Nobuyuki OKAHASHI, Ph.D.

• Osaka University HP
• ORCID
• researchmap

Research

• ¹³C-metabolic flux analysis
• Mass spectrometry
• Metabolomics and lipidomics
• Cancer metabolism
• Gut microbiome
• Metabolic engineering

CV

• 2018.4 - present Associate Professor, Analytical Biotechnology Laboratory, Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
• 2018.4 - present Visiting Scientist, Laboratory for Metabolomics, Center for Integrative Medical Science, Riken
• 2018.4 - 2019.11 Assistant Professor, Analytical Biotechnology Laboratory, Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
• 2017.4 - 2018.3 Postdoctoral Scientist, Laboratory for Metabolomics, Center for Integrative Medical Science, Riken
• 2015.4 - 2017.3 JSPS Reserach Fellow (DC2), Japan Society for the Promotion of Science
• 2014.4 - 2017.3 Doctor Course, Metabolic Engineering Laboratory, Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
• 2012.4 - 2014.3 Master Course, Metabolic Engineering Laboratory, Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
• 2008.4 - 2012.3 Department of Biotechnology, Division of Advanced Science and Biotechnology, School of Engineering, Osaka University

Contact

• Adress: 1-5, Yamadaoka, Suita, Osaka, Japan 565-0871, Analytical Biotechnology Laboratory, Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
• Tel: +81-6-6879-4339

Commentary

"¹³C-Metabolic Flux Analysis of Central Carbon Metabolism Using GC-MS"

