Comparative Metabolomics Revealing the Metabolic Responses of Pathogenic Bacteria to Different Antibiotics

This protocol describes the extraction and analysis of bacterial metabolites to determine the metabolic changes pertaining to their responses to different types of antibiotics. Polar metabolites are extracted using a methanol-based extraction. Sensitive, specific, and semi-quantitative metabolite analysis was performed using a high-performance liquid chromatography coupled to a high-resolution quadrupole-Orbitrap mass spectrometry. Using our example bacteria as a demonstration, 14,528 metabolic features can be detected, and 1448 metabolites were putatively identified via basic database search. Additionally, 93 metabolites can be confidently identified via high-purity standards. Statistical analysis of these metabolites can pinpoint crucial changes in metabolic states of pathogens going through antibiotic treatment, which may assist our understanding of the antibiotic mechanism of actions from a metabolic perspective.