Gut microbiota the “virtual organ” plays a contributory role in the maintaining of human health as well as in the development of gastrointestinal diseases due to intervenes in digestion and metabolism. In this context is relevant to clarify the mechanisms of interaction of the intestinal microbiota with macromolecules for potential therapeutic applications and how bacterial growth or inhibition affect human health. This article reviewed the interaction of beneficial gut microbiota bacteria such as the bifidobacterium, eubacterium, roseburia, bacteroides, faecalibacteriummand lactobacillus genera with food macromolecules (carbohydrates, protein, lipids). It also summarized the way in which gastrointestinal diseases and gut microbiota are related in diabetes, obesity and irritable bowel syndrome as well as the perspectives of how functional foods such as prebiotics, probiotics and synbiotics can be used as a dietary therapy for the modulation of gut microbiota.