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Microbial metabolomics: past, present and future methodologies

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Abstract

Microbial metabolomics has received much attention in recent years mainly because it supports and complements a wide range of microbial research areas from new drug discovery efforts to metabolic engineering. Broadly, the term metabolomics refers to the comprehensive (qualitative and quantitative) analysis of the complete set of all low molecular weight metabolites present in and around growing cells at a given time during their growth or production cycle. This review focuses on the past, current and future development of various experimental protocols in the rapid developing area of metabolomics in the ongoing quest to reliably quantify microbial metabolites formed under defined physiological conditions. These developments range from rapid sample collection, instant quenching of microbial metabolic activity, extraction of the relevant intracellular metabolites as well as quantification of these metabolites using enzyme based and or modern high tech hyphenated analytical protocols, mainly chromatographic techniques coupled to mass spectrometry (LC-MSn, GC-MSn, CE-MSn), where n indicates the number of tandem mass spectrometry, and nuclear magnetic resonance spectroscopy (NMR).

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Abbreviations

Metabolomics:

Quantification of the total metabolites complement inside and outside a cell under defined growth conditions

Exometabolome:

Total metabolites excreted outside the cell (culture supernatant)

Endometabolome:

Total metabolites located inside the cell (Intracellularly)

Footprinting:

Qualitative analysis of exometabolome

Fingerprinting:

Qualitative analysis of endometabolome

Target analysis:

Quantitative analysis of known pre-defined metabolites concentrations

Quenching:

Instantaneous arrest of endogenous metabolic activity

GC-MS:

Gas chromatography coupled to mass spectrometry

LC-ESI-MS:

Liquid chromatography coupled to electrospray ionisation mass spectrometry

Q-TOF:

uattro Time of light

FT-ICR:

Fourier transform-ion cyclotron resonance

CE-MS:

Capillary electrophoresis coupled to mass spectrometry

Metabolite turnover rate:

The inverse of the metabolite pool size to metabolite flux ratio

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Authors and Affiliations

  1. Department of Biotechnology, Faculty of Applied Sciences, Technical University of Delft, Julianalaan 67, 2628 BC, Delft, The Netherlands

    Mlawule R. Mashego & Joseph J. Heijnen

  2. Department of Biochemical and Microbial Technology, Laboratory of Industrial Microbiology and Biocatalysis, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000, Gent, Belgium

    Mlawule R. Mashego, Karl Rumbold, Marjan De Mey, Erick Vandamme & Wim Soetaert

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  1. Mlawule R. Mashego
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  2. Karl Rumbold
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Mashego, M.R., Rumbold, K., De Mey, M. et al. Microbial metabolomics: past, present and future methodologies. Biotechnol Lett 29, 1–16 (2007). https://doi.org/10.1007/s10529-006-9218-0

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