Publications
2024
Maeda, T., Furusawa, C. Laboratory Evolution of Antimicrobial Resistance in Bacteria to Develop Rational Treatment Strategies. Antibiotics. 19;13(1):94. (2024)
Shimada, M., Kawase, Y., Sonoyama, K., Ogura, Y., Hayashi, T., Yokota A., Fukiya, S.*
Development of an improved colonization system for human-derived Bifidobacterium longum subsp. longum in conventional mice through the feeding of raffinose or 1-kestose. Biosci Microbiota Food Health. 43:110-119 (2024). https://pubmed.ncbi.nlm.nih.gov/38562544/
Shinmori, A., Guo, Z., Maeda, T., Fukiya, S., Wada, M., Yokota, A. Contributions of the anaplerotic reaction enzymes pyruvate carboxylase and phosphoenolpyruvate carboxylase to l-lysine production in Corynebacterium glutamicum, J. Biosci. Bioeng. in press. (2024)
https://www.sciencedirect.com/science/article/pii/S1389172324001634?via%3Dihub
2023
Gowda, S.G.B, Hou, F., Gowda, D., Chiba, H., Kawakami, K., Fukiya, S., Yokota, A., Hui, S.P. *
Synthesis and quantification of short-chain fatty acid esters of hydroxy fatty acids in rat intestinal contents and fecal samples by LC-MS/MS. Anal Chim Acta. 1288:342145 (2023). https://pubmed.ncbi.nlm.nih.gov/38220280/
Hisatomi, A., Kastawa, N.W.E.P.G., Song, I., Ohkuma, M., Fukiya, S., Sakamoto, M.
Claveliimonas bilis gen. nov., sp. nov., deoxycholic acid-producing bacteria isolated from human faeces, and reclassification of Sellimonas monacensis Zenner et al. 2021 as Claveliimonas monacensis comb. nov. Int J Syst Evol Microbiol. 73:006030 (2023). doi:10.1099/ijsem.0.006030. PMID: 37737068. https://pubmed.ncbi.nlm.nih.gov/37737068/
Furusawa, C., Iwasawa, J., Maeda, T. Inference of Fitness Landscape Based on Multi-Dimensional Phenotype Measurements of Escherichia coli. Seibutsu Butsuri. 63(5) 263-265. (2023)
2022
Maeda, T., Furusawa, C. Laboratory Evolution of Antimicrobial Resistance in Bacteria to Develop Rational Treatment Strategies. Antibiotics. 19;13(1):94. (2024)
Maegawa, K., Koyama, H., Fukiya, S., Yokota, A., Ueda, K., and Ishizuka, S. Dietary raffinose ameliorates hepatic lipid accumulation induced by cholic acid via modulation of enterohepatic bile acid circulation in rats. British Journal of Nutrition, 127, 1621-1630 (2022). https://pubmed.ncbi.nlm.nih.gov/34256877/
Kawai, R., Toya, Y., Miyoshi, K., Murakami, M., Niide, T., Horinouchi, T., Maeda, T., Shibai, A., Furusawa, C., Shimizu, H. Acceleration of target production in co-culture by enhancing intermediate consumption through adaptive laboratory evolution. Biotechnol. Bioeng. 119. 936-945 (2022).
