Ph.D., Tokyo Institute of Technology

microbiome

microbial interactions

Antibiotic resistance

Protoplast fusion

Metabolic engineering

RNase

Escherichia coli

Corynebacterium glutamicum

Laboratory evolution

Life Science, Bacteriology

Life Science, Evolutionary biology

Life Science, Applied microbiology

Life Science, System genome science

Bachelor's degree program, School of Agriculture

Master's degree program, Graduate School of Agriculture

Doctoral (PhD) degree program, Graduate School of Agriculture

Mar. 2026, Japan Society for Bioscience, Biotechnology, and Agrochemistry, JSBBA Award for Young Scientists
進化の方向性解明に基づく微生物機能の予測的制御と応用
Tomoya Maeda

Jan. 2021, RIKEN, Presentation award Biology Prize
Tomoya Maeda

Mar. 2012, 生物工学研究会, 鎌田泉博士論文賞
前田 智也

Standardized and batch effect-independent technologies enable global collaboration in microbiome research
Muzi Ge; Tomoya Maeda; Jingdi Li; Maryam Chaib De Mares; Emmanuel George Kifaro; Gizachew Haile Gidamo; Katsuyuki Shiroguchi; Andrew H Moeller; Zhibin Zhang; Jianshi Jin
The ISME Journal, Oxford University Press (OUP), 13 May 2026, [Peer-reviewed]
English, Scientific journal

Identification and characterization of Dorea ammoniilytica as a novel deoxycholic acid-producing bacterial species in the human gut microbiota.
Ni Wayan Eka Putri Gayatri Kastawa; Yasuhiro Gotoh; Isaiah Song; Tomoya Maeda; Satoru Fukiya
Bioscience, biotechnology, and biochemistry, 18 Dec. 2025, [Peer-reviewed], [International Magazine]
English, Scientific journal, Deoxycholic acid (DCA), a representative secondary bile acid, is produced by specific gut bacteria through bile acid 7α-dehydroxylation of cholic acid, catalyzed by enzymes encoded in the bai gene operon. Exploration of diversity and functional characteristics of DCA-producing bacteria is crucial for understanding the "in vivo" mechanisms of DCA production in the human intestine. Here, we have identified and characterized two strains derived from human feces as a novel DCA-producing species, Dorea ammoniilytica. These strains harbored segmented bai gene operons in their complete genome sequences and showed high DCA production activity from cholic acid in the culture experiments. Biochemical, phylogenetic, and average nucleotide identity analyses categorized them as D. ammoniilytica, which belongs to a distinct lineage from other known DCA producers and Dorea species. These findings expand the diversity of secondary bile acid-producing bacteria in the human gut microbiota and provide clues for clarifying the in vivo DCA production mechanisms.

EASY-edit: a toolbox for high-throughput single-step custom genetic editing in bacteria.
Maxence Lejars; Tomoya Maeda; Maude Guillier
Nucleic acids research, 53, 17, 05 Sep. 2025, [Peer-reviewed], [International Magazine]
English, Scientific journal, Targeted gene editing can be achieved using CRISPR-Cas9-assisted recombineering. However, high-efficiency editing requires careful optimization for each locus to be modified, which can be tedious and time-consuming. In this work, we developed a simple, fast and cheap method: Engineered Assembly of SYnthetic operons for targeted editing (EASY-edit) in Escherichia coli. Highly efficient editing of the different constitutive elements of the operons can be achieved by using a set of optimized guide RNAs and single- or double-stranded DNA repair templates carrying relatively short homology arms. This facilitates the construction of multiple genetic tools, including mutant libraries or reporter genes. EASY-edit is also highly modular, as we provide alternative and complementary versions of the operon inserted in three loci which can be edited iteratively and easily combined. As a proof of concept, we report the construction of several fusions with reporter genes confirming known post-transcriptional regulation mechanisms and the construction of saturated and unbiased mutant libraries. In summary, the EASY-edit system provides a flexible genomic expression platform that can be used both for the understanding of biological processes and as a tool for bioengineering applications.

EASY-CRISPR: a toolbox for high-throughput single-step custom genetic editing in bacteria
Maxence Lejars; Tomoya Maeda; Maude Guillier
bioRxiv, Cold Spring Harbor Laboratory, 20 Mar. 2025
Abstract

Targeted gene editing can be achieved using CRISPR/Cas9-assisted recombineering. However, high-efficiency editing requires careful optimization for each locus to be modified which can be tedious and time-consuming. In this work, we developed a simple, fast and cheap method for theEditing andAssembly ofSYnthetic operons using CRISPR/Cas9-assisted recombineering (EASY-CRISPR) inEscherichia coli. Highly efficient editing of the different constitutive elements of the operons can be achieved by using a set of optimized guide RNAs and single- or double-stranded DNA repair templates carrying relatively short homology arms. This facilitates the construction of multiple genetic tools, including mutant libraries or reporter genes. EASY-CRISPR is also highly modular, as we provide alternative and complementary versions of the operon inserted in three loci which can be edited iteratively and easily combined. As a proof of concept, we report the construction of several fusions with reporter genes confirming known post-transcriptional regulation mechanisms and the construction of saturated and unbiased mutant libraries.

In summary, the EASY-CRISPR system provides a flexible genomic expression platform that can be used both for the understanding of biological processes and as a tool for bioengineering applications.

Methodology and Application of Adaptive Laboratory Evolution for Antimicrobial Resistance and Bioproduction
前田智也; 古澤力
Kagaku to Seibutsu, 63, 3, 114, 122, 01 Mar. 2025, [Peer-reviewed], [Invited], [Lead author, Corresponding author]
Japanese

Improved fermentative gamma-aminobutyric acid production from glucose by the inactivation of respiratory chain components NDH-I and Cytbo₃ in Escherichia coli.
Hiroki Wakahara; Takuya Mizokoshi; Kotaro Yamagami; Satoru Fukiya; Atsushi Yokota; Tomoya Maeda
Journal of bioscience and bioengineering, 07 Sep. 2024, [Peer-reviewed], [Last author, Corresponding author], [Domestic magazines]
English, Scientific journal, Gamma-aminobutyric acid (GABA), which is synthesized from l-glutamic acid via glutamate decarboxylase (Gad), is used as food, supplements, and biodegradable plastics. Our previous study demonstrated an Escherichia coli mutant (ΔΔ) strain, lacking type I NADH dehydrogenase (NDH-I) and cytochrome bo3 oxidase (Cytbo3), produced 7 g/L glutamic acid on MS1 glucose-minimal medium. In this study, the ΔΔ strain was used for improving GABA production. A plasmid (pMBL19-gadB') expressing a mutated E. coli GadB (Glu89Gln/Δ452-466), retaining activity at neutral pH, was introduced into the ΔΔ strain and its parent strain (W1485). The ΔΔ strain carrying pMBL19-gadB' exhibited a twofold increase in GABA production compared to the W1485 strain carrying pMBL19-gadB'. Deleting the C-terminal (Δ471-511) of GadC antiporter in the ΔΔ strain further improved GABA yield by 1.5 g/L when cultured in MS1 glucose-minimal medium. On the other hand, a large amount of glutamic acid produced by the ΔΔ strain was not fully converted to GABA, likely due to the inhibition of GadB activity by the accumulation of acetic acid. Although there is room for improvement, these results indicate the efficacy of the ΔNDH-IΔCytbo3 double mutation in augmenting GABA production.

