Nowadays, the literature provides evidence that obesity, type 2 diabetes and insulin resistance are characterized by a low grade inflammation. Among the environmental factors involved in such diseases, the gut microbiota has been proposed as a key player. This neglected "organ" has been found to be different between healthy and or obese and type 2 diabetic patients. For example, recent data have proposed that dysbiosis of gut microbiota (at phyla, genus, or species level) affects host metabolism and energy storage. Among the mechanisms, metabolic endotoxemia (higher plasma LPS levels), gut permeability and the modulation of gut peptides (GLP-1 and GLP-2) have been proposed as putative targets. Here we discuss 1 degrees the specific modulation of the gut microbiota composition by using prebiotics and 2 degrees the novel findings that may explain how gut microbiota can be involved in the development or in the control of obesity and associated low-grade inflammation.