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

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.