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Total Metabolome Extraction from Mycobacterial Cells for GC-MS Metabolomics Analysis

Part of the Methods in Molecular Biology book series (MIMB,volume 1859)


Over the past 10 years, the number of metabolomics based publications in the available scientific literature has exponentially grown, a large portion of which describing new biomarkers better elucidating microbial disease mechanisms and improved diagnostics and treatment thereof. Here, we describe a metabolomics method for extracting the total metabolome (all compounds present in the microbial cell irrespective of the compound class), for analysis in a single analytical run using only one analytical instrument. This method includes disruption of robust microbial cell walls, and the precipitation of proteins and cell debris using a combination of mechanical methods and solvents. These extracts are subsequently derivatized, in order to improve the volatility of polar compounds for efficient gas chromatography-mass spectrometry (GC-MS) analysis. This methodology can be applied to all microbes, including those with robust cell walls, such as M. tuberculosis. To date, the biomarkers identified using this approach have led to improved tuberculosis (TB) diagnostics, improved TB treatment approaches, and better understanding of host–microbe interactions and associated mycobacterial genomics.

Key words

  • Metabolomics
  • Total metabolome extraction
  • GC-MS
  • Mycobacteria

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  • DOI: 10.1007/978-1-4939-8757-3_6
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The financial assistance of the National Research Foundation (NRF) of South Africa for this research is gratefully acknowledged (UID: 95269). The opinions expressed and conclusions derived are those of the authors and are not necessarily those of the NRF.

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Correspondence to Du Toit Loots .

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Beukes, D., du Preez, I., Loots, D.T. (2019). Total Metabolome Extraction from Mycobacterial Cells for GC-MS Metabolomics Analysis. In: Baidoo, E. (eds) Microbial Metabolomics. Methods in Molecular Biology, vol 1859. Humana Press, New York, NY.

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  • Print ISBN: 978-1-4939-8756-6

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