.01132-19
• Draft genome sequence of Comamonas testosteroni TA441, a bacterium that has a cryptic phenol degradation gene cluster
  Hiroyuki Arai and Masaharu Ishii
  Microbiol. Resour. Announc., 8, e00946-19 (2019)
  doi: 10.1128/MRA.00946-19
• Physiological characterization of poly-β-hydroxybutyrate accumulation in the moderately thermophilic hydrogen-oxidizing bacterium Hydrogenophilus thermoluteolus TH-1
  Tri Huu Nguyen, Fumiko Ishizuna, Yuya Sato, Hiroyuki Arai, and Masaharu Ishii
  J. Biosci. Bioeng., 127, 686-689 (2019)
  doi: 10.1016/j.jbiosc.2018.11.011
• Discovery and analysis of a novel-type serine biosynthetic enzyme, phosphoserine phosphatase in Thermus thermophilus
  Yoko Chiba, Ayako Yoshida, Shigeru Shimamura, Masafumi Kameya, Takeo Tomita, Makoto Nishiyama, and Ken Takai
  FEBS J., 286, 726-736 (2019)
  doi: 10.1111/febs.14703
  Preprint

2018

• Complete genome sequence of a moderately thermophilic facultative chemolithoautotrophic hydrogen-oxidizing bacterium, Hydrogenophilus thermoluteolus TH-1
  Hiroyuki Arai, Yasuhito Shomura, Yoshiki Higuchi, and Masaharu Ishii
  Microbiol. Res. Announc., 7, e00857-18 (2018)
  doi: 10.1128/MRA.00857-18
• Protein engineering for improving the thermostability of tryptophan oxidase and insights from structural analysis
  Hiroki Yamaguchi, Moemi Tatsumi, Kazutoshi Takahashi, Uno Tagami, Masayuki Sugiki, Tatsuki Kashiwagi, Masafumi Kameya, Seiji Okazaki, Toshimi Mizukoshi, and Yasuhisa Asano
  J. Biochem., 164, 359-367 (2018)
  doi: 10.1093/jb/mvy065
• Function of three RuBisCO enzymes under different CO₂ conditions in Hydrogenovibrio marinus
  Koichi Toyoda, Masaharu Ishii, and Hiroyuki Arai
  J. Biosci. Bioeng., 126, 730-735 (2018)
  doi: 10.1016/j.jbiosc.2018.06.005
• Earth without life: a systems model of a global abiotic nitrogen cycle
  Matthieu Laneuville, Masafumi Kameya, and H. James Cleaves II
  Astrobiology, 18 (7), 897-914 (2018)
  doi: 10.1089/ast.2017.1700
• Pseudomonas aeruginosa overexpression system of nitric oxide reductase for in vivo and in vitro mutational analyses
  Raika Yamagiwa, Takuya Kurahashi, Mariko Takeda, Mayuho Adachi, Hiro Nakamura, Hiroyuki Arai, Yoshitsugu Shiro, Hitomi Sawai, and Takehiko Tosha
  Biochim. Biophys. Acta, 1859 (5), 333–341 (2018)
  ISSN 0005-2728
  doi: 10.1016/j.bbabio.2018.02.009

