It is well established that gut microbes and their metabolic products
regulate host metabolism. The interactions between the host and its gut
microbiota are highly dynamic and complex. In this review we present and
discuss the metabolomic strategies to study the gut microbial
ecosystem. We highlight the metabolic profiling approaches to study
faecal samples aimed at deciphering the metabolic product derived from
gut microbiota. We also discuss how metabolomics data can be integrated
with metagenomics data derived from gut microbiota and how such
approaches may lead to better understanding of the microbial functions.
Finally, the emerging approaches of genome-scale metabolic modelling to
study microbial co-metabolism and host–microbe interactions are
highlighted.