Cited by 208Metabolomics and Mass Spectrometry StudiesMicrobial Metabolic Engineering and BioproductionBacterial Identification and Susceptibility Testing

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Microbial metabolomics: Toward a platform with full metabolome coverage

Werf, Mariët J. van der, Overkamp, Karin M., Muilwijk, Bas, Coulier, Leon, Hankemeier, Thomas·2007·Analytical Biochemistry

DOI 10.1016/j.ab.2007.07.022

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Abstract

Achieving metabolome data with satisfactory coverage is a formidable challenge in metabolomics because metabolites are a chemically highly diverse group of compounds. Here we present a strategy for the development of an advanced analytical platform that allows the comprehensive analysis of microbial metabolomes. Our approach started with in silico metabolome information from three microorganisms-Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae-and resulted in a list of 905 different metabolites. Subsequently, these metabolites were classified based on their physicochemical properties, followed by the development of complementary gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry methods, each of which analyzes different metabolite classes. This metabolomics platform, consisting of six different analytical methods, was applied for the analysis of the metabolites for which commercial standards could be purchased (399 compounds). Of these 399 metabolites, 380 could be analyzed with the platform. To demonstrate the potential of this metabolomics platform, we report on its application to the analysis of the metabolome composition of mid-logarithmic E. coli cells grown on a mineral salts medium using glucose as the carbon source. Of the 431 peaks detected, 235 (=176 unique metabolites) could be identified. These include 61 metabolites that were not previously identified or annotated in existing E. coli databases.

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Kunst, F., Ogasawara, N., Moszer, I., Albertini, A. M., Alloni, G., Azevedo, V., Bertero, M. G., Bessières, P., Bolotin, A., Borchert, S., et al. (1997) · Nature · doi:10.1038/36786 · Cited by 3,679
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Authors: Werf, M. J. V. D., Overkamp, K. M., Muilwijk, B., Coulier, L., & Hankemeier, T.
Corresponding author: Werf, Mariët J. van der
ORCID: Coulier, Leon
Hankemeier, Thomas
Venue: Analytical Biochemistry
Publisher: Elsevier BV
Published: 2007-11
Volume: 370
Issue: 1
Pages: 17-25
ISSN: 0003-2697 (ISSN-L)
DOI: 10.1016/j.ab.2007.07.022
OpenAlex: W1965468642
Cited by: 207
References: 37
Citations by year: 2025: 3 · 2024: 4 · 2023: 3 · 2022: 4 · 2021: 5 · 2020: 3 · 2019: 9 · 2018: 4 · 2017: 4 · 2016: 11 · 2015: 20 · 2014: 16 · 2013: 18 · 2012: 20
FWCI: 8.73
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
Locations: Analytical Biochemistry (publishedVersion)
PubMed (publishedVersion)
TNO Repository (submittedVersion)
Repository hosted by TU Delft Library (TU Delft) (submittedVersion)
Data Archiving and Networked Services (DANS) (submittedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
Health Sciences › Medicine › Microbiology (medical) › Bacterial Identification and Susceptibility Testing
Keywords: microbial metabolomics, Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, metabolite classification, gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, metabolite identification
MeSH terms: Bacillus subtilis, Chromatography, Liquid, Escherichia coli, Gas Chromatography-Mass Spectrometry, Saccharomyces cerevisiae, Databases, Factual

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Microbial metabolomics: Toward a platform with full metabolome coverage

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