A comparison of two extraction methods for differentiating and characterising various Mycobacterium species and Pseudomonas aeruginosa using GC-MS metabolomics

Abstract

We investigated the capacity of a metabolomics research approach to characterise and differentiate between various infectious Mycobacterium species and Pseudomonas aeruginosa, and compared two extraction procedures; 1) extracting the fatty acid metabolome, and 2) extracting the total metabolome, prior to gas chromatography mass spectrometry (GC-MS) and statistical data analyses. Both extraction procedures, as part of a metabolomics study, were able to successfully differentiate between all bacterial groups investigated. The total metabolome extraction method proved the better of the two methods due to its comparative: simplicity; speed (taking less than 4 h), repeatability; extraction capacity (considering the range of compounds extracted and their relative concentrations), and; ability to extract those compounds which allow a better differentiation and characterisation of the investigated sample groups.