Unlocking the secrets of the microbiome: exploring the dynamic microbial interplay with humans through metabolomics and their manipulation for synthetic biology applications

Metabolomics is a powerful research discovery tool with the potential to measure hun-dreds to low thousands of metabolites. In this review, we discuss the application of GC- MS and LC-MS in discovery-based metabolomics research, we define metabolomics workflows and we highlight considerations that need to be addressed in order to generate robust and reproducible data. We stress that metabolomics is now routinely applied across the biological sciences to study microbiomes from relatively simple microbial systems to their complex interactions within consortia in the host and the environment and highlight this in a range of biological species and mammalian systems including humans. However, challenges do still exist that need to be overcome to maximise the potential for metabolomics to help us understanding biological systems. To demonstrate the potential of the approach we discuss the application of metabolomics in two broad research areas: (1) synthetic biology to increase the production of high-value fine chemi-cals and reduction in secondary by-products and (2) gut microbial interaction with the human host. While burgeoning in importance, the latter is still in its infancy and will benefit from the development of tools to detangle host-gut-microbial interactions and their impact on human health and diseases.

Automated summary

Metabolomics is a powerful research tool that can measure hundreds to thousands of metabolites. This review discusses the use of GC-MS and LC-MS in discovery-based metabolomics research, defines metabolomics workflows, and highlights considerations for generating robust and reproducible data. It emphasizes the routine application of metabolomics across various biological species and systems, including the study of microbial interactions and their impact on human health. The review also discusses the challenges and potential applications of metabolomics in synthetic biology and gut microbial interactions with the human host.