| Summary: | Over the past few years, metabolomics has been employed in a broad range of applications in different research fields. Microbial metabolomics has been applied in several microbiological areas, such as identification of microorganisms, cell mutations, functional gene approach, identification of unique metabolic pathways and microbial engineering, leading to a better understanding of the global metabolism and metabolic regulation of certain systems. Metabolites produced by microorganisms constitute a large promising group with diverse applications; however, most of these systems are still unknown and underexplored. In this context, the overall analysis of metabolites involved in a biological system can be used to discover potential biomarkers or specific metabolic changes due to a biological phenomenon studied. In this sense, this review aims to understand the main challenges faced by each step of the workflow in the metabolic analysis of microorganisms and how these difficulties have been overcome. A critical analysis of the articles published within the last five years will be accomplished in this paper to understand how these studies have contributed to the microbial metabolomics research. Moreover, major trends observed in this area will be highlighted here in order to guide readers interested in microbial metabolomics in their future researches.
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