2026
Nobuhiro Takahashi, Yasunari Kita, Rei Hojo, Reika Mimoto, Ayaka Sugiura, Ryota Moriuchi, Hideo Dohra, and Hiroyuki Futamata 2026. Complete genome sequence of phenol-degrading Burkholderia anthina strain IK3-12. Microbial Resource Announcement投稿中-revise260502
Rin Yamazaki, Maho Tokuda, Singh Shweta, Koichiro Nakamichi, Ryota Moriuchi, Hideo Dora, Hiroyuki Futamata, Kazuhide Kimbara, Masaki Shintani* 2026. Global dissemination potential of multidrug resistance plasmids captured from the Tama River flowing through the Tokyo megalopolis. Antibiotics. 15, 241.
2025
Kenshi Suzuki, Fatma Azwani Abdul Aziz,·Masahiro Honjo,·Abd Rahman Jabir bin Mohd Din, Koki Amano, Yosuke Tashiro, Hiroyuki Futamata*. Stable coexistence and phenol-degradation expression of Cupriavidus sp. strain P-10 and Comamonas thiooxydans strain R2 in phenol-competitive chemostat culture. Applied Microbiol. Biotech. 109 (1):243. doi.org/10.1007/s00253-025-13629-5
Makoto Kawano, Kohei Ikeura, Hiroki Taniguchi, Minako Terao, Kota Ichikawa, Takumi Higashi, Hiroyuki Futamata, and Hiroyuki Kimura. 2025. Role of organic acid-degrading bacteria in a microbial methanation system using a subterranean microbial community. World Journal of Microbiology and Biotechnology 41:286. doi.org/10.1007/s11274-025-04496-3
Yui Arashi, Hiroki Mochihara, Hiroko Kubota, Kei Suzuki, Yusuke Chiba, Yutaka Kato, Toshihiro Kogure, Ryota Moriuchi, Hideo Dohra, Yuto Nakamura, Yosuke Tashiro, and Hiroyuki Futamata*. 2025. A Rechargeable Biomineral Induced by Sulfate-reducing Bacterium Nitratidesulfovibrio HK-II. Microbes Environ. 2025 40(2): Article ME24022. doi:10.1264/jsme2.ME24022
2024
Hidehiro Ishizawa*, Yosuke Tashiro, Takashi Okada, Daisuke Inoue, Michihiko Ike, Hiroyuki Futamata. 2024.Uncovering the causal relationships in plant-microbe ecosystems: A time series analysis of the duckweed cultivation system for biomass production and wastewater treatment. Science of the Total Environment (Sci. Total Environ.) Dec 20:957:177717 doi: 10.1016/j.scitotenv.2024.177717.
So Ueno, Mizuki Kanno, Shakhina Sharan, Hiroyuki Futamata, Ryoma Nakano and Yosuke Tashiro*. 2024. Biofilm-derived membrane vesicles exhibit potent immunomodulatory activity in Pseudomonas aeruginosa Microbiol. Immunol. Jul; 68(7):224-236. DOI: 10.1111/1348-0421.13156
So Ueno, Mizuki Kanno, Shakhina Zaman Sharan, Hiroyuki Futamata, Yosuke Tashiro. 2024 Sep.. Pyocianin stimulates membrane vesicle formation in Pseudomonas aerugnosa, but the synthesis is not required for enhanced vesiculation in biofilms. The Microbe 4(2024): 100137 https://doi.org/10.1016/j.microb.2024.100137
Hidehiro Ishizawa*, Minami Tada, Yosuke Tashiro, Masashi Kuroda, Daisuke Inoue, Hideo Dohra, Hiroyuki Futamata, and Michihiko Ike. 2024. Complete genome sequences of six duckweed-associated bacterial strains for studying community assembly in synthetic plant microbiome. Microbial Resource Announcement. 2024 Mar 1:e0128023 doi: 10.1128/mra.01280-23.
