Publications

Journal Articles

1. X. Shen, K.  Hashiba, T. Yakata, K. Yoshida, H. Kobayashi (2025) "Characterization of indigenous bacteria for microbially induced carbonate precipitation in a limestone mine" Microorganisms,in press

2. A.Goto, S. Watanabe, K. Uruma, Y. Momoi, T. Oomukai, H. Kobayashi (2025) “Microbial DNA-based monitoring of underground crude oil storage bases using water-sealed rock-cavern tanks.” Water,17:2197. doi.org/10.3390/w17152197. 

3. X. Shen, S. He, Y. Takaya, T. Yakata, K. Yoshida, H. Kobayashi (2025) "Ureolysis-driven microbially induced carbonate precipitation by a facultatively anaerobic thermophilic bacterium under high-temperature and anaerobic conditions. Microorganisms, 13:1102. doi.org/10.3390/microorganisms13051102.

4. X. Feng, D. Kazama, K. Sato and H. Kobayashi (2023) “Complete genome sequence of an Achromobacter xylosoxidans strain H1_3_1 isolated from a hybrid biological-inorganic system reactor” Microbiol Res Announce,10.1128/MRA.006-1223.

5. X. Feng, D. Kazama, K. Sato and H. Kobayashi (2023) “Complete genome sequence of a Mycolicibacterium mageritense strain H4_3_1 isolated from a hybrid biological-inorganic system reactor” Microbiol Res Announce, 10.1128/MRA.00230-23.

6. X. Feng, D. Kazama, S. He, H. Nakayama, T. Hayashi, T. Tokunaga, K. Sato and H. Kobayashi (2023) "Enrichment of halotolerant hydrogen-oxidizing bacteria and production of high-value chemical hydroxyectoine using a hybrid biological–inorganic system" Front Microbiol, 14: doi.org/10.3389/fmicb.2023.1254451.

7. H. Kobayashi, A. Goto, X. Feng, K. Uruma, Y. Momoi, S. Watanabe, K. Sato, Y. Zhang, R.N. Horne, T. Shibuya and Y. Okano (2023) "Long-term microbial DNA-based monitoring of the mature Sarukawa oilfield in Japan" SPE Reserv Evaluation Eng, 3:1110-9.

8. X. Feng, S. He, T. Sato, T. Kondo, K. Uema, K. Sato and H. Kobayashi (2023) "Enrichment of hydrogen-oxidizing bacteria using a hybrid biological-inorganic system" J Biosci Bioeng, 135: 250-7.

9. H. Kobayashi, R. Toyoda, H. Miyamoto, Y. Nakasugi, Y. Momoi, K. Nakamura, Q. Fu, H. Maeda, T. Goda and K. Sato (2021) "Analysis of a methanogen and an actinobacterium dominating the thermophilic microbial community of an electromethanogenic biocathode" Archaea, 2021:Article ID 8865133.

10. Q. Li, Y. He, Q. Fu, H. Kobayashi, J. Li, L. Zhang, Q. Liao, X. Zhu (2020) "PEDOT/GO modified biocathode promotes CO2 reduction to CH4 in microbial electrosynthesis" Sustain Energ Fuels, 4:2987-97.

11. J. Li, Z., Li, S. Xiao, Q. Fu, H. Kobayashi, L. Zhang, Q. Liao, X. Zhu (2020) "Startup cathode potentials determine electron transfer behaviours of biocathodes catalysing CO2 reduction to CH4 in microbial electrosynthesis" J CO2 Utilization, 35:169-75.

12. Z. Li, Q. Fu, H. Kobayashi, S. Xiao, J. Li, L. Zhang, Q. Liao, X. Zhu (2019) "Polarity reversal facilitates the development of biocathodes in microbial electrosynthesis systems for biogas production" Int J Hydrogen Energ, 44: 26226-36.

