Updated on 2025/06/11

Information

 

写真a

 
SUZUKI KENSHI
 
Organization
Faculty of Agriculture Department of Bioscience and Biotechnology Assistant Professor
Graduate School of Bioresource and Bioenvironmental Sciences Department of Bioscience and Biotechnology（Concurrent）
School of Agriculture Department of Bioresource and Bioenvironment（Concurrent）
Title
Assistant Professor
Homepage

Research Areas

  • Life Science / Applied microbiology

  • Environmental Science/Agriculture Science / Conservation of biological resources

Degree

  • 博士（工学） （ 2019.9 Shizuoka University ）

Research History

  • Kyushu University Faculty of Agriculture Department of Bioscience and Biotechnology  Assistant Professor 

    2025.1 - Present

  • The University of Tokyo Graduate School of Agricultural and Life Sciences Specially Appointed Assistant Professor 

    2021.4 - 2024.12

  • The University of Tokyo 生物生産工学研究センター Academic Researcher 

    2020.4 - 2021.3

  • Shizuoka University Research Institute of Green Science and Technology Academic Researcher 

    2019.10 - 2020.3

Education

  • Shizuoka University   創造科学技術大学院  

    2015.4 - 2019.9

  • Shizuoka University   Graduate School of Engineering  

    2013.4 - 2015.3

  • Shizuoka University   Faculty of Engineering  

    2009.4 - 2013.3

Research Interests・Research Keywords

  • Research theme： Control of phenotypic heterogeneity of microorganism

    Keyword： phenotypic heterogeneity, metabolic network

    Research period： 2019.4 - Present

  • Research theme： Dynamics and control of the function of microbial community

    Keyword： 複合微生物群、微生物間相互作用、代謝ネットワーク

    Research period： 2015.4 - Present

  • Research theme： Bio-degradation and Bio-production using microbes

    Keyword： 難分解性化合物、微生物生理物質、微生物間相互作用

    Research period： 2013.4 - Present

Awards

  • 日本微生物生態学会第33回大会 Best prezenter Award

    2019  

  • ASMmicrobe2018 Outstanding Abstract Award

    2018  

  • 創造科学技術大学院長賞

    2018   静岡大学  

  • 環境微生物系合同大会2017 優秀ポスター賞

    2017  

Papers

  • Stable States of a Microbial Community Are Formed by Dynamic Metabolic Networks with Members Functioning to Achieve Both Robustness and Plasticity Invited Reviewed

    Masahiro Honjo, Kenshi Suzuki, Junya Katai, Yosuke Tashiro, Tomo Aoyagi, Tomoyuki Hori, Takashi Okada, Yasuhisa Saito, Hiroyuki Futamata

    Microbes and Environments   39 ( 1 )   n/a - n/a   2024   （ ISSN:1342-6311 eISSN:1347-4405 ）

    　More details

    Publishing type：Research paper (scientific journal)   Publisher：Japanese Society of Microbial Ecology  

    DOI： 10.1264/jsme2.me23091

  • Metabolic Pathway of Phenol Degradation of a Cold-Adapted Antarctic Bacteria, Arthrobacter sp. Invited Reviewed

    Gillian Li Yin Lee, Nur Nadhirah Zakaria, Hiroyuki Futamata, Kenshi Suzuki, Azham Zulkharnain, Noor Azmi Shaharuddin, Peter Convey, Khadijah Nabilah Mohd Zahri, Siti Aqlima Ahmad

    Catalysts   12 ( 11 )   2022.11   （ eISSN:2073-4344 ）

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    Publishing type：Research paper (scientific journal)  

    DOI： 10.3390/catal12111422

    Scopus

  • Coexisting mechanisms of bacterial community are changeable even under similar stable conditions in a chemostat culture. Invited Reviewed

    Fatma Azwani Abdul Aziz, Kenshi Suzuki, Masahiro Honjo, Koki Amano, Abd Rahman Jabir Bin Mohd Din, Yosuke Tashiro, Hiroyuki Futamata

    Journal of bioscience and bioengineering   131 ( 1 )   77 - 83   2021.1

    　More details

    Language：English   Publishing type：Research paper (scientific journal)  

