Biotechnology Letters

, Volume 29, Issue 1, pp 1–16

Microbial metabolomics: past, present and future methodologies

Authors

    • Department of Biotechnology, Faculty of Applied SciencesTechnical University of Delft
    • Department of Biochemical and Microbial Technology, Laboratory of Industrial Microbiology and Biocatalysis, Faculty of Bioscience EngineeringGhent University
  • Karl Rumbold
    • Department of Biochemical and Microbial Technology, Laboratory of Industrial Microbiology and Biocatalysis, Faculty of Bioscience EngineeringGhent University
  • Marjan De Mey
    • Department of Biochemical and Microbial Technology, Laboratory of Industrial Microbiology and Biocatalysis, Faculty of Bioscience EngineeringGhent University
  • Erick Vandamme
    • Department of Biochemical and Microbial Technology, Laboratory of Industrial Microbiology and Biocatalysis, Faculty of Bioscience EngineeringGhent University
  • Wim Soetaert
    • Department of Biochemical and Microbial Technology, Laboratory of Industrial Microbiology and Biocatalysis, Faculty of Bioscience EngineeringGhent University
  • Joseph J. Heijnen
    • Department of Biotechnology, Faculty of Applied SciencesTechnical University of Delft
Review

DOI: 10.1007/s10529-006-9218-0

Cite this article as:
Mashego, M.R., Rumbold, K., De Mey, M. et al. Biotechnol Lett (2007) 29: 1. doi:10.1007/s10529-006-9218-0

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).

Keywords

BacteriaChromatographyFilamentous fungiMass spectrometryMetabolomicsMetabolite extractionQuenchingRapid samplingYeast

Glossary

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

Copyright information

© Springer Science+Business Media B.V. 2006