Masahiro Honjo, Kenshi Suzuki, Junya Katai, Yosuke Tashiro, Tomo Aoyagi, Tomoyuki Hori, Takashi Okada, Yasuhisa Saito, and Hiroyuki Futamata*. 2024. Stable states of microbial community are formed by dynamic metabolic networks with members functioning as both robustness and plasticity. Microbes and Environ. 2024;39(1):ME23091. doi:10.1264/jsme2.ME23091 （リポジトリ登録 http://hdl.handle.net/10297/0002000607） M&E論文賞佳作
Hidehiro Ishizawa*, Yosuke Tashiro, Daisuke Inoue, Michihiko Ike, Hiroyuki Futamata.2024. Learning beyond-pairwise interactions enables the bottom-up prediction of microbial community structure. Proc. Natl. Acad. Sci. USA 2024 Feb 13;121(7):e2312396121 DOI: 1073/pnas.2312396121
2023
Mizuki Kanno, Takuya Shiota, So Ueno, Minato Takahara, Keisuke Haneda, Yuhei O Tahara, Masaki Shintani, Ryoma Nakao, Makoto Miyata, Kazuhide Kimbara, Hiroyuki Futamata, Yosuke Tashiro*. 2023. Identification of genes involved in enhanced membrane vesicle formation in Pseudomonas aeruginosa biofilms: Surface sensing facilitates vesiculation. Frontiers in Microbiology. 2023 Dec 1:14:1252155 DOI: 3389/fmicb.2023.1252155
Yuya Sato, Teruhiko Miwa, Tomohiro Inaba, Takuto Akachi, Eiji Tanaka, Tomoyuki Hori, Keita Murofushi, Hiroshi Takagi, Hiroyuki Futamata, Tomo Aoyagi, Hiroshi Habe. 2023. Microbially produced fertilizer provides rhizobacteria to hydroponic tomato roots by forming benefical biofilms. Appl. Microbiol. Biotech. 107(23):7365-7374. https://doi.org/10.1007/s00253-023-12794-9
2022
Masaya Hayakawa, Maho Tokuda, Kensei Kaneko, Koichiro Nakamichi, Yukie Yamamoto, Tatsuya Kamijo, Honoka Umeki, Reimi Chiba, Ryo Yamada, Mitsuya Mori, Kosuke Yanagiya, Ryota Moricuhi, Msahiro Yuki, Hideo Dohra, Hiroyuki Futamata, Moriya Ohkuma, Kazuhide Kimbara, Masaki Shintani. 2022. Hitheto-unnoticed self-transissible plasmids widely distributed among different environments in Japan. Environ. Microbiol. aem.01114-22 2022 88(18):10.1128/aem.01114-22 DOI: 10.1128/aem.01114-22
2021
Sharmin Aktar, Yuhi Okamoto, So Ueno, Yuhei O Tahara, Masayoshi Imaizumi, Masaki Shintani, Makoto Miyata, Hiroyuki Futamata, Hideaki Nojiri, and Yosuke Tashiro. 2021. Incorporation of plasmid DNA into bacterial membrane vesicles by peptidoglycan defects in Escherichia coli. Frontiers in Microbiology 12: Article 747606 DOI: 3389/fmicb.2021.747606
Abd Rahman Jabir Mohd Din, Kenshi Suzuki, Masahiro Honjo, Koki Amano, Tomoka Nishimura, Ryota Moriuchi, Hideo Dohra, Hidehiro Ishizawa, Motohiko Kimura, Yosuke Tashiro, and Hiroyuki Futamata*. 2021. Imbalance in carbon and nitrogen metabolism in Comamonas testosteroni R2 is caused by negative feedback and rescued by L-arginine. Microbes Environ. 36: Article ME21050 DOI: 1264/jsme2.ME21050 （リポジトリ登録 http://hdl.handle.net/10297/0002000608 ）M&E論文賞佳作
Thien V. Le, Chau N. T. Ngo, and Hiroyuki Futamata. 2021. Effect of fly ash amendment on sandy soil properties and peanut yields. ScienceAsia 47:357-365.