13. Q. Fu, S. Xiao, Z. Li, Y. Li, H. Kobayashi, J. Li, Y. Yang, Q. Liao, X. Zhu, X. He, D. Ye, L. Zhang, M. Zhong (2018) "Hybrid solar-to-methane conversion system with a Faradaic efficiency of up to 96%." Nano Energy, 53: 232-9.

14. H. Kobayashi, X. Sun, Q. Fu, H. Maeda and K. Sato (2017) “Draft genome sequence of Methanothermobacter species strain EMTCatA1 reconstructed from the metagenome of a thermophilic biocathode catalyzing electromethanogenesis.” Genome Announc, 5: e00892-17.

15. J. Li, H. Li, Q. Fu, Q. Liao, X. Zhu, H. Kobayashi, D. Ye (2017) “Voltage reversal causes bioanode corrosion in microbial fuel cell stacks.” Int J Hydrogen Energ, 42:27649-56.

16. H. Kobayashi, A. Nagashima, M. Kouyama, Q. Fu, M. Ikarashi, H. Maeda and K. Sato (2017) “A high-pressure thermophilic electromethanogenic system producing methane at 5 MPa, 55℃.” J Biosci Bioeng, 124:327-32.

17. H. Kobayashi, Q. Fu, H. Maeda and K. Sato (2017) “Draft genome sequence of a novel Coriobacteriaceae sp. strain EMTCatB1 reconstructed from the metagenome of a thermophilic electromethanogenic biocathode.” Genome Announc, 5: e00022-17.

18. Q. Fu, N. Fukushima, H. Maeda, K. Sato and H. Kobayashi (2015) “Bioelectrochemical analysis of a hyperthermophilic microbial fuel cell generating electricity at temperatures above 80℃.” Biosci Biotechnol Biochem, 79:1200-6.

19. Q. Fu, Y. Kuramochi, N. Fukushima, H. Maeda, K. Sato and H. Kobayashi (2015) “Bioelectrochemical analyses of the development of a thermophilic biocathode catalyzing electromethanogenesis.” Environ Sci Technol, 49:1225-32.

20. Q. Fu, H. Kobayashi, Y. Kuramochi, J. Xu, T. Wakayama, H. Maeda and K. Sato (2013) “Bioelectrochemical analyses of a thermophilic biocathode catalyzing sustainable hydrogen production.” Int J Hydrogen Energ, 38:15638-45.

21. Q. Fu, H. Kobayashi, H. Kawaguchi, T. Wakayama, H. Maeda and K. Sato (2013) “A thermophilic Gram-negative nitrate-reducing bacterium, Calditerrivibrio nitroreducens, exhibiting electricity generation capability.” Environ Sci Technol, 47:12583-90.

22. H. Kobayashi†/N. Saito†/Q. Fu† (†contributed equally), H. Kawaguchi, J. Vilcaez, T. Wakayama, H. Maeda and K. Sato (2013) “Bio-electrochemical property and phylogenetic diversity of microbial communities associated with bioelectrodes of an electromethanogenic reactor.” J Biosci Bioeng, 116:114-7.

23. K. Sato, H. Kawaguchi and H. Kobayashi (2013) “Bio-electrochemical conversion of carbon dioxide to methane in geological storage reservoirs.” Energ Convers Manage 66:343-50.

24. Q. Fu, H. Kobayashi, H. Kawaguchi, J. Vilcaez, T. Wakayama, H. Maeda and K. Sato (2012) “Electrochemical and phylogenetic analyses of current-generating microorganisms in a thermophilic microbial fuel cell.” J Biosci Bioeng, 115:268-71.

25. H. Kawaguchi, H. Kobayashi and K. Sato (2012) “Metabolic engineering of hydrophobic Rhodococcus opacus for biodesulfurization in oil-water biphasic reaction mixtures.” J Biosci Bioeng 113:360-6.

