The contribution of the gut microbiota to the development of a large number of diseases, including obesity, is being explored. Although mechanisms are not fully understood, perturbations on gut microbiota composition seem to be an important factor. Therefore, modulation of gut bacterial community with approaches (i.e. supplementation with polyphenols) that could enhance the growth of ¿friendly¿ bacteria and reduce harmful bacteria might be an effective therapeutic tool. This thesis aimed to provide a snapshot of the complex system consisting of gut microbiota, diet and polyphenols, host metabolism and health. For this purpose, this work has taken advantage of advanced technologies namely next-generation sequencing and untargeted metabolomics In the present work it is demonstrated that consumption of a high-fat high-sucrose diet strongly affects host metabolome altering serum levels of a different set of metabolites, which might be reflective of the physiopathology of diet-induced obesity. Moreover, the obesogenic diet strongly impacts gut microbiota composition perturbing the bacterial balance towards an obesity-associated gut microbial pattern. Remarkably, the use of pure natural compounds, particularly quercetin, could counteract the disturbance of gut microbiota related to diet-induced obesity. In contrast, trans-resveratrol significantly influences gene expression level in the intestine in vivo, without notably modifying gut microbial profile. In this context, trans-resveratrol seems to favour intestinal epithelial homeostasis promoting the repair of intestinal epithelial barrier, upon damage. Furthermore, from the in vitro studies conducted in Caco-2 cells, the inhibitory action of the stilbene on genes implicated in lipid metabolism has been observed. Finally, biological outcomes exerted by polyphenols on global host metabolome might be distinguished through a faecal non-targeted metabolomic analysis, proposing the potential of this technique to elucidate interactions between gut bacteria and polyphenols, and also to discriminate individuals in different groups based on the dietary intervention they have been subjected to.