Nao Nakamichi, Ryota Moriuchi, Hideo Dohra, Hiroyuki Futamata, Yosuke Tashiro. 2021. Complete genome sequence of Buttiauxella agrestis DSM 9389. Microbiology Resource Announcement. DOI:10.1128/MRA.00301-21
Yuya Sato, Eiji Tanaka, Tomoyuki Hori, Hiroyuki Futamata, Keita Murofushi, Hiroshi Takagi, Takuto Akachi, Teruhiko Miwa, Tomohiro Inaba, Tomo Aoyagi, and Hiroshi Habe. 2021 Efficient conversion of organic nitrogenous wastewater to nitrate solution driven by comamox Nitrospira. Water Res. 197:117088. doi. 10.1016/j.waters.2021.117088
Fatma Azwani Abdul Aziz, Kenshi Suzuki, Masahiro Honjo, Koki Amano, Abd Rahman Jabir Bin Mohd Din, Yosuke Tashiro, and Hiroyuki Futamata* 2021 Coexisting mechanisms of bacterial community are changeable even under similar stable conditions in a chemostat culture. Biosci. Bioeng. 131(1):77-83. doi:10.1016/j.jbiosc.2020.09.009
2020
Lee, GLY, NN Zakaria, P. Convey, H. Futamata, A. Zulkharnain, K. Suzuki, KA Khalil, NA Shaharuddin, SA, Alias, G. Gonzalez-Rocha, and SA. Ahamad. 2020 Statistical optimization of phenol degradation and pathway identification through whole genome sequencing of the cold-adapted Antarctic bacterium, Rhodococcus strain AQ5-07. Int. J. Mol. Sci. 21(24):9369. doi: 10.3390/ ijms21249363 (IF 4.556 on Journal Citation Reports)
Hidehiro Ishizawa, Minami Tada, Masashi Kuroda, Daisuke Inoue, Hiroyuki Futamata, and Michihiko Ike. 2020 Synthetic bacterial community of duckweed: A simple and stable system to study plant-microbe interactions. Microbes Environ. 35(4): doi:10.1264/jsme2.ME20112.
Fatma Azwani Abdul Aziz, Kenshi Suzuki, Koki Amano, Ryota Moriuchi, Hideo Dohra, Yosuke Tashiro, Hiroyuki Futamata* 2020 Draft genome sequence of phenol-degrading Variovorax boronicumulans strain c24. Microbiology Resource Announcements. Sep 10;9(37):e00597-20. doi: 10.1128/MRA.00597-20.
Takaki K, Tahara YO, Nakamichi N, Hasegawa Y, Shintani M, Ohkuma M, Miyata M, Futamata H, Tashiro Y. 2020 Multilamellar and multivesicular outer membrane vesicles produced by a Buttiauxella agrestis tolB Appl. Environ. Microbiol. 86(20):e01131-20. doi: 10.1128/AEM.01131-20
Fatma Azwani Abdul Aziz, Kenshi Suzuki, Ryota Moriuchi, Hideo Dohra, Yosuke Tashiro, Hiroyuki Futamata* 2020 Draft genome sequence of phenol-degrading Variovorax boronicumulans strain HAB-30. Microbiology Resource Announcements DOI: 10.1128/MRA.01478-19 2020 9(7) e01478-19.
2019
Yosuke Tashiro*, Kotaro Takaki, Hiroyuki Futamata. 2019. Targeted delivery using membrane vesicles in prokaryotes. Biophys. Physicobiol. (Apr. 19) 16:114-120 Review. DOI: 10.2142/biophysico.16.0_114
Le Van Thien*, Ngo Thi Tuong Chau, Le Thi Tham Hong, Nguyen Thu Trang, Hiroyuki Futamata. 2019. Properties of fly ashes from thermal power stations in relation to use as soil amendments. Sains Malasysiana 48(4): 745-755. (IF 0.540)
2018
Abd Rahaman Jabir Mohd Din, Siti Zulaiha Hanapi, Hiroyuki Futamata, and Mohamad roji Sarmidi*. 2018. Utilization of compost tea for biochemical response assessment associated with resistance to phytopathogen causing leaf spot in Melicope ptelefolia. Organic Agriculture https://doi.org/10.1007/s13165-018-0235-9 10. 30. (IF未)
