13C-metabolic flux analysis of Saccharomyces cerevisiae in complex media

Hayato Fujiwara, Nobuyuki Okahashi, Taisuke Seike, Fumio Matsuda

Metabolic Engineering Communications　Vol. 20　p. e00260-e00260　2025/04　Research paper (scientific journal)

ΔΔG Method for Elucidating Key Control Reactions from Relative Quantification Metabolome Data: Comparative Analysis of Yeast Glycolysis.

Fumio Matsuda, Ayumu Kamiyama, Kazuki Yamasaki, Taisuke Seike, Nobuyuki Okahashi

Analytical chemistry　Vol. 97　No. 12　p. 6391-6398　2025/04/01　Research paper (scientific journal)

Combinatorial Nonribosomal Peptide Synthetase Libraries Using the SEAM-Combi-OGAB Method.

Varada Jagadeesh, Nobuyuki Okahashi, Fumio Matsuda, Kenji Tsuge, Akihiko Kondo

ACS synthetic biology　Vol. 14　No. 2　p. 520-530　2025/02/21　Research paper (scientific journal)

Commensal consortia decolonize Enterobacteriaceae via ecological control

Munehiro Furuichi, Takaaki Kawaguchi, Marie-Madlen Pust, Keiko Yasuma-Mitobe, Damian R. Plichta, Naomi Hasegawa, Takashi Ohya, Shakti K. Bhattarai, Satoshi Sasajima, Yoshimasa Aoto, Timur Tuganbaev, Mizuki Yaginuma, Masahiro Ueda, Nobuyuki Okahashi, Kimiko Amafuji, Yuko Kiridoshi, Kayoko Sugita, Martin Stražar, Julian Avila-Pacheco, Kerry Pierce, Clary B. Clish, Ashwin N. Skelly, Masahira Hattori, Nobuhiro Nakamoto, Silvia Caballero, Jason M. Norman, Bernat Olle, Takeshi Tanoue, Wataru Suda, Makoto Arita, Vanni Bucci, Koji Atarashi, Ramnik J. Xavier, Kenya Honda

Nature　Vol. 633　p. 878-886　2024/09/18　Research paper (scientific journal)

13C-metabolic flux analysis reveals metabolic rewiring in HL-60 neutrophil-like cells through differentiation and immune stimulation

Takeo Taniguchi, Nobuyuki Okahashi, Fumio Matsuda

Metabolic Engineering Communications　Vol. 18　p. e00239-e00239　2024/05　Research paper (scientific journal)

Metabolome analysis of metabolic burden in Escherichia coli caused by overexpression of green fluorescent protein and delta-rhodopsin

Chinatsu Matsuyama, Taisuke Seike, Nobuyuki Okahashi, Teppei Niide, Kiyotaka Y. Hara, Yoko Hirono-Hara, Jun Ishii, Hiroshi Shimizu, Yoshihiro Toya, Fumio Matsuda

Journal of Bioscience and Bioengineering　Vol. 137　No. 3　p. 187-194　2024/03　Research paper (scientific journal)

Improved 2,3-Butanediol Production Rate of Metabolically Engineered Saccharomyces cerevisiae by Deletion of RIM15 and Activation of Pyruvate Consumption Pathway

Masahiko Sugimura, Taisuke Seike, Nobuyuki Okahashi, Yoshihiro Izumi, Takeshi Bamba, Jun Ishii, Fumio Matsuda

International Journal of Molecular Sciences　Vol. 24　No. 22　p. 16378-16378　2023/11/15　Research paper (scientific journal)

Lipidome and metabolome analyses reveal metabolic alterations associated with MCF-7 apoptosis upon 4-hydroxytamoxifen treatment

Kazuki Nishimoto, Nobuyuki Okahashi, Masaharu Maruyama, Yoshihiro Izumi, Kohta Nakatani, Yuki Ito, Junko Iida, Takeshi Bamba, Fumio Matsuda

Scientific Reports　Vol. 13　No. 1　2023/10/29　Research paper (scientific journal)

Rationally-defined microbial consortia suppress multidrug-resistant proinflammatory Enterobacteriaceae via ecological control.