2017

• Transcriptome profiles of central carbon metabolism under autotrophic, heterotrophic, and mixotrophic conditions in Hydrogenophilus thermoluteolus TH-1
  Tri Huu Nguyen, Shin-ichi Hirano, Hiroyuki Arai, Hirofumi Nishihara, and Masaharu Ishii
  J. Jpn. Soc. Extremophiles, 16, 27-36 (2017)
• The Arnon-Buchanan cycle: a retrospective, 1966-2016.
  Bob B. Buchanan, Reidun Sirevåg, Georg Fuchs, Ruslan N. Ivanovsky, Yasuo Igarashi, Masaharu Ishii, F. Robert Tabita, and Ivan A. Berg
  Photosynth. Res., 134, 117–131 (2017)
  doi: 10.1007/s11120-017-0429-0
• Origin of the reductive tricarboxylic acid (rTCA) cycle-type CO₂ fixation: a perspective
  Norio Kitadai, Masafumi Kameya, and Kosuke Fujishima
  Life 7, 39 (2017)
  doi: 10.3390/life7040039
• Structural basis of the redox switches in the NAD⁺-reducing soluble [NiFe]-hydrogenase
  Y. Shomura, M. Taketa, H. Nakashima, H. Tai, H. Nakagawa, Y. Ikeda, M. Ishii, Y. Igarashi, H. Nishihara, K-S. Yoon, S. Ogo, S. Hirota, and Y. Higuchi
  Science, 357 (6354), 928-932 (2017)
  doi: 10.1126/science.aan4497
  研究科トピックス
  日本語解説
• Dynamics of nitric oxide controlled by protein complex in bacterial system
  Erina Terasaka, Kenta Yamada, Po-Hung Wang, Kanta Hosokawa, Raika Yamagiwa, Kimi Matsumoto, Shoko Ishii, Takaharu Mori, Kiyoshi Yagi, Hitomi Sawai, Hiroyuki Arai, Hiroshi Sugimoto, Yuji Sugita, Yoshitsugu Shiro, and Takehiko Tosha
  Proc. Natl. Acad. Sci. USA, 114, 9888–9893 (2017)
  doi: 10.1073/pnas.1621301114
  研究科トピックス
• Phosphoserine phosphatase is required for serine and one-carbon unit synthesis in Hydrogenobacter thermophilus
  Keugtae Kim, Yoko Chiba, Azusa Kobayashi, Hiroyuki Arai, and Masaharu Ishii
  J. Bacteriol., 199, e00409-17 (2017)
  doi: 10.1128/JB.00409-17
• Nitrate reductase in Hydrogenobacter thermophilus with evolutionarily ancient features: distinctive localization and electron transfer
  Masafumi Kameya, Haruna Kanbe, Yasuo Igarashi, Hiroyuki Arai, and Masaharu Ishii
  Mol. Microbiol., 106, 129-141 (2017)
  doi: 10.1111/mmi.13756　ReadCube
  Preprint　概要
• Specific expression and function of the A-type cytochrome c oxidase under starvation conditions in Pseudomonas aeruginosa
  Tatsuya Osamura, Takuro Kawakami, Reiko Kido, Masaharu Ishii, and Hiroyuki Arai
  PLoS ONE, 112(5): e0177957 (2017)
  doi: 10.1371/journal.pone.0177957
  PubMed
• 古くて新しい酢酸菌の酸化発酵
  桜井健太、石井正治、新井博之
  バイオサイエンスとインダストリー、75 (1), 17-21 (2017)

2016

• Expression of multiple cbb3 cytochrome c oxidase isoforms by combinations of multiple isosubunits in Pseudomonas aeruginosa
  Takehiro Hirai, Tatsuya Osamura, Masaharu Ishii, and Hiroyuki Arai
  Proc. Natl. Acad. Sci. USA, 113 (45), 12815-12819 (2016)
  doi/10.1073/pnas.1613308113
  PubMed
  研究科トピックス
• Metabolic features of Acetobacter aceti
  Hiroyuki Arai, Kenta Sakurai, and Masaharu Ishii
  In “Acetic acid Bacteria: Ecology and physiology” Matsushita, K. et al. (eds.) , pp. 225-271. Springer (2016)
  doi: 10.1007/978-4-431-55933-7_12
  Link
• Discovery of an intermolecular disulfide bond required for the thermostability of a heterodimeric protein from the thermophile Hydrogenobacter thermophilus
  Keug Tae Kim, Yoko Chiba, Hiroyuki Arai, and Masaharu Ishii
  Biosci. Biotechnol. Biochem., 80 (2), 232-240 (2016)
  doi: 10.1080/09168451.2015.1079476
  PubMed

2015

• Crystallization and preliminary X-ray analysis of the NAD⁺-reducing [NiFe] hydrogenase from Hydrogenophilus thermoluteolus TH-1.
  Taketa, M., Nakagawa, H., Habukawa, M., Osuka, H., Kihira, K., Komori, H., Shibata, N., Ishii, M., Igarashi, Y., Nishihara, H., Yoon, K. S., Ogo, S., Shomura, Y. and Higuchi, Y.
  Acta Crystallogr. F Struct. Biol. Commun. 71, 96-99 (2015)
• Conductive iron oxides accelerate thermophilic methanogenesis from acetate and propionate
  Chihaya Yamada, Souichiro Kato, Yoshiyuki Ueno, Masaharu Ishii, and Yasuo Igarashi
  J. Biosci. Bioeng., 119 (6), 678-82.1 (2015)
  doi: 10.1016/j.jbiosc.2014.11.00
• Reorganization of the bacterial and archaeal populations associated with organic loading conditions in a thermophilic anaerobic digester
  Tomoyuki Hori, Shin Haruta, Daisuke Sasaki, Dai Hanajima, Yoshiyuki Ueno, Atsushi Ogata, Masaharu Ishii, and Yasuo Igarashi
  J. Biosci. Bioeng., 119 (3), 337-344 (2015)
  PubMed