    The coexisting mechanism of a synthetic bacterial community (SBC) was investigated to better understand how to manage microbial communities. The SBC was constructed with three kinds of phenol-utilizing bacteria, Pseudomonas sp. LAB-08, Comamonas testosteroni R2, and Cupriavidus sp. P-10, under chemostat conditions supplied with phenol as a sole carbon and energy source. Population densities of all strains were monitored by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase. Although the supply of phenol was stopped to allow perturbation in the SBC, all of the strains coexisted and the degradation of phenol was maintained for more than 800 days. The qPCR analyses showed that strains LAB-08 and R2 became dominant simultaneously, whereas strain P-10 was a minor population. This phenomenon was observed before and after the phenol-supply stoppage. The kinetic parameters for phenol of the SBC changed before and after the phenol-supply stoppage, which suggests a change in functional roles of strains in the SBC. Transcriptional levels of phenol hydroxylase and catechol dioxygenases of three strains were monitored by reverse-transcription qPCR (RT-qPCR). The RT-qPCR analyses revealed that all strains shared phenol and survived independently before the phenol-supply stoppage. After the stoppage, strain P-10 would incur the cost for degradation of phenol and catechol, whereas strains LAB-08 and R2 seemed to be cheaters using metabolites, indicating the development of the metabolic network. These results indicated that it is important for the management and redesign of microbial communities to understand the metabolism of bacterial communities.

    DOI： 10.1016/j.jbiosc.2020.09.009

    PubMed

  • Imbalance in Carbon and Nitrogen Metabolism in <i>Comamonas testosteroni</i> R2 Is Caused by Negative Feedback and Rescued by L-arginine Invited Reviewed

    Abd Rahman Jabir Mohd Din, Kenshi Suzuki, Masahiro Honjo, Koki Amano, Tomoka Nishimura, Ryota Moriuchi, Hideo Dohra, Hidehiro Ishizawa, Motohiko Kimura, Yosuke Tashiro, Hiroyuki Futamata

    Microbes and Environments   36 ( 4 )   n/a - n/a   2021   （ ISSN:1342-6311 eISSN:1347-4405 ）

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    Publishing type：Research paper (scientific journal)   Publisher：Japanese Society of Microbial Ecology  

    DOI： 10.1264/jsme2.me21050

  • Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07. Invited Reviewed International journal

    Gillian Li Yin Lee, Nur Nadhirah Zakaria, Peter Convey, Hiroyuki Futamata, Azham Zulkharnain, Kenshi Suzuki, Khalilah Abdul Khalil, Noor Azmi Shaharuddin, Siti Aisyah Alias, Gerardo González-Rocha, Siti Aqlima Ahmad

    International journal of molecular sciences   21 ( 24 )   2020.12

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    Language：English   Publishing type：Research paper (scientific journal)  

    Study of the potential of Antarctic microorganisms for use in bioremediation is of increasing interest due to their adaptations to harsh environmental conditions and their metabolic potential in removing a wide variety of organic pollutants at low temperature. In this study, the psychrotolerant bacterium Rhodococcus sp. strain AQ5-07, originally isolated from soil from King George Island (South Shetland Islands, maritime Antarctic), was found to be capable of utilizing phenol as sole carbon and energy source. The bacterium achieved 92.91% degradation of 0.5 g/L phenol under conditions predicted by response surface methodology (RSM) within 84 h at 14.8 °C, pH 7.05, and 0.41 g/L ammonium sulphate. The assembled draft genome sequence (6.75 Mbp) of strain AQ5-07 was obtained through whole genome sequencing (WGS) using the Illumina Hiseq platform. The genome analysis identified a complete gene cluster containing catA, catB, catC, catR, pheR, pheA2, and pheA1. The genome harbours the complete enzyme systems required for phenol and catechol degradation while suggesting phenol degradation occurs via the β-ketoadipate pathway. Enzymatic assay using cell-free crude extract revealed catechol 1,2-dioxygenase activity while no catechol 2,3-dioxygenase activity was detected, supporting this suggestion. The genomic sequence data provide information on gene candidates responsible for phenol and catechol degradation by indigenous Antarctic bacteria and contribute to knowledge of microbial aromatic metabolism and genetic biodiversity in Antarctica.