Contributions of the anaplerotic reaction enzymes pyruvate carboxylase and phosphoenolpyruvate carboxylase to l-lysine production in Corynebacterium glutamicum.
Akinobu Shinmori; Zhen Guo; Tomoya Maeda; Satoru Fukiya; Masaru Wada; Atsushi Yokota
Journal of bioscience and bioengineering, 27 Jun. 2024, [Peer-reviewed], [Domestic magazines]
English, Scientific journal, Anaplerotic reactions catalyzed by pyruvate carboxylase (PC) and phosphoenolpyruvate carboxylase (PEPC) have important roles in the production of l-lysine to replenish oxaloacetic acid (OAA) in Corynebacterium glutamicum. However, the relative contributions of these enzymes to l-lysine production in C. glutamicum are not fully understood. In this study, using a parent strain (P) carrying a feedback inhibition-resistant aspartokinase with the T311I mutation, we constructed a PC gene-deleted mutant strain (PΔPC) and a PEPC gene-deleted mutant strain (PΔPEPC). Although the growth of both mutant strains was comparable to the growth of strain P, the maximum l-lysine production in strains PΔPC and PΔPEPC decreased by 14% and 49%, respectively, indicating that PEPC strongly contributed to OAA supply. l-Lysine production in strain PΔPC slightly decreased during the logarithmic phase, while production during the early stationary phase was comparable to production in strain P. By contrast, strain PΔPEPC produced l-lysine in an amount comparable to the production of strain P during the logarithmic phase; l-lysine production after the early stationary phase was completely stopped in strain PΔPEPC. These results indicate that OAA is supplied by both PC and PEPC during the logarithmic phase, while only PEPC can continuously supply OAA after the logarithmic phase.

Laboratory Evolution of Antimicrobial Resistance in Bacteria to Develop Rational Treatment Strategies
Tomoya Maeda; Chikara Furusawa
Antibiotics, 13, 1, 94, 94, MDPI AG, 18 Jan. 2024, [Peer-reviewed], [Invited], [Lead author, Corresponding author]
Scientific journal, Laboratory evolution studies, particularly with Escherichia coli, have yielded invaluable insights into the mechanisms of antimicrobial resistance (AMR). Recent investigations have illuminated that, with repetitive antibiotic exposures, bacterial populations will adapt and eventually become tolerant and resistant to the drugs. Through intensive analyses, these inquiries have unveiled instances of convergent evolution across diverse antibiotics, the pleiotropic effects of resistance mutations, and the role played by loss-of-function mutations in the evolutionary landscape. Moreover, a quantitative analysis of multidrug combinations has shed light on collateral sensitivity, revealing specific drug combinations capable of suppressing the acquisition of resistance. This review article introduces the methodologies employed in the laboratory evolution of AMR in bacteria and presents recent discoveries concerning AMR mechanisms derived from laboratory evolution. Additionally, the review outlines the application of laboratory evolution in endeavors to formulate rational treatment strategies.

Inference of Fitness Landscape Based on Multi-Dimensional Phenotype Measurements of Escherichia coli
Chikara FURUSAWA; Junichiro IWASAWA; Tomoya MAEDA
Seibutsu Butsuri, 63, 5, 263, 265, Biophysical Society of Japan, 2023
Scientific journal

Adaptive Laboratory Evolution of Microorganisms: Methodology and Application for Bioproduction.
Takashi Hirasawa; Tomoya Maeda
Microorganisms, 11, 1, 29 Dec. 2022, [Peer-reviewed], [Invited], [International Magazine]
English, Scientific journal, Adaptive laboratory evolution (ALE) is a useful experimental methodology for fundamental scientific research and industrial applications to create microbial cell factories. By using ALE, cells are adapted to the environment that researchers set based on their objectives through the serial transfer of cell populations in batch cultivations or continuous cultures and the fitness of the cells (i.e., cell growth) under such an environment increases. Then, omics analyses of the evolved mutants, including genome sequencing, transcriptome, proteome and metabolome analyses, are performed. It is expected that researchers can understand the evolutionary adaptation processes, and for industrial applications, researchers can create useful microorganisms that exhibit increased carbon source availability, stress tolerance, and production of target compounds based on omics analysis data. In this review article, the methodologies for ALE in microorganisms are introduced. Moreover, the application of ALE for the creation of useful microorganisms as cell factories has also been introduced.

Analysis of the evolution of resistance to multiple antibiotics enables prediction of the Escherichia coli phenotype-based fitness landscape.
Junichiro Iwasawa; Tomoya Maeda; Atsushi Shibai; Hazuki Kotani; Masako Kawada; Chikara Furusawa
PLoS biology, 20, 12, e3001920, Dec. 2022, [Peer-reviewed], [International Magazine]
English, Scientific journal, The fitness landscape represents the complex relationship between genotype or phenotype and fitness under a given environment, the structure of which allows the explanation and prediction of evolutionary trajectories. Although previous studies have constructed fitness landscapes by comprehensively studying the mutations in specific genes, the high dimensionality of genotypic changes prevents us from developing a fitness landscape capable of predicting evolution for the whole cell. Herein, we address this problem by inferring the phenotype-based fitness landscape for antibiotic resistance evolution by quantifying the multidimensional phenotypic changes, i.e., time-series data of resistance for eight different drugs. We show that different peaks of the landscape correspond to different drug resistance mechanisms, thus supporting the validity of the inferred phenotype-fitness landscape. We further discuss how inferred phenotype-fitness landscapes could contribute to the prediction and control of evolution. This approach bridges the gap between phenotypic/genotypic changes and fitness while contributing to a better understanding of drug resistance evolution.

A manually curated compendium of expression profiles for the microbial cell factory Corynebacterium glutamicum.
Angela Kranz; Tino Polen; Christian Kotulla; Annette Arndt; Graziella Bosco; Michael Bussmann; Ava Chattopadhyay; Annette Cramer; Cedric-Farhad Davoudi; Ursula Degner; Ramon Diesveld; Raphael Freiherr von Boeselager; Kim Gärtner; Cornelia Gätgens; Tobias Georgi; Christian Geraths; Sabine Haas; Antonia Heyer; Max Hünnefeld; Takeru Ishige; Armin Kabus; Nicolai Kallscheuer; Larissa Kever; Simon Klaffl; Britta Kleine; Martina Kočan; Abigail Koch-Koerfges; Kim J Kraxner; Andreas Krug; Aileen Krüger; Andreas Küberl; Mohamed Labib; Christian Lange; Christina Mack; Tomoya Maeda; Regina Mahr; Stephan Majda; Andrea Michel; Xenia Morosov; Olga Müller; Arun M Nanda; Jens Nickel; Jennifer Pahlke; Eugen Pfeifer; Laura Platzen; Paul Ramp; Doris Rittmann; Steffen Schaffer; Sandra Scheele; Stephanie Spelberg; Julia Schulte; Jens-Eric Schweitzer; Georg Sindelar; Ulrike Sorger-Herrmann; Markus Spelberg; Corinna Stansen; Apilaasha Tharmasothirajan; Jan van Ooyen; Philana van Summeren-Wesenhagen; Michael Vogt; Sabrina Witthoff; Lingfeng Zhu; Bernhard J Eikmanns; Marco Oldiges; Georg Schaumann; Meike Baumgart; Melanie Brocker; Lothar Eggeling; Roland Freudl; Julia Frunzke; Jan Marienhagen; Volker F Wendisch; Michael Bott
Scientific data, 9, 1, 594, 594, 01 Oct. 2022, [Peer-reviewed], [International Magazine]
English, Scientific journal, Corynebacterium glutamicum is the major host for the industrial production of amino acids and has become one of the best studied model organisms in microbial biotechnology. Rational strain construction has led to an improvement of producer strains and to a variety of novel producer strains with a broad substrate and product spectrum. A key factor for the success of these approaches is detailed knowledge of transcriptional regulation in C. glutamicum. Here, we present a large compendium of 927 manually curated microarray-based transcriptional profiles for wild-type and engineered strains detecting genome-wide expression changes of the 3,047 annotated genes in response to various environmental conditions or in response to genetic modifications. The replicates within the 927 experiments were combined to 304 microarray sets ordered into six categories that were used for differential gene expression analysis. Hierarchical clustering confirmed that no outliers were present in the sets. The compendium provides a valuable resource for future fundamental and applied research with C. glutamicum and contributes to a systemic understanding of this microbial cell factory. Measurement(s) Gene Expression Analysis Technology Type(s) Two Color Microarray Factor Type(s) WT condition A vs. WT condition B • Plasmid-based gene overexpression in parental strain vs. parental strain with empty vector control • Deletion mutant vs. parental strain Sample Characteristic - Organism Corynebacterium glutamicum Sample Characteristic - Environment laboratory environment Sample Characteristic - Location Germany.