2014

• Involvement of a novel fermentative bacterium in acidification in a thermophilic anaerobic digester
  Tomoyuki Hori, Masateru Akuzawa, Shin Haruta, Yoshiyuki Ueno, Atsushi Ogata, Masaharu Ishii, and Yasuo Igarashi
  FEMS Microbiology Letters, 361 (1), 62–67, (2014)
  doi: 10.1111/1574-6968.12611
  PubMed
• Enzymatic characterization and in-vivo function of five terminal oxidases in Pseudomonas aeruginosa
  Hiroyuki Arai, Takuro Kawakami, Tatsuya Osamura, Takehiro Hirai, Yoshiaki Sakai, and Masaharu Ishii
  J Bacteriol., 196 (24), 4206-4215 (2014)
  PubMed
  Journal of Bacteriology誌のCommentaryで紹介されました。
  PubMed
• Fine-tuned regulation of the dissimilatory nitrite reductase gene by oxygen and nitric oxide in Pseudomonas aeruginosa
  Miho Kuroki, Yasuo Igarashi, Masaharu Ishii, and Hiroyuki Arai
  Environ. Microbiol. Rep., 6 (6), 792-801 (2014)
  PubMed
• The crystal structure of siroheme decarboxylase in complex with iron-uroporphyrin III reveals two essential histidine residues
  Kristin Haufschildt, Stefan Schmelz, Theresa M. Kriegler, Alexander Neumann, Judith Streif, Hiroyuki Arai, Dirk W. Heinz, and Gunhild Layer
  J. Mol. Biol., 426 (19), 3272-3286 (2014)
  PubMed
• Reduction of Fe(III) oxides by phylogenetically and physiologically diverse thermophilic methanogens
  Chihaya Yamada, Souichiro Kato, Satoshi Kimura, Masaharu Ishii, and Yasuo Igarashi
  FEMS Microbiol. Ecol., 89 (3), :637-645 (2014)
  PubMed
• Inhibitory effects of ferrihydrite on a thermophilic methanogenic community
  Chihaya Yamada, Souichiro Kato, Yoshiyuki Ueno, Masaharu Ishii, and Yasuo Igarashi
  Microbes Environ., 29 (2), 227-230 (2014)
  PubMed
• Adaptation of Hydrogenobacter thermophilus toward oxidative stress triggered by high expression of alkyl hydroperoxide reductase
  Yuya Sato, Hiroyuki Arai, Yasuo Igarashi, and Masaharu Ishii
  Biosci. Biotechnol. Biochem., 78 (9) 1619-1622 (2014)
  PubMed
• Enrichment of amino acid-oxidizing, acetate-reducing bacteria
  Makoto Ato, Masaharu Ishii, and Yasuo Igarashi
  J. Biosci. Bioeng. 118 (2), 160-165 (2014)
  PubMed

2013

• Structural units important for activity of a novel-type phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6 revealed by crystal structure analysis
  Yoko Chiba, Shoichiro Horita, Jun Ohtsuka, Hiroyuki Arai, Koji Nagata, Yasuo Igarashi, Masaru Tanokura, and Masaharu Ishii
  J. Biol. Chem., 288 (16), 11448-11458 (2013)
  PubMed
• Role of nitric oxide-detoxifying enzymes in virulence of Pseudomonas aeruginosa against the silkworm, Bombyx mori
  Hiroyuki Arai and Kazuhiro Iiyama
  Biosci. Biotechnol. Biochem., 77 (1), 198-200 (2013)
  PubMed
• Transcriptome response to nitrosative stress in Rhodobacter sphaeroides 2.4.1
  Hiroyuki Arai, Jung Hyeob Roh, Jesus M. Eraso, and Samuel Kaplan
  Biosci. Biotechnol. Biochem., 77 (1), 111-118 (2013)
  PubMed
• Role of the glyoxylate pathway in acetic acid production by Acetobacter aceti
  Kenta Sakurai, Shoko Yamazaki, Masaharu Ishii, Yasuo Igarashi, and Hiroyuki Arai
  J. Biosci. Bioeng. 115 (1), 32-36 (2013)
  PubMed
• “電子の流れ”で代謝を読み解く：Hydrogenobacter thermophilusの新規peroxidaseの発見
  佐藤由也、新井博之、石井正治
  バイオサイエンスとインダストリー、71 (4), 308-313 (2013)