    DOI： 10.3390/ijms21249363

    PubMed

  • Draft Genome Sequence of Phenol-Degrading Variovorax boronicumulans Strain c24. Invited Reviewed International journal

    Fatma Azwani Abdul Aziz, Kenshi Suzuki, Koki Amano, Ryota Moriuchi, Hideo Dohra, Yosuke Tashiro, Hiroyuki Futamata

    Microbiology resource announcements   9 ( 37 )   2020.9

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    Language：English   Publishing type：Research paper (scientific journal)  

    We report the draft genome sequence of Variovorax boronicumulans strain c24, which was isolated from a soil-inoculated chemostat culture amended with phenol as a sole carbon and energy source. The genome data will provide insights into phenol and other xenobiotic compound degradation mechanisms for bioremediation applications.

    DOI： 10.1128/MRA.00597-20

    PubMed

  • Draft Genome Sequence of Phenol-Degrading Variovorax boronicumulans Strain HAB-30. Invited Reviewed International journal

    Fatma Azwani Abdul Aziz, Kenshi Suzuki, Ryota Moriuchi, Hideo Dohra, Yosuke Tashiro, Hiroyuki Futamata

    Microbiology resource announcements   9 ( 7 )   2020.2

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    Language：English   Publishing type：Research paper (scientific journal)  

    We report the draft genome sequence of Variovorax boronicumulans strain HAB-30, which was isolated from a phenol-degrading chemostat culture. This strain contains genes encoding a multicomponent type of phenol hydroxylase, with degradation pathways for catechol and other aromatic compounds. The genome sequence will be useful for understanding the metabolic pathways involved in phenol degradation.

    DOI： 10.1128/MRA.01478-19

    PubMed

  • Draft Genome Sequence of the Phenol-Degrading Bacterium Cupriavidus sp. Strain P-10, Isolated from Trichloroethene-Contaminated Aquifer Soil. Invited Reviewed International journal

    Kenshi Suzuki, Fatma A A Aziz, Masahiro Honjo, Tomoka Nishimura, Kensei Masuda, Ayaka Minoura, Yuki Kudo, Ryota Moriuchi, Hideo Dohra, Yosuke Tashiro, Hiroyuki Futamata

    Microbiology resource announcements   7 ( 18 )   2018.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    A batch culture was enriched on phenol with trichloroethene-contaminated aquifer soil as an inoculum. Cupriavidus sp. strain P-10 was isolated from the culture using a diluted plating method. Here, we report the draft genome sequence and annotation of strain P-10, which provides insights into the metabolic processes of phenol degradation.

    DOI： 10.1128/MRA.01009-18

    PubMed

  • Draft Genome Sequence of Comamonas testosteroni R2, Consisting of Aromatic Compound Degradation Genes for Phenol Hydroxylase. Invited Reviewed International journal

    Fatma Azwani, Kenshi Suzuki, Masahiro Honjyo, Yosuke Tashiro, Hiroyuki Futamata

    Genome announcements   5 ( 36 )   2017.9

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    Language：English   Publishing type：Research paper (scientific journal)  

    Comamonas testosteroni strain R2 was isolated from a continuous culture enriched by a low concentration of phenol-oxygenating activities with low K
    s
    values (below 1 μM). The draft genome sequence of C. testosteroni strain R2 reported here may contribute to determining the phenol degradation gene cluster.

    DOI： 10.1128/genomeA.00875-17

    PubMed

  • Draft Genome Sequence of Pseudomonas sp. LAB-08 Isolated from Trichloroethene-Contaminated Aquifer Soil. Invited Reviewed International journal

    Kenshi Suzuki, Fatma A A Aziz, Yuma Inuzuka, Yosuke Tashiro, Hiroyuki Futamata

    Genome announcements   4 ( 5 )   2016.9

    　More details

    Language：English   Publishing type：Research paper (scientific journal)  

    Pseudomonas sp. LAB-08 was isolated from a phenol-fed bioreactor constructed with contaminated aquifer soil as the inoculum. Strain LAB-08 utilized phenol as a sole carbon and energy source. Here, we report the genome sequence and annotation of Pseudomonas sp. LAB-08.