Kenshi Suzuki, Fatma A. A. Azizi, Masahiro Honjo, Tomoka Nishimura, Ryota Moriuchi, Hideo Dohra, Kensei Masuda, Ayaka Minoura, Yuki Kudo, Yosuke Tashiro, and Hiroyuki Futamata*. 2018. Draft genome sequence of the phenol-degrading bacterium Cupriavidus P-10 isolated from trichloroethene-contaminated aquifer soil. Microbiology Resource Announcement 7 (18): e01009-18. doi: 10.1128/MRA.01009-18 (IF未)
Ngo Thi Tuong Chau, Le Van Thien, Le Thi Tham Hong, and Hiroyuki Futamata. 2018. Effect of using thermophilic bacteria as start inoculum on microbial aspect of pulp and paper mill sludge compositing process. Chiang Mai J. Sci. 45: 1-14. (IF 0.409)
Chau Ngo, Van Thien Le, Ngoc Lan Pham Thi, and Hiroyuki Futamata. 2018. Characterization and utilization of pulp and paper mill sludge digesting thermophilic bacteria in compositing process. Sains Malaysiana 47(5): 1051-1060. (IF 0.565)
Kei Suzuki, Yutaka Kato, Shuji Yamamoto, Owen Rubaba, Hiroki Mochihara, Takuya Hosokawa, Hiroko Kubota, Arashi Yui, Yosuke Tashiro, and Hiroyuki Futamata*. 2018. Bacterial communities adapted to higher external resistance can reduce the onset potential of anode in microbial fuel cells. J. Biosci. Bioeng. 125(5): 565-571.(IF 2.015) doi: 10.1016/j.jbiosc.2017.12.018
2017
Yosuke Tashiro, Hiroaki Eida, Satoshi Ishii, Hiroyuki Futamata, and Satoshi Okabe. 2017. Generation of small colony variants in biofilms by Escherichia coli harboring a conjugative F plasmid. Microbes and Environments.
Yosuke Tashiro, Yusuke Hasegawa, Masaki Shintani, Kotaro Takaki, Moriya Ohkuma, Kazuhide Kimbara and Hiroyuki Futamata. 2017. Interaction of bacterial membrane vesicles with specific species and their potential for delivery to target cells. Frontiers in Microbiology
2016
Shin Haruta, Yasuhisa Saito and Hiroyuki Futamata. 2016 Editorial: Development of microbial ecological theory: stability, plasticity and evolution of microbial ecosystems. Frontiers in Microbiology
Kenshi Suzuki, Fatma A. A. Aziz, Yuma Inuzuka, Yosuke Tashiro, and Hiroyuki Futamata* 2016. Draft genome sequence of Pseudomonas LAB-08 isolated from trichloroethene contaminated aquifer soil. Genome Announcements. Sep 22: 4(5) e00948-16.(http://hdl.handle.net/10297/9859)
Kei Suzuki, Rubaba Owen, Joann Mork, Hiroki Mochihara, Takuya Hosokawa, Hiroko Kubota, Hisatosihi Sakamoto, Atsunori Matsuda, Yosuke Tashiro, and Hiroyuki Futamata* 2016. Comparison of electrochemical and microbiological characterization of microbial fuel cells equipped with SPEEK and Nafion membrane electrode assemblies. J. Bioscience Bioeng. 122(3); 322-328. doi: 10.1016/j.jbiosc.2016.02.005
2015
Fatma Azwani Abdul Aziz*, Kenshi Suzuki, Akihiro Ohtaki, Keita Sagegami, Hidetaka Hirai, Jun Seno, Naoko Mizuno, Yuma Inuzuka, Yasuhisa Saito, Yosuke Tashiro, Akira Hiraishi and Hiroyuki Futamata*
Interspecies interactions are an integral determinant of microbial community dynamics.
Frontiers in Microbiology 6:1148 (2015) doi: 10.3389/fmicb.2015.01148
Yusuke Hasegawa, Hiroyuki Futamata, Yosuke Tashiro.
Complexities of cell-to-cell communication through membrane vesicles: implications for selective interaction of membrane vesicles with microbial cells.
Frontiers in Microbiology 6:633 (2015)
Keitaro Yoshida, Yosuke Tashiro, Thithiwat May, Satoshi Okabe.
Impacts of hydrophilic colanic acid on bacterial attachment to microfiltration membranes and subsequent membrane biofouling.