Kranz, A.,* Polen T., Kotulla, C., Arndt, A., Bosco, G., Bussmann, M., Chattopadhyay, A., Cramer, A., Davoudi, CF., Degner, U., Diesveld, R., von Boeselager, RF., Gärtner, K., Gätgens, C., Georgi, T., Geraths, C., Haas, S., Heyer, A., Hünnefeld, M., Ishige,T., Kabus, A., Kallscheuer, N., Kever, L., Klaffl, S., Kleine, B., Kočan, M., Koch-Koerfges, A., Kraxner, KJ., Krug, A., Krüger, A., Küberl, A., Labib, M., Lange, C., Mack, C., Maeda, T., Mahr, R., Majda, S., Michel, A., Morosov, X., Müller, O., Nanda, AM., Nickel, J., Pahlke, J., Pfeifer, E., Platzen, L., Ramp, P., Rittmann, D., Schaffer, S., Scheele, S., Spelberg, S., Schulte, J., Schweitzer, JE., Sindelar, G., Sorger-Herrmann, U., Spelberg, M., Stansen, C., Tharmasothirajan, A., van Ooyen, J., van Summeren-Wesenhagen, O., Vogt, M., Witthoff, S., Zhu, L., Eikmanns, BJ., Oldiges, M., Schaumann, G., Baumgart, M., Brocker, M., Eggeling, L., Freudl, R., Frunzke, J., Marienhagen, J., Wendisch, VF., Bott, M.* A manually curated compendium of expression profiles for the microbial cell factory Corynebacterium glutamicum. Sci. Data., 9, 594. (2022).
Iwasawa, J., Maeda, T., Shibai, A., Kotani, H., Kawada, M., Furusawa, C*. Analysis of the evolution of resistance to multiple antibiotics enables prediction of the Escherichia coli phenotype-based fitness landscape. PLoS Biol. 20. e3001920. (2022).
Hirasawa, T.,* Maeda, T. Adaptive Laboratory Evolution of Microorganisms: Methodology and Application for Bioproduction. Microorganisms. 11:92. (2022).
2021
Song, I., Gotoh, Y., Ogura, Y., Hayashi, T., Fukiya, S.*, and Yokota, A. Comparative genomic and physiological analysis against Clostridium scindens reveals Eubacterium sp. c-25 as an atypical deoxycholic acid producer of the human gut microbiota. Microorganisms, 9, 2254 (2021). https://pubmed.ncbi.nlm.nih.gov/34835380/
Hori, S., Satake, M., Kohmoto, O., Takagi, R., Okada, K., Fukiya, S., Yokota, A., and Ishizuka, S. * Primary 12α-hydroxylated bile acids lower hepatic iron concentration in rats. Journal of Nutrition, 151, 523-530 (2021). https://pubmed.ncbi.nlm.nih.gov/33438034/
Wada, M.,* Fukiya, S., Suzuki, A., Matsumoto, N., Matsuo, M., and Yokota, A. Methionine utilization by bifidobacteria: possible existence of a reverse transsulfuration pathway. Bioscience, Microbiota, Food and Health, 40, 80-83 (2021). https://pubmed.ncbi.nlm.nih.gov/33520573/
Hirano, R., Sakanaka, M., Yoshimi, K., Sugimoto, N., Eguchi, S., Yamauchi, Y., Nara, M., Maeda, S., Ami, Y., Gotoh, A., Katayama, T., Iida, N., Kato, T., Ohno, H., Fukiya, S., Yokota, A., Nishimoto, M., Kitaoka, M., Nakai, H.*, and Kurihara, S.* Next-generation prebiotic promotes selective growth of bifidobacteria, suppressing Clostridioides difficile. 13, 1973835 (2021). https://pubmed.ncbi.nlm.nih.gov/34553672/
Maeda, T. &, Koch-Koerfges, A. &, and Bott, M.* Relevance of NADH dehydrogenase and alternative two-enzyme systems for growth of Corynebacterium glutamicum with glucose, lactate, and acetate. Frontiers in Bioengineering and Biotechnology 8, DOI: 10.3389/fbioe.2020.621213 (2021).
Maeda, T.*, Shibai, A., Yokoi, N., Tarusawa, Y., Kawada, M., Kotani, H., Furusawa, C. Mutational property of newly identified mutagen L-glutamic acid γ-hydrazide in Escherichia coli. Mutat. Res., 823, 111759 (2021).
Maeda, T.*, Kawada, M., Sakata, N., Kotani, H., Furusawa, C. Laboratory evolution of Mycobacterium on agar plates for analysis of resistance acquisition and drug sensitivity profiles. Sci. Rep., 11, 15136 (2021).
