Microbial metabolomics: Toward a platform with full metabolome coverage
Section snippets
In silico metabolomes
The complete lists of metabolites present in the in silico metabolomes of E. coli and Bacillus subtilis were deduced from the metabolite databases for these microorganisms as downloaded in April 2005 from http://www.ecocyc.org (version 9.0 [15]) and http://biocyc.org/BSUB/organism-summary?object=BSUB and the metabolite database for yeast as downloaded in August 2006 from http://systemsbiology.ucsd.edu/organisms/yeast.html[16]. These metabolite lists were curated manually; compounds with
Metabolite composition of microbial metabolomes
For the development of an analytical platform that allows the detection of all metabolites present in microbial metabolomes, it is essential to have access to information about the type and number of metabolites potentially present in microorganisms. To this end, we established the in silico metabolomes of three phylogenetically different and commonly applied microorganisms: E. coli, B. subtilis, and Saccharomyces cerevisiae. Metabolite lists were downloaded from the compounds sub-databases in
Discussion
We have presented a strategy for the development of a metabolomics platform toward the analysis of full microbial metabolomes. Notwithstanding the large chemical diversity of metabolites, using a combination of six different GC–MS and LC–MS methods only, of the 399 metabolites for which commercial standards could be purchased, 380 could be analyzed with this metabolomics platform. Notably, two of the methods of our metabolomics platform, the OS–GC–MS and IP–LC–MS methods, were very powerful and
Acknowledgments
The authors thank Nicole van Luijk and Anna Conesa for downloading the Bacillus subtilis metabolite database; Roelie Bijl for cultivating Escherichia coli and extracting the samples; Maud Koek, Leo van Stee, and Richard Bas for GC–MS and LC–MS analysis; Roche Vitamins (currently DSM DNP, Basel, Switzerland) for financial support; and Markus Wyss and Werner Bretzel (currently DSM DNP) for fruitful discussions.
References (37)
- et al.
Metabolomics by numbers: Acquiring and understanding global metabolite data
Trends Biotechnol.
(2004) Towards replacing closed with open target selection approaches
Trends Biotechnol.
(2005)- et al.
Metabolomics or metabolite profiles?
Trends Biotechnol.
(2005) - et al.
A structure-based anatomy of the Escherichia coli metabolome
J. Mol. Biol.
(2003) - et al.
Negative mode sheatless capillary electrophoresis electrospray ionization–mass spectrometry for metabolite analysis of prokaryotes
J. Chromatogr. A
(2006) - et al.
Simultaneous analysis of the majority of low-molecular-weight, redox-active compounds from mitochondria
Anal. Chem.
(1998) - et al.
Quenching of microbial samples for increased reliability of microarray data
J. Microbiol. Methods
(2006) - et al.
Determination of intermediary metabolites in Aspergillus niger
J. Microbiol. Methods
(1996) - et al.
Characterization of anti-inflammatory compounds using transcriptomics, proteomics, and metabolomics in combination with multivariate data analysis
Int. Immunopharmacol.
(2004) - et al.
Impact of the cold shock phenomenon on quantification of intracellular metabolites in bacteria
Anal. Chem.
(2004)
Microbial metabolomics: Replacing trial-and-error by the unbiased selection and ranking of targets
J. Ind. Microbiol. Biotechnol.
Metabolic engineering in the -omics era: Elucidating and modulating regulatory networks
Microbiol. Mol. Biol. Rev.
Metabolome and proteome profiling for microbial characterization
Metabolite profiling for plant functional genomics
Nat. Biotechnol.
Two-dimensional separation system of coupling capillary liquid chromatography to capillary electrophoresis for analysis of Escherichia coli metabolites
Electrophoresis
Quantitative metabolome analysis using capillary electrophoresis mass spectrometry
J. Proteome Res.
Comprehensive analysis of metabolites in Corynebacterium glutamicum by gas chromatography/mass spectrometry
Biol. Chem.
High-throughput metabolic state analysis: The missing link in integrated functional genomics of yeasts
Biochem. J.
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Current address: Division of Analytical Biosciences, Leiden/Amsterdam Center for Drug Research, 2300 RA Leiden, The Netherlands.