Multi-dimensional antibiotic resistance time series reveals the phenotype-based fitness landscape for Escherichia coli
Junichiro Iwasawa; Tomoya Maeda; Atsushi Shibai; Hazuki Kotani; Masako Kawada; Chikara Furusawa
24 Aug. 2022

Acceleration of target production in co-culture by enhancing intermediate consumption through adaptive laboratory evolution.
Ryutaro Kawai; Yoshihiro Toya; Kenta Miyoshi; Manami Murakami; Teppei Niide; Takaaki Horinouchi; Tomoya Maeda; Atsushi Shibai; Chikara Furusawa; Hiroshi Shimizu
Biotechnology and bioengineering, 119, 3, 936, 945, 16 Dec. 2021, [Peer-reviewed], [International Magazine]
English, Scientific journal, Co-culture is a promising way to alleviate metabolic burden by dividing the metabolic pathways into several modules and sharing the conversion processes with multiple strains. Since an intermediate is passed from the donor to the recipient via the extracellular environment, it is inevitably diluted. Therefore, enhancing the intermediate consumption rate is important for increasing target productivity. In the present study, we demonstrated the enhancement of mevalonate consumption in Escherichia coli by adaptive laboratory evolution and applied the evolved strain to isoprenol production in an E. coli (upstream: glucose to mevalonate)-E. coli (downstream: mevalonate to isoprenol) co-culture. An engineered mevalonate auxotroph strain was repeatedly sub-cultured in a synthetic medium supplemented with mevalonate, where the mevalonate concentration was decreased stepwise from 100 to 20 µM. In five parallel evolution experiments, all growth rates gradually increased, resulting in five evolved strains. Whole-genome re-sequencing and reverse engineering identified three mutations involved in enhancing mevalonate consumption. After introducing nudF gene for producing isoprenol, the isoprenol-producing parental and evolved strains were respectively co-cultured with a mevalonate-producing strain. At an inoculation ratio of 1:3 (upstream:downstream), isoprenol production using the evolved strain was 3.3 times higher than that using the parental strain.

Laboratory evolution of Mycobacterium on agar plates for analysis of resistance acquisition and drug sensitivity profiles.
Tomoya Maeda; Masako Kawada; Natsue Sakata; Hazuki Kotani; Chikara Furusawa
Scientific reports, 11, 1, 15136, 15136, 23 Jul. 2021, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
English, Scientific journal, Drug-resistant tuberculosis (TB) is a growing public health problem. There is an urgent need for information regarding cross-resistance and collateral sensitivity relationships among drugs and the genetic determinants of anti-TB drug resistance for developing strategies to suppress the emergence of drug-resistant pathogens. To identify mutations that confer resistance to anti-TB drugs in Mycobacterium species, we performed the laboratory evolution of nonpathogenic Mycobacterium smegmatis, which is closely related to Mycobacterium tuberculosis, against ten anti-TB drugs. Next, we performed whole-genome sequencing and quantified the resistance profiles of each drug-resistant strain against 24 drugs. We identified the genes with novel meropenem (MP) and linezolid (LZD) resistance-conferring mutation, which also have orthologs, in M. tuberculosis H37Rv. Among the 240 possible drug combinations, we identified 24 pairs that confer cross-resistance and 18 pairs that confer collateral sensitivity. The acquisition of bedaquiline or linezolid resistance resulted in collateral sensitivity to several drugs, while the acquisition of MP resistance led to multidrug resistance. The MP-evolved strains showed cross-resistance to rifampicin and clarithromycin owing to the acquisition of a mutation in the intergenic region of the Rv2864c ortholog, which encodes a penicillin-binding protein, at an early stage. These results provide a new insight to tackle drug-resistant TB.

Mutational property of newly identified mutagen l-glutamic acid γ-hydrazide in Escherichia coli.
Tomoya Maeda; Atsushi Shibai; Naomi Yokoi; Yumeko Tarusawa; Masako Kawada; Hazuki Kotani; Chikara Furusawa
Mutation research, 823, 111759, 111759, 21 Jul. 2021, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
English, Scientific journal, We previously found that an l-glutamine analog l-glutamic acid γ-hydrazide has high mutagenic activity through the high-throughput laboratory evolution of Escherichia coli. In this study, mutagenicity and mutational property of l-glutamic acid γ-hydrazide were examined by the Ames test and mutation accumulation experiments using E. coli. The Ames test revealed that l-glutamic acid γ-hydrazide showed higher mutagenic activity without metabolic activation than known mutagens 2-aminoanthracene, and cobalt(II) acetate tetrahydrate. This result indicates that l-glutamic acid γ-hydrazide does not require metabolic activation for mutagenic activity in E. coli. Mutation accumulation experiments and whole-genome sequencing analysis revealed the number and spectrum of the accumulated mutations with or without l-glutamic acid γ-hydrazide. In the presence of l-glutamic acid γ-hydrazide, MDS42 strain accumulated 392.3 ± 116.2 point mutations during 30 passages corresponding to 777 generations, while MDS42 strain accumulated 1.5 ± 2.5 point mutations without l-glutamic acid γ-hydrazide during 50 passages corresponding to 1341 generations. The mutational spectrum of l-glutamic acid γ-hydrazide was G/C to A/T transition (82.2 ± 4.3 %) and A/T to G/C transition (17.4 ± 4.3 %). These results indicated that l-glutamic acid γ-hydrazide has a strong mutagenic activity.