Maeda, T.*, Kotani, H., Furusawa, C. Morphological change of coiled bacterium Spirosoma linguale with acquisition of β-lactam resistance. Sci. Rep., 11. 13278 (2021).
2020
Wada M, Fukiya S, Suzuki A, Matsumoto N, Matsuo M, and Atsushi Yokota. Methionine utilization by bifidobacteria: Possible existence of a reverse transsulfuration pathway. Biosci Microbiota Food Health, in press (2020)
Lee JY, Shimizu H, Hagio M, Fukiya S, Watanabe M, Tanaka Y, Joe GH, Iwaya H,Yoshitsugu R, Kikuchi K, Tsuji M, Baba N, Nose T, Tada K, Hanai T, Hori S, Takeuchi A, Furukawa Y, Shirouchi B, Sato M, Ooka T, Ogura Y, Hayashi T, Yokota A, Ishizuka S. 12α-hydroxylated bile acid induces hepatic steatosis with dysbiosis in rats.
Biochim Biophys Acta Mol Cell Biol Lipids.2020 Sep;4:158811
Hori S, Abe T, Lee DG, Fukiya S, Yokota A, Aso N, Shirouchi B, Sato M,Ishizuka S. Association between 12α-hydroxylated bile acids and hepatic steatosis in rats fed a high-fat diet.
J Nutr Biochem. 2020 Sep;83:108412
Gowda SGB, Liang C, Gowda D, Hou F, Kawakami K, Fukiya S, Yokota A, Chiba H, Hui SP. Identification of short chain fatty acid esters of hydroxy fatty acids (SFAHFAs) in murine model by nontargeted analysis using ultra-high-performance liquid chromatography/linear trap quadrupole-Orbitrap mass spectrometry.
Rapid Commun Mass Spectrom. 2020 May;15
Koguchi H, Ishigami N, Sakanaka M, Yoshida K, Hiratou S, Shimada M, Fukiya S, Sonoyama K, Yokota A. Application of recombinase-based in vivo expression technology to Bifidobacterium longum subsp. longum for Identification of genes induced in the gastrointestinal tract of mice.
Microorganisms. 2020 Mar 13;8(3):410
Gowda SGB, Gao ZJ, Chen Z, Abe T, Hori S, Fukiya S, Ishizuka S, Yokota A, Chiba H, Hui SP. Untargeted lipidomic analysis of plasma from high fat diet-induced obese rats using UHPLC- linear trap quadrupole -Orbitrap MS.
Anal Sci. 2020 Jan;17
Gowda, S.G.B., Gowda, D., Liang, C., Li, Y., Kawakami, K., Fukiya, S., Yokota, A., Chiba, H., and Hui, S.P. * Chemical Labeling assisted detection and identification of short chain fatty acid esters of hydroxy fatty acid in rat colon and cecum contents. Metabolites, 10, 398 (2020). https://pubmed.ncbi.nlm.nih.gov/33050007/
Yoshioka, H., Watanabe, M., Nanba, F., Suzuki, T., Fukiya, S., Yokota, A., and Toda, T. * Administration of cholic acid inhibits equol production from daidzein in mice. Journal of Nutritional Science and Vitaminology, 66, 571-576 (2020). https://pubmed.ncbi.nlm.nih.gov/33390399/
2019
Kato, S., Tobe, H., Matsubara, H., Sawada, M., Sasaki, Y., Fukiya, S., et al. The membrane phospholipid cardiolipin plays a pivotal role in bile acid adaptation by Lactobacillus gasseri JCM1131T.
Biochim Biophys Acta - Mol Cell Biol Lipids 1864: 403-412(2019)
Kataoka N, Vangnai AS, Pongtharangkul T, Yakushi T, Wada M, Yokota A, Matsushita K.Engineering of Corynebacterium glutamicum as a prototrophic pyruvate-producing strain: Characterization of a ramA-deficient mutant and its application for metabolic engineering.