    DOI： 10.1128/genomeA.00948-16

    PubMed

  • Interspecies interactions are an integral determinant of microbial community dynamics. Invited Reviewed International journal

    Fatma A A Aziz, Kenshi Suzuki, Akihiro Ohtaki, Keita Sagegami, Hidetaka Hirai, Jun Seno, Naoko Mizuno, Yuma Inuzuka, Yasuhisa Saito, Yosuke Tashiro, Akira Hiraishi, Hiroyuki Futamata

    Frontiers in microbiology   6   1148 - 1148   2015

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    Language：English   Publishing type：Research paper (scientific journal)  

    This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and "interspecies interaction," were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, "interspecies interaction," a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem.

    DOI： 10.3389/fmicb.2015.01148

    PubMed

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Presentations

MISC

  • 微生物の適応と多種共存

    2019

  • American Society for Microbiology 学会　ASM Microbe2018 参加報告

    2018.3

Professional Memberships

  • 日本農芸化学会

  • 環境バイオテクノロジー学会

  • 日本生物工学会

  • 日本微生物生態学会

Other

  • 日本微生物生態学会2024年度大会　シンポジウム企画

    2024.10

  • 日本微生物生態学会2023年度大会　シンポジウム企画

    2023.11

Research Projects

  • 複合微生物群における種多様性と機能的頑健性

    Grant number：JPMJAX22BD  2022.10 - 2025.3

    科学技術振興機構  戦略的な研究開発の推進 戦略的創造研究推進事業 ACT-X 

  • 複合微生物群における機能の最適化と定量的安定性評価

    Grant number：24K01776  2024.4 - 2027.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    鈴木 研志, 岡橋 伸幸

    　 More details

    Grant type：Scientific research funding

    本研究では微生物利用技術の確立に向けて、複合微生物群の制御を可能にするための枠組みの構築を目指し、微生物間に形成される代謝ネットワークを個体群・1細胞レベルで解析することを目的とする。そのために、個体群でありながら複合微生物群様の振る舞いをする微生物を用いる。基質を積極的に分解する細胞と代謝経路を部分的に破壊した変異株を組み合わせ、増殖量や分解速度が増大・減少するものをマイクロドロップレット技術でスクリーニングする。得られた情報とゲノム情報から形成されたネットワークを予測し実証する。以上の結果から最安定な代謝状態を熱力学の観点から解析し定量的に評価する。

  • Challenge to control environmental microorganisms based on analysis of dissolved organic matter in water

    Grant number：23K17329  2023.6 - 2026.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Challenging Research (Pioneering)

