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

Ya-Ting Lin, School of Pharmacy, National Taiwan University, Taipei, Taiwan
Huai-Hsuan Chiu, Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
Chih-Ning Cheng, School of Pharmacy, National Taiwan University, Taipei, Taiwan
Ching-Hua Kuo, The Metabolomics Core Laboratory, Center of Genomic and Precision Medicine, National Taiwan University, Taipei, TaiwanFollow

Keywords

biological samples; chromatography; gut microbiota; metabolomics; mass spectrometry

Abstract

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.

Recommended Citation

Lin, Ya-Ting; Chiu, Huai-Hsuan; Cheng, Chih-Ning; and Kuo, Ching-Hua (2026) "Mass spectrometry-based metabolomics for studying gut microbiota-derived metabolites in biological samples," Journal of Food and Drug Analysis: Vol. 34 : Iss. 1 , Article 2.
Available at: https://doi.org/10.38212/2224-6614.3568