Biosci Biotechnol Biochem. 2019 Feb;83(2):372-380
Sakanaka M, Hansen ME, Gotoh A, Katoh T, Yoshida K, Odamaki T, Yachi H, Sugiyama Y, Kurihara S, Hirose J, Urashima T, Xiao JZ, Kitaoka M, Fukiya S, Yokota A, Lo Leggio L, Abou Hachem M, Katayama T. Evolutionary adaptation in fucosyllactose uptake systems supports bifidobacteria-infant symbiosis.
Sci Adv. 2019 Aug 28;5(8):eaaw7696
Lee DG, Hori S, Kohmoto O, Kitta S, Yoshida R, Tanaka Y, Shimizu H, Takahashi K, Nagura T, Uchino H, Fukiya S, Yokota A, Ishizuka S. Ingestion of difructose anhydride III partially suppresses the deconjugation and 7α-dehydroxylation of bile acids in rats fed with a cholic acid-supplemented diet.
Biosci Biotechnol Biochem. 2019 Jul;83(7):1329-1335
2018
Sakanaka, M., Nakakawaji, S., Nakajima, S., Fukiya, S., Abe, A., Saburi, W., et al. A Transposon Mutagenesis System for Bifidobacterium longum subsp. longum based on an IS3 family insertion sequence, IS
Blo11. Appl Environ Microbiol 84: e00824-18(2018)
Shiraishi, T., Yokota, S., Sato, Y., Ito, T., Fukiya, S., Yamamoto, S., et al. Lipoteichoic acids are embedded in cell walls during logarithmic phase, but exposed on membrane vesicles in Lactobacillus gasseri JCM 1131T.
Benef Microbes 9: 653-662(2018)
2017
Tawthep S, Fukiya S, Lee JY, Hagio M, Ogura Y, Hayashi T, Yokota A. Isolation of six novel 7-oxo- or urso-type secondary bile acid-producing bacteria from rat cecal contents. Journal of Bioscience and Bioengineering in press (2017) doi: 10.1016/j.jbiosc.2017.06.002. >>pubmed
Watanabe M, Fukiya S, Yokota A. Comprehensive evaluation of the bactericidal activities of free bile acids in the large intestine of humans and rodents. Journal of LIPID RESEARCH. 58: 1143-1152(2017) doi: 10.1194/jlr.M075143 >>pubmed
Nagano S, Shibano K, Matsumoto Y, Yokota A, Wada M. Isolation and amino acid sequence of a dehydratase acting on D-erythro-3-hydroxyaspartate from Pseudomonas sp. N99, and its application in the production of optically active 3-hydroxyaspartate. Bioscience, Biotechnology, and Biochemistry. 81(6): 1156-1164 (2017) doi:10.1080/09168451.2017.1295804 >>Taylor Francis Online
Yokota A, Sawada K, Wada M. Boosting Anaplerotic Reactions by Pyruvate Kinase Gene Deletion and Phosphoenolpyruvate Carboxylase Desensitization for Glutamic Acid and Lysine Production in Corynebacterium glutamicum. Advances in Biochemical Engineering/Biotechnology. 159: 181-198 (2017) doi:10.1007/10_2016_31 >>pubmed
Maeda, S., Shimizu, K., Kihira, C., Iwabu, Y., Kato, R., Sugimoto, M., et al. Pyruvate dehydrogenase complex regulator (PdhR) gene deletion boosts glucose metabolism in Escherichia coli under oxygen-limited culture conditions. J Biosci Bioeng 123: 437-443(2017)
Nishiyama, K., Yamamoto, Y., Sugiyama, M., Takaki, T., Urashima, T., Fukiya, S., et al. Bifidobacterium bifidum extracellular sialidase enhances adhesion to the mucosal surface and supports carbohydrate assimilation. MBio 8: e00928-17(2017)
2016
Maeda S, Shimizu K, Kihira C, Iwabu Y, Kato R, Sugimoto M, Fukiya S, Wada M, Yokota A. Pyruvate dehydrogenase complex regulator (PdhR) gene deletion boosts glucose metabolism in Escherichia coli under oxygen-limited culture conditions. Journal of Bioscience and Bioengineering. 123(4):437-443 (2016) doi:10.1016/j.jbiosc.2016.11.004 >>pubmed
Yanase M, Aikoh T, Sawada K, Ogura K, Hagiwara T, Imai K, Wada M, Yokota A. Pyruvate kinase deletion as an effective phenotype to enhance lysine production in Corynebacterium glutamicum ATCC13032: Redirecting the carbon flow to a precursor metabolite. Journal of Bioscience and Bioengineering. 122 (2):160-167 (2016) doi:10.1016/j.jbiosc.2015.12.023 >>ScienceDirect
2015
Sawada K, Wada M, Hagiwara T, Zen-in S, Imai K, Yokota A. Effect of pyruvate kinase gene deletion on the physiology of Corynebacterium glutamicum ATCC13032 under biotin-sufficient non-glutamate-producing conditions: Enhanced biomass production.
