Review on microbial metabolomics of probiotics and pathogens: Methodologies and applications

In recent years, microbial metabolomics, a new field that has attracted wide attention, provides a map of metabolic pathways and clarifies the interaction mechanism between microorganisms and hosts. Many microorganisms are found in the human intestine, oral cavity, vagina, etc. Probiotics could maintain the good health of the host, while pathogens and an imbalance of bacterial flora lead to a series of diseases of the body and mind. Metabolomics is a science for qualitative and quantitative analysis of all metabolites in an organism or biological system, which could provide key information to understand the related metabolic pathways and associated changes. This approach analyzes the final products of cellular regulatory processes, the level of which can be regarded as the ultimate response of the biological system to genetic or environmental changes. Microbial metabolomics has been widely used in different research fields, such as microbial phenotypic classification, mutant screening, metabolic pathways, microbial metabolic engineering, fermentation engineering monitoring and optimization, microbial environmental pollution, and so on. However, there are only a few reviews on microbial metabolomics of probiotics and pathogens. This review summarizes the main methodologies, including sample preparation, identification of metabolites, data processing, and analysis. Recent applications in microbial metabolomics of probiotics and pathogens are also described. This paper first summarized the research progress and application of microbial metabolomics from two aspects: probiotics and pathogenic bacteria. Probiotics and pathogenic bacteria do not exist independently most of the time; hence, these were reviewed in the research field of coexistence of probiotics and pathogenic bacteria, which was subdivided into important microbial research fields closely related to human health, including the human gut, oral cavity, food, and nutrition-related microorganisms. Then, the main problems and trends associated with microbial metabolomics are discussed.