Kenya Honda, Munehiro Furuichi, Takaaki Kawaguchi, Marie-Madlen Pust, Keiko Yasuma-Mitobe, Damian Plichta, Naomi Hasegawa, Takashi Ohya, Shakti Bhattarai, Satoshi Sasajima, Aoto Yoshimasa, Timur Tuganbaev, Mizuki Yaginuma, Masahiro Ueda, Nobuyuki Okahashi, Kimiko Amafuji, Yuuko Kiridooshi, Kayoko Sugita, Martin Stražar, Ashwin Skelly, Wataru Suda, Masahira Hattori, Nobuhiro Nakamoto, Silvia Caballero, Jason Norman, Bernat Olle, Takeshi Tanoue, Makoto Arita, Vanni Bucci, Koji Atarashi, Ramnik Xavier

Research square　2023/10/23

Improvement of ethanol and 2,3-butanediol production in Saccharomyces cerevisiae by ATP wasting

Futa Yatabe, Taisuke Seike, Nobuyuki Okahashi, Jun Ishii, Fumio Matsuda

Microbial Cell Factories　Vol. 22　No. 1　2023/10/08　Research paper (scientific journal)

Comprehensive analysis of the composition of the major phospholipids during the asexual life cycle of the filamentous fungus Aspergillus nidulans

Ryo Iwama, Nobuyuki Okahashi, Tetsuki Suzawa, Chuner Yang, Fumio Matsuda, Hiroyuki Horiuchi

Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids　Vol. 1868　No. 10　p. 159379-159379　2023/08　Research paper (scientific journal)

Simple and Rapid Non-ribosomal Peptide Synthetase Gene Assembly Using the SEAM–OGAB Method

Varada Jagadeesh, Takanobu Yoshida, Misugi Uraji, Nobuyuki Okahashi, Fumio Matsuda, Christopher J. Vavricka, Kenji Tsuge, Akihiko Kondo

ACS Synthetic Biology　Vol. 12　No. 1　p. 305-318　2022/12/23　Research paper (scientific journal)

Data Processing of Product Ion Spectra: Quality Improvement by Averaging Multiple Similar Spectra of Small Molecules

Fumio Matsuda, Shuka Komori, Yuki Yamada, Daiki Hara, Nobuyuki Okahashi

Mass Spectrometry　Vol. 11　No. 1　p. A0106-A0106　2022/12/15　Research paper (scientific journal)

Lipidome variation of industrial Saccharomyces cerevisiae strains analyzed by LC-QTOF/MS-based untargeted lipidomics

Shuka Komori, Nobuyuki Okahashi, Junko Iida, Fumio Matsuda

Journal of Bioscience and Bioengineering　Vol. 135　No. 2　p. 102-108　2022/12　Research paper (scientific journal)

Isotope Calculation Gadgets: A Series of Software for Isotope-Tracing Experiments in Garuda Platform

Nobuyuki Okahashi, Yuki Yamada, Junko Iida, Fumio Matsuda

Metabolites　Vol. 12　No. 7　p. 646-646　2022/07/14　Research paper (scientific journal)

Structures and functions of the gut microbial lipidome

Satoshi Morozumi, Masahiro Ueda, Nobuyuki Okahashi, Makoto Arita

Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids　Vol. 1867　No. 3　p. 159110-159110　2022/03　Research paper (scientific journal)

Comparative Evaluation of Plasma Metabolomic Data from Multiple Laboratories

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 Yokota Hirai, Masaru Yoshida, Yoshiya Oda, Fumio Matsuda, Takeshi Bamba

Metabolites　Vol. 12　No. 2　p. 135-135　2022/02/01　Research paper (scientific journal)

mfapy: An open-source Python package for 13C-based metabolic flux analysis

Fumio Matsuda, Kousuke Maeda, Takeo Taniguchi, Yuya Kondo, Futa Yatabe, Nobuyuki Okahashi, Hiroshi Shimizu

Metabolic Engineering Communications　Vol. 13　p. e00177-e00177　2021/12　Research paper (scientific journal)

Metabolic flux and flux balance analyses indicate the relevance of metabolic thermogenesis and aerobic glycolysis in cancer cells

Nobuyuki Okahashi, Tomoki Shima, Yuya Kondo, Chie Araki, Shuma Tsuji, Akane Sawai, Hikaru Uehara, Susumu Kohno, Hiroshi Shimizu, Chiaki Takahashi, Fumio Matsuda