Morphological change of coiled bacterium Spirosoma linguale with acquisition of β-lactam resistance.
Tomoya Maeda; Hazuki Kotani; Chikara Furusawa
Scientific reports, 11, 1, 13278, 13278, 24 Jun. 2021, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
English, Scientific journal, Spirosoma linguale is a gram-negative, coiled bacterium belonging to the family Cytophagaceae. Its coiled morphology is unique in contrast to closely related bacteria belonging to the genus Spirosoma, which have a short, rod-shaped morphology. The mechanisms that generate unique cell morphology are still enigmatic. In this study, using the Spirosoma linguale ATCC33905 strain, we isolated β-lactam (cefoperazone and amoxicillin)-resistant clones. These clones showed two different cell morphological changes: relatively loosely curved cells or small, horseshoe-shaped cells. Whole-genome resequencing analysis revealed the genetic determinants of β-lactam resistance and changes in cell morphology. The loose-curved clones commonly had mutations in Slin_5958 genes encoding glutamyl-tRNA amidotransferase B subunit, whereas the small, horseshoe-shaped clones commonly had mutations in either Slin_5165 or Slin_5509 encoding pyruvate dehydrogenase (PDH) components. Two clones, CFP1ESL11 and CFL5ESL4, which carried only one mutation in Slin_5958, showed almost perfectly straight, rod-shaped cells in the presence of amoxicillin. This result suggests that penicillin-binding proteins targeted by amoxicillin play an important role in the formation of a coiled morphology in this bacterium. In contrast, supplementation with acetate did not rescue the growth defect and abnormal cell size of the CFP5ESL9 strain, which carried only one mutation in Slin_5509. These results suggest that PDH is involved in cell-size maintenance in this bacterium.

Relevance of NADH Dehydrogenase and Alternative Two-Enzyme Systems for Growth of Corynebacterium glutamicum With Glucose, Lactate, and Acetate
Tomoya Maeda; Abigail Koch-Koerfges; Michael Bott
Frontiers in Bioengineering and Biotechnology, 8, Frontiers Media SA, 20 Jan. 2021, [Peer-reviewed], [Lead author]
Scientific journal, The oxidation of NADH with the concomitant reduction of a quinone is a crucial step in the metabolism of respiring cells. In this study, we analyzed the relevance of three different NADH oxidation systems in the actinobacterial model organism Corynebacterium glutamicum by characterizing defined mutants lacking the non-proton-pumping NADH dehydrogenase Ndh (Δndh) and/or one of the alternative NADH-oxidizing enzymes, L-lactate dehydrogenase LdhA (ΔldhA) and malate dehydrogenase Mdh (Δmdh). Together with the menaquinone-dependent L-lactate dehydrogenase LldD and malate:quinone oxidoreductase Mqo, the LdhA-LldD and Mdh-Mqo couples can functionally replace Ndh activity. In glucose minimal medium the Δndh mutant, but not the ΔldhA and Δmdh strains, showed reduced growth and a lowered NAD⁺/NADH ratio, in line with Ndh being the major enzyme for NADH oxidation. Growth of the double mutants ΔndhΔmdh and ΔndhΔldhA, but not of strain ΔmdhΔldhA, in glucose medium was stronger impaired than that of the Δndh mutant, supporting an active role of the alternative Mdh-Mqo and LdhA-LldD systems in NADH oxidation and menaquinone reduction. In L-lactate minimal medium the Δndh mutant grew better than the wild type, probably due to a higher activity of the menaquinone-dependent L-lactate dehydrogenase LldD. The ΔndhΔmdh mutant failed to grow in L-lactate medium and acetate medium. Growth with L-lactate could be restored by additional deletion of sugR, suggesting that ldhA repression by the transcriptional regulator SugR prevented growth on L-lactate medium. Attempts to construct a ΔndhΔmdhΔldhA triple mutant were not successful, suggesting that Ndh, Mdh and LdhA cannot be replaced by other NADH-oxidizing enzymes in C. glutamicum.

High-throughput laboratory evolution reveals evolutionary constraints in Escherichia coli
Tomoya Maeda; Junichiro Iwasawa; Hazuki Kotani; Natsue Sakata; Masako Kawada; Takaaki Horinouchi; Aki Sakai; Kumi Tanabe; Chikara Furusawa
Nature Communications, 11, 1, 5970, 5970, Springer Science and Business Media LLC, Nov. 2020, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
English, Scientific journal, Understanding the constraints that shape the evolution of antibiotic resistance is critical for predicting and controlling drug resistance. Despite its importance, however, a systematic investigation of evolutionary constraints is lacking. Here, we perform a high-throughput laboratory evolution of Escherichia coli under the addition of 95 antibacterial chemicals and quantified the transcriptome, resistance, and genomic profiles for the evolved strains. Utilizing machine learning techniques, we analyze the phenotype–genotype data and identified low dimensional phenotypic states among the evolved strains. Further analysis reveals the underlying biological processes responsible for these distinct states, leading to the identification of trade-off relationships associated with drug resistance. We also report a decelerated evolution of β-lactam resistance, a phenomenon experienced by certain strains under various stresses resulting in higher acquired resistance to β-lactams compared to strains directly selected by β-lactams. These findings bridge the genotypic, gene expression, and drug resistance gap, while contributing to a better understanding of evolutionary constraints for antibiotic resistance.

Suppression of antibiotic resistance evolution by single-gene deletion.
Takaaki Horinouchi; Tomoya Maeda; Hazuki Kotani; Chikara Furusawa
Scientific reports, 10, 1, 4178, 4178, 06 Mar. 2020, [Peer-reviewed], [International Magazine]
English, Scientific journal, Antibiotic treatment generally results in the selection of resistant bacterial strains, and the dynamics of resistance evolution is dependent on complex interactions between cellular components. To better characterize the mechanisms of antibiotic resistance and evaluate its dependence on gene regulatory networks, we performed systematic laboratory evolution of Escherichia coli strains with single-gene deletions of 173 transcription factors under three different antibiotics. This resulted in the identification of several genes whose deletion significantly suppressed resistance evolution, including arcA and gutM. Analysis of double-gene deletion strains suggested that the suppression of resistance evolution caused by arcA and gutM deletion was not caused by epistatic interactions with mutations known to confer drug resistance. These results provide a methodological basis for combinatorial drug treatments that may help to suppress the emergence of resistant pathogens by inhibiting resistance evolution.

Complete Genome Sequences of Three Star-Shaped Bacteria, Stella humosa, Stella vacuolata, and Stella Species ATCC 35155
Atsushi Shibai; Tomoya Maeda; Masako Kawada; Hazuki Kotani; Natsue Sakata; Chikara Furusawa
Microbiology Resource Announcements, 8, 32, American Society for Microbiology, 08 Aug. 2019, [Peer-reviewed], [Corresponding author], [International Magazine]
English, Scientific journal, Stella species are unique star-shaped alphaproteobacteria found in various environments. We report the complete genome sequences of three Stella strains, Stella humosa ATCC 43930, Stella vacuolata ATCC 43931, and Stella species ATCC 35155. These are the first complete genome sequences of members of the genus Stella.

High-throughput identification of the sensitivities of an Escherichia coli ΔrecA mutant strain to various chemical compounds.
Maeda T; Horinouchi T; Sakata N; Sakai A; Furusawa C
The Journal of antibiotics, 72, 7, 566, 573, Feb. 2019, [Peer-reviewed], [Lead author, Corresponding author], [Domestic magazines]
English, Scientific journal, Antibiotic resistance is considered a global threat to public health. Adaptive resistance mutations and the acquisition of resistance genes by horizontal gene transfer are known to be facilitated by the RecA-dependent SOS response during antibiotic treatment, making RecA inhibitors promising agents for the prevention of antibiotic resistance. However, the impact of RecA inactivation on antibiotic sensitivities remains unclear. Therefore, in this study, we performed high-throughput screening to determine the minimum inhibitory concentrations (MICs) of 217 chemicals, including both antibiotics and toxic chemicals of unknown drug action, in the wild-type MDS42 and the ΔrecA mutant strains of Escherichia coli. The ΔrecA mutant showed increased sensitivity to DNA-damaging agents, DNA replication inhibitors, and chromate stress, as well as to other chemicals, such as S-(2-aminoethyl)-L-cysteine, L-histidine, ruthenium red, D-penicillamine, carbonyl cyanide 3-chlorophenylhydrazone (CCCP), cerulenin, and L-cysteine. Microarray analysis showed further that the ΔrecA mutant had lower expressions of glnK, nac, and glnLG, which encode nitrogen assimilation regulators, as well as amtB, which encodes an ammonium transporter, compared with the wild type. These findings suggest that the ΔrecA mutation affects not only the SOS response but also amino acid metabolism.