    栗栖 太, 春日 郁朗, 飛野 智宏, 鈴木 研志, 高梨 啓和

    　 More details

    Grant type：Scientific research funding

    水道水中では、滞留時間の経過とともに残留塩素が消費されると微生物が再増殖する。微生物は水道水に含まれる有機物を利用して増殖していることから、増殖に利用される有機物を特定することで、有機物を制御して再増殖を制御する技術につなげることができる。また、微生物による廃水処理において、処理される有機物と微生物種の関係はそれぞれ個別にはほとんど理解されていない。安定して処理を制御するために、それぞれの微生物種が利用する有機物を明らかにしていくことは本質的に重要な技術開発基盤となる。本研究では、精密質量分析計による有機物分析技術を最大限に活用し、微生物が利用する有機物を明らかにしていく。
    今年度においては、環境中において特定の菌株が利用する基質の探索方法の開発として、河川水中において増殖が懸念されている大腸菌をモデルケースとして、河川水中で利用する増殖基質の探索と同定を行った。増殖前後、および大腸菌植種の有無の差分について、高分解能精密質量分析計であるHPLC－四重極－Orbitrapハイブリッド型質量分析計で試料を分析し、増殖によって利用された有機物の候補を得た。これまでに代表者らが行ってきた結果とともに、候補となる有機物の構造推定を行い、ヒドロキシデカン酸をはじめとする物質の同定に成功した。
    さらにより貧栄養環境における検討として、水道水中における日和見病原細菌の１つとして懸念されている緑膿菌の増殖基質の特定を試みた。河川水よりも貧栄養条件下での実験を行う上で、水道水中に残存する細菌をいかに除く（もしくは不活化させる）かが課題となるため、除菌／不活化方法の検討を行った。無機膜で複数回ろ過したうえで、低温滅菌を行う手法を確立し、非植種の対照系において菌の増殖を最低限に抑えることに成功した。
    得られた分析結果の一部について、得られた増殖基質候補について、MS/MS分析による構造推定を試みた。候補となる異性体について、量子化学計算を行うことでMS/MSスペクトルの推定を行い、構造推定の妥当性を検証した。
    また、モデル微生物群を用いた代謝物の解析では、相互分配される代謝物を検出しその動態と微生物群集構造の変化を比較し、個々の微生物の関係性を予測した。さらに不均質な微生物個体群を用いて細胞間でやり取りされる代謝物を推定した。
    当初初年度に計画していた内容について、ほぼ予定通り進めることができた。ただし、下水処理場に設置予定であったパイロットプラントは、下水処理場当局の都合により設置が遅れている。
    貧栄養環境である水道水中での微生物再増殖現象について、研究を行うための準備が整ったことから、特に緑膿菌を用いて再増殖試験を実施する。まｔ、下水処理場内における試料採取と試験を実施し、下水処理微生物と有機物分析の解析を行う。また、モデル微生物生態系における代謝ネットワークについても、引き続き検討を進めていく。今年度前半に研究チーム会合を実施し、それぞれの研究内容について有機的につながっていくようにする。

  • Self-organization and functional stability of microbial community

    Grant number：22K14906  2022.4 - 2024.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Early-Career Scientists

    Suzuki Kenshi

    　 More details

    Grant type：Scientific research funding

    Analysis of metabolite cross-feeding within the Comamonas thiooxydans R2 population revealed the establishment of a metabolic network capable of sharing at least 51 metabolites. Furthermore, phenol, supplied to the culture as the sole carbon source, was degraded by a part of cells, and other cells probably utilized metabolites from phenol-degrading cells. It was suggested that the population of strain R2 was maintained while the network structure was altered. Investigation of the effects of metabolites on the growth of strain R2 revealed that enhancement or inhibition of growth was observed. Thus, these metabolites would alter the metabolic state of individual cells, resulting in a heterogeneous population. A model microbial community using five strains was constructed to analyze the metabolic network in a more complex microbial community. Metabolite analysis revealed that more than 150 metabolites were shared among the five strains.

  • The stability and maintenance mechanisms of the microbial ecosystem

    Grant number：20K15544  2020.4 - 2023.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Early-Career Scientists

    Suzuki Kenshi

    　 More details

    Grant type：Scientific research funding

    The maintenance mechanisms of a microbial ecosystem and its stability were investigated in this study. Since the natural microbial community is too complex to analyze, five different phenol-degrading bacteria were incubated in phenol-fed chemostat culture as a model microbial community. Several equilibrium points of microbial communities were observed when the five strains were sequentially inoculated with several patterns. RNA-seq analysis suggested that phenol was occupied by the dominant strain and others utilized metabolites from the dominant strain when the community structure stabilized at an early incubation phase. On the other hand, it was more competitive for phenol in unstable culture. These results suggested that the emergence of metabolic network among microbial strains were significantly important in stabilizing a microbial community structure. Thus, the design of the metabolic network is essential to design and to control microbial community.

  • ⾼効率な嫌気的ベンゼン分解を実現する最適微⽣物群の構築

    Grant number：G-2022-3-057 

    公益財団法⼈発酵研究所  ⼀般研究助成 

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Educational Activities

  • 合成生物学（農学部）
    システム生物工学特論（大学院生物資源環境科学府）

Class subject

  • システム生物工学特論

    2025.4 - Present  

  • 合成生物学

    2025.4 - Present