2012

• Identification of the genes encoding nitric oxide reductase in the aerobic photosynthetic bacterium Roseobacter denitrificans OCh114
  Makoto Kimura, Masaharu Ishii, Yasuo Igarashi, and Hiroyuki Arai
  Biosci. Biotechnol. Biochem., 76 (10), 1984-1986 (2012)
  PubMed
• Transcriptome analyses for metabolic enzymes in thiosulfate- and hydrogen-grown Hydrogenobacter thermophilus cells
  Yuya Sato, Haruna Kanbe, Hirosuke Miyano, Yoshihiro Sambongi, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  Biosci. Biotechnol. Biochem., 76 (9), 1677-1681 (2012)
  PubMed
• Crystallization and preliminary X-ray diffraction analysis of a novel type of phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6
  Yoko Chiba, Shoichiro Horita, Jun Ohtsuka, Hiroyuki Arai, Koji Nagata, Yasuo Igarashi, Masaru Tanokurab, and Masaharu Ishii
  Acta Cryst. F68, 911-913 (2012)
  PubMed
• Phylogenetic position of Aquificales based on the whole genome sequences of six Aquificales species
  Kenro Oshima, Yoko Chiba, Yasuo Igarashi, Hiroyuki Arai, and Masaharu Ishii
  Int. J. Evol. Biol., 2012:859264 (2012)
  PubMed
• A novel enzymatic system against oxidative stress in the thermophilic hydrogen-oxidizing bacterium Hydrogenobacter thermophilus
  Yuya Sato, Masafumi Kameya, Shinya Fushinobu, Takayoshi Wakagi, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  PLoS ONE, 7 (4), e34825 (2012)
  PubMed
  Journal
  ※農学部のホームページに研究内容が紹介されています。http://www.a.u-tokyo.ac.jp/topics/2012/20120403-1.html
• Construction of hydrogen fermentation from garbage slurry using the membrane free bioelectrochemical system
  Kengo Sasaki, Masahiko Morita, Norio Matsumoto, Daisuke Sasaki, Shin-ichi Hirano, Naoya Ohmura, Yasuo Igarashi
  J. Biosci. Bioeng., 114 (1), 64-69 (2012)
  PubMed
• Discovery and analysis of cofactor-dependent phosphoglycerate mutase homologs as novel phosphoserine phosphatases in Hydrogenobacter thermophilus
  Yoko Chiba, Kenro Oshima, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  J. Biol. Chem. 287 (15), 11934-11941 (2012)
  PubMed
  ※農学部のホームページに研究内容が紹介されています。http://www.a.u-tokyo.ac.jp/topics/2012/20120221-5.html
• Involvement of flagella-driven motility and pili in Pseudomonas aeruginosa colonization at the air-liquid interface
  Kyosuke Yamamoto, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  Microbes Environ., 27 (3), 320-323 (2012)
  PubMed
• Mechanism for folate-independent aldolase reaction catalyzed by serine hydroxymethyltransferase
  Yoko Chiba, Tohru Terada, Masafumi Kameya, Kentaro Shimizu, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  FEBS J. 279 (3), 504-514 (2012)
  PubMed
• Changes in the gene expression profile of Acetobacter aceti during growth on ethanol
  Kenta Sakurai, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  J. Biosci. Bioeng., 113 (3), 343-348 (2012).
  PubMed

