Mass spectrometry-based metabolomics for studying gut microbiota-derived metabolites in biological samples

Gut microbiota produces a wide range of metabolites and plays a critical role in maintaining host health. Dysregulation of these metabolites can influence host metabolism through systemic circulation, contributing to the development of various diseases, including immunological, neurological and cancer-related disorders. Chromatography coupled with mass spectrometry (MS) has emerged as a powerful analytical approach, offering high sensitivity and resolution for studying gut microbiota-related metabolites. This review provides a comprehensive overview of chromatographic MS-based methods applied to the study of the gut microbial metabolome. We summarize strategies for sample collection, storage, and preparation of commonly analyzed sample types, including feces, plasma/serum, urine, and tissue samples. In addition, we included the main chromatographic MS-based approaches, as well as data analysis techniques, for investigating the gut microbial metabolome. The characteristics and utility of liquid chromatographic-mass spectrometry (LC-MS), gas chromatographic-mass spectrometry (GC-MS), and capillary electrophoresis-mass spectrometry (CE-MS) were discussed in the context of providing broader coverage of gut microbiota-derived metabolites with diverse physicochemical properties. Finally, we summarize recent studies that have employed chromatographic MS-based approaches to investigate gut microbiota-related disease. Through the integration of appropriate sample handling and advanced analytical strategies, a deeper understanding of host–microbiota interactions and their roles in health and disease can be achieved.