RNase E/G-dependent degradation of metE mRNA, encoding methionine synthase, in Corynebacterium glutamicum
Satoshi Endo; Tomoya Maeda; Takahiro Kawame; Noritaka Iwai; Masaaki Wachi
The Journal of General and Applied Microbiology, 65, 1, 47, 52, Microbiology Research Foundation, 2019, [Peer-reviewed]
Scientific journal

Toward prediction and control of antibiotic-resistance evolution
Chikara Furusawa; Takaaki Horinouchi; Tomoya Maeda
Current Opinion in Biotechnology, 54, 45, 49, Elsevier Ltd, 01 Dec. 2018, [Peer-reviewed]
English

Understanding and engineering alcohol-tolerant bacteria using OMICS technology.
Horinouchi T; Maeda T; Furusawa C
World journal of microbiology & biotechnology, 34, 11, 157, 157, Oct. 2018, [Peer-reviewed], [International Magazine]
English, Scientific journal, Microbes are capable of producing alcohols, making them an important source of alternative energy that can replace fossil fuels. However, these alcohols can be toxic to the microbes themselves, retaring or inhibiting cell growth and decreasing the production yield. One solution is improving the alcohol tolerance of such alcohol-producing organisms. Advances in omics technologies, including transcriptomic, proteomic, metabolomic, and genomic technologies, have helped us understand the complex mechanisms underlying alcohol toxicity, and such advances could assist in devising strategies for engineering alcohol-tolerant strains. This review highlights these advances and discusses strategies for improving alcohol tolerance using omics analyses.

Glutamine-rich toxic proteins GrtA, GrtB and GrtC together with the antisense RNA AsgR constitute a toxin–antitoxin-like system in Corynebacterium glutamicum
Tomoya Maeda; Yuya Tanaka; Masayuki Inui
Molecular Microbiology, 108, 5, 578, 594, Blackwell Publishing Ltd, 01 Jun. 2018, [Peer-reviewed], [Lead author]
English, Scientific journal

Polynucleotide Phosphorylase, RNase E/G, and YbeY Are Involved in the Maturation of 4.5S RNA in Corynebacterium glutamicum
Tomoya Maeda; Yuya Tanaka; Masaaki Wachi; Masayuki Inui
JOURNAL OF BACTERIOLOGY, 199, 5, Mar. 2017, [Peer-reviewed], [Lead author]
English, Scientific journal

RNase III mediated cleavage of the coding region of mraZ mRNA is required for efficient cell division in Corynebacterium glutamicum
Tomoya Maeda; Yuya Tanaka; Norihiko Takemoto; Nagisa Hamamoto; Masayuki Inui
MOLECULAR MICROBIOLOGY, 99, 6, 1149, 1166, Mar. 2016, [Peer-reviewed], [Lead author]
English, Scientific journal

細菌におけるRNaseを介した代謝制御 産業微生物コリネ型細菌を例に
前田智也; 和地正明
化学と生物, 53, 2, 2015

Engineering of Corynebacterium glutamicum for growth and L-lysine and lycopene production from N-acetyl-glucosamine
Christian Matano; Andreas Uhde; Jung-Won Youn; Tomoya Maeda; Lina Clermont; Kay Marin; Reinhard Kraemer; Volker F. Wendisch; Gerd M. Seibold
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 98, 12, 5633, 5643, Jun. 2014, [Peer-reviewed]
English, Scientific journal

L-Glutamate Secretion by the N-Terminal Domain of the Corynebacterium glutamicum NCgl1221 Mechanosensitive Channel
Chikako Yamashita; Ken-ichi Hashimoto; Kosuke Kumagai; Tomoya Maeda; Ayako Takada; Isamu Yabe; Hisashi Kawasaki; Masaaki Wachi
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 77, 5, 1008, 1013, May 2013, [Peer-reviewed]
English, Scientific journal

Glucosamine as carbon source for amino acid-producing Corynebacterium glutamicum
Andreas Uhde; Jung-Won Youn; Tomoya Maeda; Lina Clermont; Christian Matano; Reinhard Kraemer; Volker F. Wendisch; Gerd M. Seibold; Kay Marin
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 97, 4, 1679, 1687, Feb. 2013, [Peer-reviewed]
English, Scientific journal

A role of the transcriptional regulator LldR (NCgl2814) in glutamate metabolism under biotin-limited conditions in Corynebacterium glutamicum
Tanyanut Supkulsutra; Tomoya Maeda; Kosuke Kumagai; Masaaki Wachi
JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY, 59, 3, 207, 214, 2013, [Peer-reviewed]
English, Scientific journal

3 ' Untranslated Region-Dependent Degradation of the aceA mRNA, Encoding the Glyoxylate Cycle Enzyme Isocitrate Lyase, by RNase E/G in Corynebacterium glutamicum
Tomoya Maeda; Masaaki Wachi
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 78, 24, 8753, 8761, Dec. 2012, [Peer-reviewed], [Lead author]
English, Scientific journal

Corynebacterium glutamicum RNase E/G-type endoribonuclease encoded by NCgl2281 is involved in the 5 ' maturation of 5S rRNA
Tomoya Maeda; Masaaki Wachi
ARCHIVES OF MICROBIOLOGY, 194, 2, 65, 73, Feb. 2012, [Peer-reviewed], [Lead author]
English, Scientific journal

The Corynebacterium glutamicum NCgl2281 Gene Encoding an RNase E/G Family Endoribonuclease Can Complement the Escherichia coli rng::cat Mutation but Not the rne-1 Mutation
Tomoya Maeda; Taro Sakai; Masaaki Wachi
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 73, 10, 2281, 2286, Oct. 2009, [Peer-reviewed], [Lead author]
English, Scientific journal

Gene function analysis to elucidate the metabolic mechanism of 1-kestose in Bifidobacterium longum subsp. longum.
樋野優子; 難波有希; 宮下聖也; 前田智也; 吹谷智, 日本乳酸菌学会誌, 35, 2, 2024

Adaptive laboratory evolution of Escherichia coli mutants lacking the enzymes involved in the maintenance of energy and redox balance
山上晃汰郎; 小谷葉月; 吹谷智; 古澤力; 古澤力; 前田智也; 前田智也, 日本生物工学会大会講演要旨集, 76th, 2024

Adaptive laboratory evolution of Corynebacterium glutamicum lacking the enzymes involved in the oxidation of NADH
中堀祥悟; 小谷葉月; 吹谷智; 古澤力; 古澤力; BOTT Michael; 前田智也; 前田智也, 日本生物工学会大会講演要旨集, 76th, 2024

Laboratory evolution of Escherichia coli under antibiotic treatments when embedded in a synthetic gut bacterial community
永野有佳理; 小谷葉月; 吹谷智; 古澤力; 古澤力; 前田智也; 前田智也, 日本農芸化学会大会講演要旨集(Web), 2024, 2024