2011

• Detecting weak protein-protein interactions by modified far-western blotting
  Yuya Sato, Masafumi Kameya, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  J. Biosci. Bioeng., 112 (3) 304-307 (2011)
  PubMed
• A bioelectrochemical reactor containing carbon fiber textiles enables efficient methane fermentation from garbage slurry
  Kengo Sasaki, Masahiko Morita, Daisuke Sasaki, Shin-ichi Hirano, Norio Matsumoto, Atushi Watanabe, Naoya Ohmura, and Yasuo Igarashi
  Bioresour. Technol. 102 (13), 6837-6842 (2011)
  PubMed
• Decreasing ammonia inhibition in thermophilic methanogenic bioreactors using carbon fiber textiles
  Kengo Sasaki, Masahiko Morita, Shin-ichi Hirano, Naoya Ohmura, and Yasuo Igarashi
  Appl. Microbiol. Biotechnol., 90, 1555-1561(2011)
  PubMed
• Regulation and function of versatile aerobic and anaerobic respiratory metabolism in Pseudomonas aeruginosa
  Hiroyuki Arai
  Front. Microbio. 2:103 (2011)
  PubMed
• Detection of active, potentially acetate-oxidizing syntrophs in an anaerobic digester by flux measurement and FTHFS expression profiling
  Tomoyuki Hori, Daisuke Sasaki, Shin Haruta, Toru Shigematsu, Yoshiyuki Ueno, Masaharu Ishii, and Yasuo Igarashi
  Microbiology, 157 (7), 1980-1989 (2011)
  PubMed
• Trade-off between oxygen and iron acquisition in bacterial cells at the air-liquid interface
  Kyosuke Yamamoto, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  FEMS Microbiol. Ecol. 77 (1), 83-94 (2011)
  PubMed
• Bioelectrochemical system accelerates microbial growth and degradation of filter paper
  Kengo Sasaki, Shin-ichi Hirano, Masahiko Morita, Daisuke Sasaki, Norio Matsumoto, Naoya Ohmura, and Yasuo Igarashi
  Appl. Microbiol. Biotechnol. 89, 449-455 (2011)
  PubMed
• Distinctive responses of metabolically active microbiota to acidification in a thermophilic anaerobic digester
  Masateru Akuzawa, Tomoyuki Hori, Shin Haruta, Yoshiyuki Ueno, Masaharu Ishii, and Yasuo Igarashi
  Microb. Ecol. 61(3), 595-605 (2011)
  PubMed
• Transcriptome response to different carbon sources in Acetobacter aceti
  Kenta Sakurai, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  Microbiology, 157 (3), 899-910 (2011)
  PubMed
• Methanogenic pathway and community structure in a thermophilic anaerobic digestion process of organic solid waste
  Daisuke Sasaki, Tomoyuki Hori, Shin Haruta, Yoshiyuki Ueno, Masaharu Ishii, and Yasuo Igarashi
  J. Biosci. Bioeng., 111 (1), 41-46 (2011)
  PubMed
• Methanogenic communities on the electrodes of bioelectrochemical reactors without membranes
  Kengo Sasaki, Masahiko Morita, Daisuke Sasaki, Shin-ichi Hirano, Norio Matsumoto, Naoya Ohmura, and Yasuo Igarashi
  J. Biosci. Bioeng., 111 (1), 47-49 (2011)
  PubMed

