Last Updated :2024/06/12

Affiliations, Positions
Graduate School of Integrated Sciences for Life, Associate Professor
Web Site
It is generally recognized that most microorganisms are not readily cultivable in the laboratory. Thus, most of them are remaining untapped, unknown, and unused, regardless of huge potential.My research focuses on, 1) innovations for microbial cultivation: development of new cultivation methods; 2) isolation and cultivation of environmentally key but uncultivated microorganisms; 3) puzzling out the mechanism for "unculturability" or "recalcitrant for cultivation" of environmental microorganisms. The goal is to acquire a new tool for controlling microbial growth and microbial community structure. Achievements from above subjects are simultaneously applied to biotechnology, life science and environmental science.

Basic Information

Major Professional Backgrounds

  • 2019/04/01, Hiroshima University, Graduate School of Integrated Sciences for Life, Associate Professor
  • 2017/04, 2019/03/31, Hiroshima University, Graduate School of Advanced Sciences of Matter, Associate Professor
  • 2012/04, 2017/03, Hiroshima University, The Institute for Sustainable Sciences and Development, Tenure track Lecturer
  • 2012/04, 2017/03, Northeastern University, Visiting Scholar
  • 2010/04, 2012/03, Northeastern University, Visiting Scholar (JSPS Research Fellow Abroad)
  • 2007/03, 2010/03, Waseda University, Waseda Institute for Advanced Study, Assistant Professor
  • 2004/04, 2007/03, Waseda University, Research Associate
  • 2003/04, 2004/03, Waseda University, JSPS Research Fellow (PD)
  • 2001/04, 2003/03, Waseda University, Department of Chemical Engineering, JSPS fellow for doctoral course students (DC1)

Educational Backgrounds

  • Waseda University, School of Science and Engineering, Applied Chemistry, 1995/04, 1999/03
  • Waseda University, Graduate School of Science and Engineering, Deaprtment of Chemical Engineering, 1999/04, 2001/03
  • Waseda University, Graduate School of Science and Engineering, Department of Chemical Engineering, 2001/04, 2003/03

Academic Degrees

  • Doctor of Engineering, Waseda University
  • Master of Engineering, Waseda University

In Charge of Primary Major Programs

  • Program of Biotechnology

Research Fields

  • Agricultural sciences;Agricultural chemistry;Applied microbiology
  • Engineering;Process / Chemical engineering;Biofunction / Bioprocess
  • Biology;Basic biology;Biodiversity / Systematics

Research Keywords

  • Uncultivated microorganisms, Microbial cultivation, Microbial dormancy and resuscitation, Environmental microorganisms, Bioresources

Affiliated Academic Societies

  • Japan Society for Bioscience, Biotechnology, and Agrochemistry
  • Japanes Society of Microbial Ecology
  • The Society for Biotechnology, Japan
  • Japan Society on Water Environment
  • International Society for Microbial Ecology (ISME)
  • American Society for Microbiology

Educational Activity

Course in Charge

  1. 2024, Undergraduate Education, Second Semester, Basic Experiments in Chemistry
  2. 2024, Undergraduate Education, First Semester, Training of Biotechnology I
  3. 2024, Undergraduate Education, 4Term, MicrobiologyI
  4. 2024, Undergraduate Education, Year, Graduation Thesis
  5. 2024, Graduate Education (Master's Program) , Academic Year, Seminar in Biotechnology
  6. 2024, Graduate Education (Master's Program) , 1Term, Exercises in Biotechnology A
  7. 2024, Graduate Education (Master's Program) , 2Term, Exercises in Biotechnology A
  8. 2024, Graduate Education (Master's Program) , 3Term, Exercises in Biotechnology B
  9. 2024, Graduate Education (Master's Program) , 4Term, Exercises in Biotechnology B
  10. 2024, Graduate Education (Master's Program) , Academic Year, Research for Academic Degree Dissertation in Biotechnology
  11. 2024, Graduate Education (Doctoral Program) , Academic Year, Research for Academic Degree Dissertation in Integrated Life Sciences
  12. 2024, Graduate Education (Doctoral Program) , Academic Year, Research for Academic Degree Dissertation in Integrated Life Sciences