26. H. Kobayashi, K. Endo, S. Sakata, D. Mayumi, H. Kawaguchi, M. Ikarashi, Y. Miyagawa, H. Maeda and K. Sato (2012) “Phylogenetic diversity of microbial communities associated with the crude oil and formation water phases of the produced fluid from a high-temperature biodegraded petroleum reservoir.” J Biosci Bioeng 113:204-10.

27. H. Kobayashi, H. Kawaguchi, K. Endo, D. Mayumi, S. Sakata, M. Ikarashi, Y. Miyagawa, H. Maeda and K. Sato (2012) “Analysis of methane production by microorganisms indigenous to a depleted oil reservoir for application in Micobial Enchance Oil Recoverly.” J Biosci Bioeng 113:84-7.

28. S. Ardissone, H. Kobayashi, K. Kambara, C. Rummel1, D.K. Noel, G.C. Walker, W.J. Broughton and W.J. Deakin (2011) “Role of BacA in lipopolysaccharide synthesis, peptide transport and nodulation by Rhizobium sp. NGR234.” J Bacteriol 93:2218-28.

29. H. Kawaguchi, T. Sakuma, Y. Nakata, H. Kobayashi, K. Endo and K. Sato (2010) “Methane production by Methanothermobacter thermautotrophicus to recover energy from carbon dioxide sequestered in geological reservoirs.” J Biosci Bioeng 110:106-8.

30. H. Kobayashi, N.J. De Nisco, P. Chien, L.A. Simmons and G.C. Walker (2009) “Sinorhizobium meliloti CpdR1 is critical for coordinating cell-cycle progression and the symbiotic chronic infection.” Mol Microbiol 73:586-600. 表紙に選出

31. V.L. Marlow, A.F. Haag, H. Kobayashi, V. Fletcher, M. Scocchi, G.C. Walker and G.P. Ferguson (2009) “Essential role for the BacA protein in the uptake of a truncated eukaryotic peptide in Sinorhizobium meliloti.” J Bacteriol 191:1519-27.

32. L.A. Simmons, A.I. Goranov, H. Kobayashi, D.S. Yuan, A.D. Grossman, G.C. Walker (2009) “A comparison of responses to double-strand breaks between Escherichia coli and Bacillus subtilis reveals different requirements for SOS induction.” J Bacteriol 191:1152-61.

33. P. Domenech, H. Kobayashi, K. Levier, G.C. Walker, C.E. Barry III (2009) “BacA: an ABC transporter involved in maintenance of chronic murine infections with Mycobacterium tuberculosis.” J Bacteriol 191: 477-85.

34. K. Kambara, S. Ardissone, H. Kobayashi, M.M. Saad, O. Schumpp, W.J. Broughton, W.J. Deakin (2009) “Rhizobia utilize pathogenic-like effector proteins during symbiosis.” Mol Microbiol 71:92-106.

35. R. Wassem, H. Kobayashi, K. Kambara, A.L. Le Quere, G.C. Walker, W.J. Broughton and W.J. Deakin (2008) “TtsI regulates symbiotic genes in Rhizobium species NGR234 by binding to tts-boxes.” Mol Microbiol 68:736-48.

36. H. Kobayashi, L.A. Simmons, D.S. Yuan, W.J. Broughton and G.C. Walker (2008) “Multiple Ku orthologs mediate DNA non-homologous end-joining in the free-living form and during chronic infection of Sinorhizobium meliloti.” Mol Microbiol 67:350-63.

37. W.J. Broughton, M. Hanin, B. Relic, J. Kopcinska, W. Golinowski, S. Simsek, T. Ojanen-Reuhs, B. Reuhs, C. Marie, H. Kobayashi, B. Bordogna, A. Le Quere, S. Jabbouri, R. Fellay, X. Perret, and W.J. Deakin (2006) “Flavonoid-inducible modifications to rhamnan O antigens are necessary for Rhizobium sp. strain NGR234-legume symbioses.” J Bacteriol 188:3654-63.

