Recently, a number of studies have related the development of highly prevalent disorders such as type 2 diabetes and obesity to gut microbiota. Obesity itself have been associated with modifications in gut microbiota composition, and a tendency towards an overgrowth of microorganisms that obtain more efficient energy from diet. It's capacity to decompose the polysaccharides that can not be digested by the host, increase monosaccharide and short chain fatty acid (SCFA) production. However, the increase in fat mass is not only due to a more efficient harvest of energy, but also the microbiota participates in changes in endotoxemia, bowel permeability, insulin resistance, hormonal environment, expression of genes regulating lipogenesis, interaction with bile acids, as well as changes in the proportion of brown adipose tissue, and effects associated with the use of drugs such as metformin. Currently, use of prebiotics and probiotics and other innovative techniques like antibiotic therapy or gut microbiota transplant, has been proposed as suitable tools to control the development of metabolic diseases such as obesity or insulin resistance through the diet.