2010

• ゲノム解析から見えてきた好熱性絶対独立栄養細菌Hydrogenobacter thermophilusの特徴
  新井博之
  バイオサイエンスとインダストリー, 68 (5), 322-326 (2010)
• Dissimilatory Fe(III) reduction by cytochrome c-552 in a thermophilic, obligately chemolithoautotrophic bacterium, Hydrogenobacter thermophilus TK-6
  Naoki Yoshida, Naoya Ohmura, Norio Matsumoto, Kengo Sasaki, Hiroshi Saiki, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  J. Jpn. Soc. Extremophiles, 9 (2), 61-66 (2010)
• Efficient degradation of rice straw in the reacters packed by carbon fiber textiles
  Kengo Sasaki, Masahiko Morita, Shin-ichi Hirano, Daisuke Sasaki, Naoya Ohmura, and Yasuo Igarashi
  Appl. Microbiol. Biotechnol., 87 (4), 1579-1586 (2010)
• Determinative factors of competitive advantage between aerobic bacteria for niches at the air-liquid interface
  Kyosuke Yamamoto, Shin Haruta, Souichiro Kato, Masaharu Ishii, and Yasuo Igarashi
  Microbes Environ., 25 (4), 317-320 (2010)
• Bioelectrochemical system stabilizes methane fermentation from garbage slurry
  Kengo Sasaki, Daisuke Sasaki, Masahiko Morita, Shin-ichi Hirano, Norio Matsumoto, Naoya Ohmura, and Yasuo Igarashi
  Bioresour. Technol., 101 (10), 3415-3422 (2010)
• Efficient treatment of garbage slurry in methanogenic bioreactor packed by fibrous sponge with high porosity
  Kengo Sasaki, Daisuke Sasaki, Masahiko Morita, Shin-ichi Hirano, Norio Matsumoto, Naoya Ohmura, and Yasuo Igarashi
  Appl. Microbiol. Biotechnol., 86 (5), 1573-1583 (2010)
• Complete genome sequence of the thermophilic, obligately chemolithoautotrophic hydrogen oxidizing bacterium Hydrogenobacter thermophilus TK-6
  Hiroyuki Arai, Haruna Kanbe, Masaharu Ishii, and Yasuo Igarashi
  J. Bacteriol., 192 (10), 2651-2652 (2010)
  PubMed
• Purification of three aminotransferases from Hydrogenobacter thermophilus TK-6 - novel types of alanine or glycine aminotransferase
  Masafumi Kameya, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  FEBS J., 277 (8), 1876-1885 (2010)
  PubMed
• Thiosulfate oxidation by a thermo-neutrophilic hydrogen-oxidizing Bacterium Hydrogenobacter thermophilus
  Ryoko Sano, Masafumi Kameya, Satoshi Wakai, Hiroyuki Arai, Yasuo Igarashi, Masaharu Ishii, and Yoshihiro Sambongi
  Biosci. Biotechnol. Biochem., 74 (4), 892-894 (2010)
  PubMed
• Enzymatic and electron paramagnetic resonance studies of anabolic pyruvate synthesis by pyruvate:ferredoxin oxidoreductase from Hydrogenobacter thermophilus
  Takeshi Ikeda, Masahiro Yamamoto, Hiroyuki Arai, Daijiro Ohmori, Masaharu Ishii, and Yasuo Igarashi
  FEBS J., 277 (2), 501-510 (2010)
  PubMed
• Carboxylation reaction catalyzed by 2-oxoglutarate:ferredoxin oxidoreductases from Hydrogenobacter thermophilus
  Masahiro Yamamoto, Takeshi Ikeda, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  Extremophiles, 14 (1), 79-85 (2010)
  PubMed
• Differential expression of multiple terminal oxidases for aerobic respiration in Pseudomonas aeruginosa
  Takuro Kawakami, Miho Kuroki, Masaharu Ishii, Yasuo Igarashi, and Hiroyuki Arai
  Environ. Microbiol., 12 (6), 1399-1412 (2010)
  PubMed
• Identification of iron-reducing microorganisms in anoxic rice paddy soil by ¹³C-acetate probing.
  Tomoyuki Hori, Alexandra Muller, Yasuo Igarashi, Ralf Conrad, and Michael W. Friedrich
  ISME J., 4 (2), 267-278 (2010)

2009

• Effect of adding carbon fiber textiles to methanogenic bioreactors used to treat an artificial garbage slurry
  Kengo Sasaki, Masahiko Morita, Shin-ichi Hirano, Naoya Ohmura, and Yasuo Igarashi
  J. Biosci. Bioeng..108 (2), 130-135 (2009)
• Siccanin rediscovered as a species-selective succinate dehydrogenase inhibitor
  Tatsushi Mogi, Takuro Kawakami, Hiroyuki Arai, Yasuo Igarashi, Kazunobu Matsushita, Mihoko Mori, Kazuro Shiomi, Satoshi Omura, Shigeharu Harada, and Kiyoshi Kita
  J. Biochem., 146 (3), 383-387 (2009)
• Ferredoxin-NADP⁺ reductase from the thermophilic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus TK-6
  Takeshi Ikeda, Miyuki Nakamura, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  FEMS Microbiol. Lett., 297 (1), 124-130 (2009)
• Intertwined interspecies relationships: approaches to untangle the microbial network.
  Shin Haruta, Souichiro Kato, Kyosuke Yamamoto, and Yasuo Igarashi
  Environ. Microbiol., 11 (12), 2963-2969 (2009)
• Bacterial community dynamics during reduction of odorous compounds in aerated pig manure slurry
  Dai Hanajima, Shin Haruta, Tomoyuki Hori, Masaharu Ishii, Kiyonori Haga, and Yasuo Igarashi
  J. Appl. Microbiol., 106, 118-129 (2009)

