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  • Review Article
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Metabolic footprinting and systems biology: the medium is the message

Nature Reviews Microbiology volume 3, pages 557–565 (2005)Cite this article

Key Points

  • The metabolome can be defined as the quantitative complement of low-molecular-weight metabolites present in a cell under a given set of physiological conditions. As changes in a cell's physiology as a result of gene deletion or overexpression are amplified through the hierarchy of the transcriptome and the proteome, it can be argued that such changes are more easily measurable through the metabolome, and that the metabolome is more sensitive to perturbations than is either the transcriptome or proteome.

  • High-throughput measurement of a complete set of intracellular microbial metabolites would require the development of an accurate, simple and rapid method with a broad dynamic range suitable for detecting and quantifying large numbers of metabolites that can be present at different concentrations.

  • Instead, the global exometabolome – or secreted metabolites - can be analysed using metabolic footprinting, a convenient and reproducible technique to monitor metabolites consumed from, and secreted into, the growth medium by batch cultures of yeast using direct-injection mass spectrometry. The principles of the technique, and results obtained using it, are described.

  • Metabolic footprinting can therefore be used to generate metabolomic data, which, in the era of systems biology, should be able to be integrated with transcriptomic and proteomic data. The current available data models and data standards for systems biology, and the need for the metabolomics community to follow the lead of transcriptomics and proteomics researchers, are also discussed.

Abstract

One element of classical systems analysis treats a system as a black or grey box, the inner structure and behaviour of which can be analysed and modelled by varying an internal or external condition, probing it from outside and studying the effect of the variation on the external observables. The result is an understanding of the inner make-up and workings of the system. The equivalent of this in biology is to observe what a cell or system excretes under controlled conditions — the 'metabolic footprint' or exometabolome — as this is readily and accurately measurable. Here, we review the principles, experimental approaches and scientific outcomes that have been obtained with this useful and convenient strategy.

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Figure 1: The basis of metabolic footprinting.
Figure 2: Patterns of m/z (mass/charge ratio) values in large-scale gene-knockout metabolic footprinting experiments.
Figure 3: Modern technology applied to metabolic footprinting.

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Acknowledgements

We thank the Biotechnology and Biological Sciences Research Council and the Natural Environment Research Council for financial support. D.B.K. is supported by the Royal Society of Chemistry and the Engineering and Physical Sciences Research Council. We thank N. Bukowski, J. Heald and H. Major for assistance with chromatographic and mass spectrometric analyses, and N. Burton for assistance with yeast microbiology and genetics.

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Authors and Affiliations

  1. School of Chemistry, University of Manchester, Faraday Building, PO Box 88, Sackville Street, Manchester, M60 1QD, UK

    Douglas B. Kell, Marie Brown, Warwick B. Dunn & Irena Spasic

  2. Institute of Biological Sciences, University of Wales, Cledwyn Building, Aberystwyth, SY23 3DD, UK

    Hazel M. Davey

  3. Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK

    Stephen G. Oliver

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  1. Douglas B. Kell
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Correspondence to Douglas B. Kell.

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Competing interests

D.B.K. is a Director of Predictive Solutions Ltd (http://www.abergc.com and http://www.predictivesolutions.co.uk), a company that sells Genetic Programming software.

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FURTHER INFORMATION

Douglas Kell's laboratory

AGML

AnIML

ArMet

GAML

Java Web Services Developer Pack

MAGE-OM

The Metabolic Control Analysis Web

MIAME

mzXML

PEDRo/PSI

SBML

SysBioOM

XML schemas

Glossary

METABOLOME

Nominally all of the small-molecular-weight metabolites in a sample. For practical reasons, this is rarely, if ever, achieved using a single extraction method, and subsets of metabolites ('metabolic profiles') are more typically obtained.

TRANSCRIPTOME

All the mRNA molecules (transcripts) in a sample.

PROTEOME

Nominally all the proteins in a sample. This measurement is not usually achieved because of poor solubilities, especially of membrane proteins, and sometimes protein digests are used, from which peptides representing the proteome are analysed. The concept of the proteome should also include all the post-translational modifications that might occur.

CE-MS

A technique in which metabolites are separated using capillary electrophoresis and then analysed using mass spectrometry. Two different runs are used for cations and anions, whereas neutral molecules can be separated using techniques that give them an effective charge.

GC-MS

A high-resolution analytical technique in which molecules, typically derivatized to enhance their volatility, are separated and then identified using mass spectrometry.

LC-MS

A technique in which metabolites are separated according to their polarity. In metabolomics, reverse-phase chromatography (in which the column is hydrophobic and an organic solvent such as methanol or acetonitrile is used for elution) is most popular, although polar chromatographies are also used.

METABOLIC FOOTPRINTING

A strategy for analysing the properties of cells or tissues by looking in a high-throughout manner at the metabolites that they excrete or fail to take up from their surroundings.

METABOLIC FINGERPRINTING

Classification of samples on the basis of their biological status or origin, using high-throughput methods, usually spectroscopic.

GENETIC PROGRAMMING

A powerful but simple computational technique with which rules are evolved that can be used to solve classification or regression problems, for instance by using the metabolome or metabolic fingerprinting data as the inputs.

GC-TOF MS

A high-resolution analytical technique in which molecules, typically derivatized to enhance their volatility, are separated and then identified using time-of-flight mass spectrometry.

GC × GC-tof MS

Similar to GC-tof MS, but involving two stages of gas-chromatographic separation in which a sample is taken (split) from the first dimension of the separation (typically carried out using a non-polar stationary-phase material) and effecting further ‘orthogonal’ separation (typically using a more polar stationary phase).

2DE/MS

A proteomics technique in which proteins are separated according to their mass and charge, using two-dimensional gel electrophoresis, and subsequently identified, and sometimes quantified, using mass spectrometric methods.

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Kell, D., Brown, M., Davey, H. et al. Metabolic footprinting and systems biology: the medium is the message. Nat Rev Microbiol 3, 557–565 (2005). https://doi.org/10.1038/nrmicro1177

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