Shifts in the bacterial composition of the human gut microbiota (i.e. dysbiosis) have been associated with digestive tract dysfunctions such as inflammatory bowel diseases. More strikingly, strong evidence, from both human studies and germ-free animal models, links intestinal microbiota dysbiosis with metabolic disorders, such as obesity and liver diseases. This chapter focuses on the changes and impact of the gut microbiota during these diseased states, and describes the possible direct and indirect mechanisms that an aberrant gut microbiota can promote metabolic dysregulations. The possible involvement of the 'microbiota-gut-brain' axis in the development of obesity is further discussed, as is the perspective of meta-omic technologies that give insight into the functions and potential effect of the non-cultured intestinal bacteria on the host health. Understanding how modifications in this finely tuned ecosystem lead to these pathological processes is crucial for the development of new therapeutic approaches to treat and hopefully ameliorate these metabolic diseases.