GCMS Technical Report, Shimadzu Corporation

Publications

• Takeo Taniguchi, Nobuyuki Okahashi^*, Fumio Matsuda. ¹³C-metabolic flux analysis reveals metabolic rewiring in HL-60 neutrophil-like cells through differentiation and immune stimulation. Metabolic Engineering Communications, e00239, 2024.
• Chinatsu Matsuyama, Taisuke Seike, Nobuyuki Okahashi, Teppei Niide, Kiyotaka Y. Hara, Yoko Hirono-Hara, Jun Ishii, Hiroshi Shimizu, Yoshihiro Toya, Fumio Matsuda. Metabolome analysis of metabolic burden in Escherichia coli caused by overexpression of green fluorescent protein and delta-rhodopsin. Journal of Bioscience and Bioengineering, 137, 3, 187-194, 2024
• Masahiko Sugimura, Taisuke Seike, Nobuyuki Okahashi, Yoshihiro Izumi, Takeshi Bamba, Jun Ishii, Fumio Matsuda. Improved 2,3-butanediol production rate of metabolically engineered Saccharomyces cerevisiae by deletion of RIM15 and activation of pyruvate consumption pathway. International Journal of Molecular Science, 24, 22, 2023.
• Kazuki Nishimoto, Nobuyuki Okahashi, Masaharu Maruyama, Yoshihiro Izumi, Kohta Nakatani, Yuki Ito, Junko Iida, Takeshi Bamba, Fumio Matsuda. Lipidome and metabolome analyses reveal metabolic alterations associated with MCF-7 apoptosis upon 4-hydroxytamoxifen treatment. Scientific reports, 13, 1, 2023.
• Yatabe Futa, Seike Taisuke, Okahashi Nobuyuki, Ishii Jun, Matsuda Fumio. Improvement of ethanol and 2, 3‑butanediol production in Saccharomyces cerevisiae by ATP wasting. Microbial Cell Factories, 22, 204, 2023.
• Ryo Iwama, Nobuyuki Okahashi, Tetsuki Suzawa, Chuner Yang, Fumio Matsuda, Hiroyuki Horiuchi. Comprehensive analysis of the composition of the major phospholipids during the asexual life cycle of the filamentous fungus Aspergillus nidulans. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, 1868, 159379, 2023.
• Varada Jagadeesh, Takanobu Yoshida, Misugi Uraji, Nobuyuki Okahashi, Fumio Matsuda, Christopher J. Vavricka, Kenji Tsuge, Akihiko Kondo. Simple and Rapid Non-ribosomal Peptide Synthetase Gene Assembly Using the SEAM–OGAB Method. ACS Synthetic Biology, 12, 2022.
• Shuka Komori, Nobuyuki Okahashi, Junko Iida, Fumio Matsuda. Lipidome variation of industrial Saccharomyces cerevisiae strains analyzed by LC-QTOF/MS-based untargeted lipidomics. Journal of Bioscience and Bioengineering, 135, 2, 2022.
• Fumio Matsuda, Shuka Komori, Yuki Yamada, Daiki Hara, Nobuyuki Okahashi. Data processing of product ion spectra: Quality improvement by averaging multiple similar spectra of small molecules. Mass spectrometry, 11, 1, A0106, 2022.
• Nobuyuki Okahashi, Yuki Yamada, Junko Iida, Fumio Matsuda. Isotope Calculation Gadgets : A Series of Software for Isotope-Tracing Experiments in Garuda Platform.Metabolites 12, 646, 2022.
• Shin Nishiumi, Yoshihiro Izumi, Akiyoshi Hirayama, Masatomo Takahashi, Motonao Nakao,Kosuke Hata, Daisuke Saigusa, Eiji Hishinuma, Naomi Matsukawa, Suzumi M. Tokuoka, Yoshihiro Kita, Fumie Hamano, Nobuyuki Okahashi, Kazutaka Ikeda, Hiroki Nakanishi, Kosuke Saito, Masami Y. Hirai, Masaru Yoshida, Yoshiya Oda, Fumio Matsuda, Takeshi Bamba. Comparative Evaluation of Plasma Metabolomic Data from Multiple Laboratories. Metabolites 12,135,2022
• Satoshi Morozumi, Masahiro Ueda, Nobuyuki Okahashi, Makoto Arita.Structures and functions of the gut microbial lipidome. BBA-Molecular Cell Biology of Lipids 1867, 3, 159110, 2022.
• Fumio Matsuda, Kousuke Maeda, Takeo Taniguchi, Yuya Kondo, Futa Yatabe, Nobuyuki Okahashi, Hiroshi Shimizu. mfapy : An open-source Python package for flux analysis 13C-based metabolic flux analysis. Metabolic Engineering Communications. 13, e00177, 2021.
• Futa Yatabe, Nobuyuki Okahashi, Taisuke Seike, Fumio Matsuda. Comparative 13C‐metabolic flux analysis indicate elevation of ATP regeneration, carbon dioxide, and heat production in industrial Saccharomyces cerevisiae strains, Biotechnology Journal, 2000438, 2021.