2021/11/19

Global profiling of gut microbiota-associated lipid metabolites in antibiotic-treated mice by LC-MS/MS-based analyses

Nobuyuki Okahashi, Masahiro Ueda, Shu Yasuda, Hiroshi Tsugawa, Makoto Arita

STAR Protocols　Vol. 2　No. 2　p. 100492-100492　2021/06　Research paper (scientific journal)

Comparative 13 C‐metabolic flux analysis indicate elevation of ATP regeneration, carbon dioxide, and heat production in industrial Saccharomyces cerevisiae strains

Futa Yatabe, Nobuyuki Okahashi, Taisuke Seike, Fumio Matsuda

Biotechnology Journal　p. 2000438-2000438　2021/05　Research paper (scientific journal)

Staphylococcus cohnii is a potentially biotherapeutic skin commensal alleviating skin inflammation

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

Cell Reports　Vol. 35　No. 4　p. 109052-109052　2021/04　Research paper (scientific journal)

Treatment of RB1‐intact hepatocellular carcinoma with CDK4/6 inhibitor combination therapy

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

Hepatology　Vol. 74　No. 4　p. 1971-1993　2021/04　Research paper (scientific journal)

Analyses of Lipid A Diversity in Gram-Negative Intestinal Bacteria Using Liquid Chromatography–Quadrupole Time-of-Flight Mass Spectrometry

Nobuyuki Okahashi, Masahiro Ueda, Fumio Matsuda, Makoto Arita

Metabolites　Vol. 11　No. 4　p. 197-197　2021/03　Research paper (scientific journal)

Synthetic production of prenylated naringenins in yeast using promiscuous microbial prenyltransferases

Shota Isogai, Nobuyuki Okahashi, Ririka Asama, Tomomi Nakamura, Tomohisa Hasunuma, Fumio Matsuda, Jun Ishii, Akihiko Kondo

Metabolic Engineering Communications　Vol. 12　p. e00169-e00169　2021/03　Research paper (scientific journal)

Senolysis by glutaminolysis inhibition ameliorates various age-associated disorders.

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, Ryuta Mikawa, Makoto Suematsu, Makoto Arita, Masataka Sugimoto, Keiichi I Nakayama, Yoichi Furukawa, Seiya Imoto, Makoto Nakanishi

Science (New York, N.Y.)　Vol. 371　No. 6526　p. 265-270　2021/01/15　Research paper (scientific journal)

Helicobacter pylori metabolites exacerbate gastritis through C-type lectin receptors

Masahiro Nagata, Kenji Toyonaga, Eri Ishikawa, Shojiro Haji, Nobuyuki Okahashi, Masatomo Takahashi, Yoshihiro Izumi, Akihiro Imamura, Koichi Takato, Hideharu Ishida, Shigenori Nagai, Petr Illarionov, 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

Journal of Experimental Medicine　Vol. 218　No. 1　2021/01/04　Research paper (scientific journal)

Elucidation of Gut Microbiota-Associated Lipids Using LC-MS/MS and 16S rRNA Sequence Analyses

Shu Yasuda, Nobuyuki Okahashi, Hiroshi Tsugawa, Yusuke Ogata, Kazutaka Ikeda, Wataru Suda, Hiroyuki Arai, Masahira Hattori, Makoto Arita

iScience　Vol. 23　No. 12　p. 101841-101841　2020/12　Research paper (scientific journal)

A lipidome atlas in MS-DIAL 4.

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

Nature biotechnology　Vol. 38　No. 10　p. 1159-1163　2020/06/15　Research paper (scientific journal)

Computational data mining method for isotopomer analysis in the quantitative assessment of metabolic reprogramming

Fumio Matsuda, Kousuke Maeda, Nobuyuki Okahashi

Scientific Reports　Vol. 10　No. 1　2020/01/14　Research paper (scientific journal)

Inter-laboratory comparison of metabolite measurements for metabolomics data integration

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

Metabolites　Vol. 9　No. 11　2019/10/31　Research paper (scientific journal)

Time-resolved analysis of short term metabolic adaptation at dark transition in Synechocystis sp. PCC 6803

Masaharu Maruyama, Hiroki Nishiguchi, Masakazu Toyoshima, Nobuyuki Okahashi, Fumio Matsuda, Hiroshi Shimizu

Journal of Bioscience and Bioengineering　Vol. 128　No. 4　p. 424-428　2019/10　Research paper (scientific journal)

Fragmentation of Dicarboxylic and Tricarboxylic Acids in the Krebs Cycle Using GC-EI-MS and GC-EI-MS/MS.