Analysis of Microbial Interactions through Extensive Serial Culturing of Human Gut Microbiota
前田智也; 前田智也; 吹谷智; 古澤力; 古澤力, 日本農芸化学会大会講演要旨集(Web), 2024, 2024

Laboratory evolution of Escherichia coli under two-drug combinations with sulfamethoxazole/trimethoprim
後藤琉; 小谷葉月; 吹谷智; 古澤力; 古澤力; 前田智也; 前田智也, 日本農芸化学会大会講演要旨集(Web), 2024, 2024

Elucidation of the abundance of deoxycholic acid-producing bacteria in human feces by quantitative PCR analysis
原田恕; 前田智也; 後藤恭宏; 林哲也; 吹谷智, 日本農芸化学会大会講演要旨集(Web), 2024, 2024

Study on 8-Prenylnaringenin production (1) Screening of novel-producing bacteria from human feces and efficient production by co-culture
丹野麻由; 植村圭祐; 大谷彬; 中島賢則; 三橋和也; 山本浩明; 前田智也; 横田篤; 吹谷智, 日本農芸化学会大会講演要旨集(Web), 2024, 2024

Study on 8-Prenylnaringenin production (2) Screening of bacteria to enhance demethylation and its application
大谷彬; 中島賢則; 三橋和也; 丹野麻由; 前田智也; 横田篤; 吹谷智; 山本浩明, 日本農芸化学会大会講演要旨集(Web), 2024, 2024

Elucidation of the metabolic mechanism of 1-Kestose in Bifidobacterium longum subsp. longum
難波有希; 倉持碧海; 山口颯人; 吉田佳鼓; 後藤恭宏; 門田吉弘; 栃尾巧; 小椋義俊; 林哲也; 前田智也; 横田篤; 吹谷智, 日本農芸化学会大会講演要旨集(Web), 2023, 2023

Elucidation of the mechanism of ursocholic acid metabolic relay by the intestinal bacteria
月舘一瑳; 北川更; 前田智也; 吹谷智; 横田篤, 日本農芸化学会大会講演要旨集(Web), 2023, 2023

Discussion about survival strategies of bifidobacteria in the gastrointestinal tract of conventional mice based on the comprehensively-identified bifidobacterial genes using insertion-sequencing
山口颯人; 倉持碧海; 後藤恭宏; 小椋義俊; 前田智也; 林哲也; 横田篤; 吹谷智, 日本農芸化学会大会講演要旨集(Web), 2023, 2023

実験室進化による大腸菌のエネルギー欠乏への潜在的な適応能力の解明
山上晃汰郎; 小谷葉月; 吹谷智; 古澤力; 古澤力; 前田智也; 前田智也, 日本農芸化学会北海道支部学術講演会講演要旨集(Web), 2023, 2023

Establishment of a selective recovery system for bifidobacteria from the gut microbiota
宮下聖也; 吉田佳鼓; 嶋田みな; 前田智也; 横田篤; 吹谷智, 日本生物工学会大会講演要旨集, 75th, 2023

Establishment of a selective recovery system for bifidobacteria from the gut microbiota.
宮下聖也; 吉田佳鼓; 嶋田みな; 前田智也; 横田篤; 吹谷智, 日本乳酸菌学会誌, 33, 2, 2022

Evaluation of the contribution of the bifidobacterial genes involved in amino acid metabolism identified by Insertion Sequencing analysis to colonization and survival in the conventional mouse intestine
井上太貴; 前田智也; 横田篤; 吹谷智, 日本農芸化学会大会講演要旨集(Web), 2022, 2022

大腸菌呼吸鎖変異株ΔNDH-IΔCytbo₃を用いたグルコースからのGABAの高生産
若原洋輝; 溝越拓哉; 前田智也; 吹谷智; 横田篤, 日本農芸化学会東北支部大会プログラム・講演要旨集, 2022, 2022

定量PCR解析によるヒト糞便中のデオキシコール酸生成菌の存在量の解明
原田恕; 前田智也; 横田篤; 吹谷智, 日本農芸化学会東北支部大会プログラム・講演要旨集, 2022, 2022

常在腸内細菌叢からのビフィズス菌の選択的回収系の確立
宮下聖也; 吉田佳鼓; 嶋田みな; 前田智也; 横田篤; 吹谷智, 日本農芸化学会東北支部大会プログラム・講演要旨集, 2022, 2022

Establishment of a selective recovery system for bifidobacteria in the gut microbiota
吉田佳鼓; 嶋田みな; 宮下聖也; 前田智也; 横田篤; 吹谷智, 日本農芸化学会大会講演要旨集(Web), 2022, 2022

Isoprenol production by co-culture with two Escherichia coli strains with consuming different carbon sources
村上茉奈美; 川井隆太郎; 三吉健太; 芝井厚; 前田智也; 堀之内貴明; 古澤力; 古澤力; 戸谷吉博; 清水浩, 日本生物工学会大会講演要旨集, 74th, 2022

Effect of deleting genes encoding glutamate dehydrogenase or glutamate synthase on unusual glutamate production in Escherichia coli mutant defective in respiratory chain enzymes NDH-I and Cytbo₃
今壮太; 前田智也; 吹谷智; 和田大; 横田篤, 日本生物工学会大会講演要旨集, 73rd, 2021

Insertion Sequencing解析により網羅的に同定されたビフィズス菌遺伝子の通常飼育マウス腸内における定着と生存への寄与の評価
井上太貴; 前田智也; 横田篤; 吹谷智, 日本農芸化学会北海道支部学術講演会講演要旨集(Web), 2021, 2021

Genomic mutation analysis of an evolved strain with enhanced mevalonate consumption
村上茉奈美; 川井隆太郎; 前田智也; 堀之内貴明; 古澤力; 古澤力; 戸谷吉博; 清水浩, 日本生物工学会大会講演要旨集, 73rd, 2021

代謝シミュレーションと指向性進化に基づく有用物質生産微生物の開発
戸谷吉博; 川井隆太郎; 三吉健太; 村上茉奈美; 一色衣香; 堀之内貴明; 前田智也; 古澤力; 清水浩, 化学工学会秋季大会研究発表講演要旨集(CD-ROM), 52nd, 2021

Directed evolution for enhancing mevalonate uptake ability in Escherichia coli under a continuous culture
村上茉奈美; 川井隆太郎; 前田智也; 堀之内貴明; 古澤力; 戸谷吉博; 清水浩, 日本農芸化学会大会講演要旨集(Web), 2021, 2021

機械学習と大腸菌実験室進化データを用いた進化拘束の解析
岩澤諄一郎; 前田智也; 堀之内貴明; 古澤力; 古澤力, 日本ゲノム微生物学会年会要旨集, 14th, 2020

Phenotypic and genotypic analysis of laboratory evolution of Escherichia coli: Toward prediction and control of ecosystem evolution
古澤力; 前田智也; 芝井厚, 実験医学, 38, 18, 2020

全自動培養システムを用いた多種ストレス環境下における大腸菌の大規模実験室進化
前田智也; 岩澤諄一郎; 堀之内貴明; 阪田奈津枝; 小谷葉月; 川田正子; 田邊久美; 古澤力; 古澤力, 日本ゲノム微生物学会年会要旨集, 13th, 2019

全自動培養システムを用いた多種ストレス環境下における大腸菌の大規模実験室進化
前田智也; 堀之内貴明; 阪田奈津江; 小谷葉月; 酒井亜希; 田邊久美; 古澤力; 古澤力, 日本ゲノム微生物学会年会要旨集, 12th, 2018