• Yoshihiro Ito, Takashi Sasaki, Youxian Li, Takeshi Tanoue, Yuki Sugiura, Ashwin N. Skelly, Wataru Suda, Yusuke Kawashima, Nobuyuki Okahashi, Eiichiro Watanabe, Hiroto Horikawa, Aiko Shiohama, Rina Kurokawa, Eiryo Kawakami, Hachiro Iseki, Hiroshi Kawasaki, Yoichiro Iwakura, Atsushi Shiota, Liansheng Yu, Junzo Hisatsune, Haruhiko Koseki, Motoyuki Sugai, Makoto Arita, Osamu Ohara, Takeshi Matsui, Makoto Suematsu, Masahira Hattori, Koji Atarashi, Masayuki Amagai, Kenya Honda. Staphylococcus cohnii is a potentially biotherapeutic skin commensal alleviating skin inflammation. Cell reports, 35, 109052, 2021.
• Jindan Sheng, Susumu Kohno, Nobuhiro Okada, Nobuyuki Okahashi, Kana Teranishi, Fumio Matsuda, Hiroshi Shimizu, Paing Linn, Naoko Nagatani, Minako Yamamura, Kenichi Harada, Shin‐ichi Horike, Hiroshi Inoue, Seiji Yano, Sharad Kumar, Shunsuke Kitajima, Itsuki Ajioka, Chiaki Takahashi.Treatment of RB1‐intact hepatocellular carcinoma with CDK4/6 inhibitor combination therapy. Hepatology, 74, 4, 2021.
• Nobuyuki Okahashi, Masahiro Ueda, Shu Yasuda, Hiroshi Tsugawa, Makoto Arita. Global profiling of gut microbiota-associated lipid metabolites in antibiotic-treated mice by LC-MS/MS-based analyses, STAR Protocols, 2, 100492, 2021.
• Nobuyuki Okahashi, Masahiro Ueda, Fumio Matsuda, Makoto Arita, Analyses of Lipid A Diversity in Gram-Negative Intestinal Bacteria Using Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry, Metabolites,11, 2021
• Shota Isogai, Nobuyuki Okahashi, Ririka Asama, Tomomi Nakamura, Tomohisa Hasunuma, Fumio Matsuda, Jun Ishii, Akihiko Kondo. Synthetic production of prenylated naringenins in yeast using promiscuous microbial prenyltransferases, Metabolic Engineering Communications, e00169, 2021
• Yoshikazu Johmura, Takehiro Yamanaka, Satotaka Omori, Teh-Wei Wang, Yuki Sugiura, Masaki Matsumoto, Narumi Suzuki, Soichiro Kumamoto, Kiyoshi Yamaguchi, Seira Hatakeyama, Tomoyo Takami, Rui Yamaguchi, Eigo Shimizu, Kazutaka Ikeda, Nobuyuki Okahashi, Mikawa Ryuta, Makoto Suematsu, Makoto Arita, Masataka Sugimoto, Keiichi I. Nakayama, Yoichi Furukawa, Seiya Imoto, Makoto Nakanishi. Senolysis by glutaminolysis inhibition ameliorates various age-associated disorders. Science, 371, 265-270, 2021.
• Masahiro Nagata, Kenji Toyonaga, Eri Ishikawa, Shojiro Haji, Nobuyuki Okahashi, Masatomo Takahashi, Yoshihiro Izumi, Akihiro Imamura, Koichi Takato, Hideharu Ishida, Shigenori Nagai, Petr Illarinov, Bridget L. Stocker, Mattie S.M. Timmer, Dylan G.M. Smith, Spencer J. Williams, Takeshi Bamba, Tomofumi Miyamoto, Makoto Arita, Ben J. Appelmelk, Sho Yamasaki. Helicobacter pylori metabolites exacerbate gastritis through C-type lectin receptors. Journal of Experimental Medicine, 218, 1, 1-15, 2020.
• Shu Yasuda#, Nobuyuki Okahashi#, Hiroshi Tsugawa, Yusuke Ogata, Kazutaka Ikeda, Wataru Suda, Hiroyuki Arai, Masahira Hattori, Makoto Arita. 2020. Elucidation of gut microbiota-associated lipids using LC-MS/MS and 16S rRNA sequence analyses. iScience. 23, 1-11, 2020. #Equally contributed.
• Hiroshi Tsugawa, Kazutaka Ikeda, Mikiko Takahashi, Aya Satoh, Yoshifumi Mori, Haruki Uchino, Nobuyuki Okahashi, Yutaka Yamada, Ipputa Tada, Paolo Bonini, Yasuhiro Higashi, Yozo Okazaki, Zhiwei Zhou, Zheng-JIang Zhu, Jeremy Koelmel, Tomas Cajka, Oliver Fiehn, Kazuki Saito, Masanori Arita, Makoto Arita. A lipidome atlas in MS-DIAL 4. Nature Biotechnology, 1-6. 2020.
• Fumio Matsuda, Kousuke Maeda, Nobuyuki Okahashi. Computational data mining method for isotopomer analysis in the quantitative assessment of metabolic reprogramming. Scientific Reports, 286, 1-10, 2020.
• Yoshihiro Izumi, Fumio Matsuda, Akiyoshi Hirayama, Kazutaka Ikeda, Yoshihiro Kita, Kanta Horie, Daisuke Saigusa, Kosuke Saito, Yuji Sawada, Hiroki Nakanishi, Nobuyuki Okahashi, Masatomo Takahashi, Motonao Nakao, Kosuke Hata, Yutaro Hoshi, Motohiko Morihara, Kazuhiro Tanabe, Takeshi Bamba, Yoshiya Oda. Inter-laboratory comparison of metabolite measurements for metabolomics data integration.Metabolites, 9, 2019