Research Activities

Academic Papers

  1. Isopropanol production via the thermophilic bioconversion of sugars and syngas using metabolically engineered Moorella thermoacetica, BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS, 17(1), 20240128
  2. Muricauda meishanensis sp. nov., a facultative anaerobic bacterium belonging to the family Flavobacteriaceae isolated from marine sediment in the East China Sea, INTERNATIONAOL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGYINTERNATIONAOL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 73(9), 20230926
  3. Enhancing acetone production from H2 and CO2 using supplemental electron acceptors in an engineered Moorella thermoacetica, JOURNAL OF BIOSCIENCE AND BIOENGINEERING, 136(1), 13-19, 202307
  4. A targeted liquid cultivation method for previously uncultured non-colony forming microbes., Frontiers in Microbiology, 14, 1194466, 20230609
  5. New microbial electrosynthesis system for methane production from carbon dioxide coupled with oxidation of sulfide to sulfate, JOURNAL OF ENVIRONMENTAL SCIENCES, 125, 786-797, 202303
  6. Cultivation of previously uncultured sponge-associated bacteria using advanced cultivation techniques: A perspective on possible key mechanisms, FRONTIERS IN MARINE SCIENCE, 9, 20220830
  7. Metabolic Potential of the Superphylum Patescibacteria Reconstructed from Activated Sludge Samples from a Municipal Wastewater Treatment Plant, MICROBES AND ENVIRONMENTS, 37(3), 20220628
  8. Biological methane production coupled with sulfur oxidation in a microbial electrosynthesis system without organic substrates, JOURNAL OF ENVIRONMENTAL SCIENCES, 116, 68-78, 202206
  9. Reversible Hydrogenase Activity Confers Flexibility to Balance Intracellular Redox in Moorella thermoacetica, FRONTIERS IN MICROBIOLOGY, 13, 897066, 20220512
  10. Environmental Factors Affecting the Community of Methane-oxidizing Bacteria, MICROBES AND ENVIRONMENTS, 37(1), 20220326
  11. Mutualistic relationship between Nitrospira and concomitant heterotrophs, ENVIRONMENTAL MICROBIOLOGY REPORTS, 14(1), 130-137, 202202
  12. Single-Cell Time-Lapse Observation Reveals Cell Shrinkage upon Cell Death in Batch Culture of Saccharomyces cerevisiae, mBio, 12(6), e03094-21, 20211221
  13. Autotrophic growth and ethanol production enabled by diverting acetate flux in the metabolically engineered Moorella thermoacetica, Journal of Bioscience and Bioengineering, 132(6), 569-574, 202112
  14. Bioelectrical Methane Production with an Ammonium Oxidative Reaction under the No Organic Substance Condition, MICROBES AND ENVIRONMENTS, 36(2), ME21007, 20210617
  15. Performance optimization of a chitosan/anammox reactor in nitrogen removal from synthetic wastewater, JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING, 9(3), 105252, 202106
  16. Reactor performance and microbial community structure of single-stage partial nitritation anammox membrane bioreactors inoculated with Brocadia and Scalindua enrichment cultures, BIOCHEMICAL ENGINEERING JOURNAL, 170, 107991, 202106
  17. Triggering Growth via Growth Initiation Factors in Nature: A Putative Mechanism for in situ Cultivation of Previously Uncultivated Microorganisms, FRONTIERS IN MICROBIOLOGY, 12, 537194, 20210504
  18. Metabolic engineering of Moorella thermoacetica for thermophilic bioconversion of gaseous substrates to a volatile chemical, AMB EXPRESS, 11, 59, 20210423
  19. Cometabolism of the Superphylum Patescibacteria with Anammox Bacteria in a Long-Term Freshwater Anammox Column Reactor, WATER, 13, 208, 202101
  20. Anti-bacterial Effects of MnO2 on the Enrichment of Manganese-oxidizing Bacteria in Downflow Hanging Sponge Reactors, Microbes and Environments, 35(4), ME20052, 20201205
  21. Multiple organic substrates support Mn(II) removal with enrichment of Mn (II)-oxidizing bacteria, Journal of Environmental Managemen, 259, 109771, 20200401
  22. Integrated anammox-biochar in synthetic wastewater treatment: Performance and optimization by artificial neural network, JOURNAL OF CLEANER PRODUCTION, 243, 118638, 20200110
  23. Mn(II) oxidation and manganese-oxide reduction on the decolorization of an azo dye, International Biodeterioration & Biodegradation, 146, 104820, 202001
  24. Integrated biological-physical process for biogas purification effluent treatment, JOURNAL OF ENVIRONMENTAL SCIENCES-CHINA, 83, 110-122, 201909
  25. Do textbook describe the "Nature of Science"? A comparative study of biology high school textbooks in Japan and Canada, Journal of Science Education in Japan, 43(2), 187-204, 201907
  26. Biogas purification performance of new water scrubber packed with sponge carriers, JOURNAL OF CLEANER PRODUCTION, 214, 103-111, 20190320
  27. Effects of Salts on the Activity and Growth of "Candidatus Scalindua sp.", a Marine Anammox Bacterium, MICROBES AND ENVIRONMENTS, 33(3), 336-339, 201809
  28. Specificities and Efficiencies of Primers Targeting Candidatus Phylum Saccharibacteria in Activated Sludge, MATERIALS, 11(7), 1129, 201807