38. P. Skorpil, M.M. Saad, N.M. Boukli, H. Kobayashi, F. Ares-Orpel, W.J. Broughton, and W.J. Deakin (2005) “NopP, a phosphorylated effector of Rhizobium sp. strain NGR234, is a major determinant of nodulation of the tropical legumes Flemingia congesta and Tephrosia vogelii.” Mol Microbiol 57:1304-17.

39. M.M. Saad, H. Kobayashi, C. Marie, I.R. Brown, J.W. Mansfield, W.J. Broughton, and W.J. Deakin (2005) “NopB, a type III secreted protein of Rhizobium sp. strain NGR234, is associated with pilus-like surface appendages.” J Bacteriol 187:1173-81.

40. M. Theunis†/H. Kobayashi† (†contributed equally), W.J. Broughton, and E. Prinsen (2004) “Flavonoids, NodD1, NodD2 and nod-box NB15 Modulate Expression of the y4wEFG Operon that is required for Indole-3-acetic acid Synthesis in Rhizobium sp. NGR234.” Mol Plant-Microbe Interact 17:1153-61.

41. H. Kobayashi, Y. Naciri-Graven, W.J. Broughton and X. Perret (2004) “Flavonoids induce temporal shifts in gene expression of nod-box controlled loci in Rhizobium sp. NGR234.” Mol Microbiol 51: 335-47. 表紙に選出

42. N. Ausmees, H. Kobayashi, W.J. Deakin, C. Marie, H.B. Krishnan, W.J. Broughton, and X. Perret (2004) “Characterization of NopP, a type III secreted effector of Rhizobium sp. NGR234.” J Bacteriol 186: 4774-80.

43. P. Kiatpapan, H. Kobayashi, M. Sakaguchi, H. Ono, M. Yamashita, Y. Kaneko, and Y. Murooka (2001) “Molecular characterization of Lactobacillus plantarum genes for beta-ketoacyl-acyl carrier protein synthase III (fabH) and acetyl coenzyme A carboxylase (accBCDA), which are essential for fatty acid biosynthesis.”  App Env Microbiol 67: 426-33.

44. H. Kobayashi, M. Sunako, M. Hayashi, and Y. Murooka (2001) “DNA synthesis and fragmentation in bacteroids during Astragalus sinicus root nodule development.”  Biosci Biotechnol Biochem 65: 510-15.

45. Y. Kaneko, H. Kobayashi, P. Kiatpapan, T. Nishimoto, R. Napitupulu, H. Ono, and Y. Murooka (2000) “Development of a host-vector system for Lactobacillus plantarum L137 isolated from a traditional fermented food produced in the Philippines.” J Biosci Bioeng 89: 62-7.

Journal Articles（in Japanese）

1. 小林 肇, 荒木裕也, 佐藤光三 (2022) “石灰石鉱山における微生物源追跡技術の利用” 石灰石, 437:30-37.

2. 小林 肇, 宮本寛之, 渡辺駿一, 佐藤光三, 岩間弘樹, 米林英治 (2020) "油ガス田における微生物源追跡技術の利用"石油技術協会誌, 85:149-56.

3. 小林 肇, 中杉康仁，姫野将徳，孙 骁晗，長嶋彩乃，宮本寛之，佐藤光三 (2017) “電気化学的メタン生成を触媒する好熱性バイオカソードの生物電気化学・数理的解析.” 資源処理技術 64:36-41. 

Reviews/Book Chapters

1. Z. Li, Q. Fu, H. Kobayashi and S. Xiao (2018) “Biofuel production from bioelectrochemical systems.” Q. Liao et al. (eds.), Bioreactors for Microbial Biomass and Energy Conversion, Green Energy and Technology, p. 435-61. in Bioreactors for Microbial Biomass and Energy Conversion, Springer, Dordrecht, The Netherlands.

2. 小林 肇, 佐藤光三 (2014) “CO2から資源を生み出す微生物電解合成システム.” 水素エネルギー協会(HESS)会誌, 39: 24-32.

