Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe

• Published in: Methods (San Diego, Calif.) Calif.), 2018-10, Vol.149, p.3-12
• Main Authors: Lamichhane, Santosh, Sen, Partho, Dickens, Alex M., Orešič, Matej, Bertram, Hanne Christine
• Format: Article
• Language: English
• Subjects: Faecal metabolites; Genome-scale metabolic models; Gut microbiota; Metabolomics; Microbiome
• ISSN: 1046-2023; 1095-9130; 1095-9130
• DOI: 10.1016/j.ymeth.2018.04.029

•Metabolomics strategy to study human gut microbial phenotype is gaining increasing attention.•Integration of metabolomics and metagenomics provides a crucial framework for interrogating the gut-microbe-metabolic axis.•Genome scale metabolic models may be a powerful tool for the deconvolution of host-gut microbial co-metabolism. 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.