Water Research 76:33-42 (2015)
Hiromu Oura†, Yosuke Tashiro† (†equally contributed), Masanori Toyofuku, Kousetsu Ueda, Tatsunori Kiyokawa, Satoshi Ito, Yurika Takahashi, Seunguk Lee, Hideaki Nojiri, Toshiaki Nakajima-Kambe, Hiroo Uchiyama, Hiroyuki Futamata and Nobuhiko Nomura.
Inhibition of Pseudomonas aeruginosa swarming motility through 1-naphthol and other bicyclic compounds bearing hydroxyl groups
Applied and Environmental Microbiology 81:2808-2818 (2015)
2014
Shuji Yamamoto, Kei Suzuki, Yoko Araki, Takuya Hosokawa, Yusuke Chiba, Hiroko Kubota, Hiroki Mochihara, Owen Rubaba, Yosuke Tashiro, Hiroyuki Futamata*.
Different communities dynamics are capable of generating sustainable electricity from microbial fuel cell with organic wastes.
Microbes and Environments 29:145-153 (2014)
Yosuke Tashiro, Aya Inagaki, Kaori Ono, Tomohiro Inaba, Yutaka Yawata, Hiroo Uchiyama, Nobuhiko Nomura.
Low concentrations of ethanol stimulate biofilm formation in Pseudomonas aeruginosa.
Bioscience, Biotechnology, and Biochemistry 78:178-181 (2014)
2013
Shin Haruta, Takehito Yoshida, Yoshiteru Aoi, Kunihiko Kaneko, Hiroyuki Futamata*.
Challenge for complex microbial ecosystems: combination of experimental approaches with mathematical modeling.
Microbes and Environments 28:285-294 (2013)
Owen Rubaba, Yoko Araki, Shuji Yamamoto, Kei Suzuki, Hisatoshi Sakamoto, Atsunori Matsuda, and Hiroyuki Futamata*.
Performance comparison of microbial fuel cells equipped with different membrane electrode assemblies.
Journal of Physics 433:012022 (2013)
Owen Rubaba, Yoko Araki, Shuji Yamamoto, Kei Suzuki, Hisatoshi Sakamoto, Atsunori Matsuda, and Hiroyuki Futamata*.
Electricity producing property and bacterial community structure in microbial fuel cells equipped with membrane electrode assembly.
Journal of Bioscience and Bioengineering 116:106-113 (2013)
Hiroyuki Futamata*, Orianna Bretschger, Andrea Cheung, Jinjun Kan, Rubaba Owen, Kenneth H. Nealson
Adaptation of soil microbes during establishment of microbial fuel cell consortia with lactate.
Journal of Bioscience and Bioengineering 115:58-63 (2013)
Yosuke Tashiro, Yutaka Yawata, Masanori Toyofuku, Hiroo Uchiyama, Nobuhiko Nomura.
Interspecies interaction between Pseudomonas aeruginosa.
Microbes and Environments 28:13-24 (2013)
＜Preprint＞
Hidehiro Ishizawa*, Rikuya Umemoto, Nanoka Yoshida, Miki Furuya, Yosuke Tashiro, Daisuke Inoue, Michihiko Ike, Masahiro Takeo, Hiroyuki Futamata. 2026. Competition-induced metabolic switching governs the interaction network in plant microbiome assembly. bioRxiv preprint doi: https://doi.org/10.64898/2026.01.26.701895; this version posted January 27, 2026.
Yui Arashi, Hiroki Mochihara, Hiroko Kubota, Kei Suzuki, Yusuke Chiba, Yutaka Kato, Toshihiro Kogure, Ryota Moriuchi, Hideo Dohra, Yosuke Tashiro, and Hiroyuki Futamata*. 2023. Rechargeable Biomineral Induced by Sulfate-reducing Bacterium Cupidesulfovibrio Strain HK-II. bioRxiv Doi: https://doi.org/10.1101/2023.08.07.552368 (The Preprint Server for Biology)
Ishizawa, H., Tashiro, Y., Inoue, D., Ike, M., Futamata, H. 2023. Learning beyond-pairwise interactions enables the bottom-up prediction of microbial community structure. bioRxiv DOI: 10.1101/2023.07.05.546222