大規模実験室進化を用いた転写因子の破壊による大腸菌の薬剤耐性化の制御
堀之内貴明; 前田智也; 小谷葉月; 酒井亜希; 古澤力; 古澤力, 日本生物工学会大会講演要旨集, 70th, 2018

全自動培養システムを用いた多種ストレス環境化における大腸菌進化ダイナミクスの解析
前田智也; 堀之内貴明; 阪田奈津枝; 小谷葉月; 酒井亜希; 田邊久美; 古澤力; 古澤力, 日本ゲノム微生物学会年会要旨集, 11th, 2017

超大規模実験室進化とオミックス解析による大腸菌のストレス耐性機構の解析
堀之内貴明; 前田智也; 古澤力; 古澤力, 日本生物工学会大会講演要旨集, 69th, 2017

大腸菌進化実験による進化的制約の解析
古澤力; 古澤力; 前田智也; 堀之内貴明, 日本進化学会大会プログラム・講演要旨集(Web), 19th, 2017

1P-046 Analysis of mRNA recognition mechanism of Corynebacterium glutamicum RNase E/G
Endo Satoshi; Maeda Tomoya; Wachi Masaaki, 日本生物工学会大会講演要旨集, 66, 28, 28, 2014
日本生物工学会, Japanese

2P-031 5'-UTR dependent degradation of mRNAs by RNase E/G in Corynebacterium glutamicum
Endo Satoshi; Maeda Tomoya; Wachi Masaaki, 日本生物工学会大会講演要旨集, 65, 111, 111, 2013
日本生物工学会, Japanese

Laboratory evolution reveals the impact of microbial interactions on antibiotic resistance evolution
Tomoya Maeda
The 48th Annual Meeting of the Molecular Biology Society of Japan, 05 Dec. 2025, Nominated symposium
31576279, [Invited]

Exploring common and unique mechanisms of antimicrobial resistance across diverse bacterial species.
Tomoya Maeda; Kumi Tanabe; Atsushi Shibai; Hazuki Kotani; Chikara Furusawa
FEMS MICRO 2025, 16 Jul. 2025, English, Poster presentation
14 Jul. 2025 - 17 Jul. 2025

抗生物質耐性進化の仕組みと多様性の解析－ 進化に潜む共通性の理解とその耐性進化抑制への試み
前田智也
環境バイオテクノロジー学会2025年度大会, 10 Jul. 2025, Nominated symposium
46295431, [Invited]

異種間相互作用が抗生物質耐性進化に及ぼす影響
前田智也
日本農芸化学会2025年度札幌大会, 07 Mar. 2025, Japanese, Nominated symposium
[Invited]

Analysis of dependence and independence of microbial community assembly on carbon sources through community assembly experiments.
Tomoya Maeda; Junpei F Yamagish; Chikara Furusawa
EMBO Workshop Molecular mechanisms in evolution and ecology, 09 Oct. 2024, English, Poster presentation

大規模継代培養実験による微生物生態系の再構成
前田 智也
第4回シンポジウム ビフィズス菌研究会, 29 Sep. 2023, Nominated symposium
38275635, [Invited]

Comparative analysis of antibiotic resistance dynamics by high-throughput laboratory evolution of 9 bacterial species
Tomoya Maeda; Kumi Tanabe; Atsushi Shibai; Hazuki Kotani; Chikara Furusawa
FEMS (Federation of European Microbiological Societies) 2023, 10 Jul. 2023, Oral presentation

Cutting-edge technologies and their applications in microbiology
Jianshi Jin; Tomoya Maeda
The 45th Annual Meeting of the Molecular Biology Society of Japan, 30 Nov. 2022, Public symposium
30 Nov. 2022 - 02 Dec. 2022, 31576279

Relationship among energy level, redox balance, and phenotype in Escherichia coli
Tomoya Maeda
日本遺伝学会第94回大会 ワークショップ「原核生物の細胞増殖研究から見えてくる遺伝学の新たな課題」, 14 Sep. 2022, Nominated symposium
[Invited]

異種間相互作用による薬剤耐性進化ダイナミクスへの影響
前田 智也; 古澤 力
新学術領域「ポストコッホ生態」－ACT-X「環境とバイオテクノロジー」合同シンポジウム, 01 Sep. 2021, Nominated symposium
31576279, [Invited]

実験室進化による薬剤耐性進化ダイナミクスの解析
前田 智也; 古澤 力
第15回細菌学若手コロッセウム, 30 Aug. 2021, Nominated symposium
31576279, [Invited]

実験室進化による薬剤耐性進化ダイナミクスの解析
前田 智也; 岩澤 諄一郎; 古澤 力
日本生物工学会【北日本支部】2021年度第一回オンライン若手シンポジウム, 26 Aug. 2021, Nominated symposium
31576279, [Invited]

大規模進化実験で解き明かす大腸菌の薬剤耐性進化における制約
前田 智也; 岩澤 諄一郎; 古澤 力
第94回日本細菌学会総会 シンポジウム「若手研究者による最先端研究：細菌学の明日を切り拓く若人たちの発想と挑戦、今此処に！」, 23 Mar. 2021, Nominated symposium
31576279, [Invited]

微生物生態学特論, 2024年, 修士課程, 農学院

応用微生物学特論, 2024年, 修士課程, 農学院

大学院共通授業科目（一般科目）：自然科学・応用科学, 2024年, 修士課程, 大学院共通科目

食品安全・機能性開発学特論, 2024年, 修士課程, 農学院

食品安全・機能性開発学特論演習, 2024年, 修士課程, 農学院

環境と人間, 2024年, 学士課程, 全学教育

生物学実験Ⅰ, 2024年, 学士課程, 農学部

化学概論, 2024年, 学士課程, 農学部

生物機能化学演習Ⅱ, 2024年, 学士課程, 農学部

基礎微生物学, 2024年, 学士課程, 農学部

微生物化学, 2024年, 学士課程, 農学部

生物学実験Ⅱ, 2024年, 学士課程, 農学部

非病原性ウシ型結核菌BCG株を用いた進化実験による多剤耐性進化可能性の検証
科学研究費助成事業
01 Apr. 2024 - 31 Mar. 2028
前田 智也
日本学術振興会, 基盤研究(B), 北海道大学, 24K02009

小分子メディエーターを活用した複合微生物系制御技術の創出
戦略的な研究開発の推進 戦略的創造研究推進事業 ALCA-Next
2025 - 2028
吉村 彩; 尾花 望; 前田 智也
細胞外膜小胞で生産誘導される新規有用代謝産物をマーカーに相互作用細菌ペアを特定する。細菌ペアごとの相互作用様式を解明・集積する。本知見をもとに有用代謝産物を生産向上させる複合微生物系を論理的に設計する。本技術を用いて新規農業用抗生物質と、複合微生物系による大量供給系をセットで提示する。本農薬を環境負荷の低い手法で大量供給し、その農業利用により経済作物の収量増加させることで大幅なCO2削減を目指す。
科学技術振興機構, 北海道大学

Development of a Structural Design Strategy to Suppress the Evolution of Antibiotic Resistance
次世代育成支援研究助成金（基礎・創薬）
Apr. 2026 - Mar. 2027
Tomoy Maeda
SHIONOGI INFECTIOUS DISEASE RESEARCH PROMOTION FOUNDATION, Hokkaido University, Principal investigator

Analysis of evolutionary dynamics of ecosystem using automated culture system
Grants-in-Aid for Scientific Research
01 Apr. 2023 - 31 Mar. 2026
古澤 力; 前田 智也
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Institute of Physical and Chemical Research, 23K27164

