The scientific literature has shown that diet is able to modify the gut microbiota and contribute to obesity and diabetes development. This process—characterized by inflammation and gut barrier disruption—can affect the immune system and alter the adipogenesis and insulin resistance. This chapter describes the advances in nutrigenomics and Human Intestinal Microbiota (HIM) modification, and its relation with diabetes mellitus type two (DM2). In context where health and feeding are the main concerns of the human being, food innovation takes a special interest to people that look for a healthy diet or demand a functional aliments, such as nutraceutical. Some products derived from diet and interaction with HIM module the expression of many genes on the host, the so-called epigenome, with favorable effects. Novel functional fiber like low-glycemic oligosaccharides and sweeteners shows a potential prebiotic activity giving a new focus of nutritional guidelines for control and prevention of DM2. The use of prebiotics derived from functional fiber sources, such as fructo-oligosaccharides and beta-glucans as well as lignin and keffir, can contribute to the development of a healthy HIM by promoting the growth of specific bacteria, some of them associated with the prevention of obesity and diabetes.