2008

• A soluble NADH-dependent fumarate reductase in the reductive tricarboxylic acid cycle of Hydrogenobacter thermophilus TK-6.
  Akane Miura, Masafumi Kameya, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  J. Bacteriol, 190, 7170-7177 (2008)
• Coexistence of antibiotic-producing and antibiotic-sensitive bacteria mediated by resistant bacteria in biofilm
  Naoki Narisawa, Shin Haruta, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  Appl. Environ. Microbiol., 74, 3887-3894 (2008)
• Nondecarboxylating and decarboxylating isocitrate dehydrogenases: oxalosuccinate reductase as an ancestral form of isocitrate dehydrogenase
  Miho Aoshima and Yasuo Igarashi
  J. Bacteriol., 190, 2050-2055 (2008)
• Network relationships of bacteria in a stable mixed culture
  Souichiro Kato, Shin Haruta, Zong Jun Cui, Masaharu Ishii, and Yasuo Igarashi
  Microb. Ecol. 56, 403-411 (2008)
• Transcriptional activity of Pseudomonas aeruginosa fhp promoter is dependent on two regulators in addition to FhpR
  Taija Koskenkorva, Niina Aro-Kärkkäinen, Daniel Bachmann, Hiroyuki Arai, Alexander D. Frey, and Pauli T. Kallio
  Arch. Microbiol. 189, 385-396 (2008)
• Transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration in Rhodobacter sphaeroides 2.4.1
  Hiroyuki Arai, Jung Hyeob Roh, and Samuel Kaplan
  J. Bacteriol., 190, 286-299 (2008)

2007

• Sequencing and reverse transcription-polymerase chain reaction (RT-PCR) analysis of four hydrogenase gene clusters from an obligately autotrophic hydrogen-oxidizing bacterium Hydrogenobacter thermophilus TK-6
  Yasufumi Ueda, Masahiro Yamamoto, Takashi Urasaki, Hiroyuki Arai, Masaharu Ishii and Yasuo Igarashi
  J. Biosci. Bioeng., 104, 470-475 (2007).
• Microbial population in the biomass adhering to supporting material in a packed-bed reactor degrading organic solid waste
  Kengo Sasaki, Shin Haruta, Yoshiyuki Ueno, Masaharu Ishii and Yasuo Igarashi
  Appl. Microbiol. Biotechnol., 75, 941-952 (2007).
• Novel enzyme reactions related to the tricarboxylic acid cycle: phylogenitic/functional implications and biotechnological application
  Miho Aoshima
  Appl. Microbiol. Biotechnol., 75, 249-255 (2007).
• The anaerobic regulatory network required for Pseudomonas aeruginosa nitrate respiration
  Kerstin Schreiber, Robert Krieger, Beatrice Benkert, Martin Eschbach, Hiroyuki Arai, Max Schobert, and Dieter Jahn
  J. Bacteriol., 189(11), 4310-4313 (2007).
• A novel ferredoxin-dependent glutamate synthase from the hydrogen-oxidizing chemoautotrophic bacterium, Hydrogenobacter thermophilus TK-6
  Masafumi Kameya, Takeshi Ikeda, Miyuki Nakamura, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  J. Bacteriol., 189(7), 2805-2812 (2007).
• Identification of acetate-assimilating microorganisms under methanogenic conditions in anoxic rice field soil by comparative stable isotope probing of RNA
  Tomoyuki Hori, Matthias Noll, Yasuo Igarashi, Michael W. Friedrich, and Ralf Conrad
  Appl. Environ. Microbiol., 73(1), 101-109 (2007).
• Traditional Pot Fermentation of Rice Vinegar -from the Viewpoint of Microbiology
  Masaharu Ishii, Shin Haruta, and Yasuo Igarashi
  J. Brew. Soc. Japan, 104, 652-657 (2007).
  doi: 10.6013/jbrewsocjapan.104.652