Nobuyuki Okahashi, Shuichi Kawana, Junko Iida, Hiroshi Shimizu, Fumio Matsuda

Mass spectrometry (Tokyo, Japan)　Vol. 8　No. 1　2019/08　Research paper (scientific journal)

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

Nobuyuki Okahashi, Kousuke Maeda, Shuichi Kawana, Junko Iida, Hiroshi Shimizu, Fumio Matsuda

Metabolic Engineering　Vol. 51　p. 43-49　2019/01　Research paper (scientific journal)

Mass Spectrometry-Based Method to Study Inhibitor-Induced Metabolic Redirection in the Central Metabolism of Cancer Cells.

Chie Araki, Nobuyuki Okahashi, Kousuke Maeda, Hiroshi Shimizu, Fumio Matsuda

Mass spectrometry (Tokyo, Japan)　Vol. 7　No. 1　2018/04

Metabolic engineering of isopropyl alcohol-producing Escherichia coli strains with ¹³C-metabolic flux analysis

Nobuyuki Okahashi, Fumio Matsuda, Katsunori Yoshikawa, Tomokazu Shirai, Yoshiko Matsumoto, Mitsufumi Wada, Hiroshi Shimizu

Biotechnology and Bioengineering　Vol. 114　No. 12　p. 2782-2793　2017/12　Research paper (scientific journal)

The RB-IL-6 axis controls self-renewal and endocrine therapy resistance by fine-tuning mitochondrial activity

S. Kitajima, A. Yoshida, S. Kohno, F. Li, S. Suzuki, N. Nagatani, Y. Nishimoto, N. Sasaki, H. Muranaka, Y. Wan, T. C. Thai, N. Okahashi, F. Matsuda, H. Shimizu, T. Nishiuchi, Y. Suzuki, K. Tominaga, N. Gotoh, M. Suzuki, M. E. Ewen, D. A. Barbie, O. Hirose, T. Tanaka, C. Takahashi

Oncogene　Vol. 36　No. 36　p. 5145-5157　2017/09/07　Research paper (scientific journal)

Investigation of useful carbon tracers for ¹³C-metabolic flux analysis of Escherichia coli by considering five experimentally determined flux distributions

Kousuke Maeda, Nobuyuki Okahashi, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu

Metabolic Engineering Communications　Vol. 3　p. 187-195　2016/12/01　Research paper (scientific journal)

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

Nobuyuki Okahashi, Shuichi Kawana, Junko Iida, Hiroshi Shimizu, Fumio Matsuda

Analytical and Bioanalytical Chemistry　Vol. 408　No. 22　p. 6133-6140　2016/09/01　Research paper (scientific journal)

Metabolic characterization of cultured mammalian cells by mass balance analysis, tracer labeling experiments and computer-aided simulations

Nobuyuki Okahashi, Susumu Kohno, Shunsuke Kitajima, Fumio Matsuda, Chiaki Takahashi, Hiroshi Shimizu

Journal of Bioscience and Bioengineering　Vol. 120　No. 6　p. 725-731　2015/12　Research paper (scientific journal)

Absolute quantitation of glycolytic intermediates reveals thermodynamic shifts in Saccharomyces cerevisiae strains lacking PFK1 or ZWF1 genes

Shunsuke Nishino, Nobuyuki Okahashi, Fumio Matsuda, Hiroshi Shimizu

Journal of Bioscience and Bioengineering　Vol. 120　No. 3　p. 280-286　2015/09/01　Research paper (scientific journal)

Reliable Metabolic Flux Estimation in Escherichia coli Central Carbon Metabolism Using Intracellular Free Amino Acids.

Nobuyuki Okahashi, Shuichi Kajihata, Chikara Furusawa, Hiroshi Shimizu

Metabolites　Vol. 4　No. 2　p. 408-20　2014/05/30