  29. Application of the filter plate microbial trap (FPMT), for cultivating thermophilic bacteria from thermal springs in Barguzin area, eastern Baikal, Russia, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 82(9), 1624-1632, 201806
  30. Draft Genome Sequence of Mn(II)-Oxidizing Pseudomonas resinovorans Strain MO-1, Genome Announcements, 6(11), e00088-18, 20180315
  31. Production of biogenic manganese oxides coupled with methane oxidation in a bioreactor for removing metals from wastewater, WATER RESEARCH, 130, 224-233, 201803
  32. pH-gradient ion-exchange microbial cell chromatography as a simple method for microbial separation, JOURNAL OF BIOSCIENCE AND BIOENGINEERING, 123(4), 431-436, 2017
  33. Dominant Candidatus Accumulibacter phosphatis Enriched in Response to Phosphate Concentrations in EBPR Process, MICROBES AND ENVIRONMENTS, 32(3), 260-267, 2017
  34. In Situ Cultivation Allows for Recovery of Bacterial Types Competitive in Their Natural Environment, MICROBES AND ENVIRONMENTS, 31(4), 456-459, 2016
  35. Research Trends in Microbial Ecology and Water Engineering, Journal of Japan Society on Water Environment, 39(12), 444-451, 2016
  36. Innovations in Microbial Cultivation, Journal of Environmental Biotechnology, 16(1), 59-64, 2016
  37. Biological oxidation of Mn(II) coupled with nitrification for removal and recovery of minor metals by downflow hanging sponge reactor, WATER RESEARCH, 68, 545-553, 2015
  38. Isolation of Microorganisms Using Sub-Micrometer Constrictions, PLOS ONE, 9(6), e101429, 2014
  39. Isolation of sublineage I Nitrospira by a novel cultivation strategy, ENVIRONMENTAL MICROBIOLOGY, 16(10), 3030-3040, 2014
  40. Selective Enrichment of Two Different Types of Nitrospira-like Nitrite-oxidizing Bacteria from a Wastewater Treatment Plant, MICROBES AND ENVIRONMENTS, 28(2), 236-243, 2013
  41. Challenges for Complex Microbial Ecosystems: Combination of Experimental Approaches with Mathematical Modeling, MICROBES AND ENVIRONMENTS, 28(3), 285-294, 2013
  42. Isolation of Nitrospira belonging to Sublineage II from a Wastewater Treatment Plant, MICROBES AND ENVIRONMENTS, 28(3), 346-353, 2013
  43. Microbial community structure in autotrophic nitrifying granules characterized by experimental and simulation analyses, ENVIRONMENTAL MICROBIOLOGY, 12(1), 192-206, 2010
  44. Microbial Population Dynamics and Community Structure during the Formation of Nitrifying Granules to Treat Ammonia-Rich Inorganic Wastewater, MICROBES AND ENVIRONMENTS, 25(3), 164-170, 2010
  45. Hollow-Fiber Membrane Chamber as a Device for In Situ Environmental Cultivation, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 75(11), 3826-3833, 2009
  46. Diversity of nitrite reductase genes in "Candidatus Accumulibacter phosphatis"-Dominated cultures enriched by flow-cytometric sorting, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 73(16), 5331-5337, 2007
  47. Experimental and simulation analysis of community structure of nitrifying bacteria in a membrane-aerated biofilm, WATER SCIENCE AND TECHNOLOGY, 55(8-9), 283-290, 2007
  48. Real-time quantitative LAMP (loop-mediated isothermal amplification of DNA) as a simple method for monitoring ammonia-oxidizing bacteria, JOURNAL OF BIOTECHNOLOGY, 125(4), 484-491, 2006
  49. Analysis of Microbial Communities in Nitrogen Removal Processes and Its Application, Journal of Japan Society on Water Environment, 28(8), 474-478, 2005
  50. Single-stage autotrophic nitrogen-removal process using a composite matrix immobilizing nitrifying and sulfur-denitrifying bacteria, APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 68(1), 124-130, 2005
  51. Comparison of spatial organization in top-down- and membrane-aerated biofilms: a numerical study, WATER SCIENCE AND TECHNOLOGY, 52(7), 173-180, 2005
  52. Expression of amoA mRNA in wastewater treatment processes examined by competitive RT-PCR, JOURNAL OF BIOTECHNOLOGY, 111(2), 111-120, 2004
  53. Transition of bacterial spatial organization in a biofilm monitored by FISH and subsequent image analysis, WATER SCIENCE AND TECHNOLOGY, 49(11-12), 365-370, 2004
  54. Quantitative analysis of amoA mRNA expression as a new biomarker of ammonia oxidation activities in a complex microbial community, LETTERS IN APPLIED MICROBIOLOGY, 39(6), 477-482, 2004
  55. In Situ Identification of Microorganisms in Bioflim Communities(ENVIRONMENTAL BIOTECHNOLOGY), Journal of bioscience and bioengineering, 94(6), 552-556, 2002
  56. Real-time monitoring of ammonia-oxidizing activity in a nitrifying biofilm by amoA mRNA analysis, WATER SCIENCE AND TECHNOLOGY, 46(1-2), 439-442, 2002
  57. Microbial Ecology of Nitrifying Bacteria in Wastewater Treatment Process Examined by Fluorescence In Sity Hybridization, Journal of bioscience and bioengineering, 90(3), 234-240, 2000
  58. Tailoring of highly efficient nitrifying biofilms in fluidized bed for ammonia-rich industrial wastewater treatment, WATER SCIENCE AND TECHNOLOGY, 42(3-4), 357-362, 2000