3. 若山 樹, 小林 肇, 前田治男 (2014) “枯渇油・ガス田をジオバイオリアクターとしたバイオエネルギー生産の可能性.” in 光合成のエネルギー利用と環境応用, 三宅淳, 佐々木健 Eds, シーエムシー出版, 東京, p. 118-30.

4. 前田治男，五十嵐雅之，宮川喜洋，小林 肇，佐藤光三，真弓大介，坂田 将. (2011) “地下常在微生物を利用した二酸化炭素のメタン変換システム構築.” 石油技術協会誌, 76: 530-7.

5. 小林 肇, 佐藤光三 (2011) “持続型炭素循環システム工学（国際石油開発帝石㈱）社会連携講座.”石油技術協会誌, 76: 176-9.

6. K. E. Gibson, H. Kobayashi and G.C. Walker (2008) “Molecular determinants of the symbiotic chronic infection.” Annu Rev Genet 42: 413-41.

7. H. Kobayashi and W.J. Broughton (2008) “Fine-tuning of symbiotic genes in rhizobia: flavonoid signal transduction cascade.” in Nitrogen-fixing Leguminous Symbioses, M.J. Dilworth, E.K. James, J.I. Sprent, and W.E. Newton Eds, Springer, Dordrecht, The Netherlands, p. 117-152.

8. K.M. Jones, H. Kobayashi, B.W. Davies, M.E. Taga, and G.C. Walker (2007) “How rhizobial symbionts invade plants: the Sinorhizobium-Medicago model.” Nature Rev Microbiol, 5:619-33.

9. A. Bartsev, H. Kobayashi, and W.J. Broughton (2004) “Rhizobial signals convert pathogens to symbionts at the legume interface.” in Plant Microbiology, M. Gillings Ed, Bios Scientific Publishers, Oxfordshire, UK, p19-31. 

10. X. Perret, H. Kobayashi, and J. Collado-Vides (2003) “Regulation of expression of symbiotic genes in Rhizobium sp. NGR234.” Indian J Exp Biol, 41: 1101-13.

Selected Other Publications

1. 小林 肇 (2019) “バイオ電極でCO2をメタンに変換する微生物たちの共生”東京大学環境報告書2019, 20.

2. 小林 肇 (2017) “温暖化の抑制のためにバイオができることは”生物工学会誌, 95:667.

3. Y. Nakasugi, M. Himeno, Q. Fu, M. Ikarashi, H. Maeda, K. Sato, H. Kobayashi (2017) “Experimental and mathematical analyses of bio-electrochemical conversion of carbon dioxide to methane.” Energy Procedia, 114:7133-40.

4. M. Hara, Y. Onaka, H. Kobayashi, Q. Fu, H. Kawaguchi, J. Vilcaez and K. Sato (2013) “Mechanism of electromethanogenic reduction of CO2 by a thermophilic methanogen.” Energy Procedia, 37:7021-8.

5. Q. Fu, H. Kobayashi, H. Kawaguchi, J. Vilcaez and K. Sato (2013) “Identification of new microbial mediators for electromethanogenic reduction of geologically-stored carbon dioxide.” Energy Procedia, 37:7006-13.

6. Y. Kuramochi, Q. Fu, H. Kobayashi, 他6名 (2013) “Electromethanogenic CO2 conversion by subsurface-reservoir microorganisms.” Energy Procedia, 37:7014-20.

7. R.S. Kobayashi, V. Champreda, L. Eurwilaichitr, S. Tanapongpipat, N. Roongsawang, and H. Kobayashi (2012) “Enzyme Technology and Application (เทคโนโลยีเอนไซม์และการประยุกต์ใช้ทางอุตสาหกรรม)” (Book). National Science and Technology Development Agency (NSTDA) printing, Pathumthani, Thailand.

8. 小林 肇 (2010) “二酸化炭素の回収・貯留からエネルギー資源を作り出す”東京大学環境報告書2010.