Metabolic Engineering Communications.2:67-75.(2015) doi:10.1016/j.meteno.2015.07.001>>ScienceDirect
Wada M, Sawada K, Ogura K, Shimono Y, Hagiwara T, Sugimoto M, Onuki A, Yokota A. Effects of phosphoenolpyruvate carboxylase desensitization on glutamic acid production in Corynebacterium glutamicum ATCC 13032.
J Biosci Bioeng.15:S1389-1723.(2015) doi: 10.1016/j.jbiosc.2015.06.008. >>PubMed
Shimizu H, Baba N, Nose T, Taguchi R, Tanaka S, Joe GH, Maseda H, Nomura N, Hagio M, Lee JY, Fukiya S, Yokota A, Ishizuka S, Miyazaki H. Activity of ERK regulates mucin 3 expression and is involved in undifferentiated Caco-2 cell death induced by 3-oxo-C12-homoserine lactone.
Biosci Biotechnol Biochem. 79:937-42.(2015) doi: 10.1080/09168451.2015.1006570.>>PubMed
Sakanaka M, Fukiya S, Kobayashi R, Abe A, Hirayama Y, Kano Y, Yokota A. Isolation and transposition properties of ISBlo11, an active insertion sequence belonging to the IS3 family, from Bifidobacterium longum 105-A.
FEMS Microbiol Lett. 362 (2015) doi: 10.1093/femsle/fnv032. >>PubMed
Matsumoto Y, Yasutake Y, Takeda Y, Tamura T, Yokota A, Wada M. Structural insights into the substrate stereospecificity of D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23: a useful enzyme for the synthesis of optically pure L-threo- and D-erythro-3-hydroxyaspartate.
Appl Microbiol Biotechnol. 99 (17):7137-50 (2015) doi: 10.1007/s00253-015-6479-3 >>PubMed
2014
Soma Y, Tsuruno K, Wada M, Yokota A, Hanai T. Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch.
Metabolic Engineering 23 :175-184 (2014) doi: 10.1016/j.ymben.2014.02.008. >>PubMed
Kanesaki Y, Masutani H, Sakanaka M, Shiwa Y, Fujisawa T, Nakamura Y, Yokota A, Fukiya S, Suzuki T, Yoshikawa H. Complete Genome Sequence of Bifidobacterium longum 105-A, a Strain with High Transformation Efficiency.
Genome Announc. 18 :01311-14 (2014) doi: 10.1128/genomeA.01311-14. >>PubMed
Hagio M, Shimizu H, Joe GH, Takatsuki M, Shiwaku M, Xu H, Lee JY, Fujii N, Fukiya S, Hara H, Yokota A, Ishizuka S. Diet supplementation with cholic acid promotes intestinal epithelial proliferation in rats exposed to γ-radiation.