• Nobuyuki Okahashi, Shuichi Kawana, Junko Iida, Hiroshi Shimizu, Fumio Matsuda. Fragmentation of dicarboxylic and tricarboxylic acids in the Krebs cycle using GC-EI-MS and GC-EI-MS/MS. Mass Spectrometry. A0073, 2019
• Masaharu Maruyama, Hiroki Nishiguchi, Masakazu Toyoshima, Nobuyuki Okahashi, Fumio Matsuda, Hiroshi Shimizu. Time-resolved analysis of short term metabolic adaptation at dark transition. Journal of Bioscience and Bioengineering. 128, 4, 424-428, 2019
• Nobuyuki Okahashi, Kousuke Maeda, Shuichi Kawana, Junko Iida, Hiroshi Shimizu, Fumio Matsuda.Sugar phosphate analysis with baseline separation and soft ionization by gas chromatography-negative chemical ionization-mass spectrometry improves flux estimation of bidirectional reactions in cancer cells,Metabolic Engineering, 51, 43-49, 2019
• Chie Araki, Nobuyuki Okahashi, Kousuke Maeda, Hiroshi Shimizu, and Fumio Matsuda. Mass spectrometry-based method to study inhibitor-induced metabolic redirection in the central metabolism of cancer cells.Mass spectrometry, 7, 1, A0067, 2018
• Nobuyuki Okahashi, Fumio Matsuda, Katsunori Yoshikawa, Tomokazu Shirai, Yoshiko Matsumoto, Mitsufumi Wada, Hiroshi Shimizu. Metabolic engineering of isopropyl alcohol-producing Escherichia coli strains with ¹³C-metabolic flux analysis, Biotechnology and Bioengineering, 114, 12, 2782-2793, 2017
• Shunsuke Kitajima, Akiyo Yoshida, Susumu Kohno, Fengkai Li, Sawako Suzuki, Naoko Nagatani, Yuuki Nishimoto, Nobunari Sasaki, Hayato Muranaka, Yuansong Wan, Tran C Thai, Nobuyuki Okahashi, Fumio Matsuda, Hiroshi Shimizu, Takumi Nishiuchi, Yutaka Suzuki, Kana Tominaga, Noriko Gotoh, Misa Suzuki, Mark E. Ewen, David A. Barbie, Osamu Hirose, Tomoaki Tanaka, Chiaki Takahashi. The RB-IL-6 axis controls self-renewal and endocrine therapy resistance by fine-tuning mitochondrial activity, Oncogene, 36, 36, 5145-5157, 2017
• Nobuyuki Okahashi, Shuichi Kawana, Junko Iida, Hiroshi Shimizu, Fumio Matsuda. GC-MS/MS survey of collision-induced dissociation of tert-butyldimethylsilyl-derivatized amino acids and its application to ¹³C-metabolic flux analysis of Escherichia coli central metabolism, Analytical and Bioanalytical Chemistry, 408, 22, 6133-6140, 2016
• Kousuke Maeda, Nobuyuki Okahashi, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu. Investigation of useful carbon tracers for ¹³C-metabolic flux analysis of Escherichia coli by considering five experimentally determined flux distributions, Metabolic Engineering Communications, 3, 187-195, 2016
• Nobuyuki Okahashi, Susumu Kohno, Shunsuke Kitajima, Fumio Matsuda, Chiaki Takahashi, Hiroshi Shimizu. Metabolic characterization of cultured mammalian cells by mass balance analysis, tracer labeling experiments and computer-aided simulations. Journal of Bioscience and Bioengineering, 120, 6, 725-731, 2015
• Shunsuke Nishino, Nobuyuki Okahashi, Fumio Matsuda, Hiroshi Shimizu. Absolute quantitation of glycolytic intermediates reveals thermodynamic s20:34 2021/03/29hifts in Saccharomyces cerevisiae strains lacking PFK1 or ZWF1 genes. Journal of Bioscience and Bioengineering, 120, 3, 280-286, 2015
• Nobuyuki Okahashi, Shuichi Kajihata, Chikara Furusawa, Hiroshi Shimizu. Reliable metabolic flux estimation in Escherichia coli central carbon metabolism using intracellular free amino acids. Metabolites, 4, 2, 408-420, 2014

Awards

• 2016.3 Most Outstanding Student Award, 81st Annual Meeting of the Society of Chemical Engineers, Japan
• 2015.6 Best Poster Presentation Award, 63rd AnnualConference on Mass Spectrometry, Japan
• 2015.3 Special Award, 80th Annual Meeting of the Society of Chemical Engineers, Japan
• 2014.5 3rd Outstanding Student Award (Hisho award), The Society for Biotechnology
• 2014.5 Best Presentation Award, 62nd AnnualConference on Mass Spectrometry, Japan