Analysis of evolutionary dynamics of ecosystem using automated culture system
Grants-in-Aid for Scientific Research
01 Apr. 2023 - 31 Mar. 2026
古澤 力; 前田 智也
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Institute of Physical and Chemical Research, 23H02471

Consolidated PHA production from marine biomass
ALCA-Next（Advanced Technologies for Carbon-Neutral）
Sep. 2024 - Mar. 2026
Takasuka Taichi; Maeda Tomoya
本研究では、独自技術である共培養系による褐藻バイオマス中の多糖および単糖類をターゲットにし、褐藻バイオマス原料からPHAの一気通貫生産を実証する。本共培養系については、育種予定の生態系微生物集団を利用する事で、褐藻バイオマスの分解向上、将来的にはPHAやそれ以外の化成品等の共培養一貫生産技術開発も視野に入れている。
Japan Science and Technology Agency, 北海道大学, Coinvestigator, JPMJAN24D6

腸内マイクロバイオームの大規模継代培養による栄養共生関係の解明
科学研究費助成事業 新学術領域研究(研究領域提案型)
01 Apr. 2022 - 31 Mar. 2024
前田 智也
日本学術振興会, 新学術領域研究(研究領域提案型), 北海道大学, 22H04876

適応的実験室進化による産業微生物のエネルギー欠乏への潜在的な適応能力の解明
科学研究費助成事業 基盤研究(C)
01 Apr. 2021 - 31 Mar. 2024
前田 智也
本研究では、発酵産業に重要な大腸菌やコリネ型細菌の発酵生産効率の向上を目的として、中枢代謝が活性化している様々な呼吸鎖酵素欠損株の適応的実験室進化を行うことで、産業微生物の細胞増殖と目的物質生産のバランスを最適化させる方法を明らかにすることを最終目的としている。
大腸菌やコリネ型細菌において、酸化的リン酸化の阻害によるエネルギー欠乏の誘導が糖代謝などの中枢代謝を活性化させる一方、著しい増殖悪化を引き起こすことが先行研究から明らかにされている。申請者は、本研究において、エネルギー欠乏株の多くが酢酸を単一炭素源として生育できない、または著しく生育が阻害されることを見出した。酢酸を単一炭素源とした場合、取り込んだ酢酸をまず活性化してアセチルリン酸へ変換する過程で1分子のATPを消費し、その後基質レベルのリン酸化では1分子のATPしか合成できないため、ATP合成は酸化的リン酸化に依存していると考えられる。そのため、酢酸を単一炭素源とする選択圧をかける実験室進化を行うことで、酸化的リン酸化が阻害されているエネルギー欠乏株において、エネルギー欠乏への潜在的な適応能力が活性化された進化株が出現し得るのではないかと考えた。そこで今年度は、まず大腸菌の様々な呼吸鎖酵素を欠損したエネルギー欠乏株6株を親株として、酢酸最少培地を用いた適応的実験室進化を行った。適応的実験室進化は、コントロールとして呼吸鎖を欠損していない野生株を用い、また同一培養条件における反復数4として合計28系列行った。このような適応的実験室進化により、酢酸最少培地における生育が回復または、増殖速度が向上した進化株を取得することに成功した。
日本学術振興会, 基盤研究(C), 国立研究開発法人理化学研究所, 21K06142

Metabolic analysis of an Escherichia coli mutant defective in respiratory chain enzymes and its application to the production of 1,3-butanediol and gamma-aminobutyric acid.
Grants-in-Aid for Scientific Research
01 Apr. 2019 - 31 Mar. 2022
Atsushi Yokota
The respiratory chain of Escherichia coli includes NADH dehydrogenase (NDH) and terminal oxidase. We previously knocked out the highest proton-motive force-generating capacity components (NADH dehydrogenase-1 and cytochrome bo3 oxidase) using the E. coli wild-type W1485 strain. In this study, we found that the double knockout mutant strain (ΔΔ strain) showed an increase in the glucose consumption rate, respiration rate, acetate production, NADH/NAD+ ratio, and glutamate production. A metabolome analysis and RNA-seq analysis revealed that genes encoding for pentose phosphate pathway, acetate metabolism, and gadAB encoding glutamate decarboxylase were significantly increased. We also demonstrated that the ΔΔ strain can be applied for the production of 1,3-butanediol and γ-aminobutyric acid (GABA).
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 19H02863

Identification of interaction network of environmental microorganisms by high-throughput laboratory evolution.
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
Apr. 2020 - Mar. 2022
前田 智也
自然界では、数多くの微生物種が共存しており、栄養や生息地の競合だけでなく、基質の分解や、代謝物の交換等、複雑な微生物相互作用を基とした共生関係が築かれている。そのため、このような微生物相互作用を明らかにすることは、マイクロバイオームにおける各微生物の役割や、存在割合の動態が何よって影響を受けているのかを理解する上で大変重要である。そこで本研究では、様々な環境下においてマイクロバイオームを継代培養し、共存状態を維持し続ける微生物の組合せを解析することで、自然界に存在し得る共生関係を大規模に同定することを目的としている。
今年度は、まず昨年度に実施した大規模継代培養実験によって得られた継代培養後の微生物集団におけるメタ16S解析を実施した。安定した微生物集団が得られた13種類の炭素源由来の継代培養後集団および、それに対応する継代前の初期集団を合わせた合計623サンプルについて、16S rRNAのV4領域をターゲットとしたアンプリコンシーケンス解析を行い、試料中に含まれていた微生物の種類をAmplicon sequence variant (ASV) として算出した。続いて継代培養後の集団が、同一炭素源と同一初期条件のどちらと類似性が高いか調べたところ、炭素源が同じ集団の方が、初期状態が同じ集団よりも菌叢構造の類似性が有意に高かった。このことから、菌叢構造は初期状態よりも、利用できる栄養による影響を強く受けることが明らかになった。また、継代培養後の集団から単離した異種を組み合わせたペアワイズな共培養試験を行ったところ、継代培養後の安定した集団には、栄養共生関係が広く見られたことから、同一環境下で安定して共存している種同士には栄養共生関係が成立していることが示唆された。
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Institute of Physical and Chemical Research, 20H05591

Construction and analysis of bacterial strains carrying heterologous bacterial genome by heterologous protoplast fusion.
Grants-in-Aid for Scientific Research Grant-in-Aid for Early-Career Scientists
01 Apr. 2018 - 31 Mar. 2020
Maeda Tomoya
In this project, I aimed to develop a new technology to construct heterologous genome fusant bacterial strain. First, protoplast fusion experiments that cause cell fusion were performed using various bacterial pairs. However, none of them produced a heterologous genome fusant. Next, to replicate and maintain heterologous genome in E. coli, the sequence of a single copy plasmid derived from E. coli was introduced to the Corynebacterium glutamicum genome. Then, the recombinant C. glutamicum strain was fused with E. coli by protoplast fusion. It was confirmed that the obtained fusant strains carry both E. coli and C. glutamicum genome sequences.
Japan Society for the Promotion of Science, Grant-in-Aid for Early-Career Scientists, Institute of Physical and Chemical Research, Principal investigator, Competitive research funding, 18K14688

Development of interspecies genome recombination method using cell fusion and CRISPR/Cas9 technique
NISR Young Investigator Research Grants
Apr. 2019 - Mar. 2020
Noda Institute for Scientific Research, Principal investigator