Toxicol Lett. 232:246-252 (2014) doi: 10.1016/j.toxlet.2014.10.011. >>PubMed
Sakanaka M, Tamai S, Hirayama Y, Onodera A, Koguchi H, Kano Y, Yokota A, Fukiya S. Functional analysis of bifidobacterial promoters in Bifidobacterium longum and Escherichia coli using the α-galactosidase gene as a reporter.
J Biosci Bioeng. 118:489-95 (2014) doi: 10.1016/j.jbiosc.2014.05.002. >>PubMed
Shimizu H, Hagio M, Iwaya H, Tsuneki I, Lee JY, Fukiya S, Yokota A, Miyazaki H, Hara H, Ishizuka S. Deoxycholic acid is involved in the proliferation and migration of vascular smooth muscle cells.
J Nutr Sci Vitaminol. 60 :450-4 (2014) doi: 10.3177/jnsv.60.450. >>PubMed
2013
Matsumoto Y, Yasutake Y, Takeda Y, Tamura T, Yokota A, Wada M. Crystallization and preliminary X-ray diffraction studies of D-threo-3-hydroxyaspartate dehydratase isolated from Delftia sp. HT23
Acta Crystallogr. Sect. F, 69:1131-1134 (2013) >>PubMed
Lee JY, Arai H, Nakamura Y, Fukiya S, Wada M, Yokota A. Contribution of the 7β-hydroxysteroid dehydrogenase from Ruminococcus gnavus N53 to ursodeoxycholic acid formation in the human colon.
J Lipid Res.(2013). >>PubMed
Sakurama H, Kiyohara M, Wada J, Honda Y, Yamaguchi M, Fukiya S, Yokota A, Ashida H, Kumagai H, Kitaoka M, Yamamoto K, Katayama T. Lacto-N-biosidase Encoded by a Novel Gene of Bifidobacterium longum Subspecies longum Shows Unique Substrate Specificity and Requires a Designated Chaperone for Its Active Expression.
J Biol Chem., 288:25194-25206 (2013) >>PubMed
Shiraishi T, Yokota S, Morita N, Fukiya S, Tomita S, Tanaka N, Okada S, Yokota A. Characterization of a Lactobacillus gasseri JCM 1131T lipoteichoic acid with a novel glycolipid anchor structure.
Appl Environ Microbiol., 79:3315-3318 (2013) >>PubMed
2012
Fukiya S, Hirayama Y, Sakanaka M, KANO Y, Yokota A. Technological Advances in Bifidobacterial Molecular Genetics: Application to Functional Genomics and Medical Treatments
Bioscience of Microbiota, Food and Health, 31:15-25 (2012) >>J-STAGE
Kihira C, Hayashi Y, Azuma N, Noda S, Maeda S, Fukiya S, Wada M, Matsushita K, Yokota A. Alterations of glucose metabolism in Escherichia coli mutants defective in respiratory-chain enzymes.
J Biotechnol, 158:215-223 (2012) >>PubMed
Hirayama Y, Sakanaka M, Fukuma H, Murayama H, Kano Y, Fukiya S, Yokota A. Development of a Double-Crossover Markerless Gene Deletion System in Bifidobacterium longum: Functional Analysis of the α-Galactosidase Gene for Raffinose Assimilation.
Appl Environ Microbiol, 78:4984-4994(2012). >>PubMed
Sawada K, Kato Y, Imai K, Li L, Wada M, Matsushita K, Yokota A. Mechanism of increased respiration in an H+-ATPase-defective mutant of Corynebacterium glutamicum.
J Biosci Bioeng, 113:467-473(2012). >>PubMed
Yokota A, Fukiya S, Ooka T, Ogura Y, Hayashi T, Ishizuka S. Is bile acid a determinant of the gut microbiota on a high-fat diet?
Gut Microbes, 3:epub ahead of print(2012). >>PubMed
2012年以前の論文はこちら（準備中です）