2006

• Purification and properties of glutamine synthetase from Hydrogenobacter thermophilus TK-6
  Masafumi Kameya, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  J. Biosci. Bioeng., 102 (4), 311-315 (2006)
• A novel oxalosuccinate-forming enzyme involved in the reductive carboxylation of 2-oxoglutarate in Hydrogenobacter thermophilus TK-6
  Miho Aoshima and Yasuo Igarashi
  Mol. Microbiol., 62, 748-759 (2006).
• Role of two 2-oxoglutarate:ferredoxin oxidoreductases in Hydrogenobacter thermophilus under aerobic and anaerobic conditions
  Masahiro Yamamoto, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  FEMS Microbiol. Lett., 263, 189-193 (2006).
• Archaeal population on supporting material in a methanogenic packed-bed reactor
  Kengo Sasaki, Shin Haruta, Yoshiyuki Ueno, Masaharu Ishi, and Yasuo Igarashi
  J. Biosci. Bioeng., 102 (3), 244-246 (2006).
• Gene structure and expression profile of cytochrome bc nitric oxide reductase from Hydrogenobacter thermophilus TK-6
  Miho Suzuki, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  Biosci. Biotechnol. Biochem. 70 (7), 1666-1671 (2006)
• Direct comparison of single-strand conformation polymorphism (SSCP) and denaturing gradient gel electrophoresis (DGGE) to characterize a microbial community on the basis of 16S rRNA gene fragments.
  Tomoyuki Hori, Shin Haruta, Yoshiyuki Ueno, Masaharu Ishii, and Yasuo Igarashi
  J. Microbiol. Methods, 66 (1), 165-169 (2006)
• Purification, characterization, and gene cloning of thermophilic cytochrome cd₁ nitrite reductase from Hydrogenobacter thermophilus TK-6
  Miho Suzuki, Tadao Hirai, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  J. Biosci. Bioeng., 101 (5), 391-397 (2006)
• Microbial community in methanogenic packed-bed reactor successfully operating at short hydraulic retention time
  Kengo Sasaki, Shin Haruta, Masahiro Tatara, Akira Yamazawa, Yoshiyuki Ueno, Masaharu Ishi, and Yasuo Igarashi
  J. Biosci. Bioeng., 101 (3), 271-273 (2006).
• Dynamic transition of a methanogenic population in response to the concentration of volatile fatty acids in a thermophilic anaerobic digester
  Tomoyuki Hori, Shin Haruta, Yoshiyuki Ueno, Masaharu Ishii, and Yasuo Igarashi
  Appl. Environ. Microbiol., 72 (2), 1623-1630 (2006)
• Anabolic five subunit-type pyruvate:ferredoxin oxidoreductase from Hydrogenobacter thermophilus TK-6
  Takeshi Ikeda, Toshiro Ochiai, Susumu Morita, Ayako Nishiyama, Eio Yamada, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  Biochem. Biophys. Res. Commun., 340 (1), 76-82 (2006)

2005

• The role of two CbbRs in the transcriptional regulation of three ribulose-1,5-bisphosphate carboxylase/oxygenase genes in Hydrogenovibrio marinus MH-110
  Koichi Toyoda, Yoichi Yoshizawa, Hiroyuki Arai, Masaharu Ishii, and Yasuo Igarashi
  Microbiology, 151 (11), 3615-3625 (2005)
• Two tandemly arranged ferredoxin genes in the Hydrogenobacter thermophilus genome: Comparatives characterization of the recombinant [4Fe-4S] ferredoxins
  Takeshi Ikeda, Masahiro Yamamoto, Hiroyuki Arai, Daijiro Ohmori, Masaharu Ishii, and Yasuo Igarashi
  Biosci. Biotechnol. Biochem., 69(6), 1172-1177 (2005)
• Stable coexistence of five bacterial strains as a cellulose-degrading community
  Souichiro Kato, Shin Haruta, Zong Jun Cui, Masaharu Ishii, and Yasuo Igarashi
  Appl. Environ. Microbiol., 71 (11), 7099-7106 (2005)
• Transcriptional regulation of the flavohemoglobin gene for aerobic nitric oxide detoxification by the second nitric oxide-responsive regulator of Pseudomonas aeruginosa
  Hiroyuki Arai, Michiko Hayashi, Azusa Kuroi, Masaharu Ishii, and Yasuo Igarashi
  J. Bacteriol., 187 (12), 3960-3967 (2005)
• Microbial diversity in biodegradation and reutilization processes of garbage
  Shin Haruta, Toru Nakayama, Kohei Nakamura, Hisashi Hemmi, Masaharu Ishii, Yasuo Igarashi, and Tokuzo Nishino
  J. Biosci. Bioeng., 99 (1), 1-11 (2005)