Publications such as books

  1. 2016, Manuals of Environmental Microbiology Fourth Edition, New devices for cultivation, ASM press, 2016, Scholarly Book, Joint work, Y. Aoi, S. Epstein Edited by M. Yates, C. Nakatsu, R. Miller, S. Pillai
  2. 2011, Nitrification, Nitrification in Wasetewater Treatment, ASM Press, 2011, Scholarly Book, Joint work, S. Okabe, Y. Aoi, H. Satoh, Y. Suwa (Ed., B. B. Ward, M. G. Klotz, D. J. Arp)

Invited Lecture, Oral Presentation, Poster Presentation

  1. Are Microbial Interactions a key for cultivation of uncultivated?, Yoshiteru Aoi, Research Workshop Microbial Ecological Theory, 2023/11/27, With Invitation, English
  2. What are uncultivables and how can we grow them?, Yoshiteru Aoi, Jung Dawoon, Koshi Machida, Yoichi Nakao, 73rd SBJ (The Society for Biotechnology, Japan) Annual meeting, 2021/10/29, With Invitation, Japanese, Okinawa
  3. Toward innovation for microbial cultivation: escaping from loneliness but not to be crowded, Yoshiteru Aoi, 2021/03/19, With Invitation
  4. Miniscule space designing for microbial cultivation, Yoshiteru Aoi, 10th ASME, 2018/07/11, With Invitation, Okinawa
  5. Innovation in microbial cultivation: nature of fastidious microbes and their potential, Yoshiteru Aoi, 2017/09/13, With Invitation
  6. Innovation in microbial cultivation and its potential importance, Yoshiteru Aoi, 2016/09/02, With Invitation
  7. Designing miniscule space for cultivation, Yoshiteru AOi, 15th International symposium on microbial ecology (ISME15), 2014/08, With Invitation, Seoul, Korea
  8. New methods for cultivation of unculutreds, Yoshiteru Aoi, International workshop on in-situ enrichment of marine microbes (IEMM), 2013/11, With Invitation, Xiamen, China
  9. New methods for cultivation of uncultured, Y. Aoi, Plant Protection and Plant Health in Europe (PPPHE 2013), 2013/06, With Invitation, Berlin
  10. Development of new technologies for cultivation of uncluturables, Y. Aoi, H. Fujitani, S. Tsuneda, 28th annual meeting of Japanese society of Microbial Ecology, the 4th Japan-Korea Joint Symposium on Microbial Ecology, 2012/09, With Invitation
  11. New cultivation methods accessing unculturables and puzzling out unculturability, Y. Aoi, 14th International symposium on microbial ecology (ISME14), 2012/08, With Invitation, Copenhagen, Danmark


