Recent advances and future directions in microbiome metabolomics

Abstract One of the ways in which the human microbiome interacts with its host is via the vast array of chemically diverse metabolites it produces. The importance of the microbiome ‘metabolome’ to the host is underscored by its associations with a diverse range of host biological processes as well as an increasing number of chronic disease states such as obesity, inflammatory bowel disease, liver disease and metabolic syndrome. These associations are often complex and, in many cases, mechanistic links remain unclear. Metabolomics is a state-of-the-art analytical technique used to identify metabolic changes in biochemical systems and can reveal mechanistic links between microbiome composition, host homoeostasis and aberrant disease states. Here, we provide an overview of current metabolomics applications investigating important human diseases linked to the microbiome. In addition, we introduce recent technical developments in metabolomics that have the potential to lead to a greater understanding of how microbiome metabolism contributes to the manifestation of host pathophysiology.