Gastrointestinal diseases are an important cause of morbidity and mortality worldwide. These include infectious pathologies, allergic and chronic inflammatory conditions such as Crohn's disease ulcerative colitis and also functional disorders such as irritable bowel syndrome, for which treatment sometimes is difficult due to multiple hypotheses for these pathologies where many factors such as psychological, social, genetic, and recently, disorders of intestinal microbiota have been described. The presence of microorganisms in the intestinal tract have been described since Fiftieth century, but its was until the use of biomolecular methods that function and nature of the gastrointestinal ecosystem of microbiota were known. This was an important contribution to the knowledge of digestion, absortion, immunologic, and protective functions of the intestinal microbioma of each organism, which is essential for the study, the treatment and prevention of numerous conditions.