  1. 2023/11/30, 36th JSME Annual Meeting & 13th ASME in Hamamatsu, JAPAN,Excellent Poster Award, 2023 Japanese Society for Microbial Ecology Annual Meeting Organizing Committee
  2. 2018, 26th JBB Best Paper Award, The Soceity for Biotechnology, Japan
  3. 2017, Best Poster Award (Awarded to supervised student), Japan Society of Water Environment
  4. 2016, D.C. White Award (The most innovative poster Award at ISME16) [Awarded to the supervised student], International Society for Microbial Ecology
  5. 2016, Best Poster Award at ISME16(Awarded to the supervised student), International Society for Microbial Ecology
  6. 2002, Best Paper Award, The Society for Biotechnology, Japan
  7. 2001/03/25, Ono Azusa Memorial Award, Waseda University


  1. Patent, JP第5316983号, P5316983, 2013/07/19
  2. Patent, US10626435B2, 2020/04/21, NanoFluidics Device for isolating, growing and characterizing microbial cells
  3. Patent, JP第6785465, 2020/10/29
  4. Patent, 6719092, 2020/06/18

External Funds

Acceptance Results of Competitive Funds

  1. 2022, 2023
  2. KAKENHI(Grant-in-Aid for Challenging Research (Exploratory)), 2020, 2022
  3. 2020, 2026
  4. AMED Drug Discovery Support Promotion Project, 2023/04, 2024/03
  5. AMED Drug Discovery Support Promotion Project, 2020, 2022
  6. AMED Drug Discovery Support Promotion Project, 2020, 2023
  7. AMED Drug Discovery Support Promotion Project, 2020, 2021
  8. 2020, 2021
  9. 2019, 2021
  10. AMED Drug Discovery Support Promotion Project, 2018/04/01, 2019/12/31
  11. KAKENHI(Grant-in-Aid for Challenging Research (Exploratory)), 2018, 2019
  12. KAKENHI(Grant-in-Aid for JSPS Research Fellow), 2017, 2018
  13. KAKENHI, 2015, 2017
  14. KAKENHI, 2014, 2018
  15. 2014/04, 2015/03
  16. KAKENHI, 2013, 2014
  17. National Science Foundation (NSF) Grant, Collaborative Research: Direction and Mechanisms of Seasonal Change in Arctic Microbial Communities (ARC-1203857) (Co-PI), 2012/09, 2015/08
  18. 2006, 2008
  19. KAKENHI, 2006, 2006
  20. 2005, 2005

Social Activities

History as Committee Members

  1. Board member, 2023/01, 2024/12, Japanese Society of Microbial Ecology
  2. Assistant to the President for Internatinal Affairs, 2022, 2025
  3. Journal of Bioscience and Biotechnology, Editor, 2021/06, 2025/05, The society for Biotechnology, Japan
  4. Board member, 2017/01, 2020/12, Japanese Society of Microbial Ecology
  5. Journal "Microbes and Environments" Associate Editor, 2017, 2025
  6. ISME Young Ambassador (Interanational Sosciety for Microbial Ecology), 2015, 2022, International Society for Microbial Ecology

Organizing Academic Conferences, etc.

  1. The 36th JSME & The 13th ASME Hamamatsu2023, Organizing Committee, 2023/11, 2023/11
  2. The 2023 Annual Meeting of The Japan Society for Bioscience, Biotechnology and Agrochemistry, Organizing committee, 2023/03, 2023/03
  3. 3rd International Conference on Nitrification (ICoN3), Organizing committee, 2013/09
  4. International Symposium on Microbial Ecology Asia 2007 (ISME Asia 2007), Organizing committee, 2007/09
  5. The 8th IWA Microbial Ecology and Water Engineering Specialist Conference (MEWE2019), organizing comittee, 2019/11, 2019/11