Clinicians have long learned of the pathogenic microorganisms that cause intestinal infections and that can be identified by culture methods from fecal, mucosa and blood samples. Nevertheless, much progress has been made due, in large part, to molecular biology which has enabled the discovery of pathogens that are not (yet) able to be cultured, but also to the protective role of some microorganisms within the microbiota. Ecological and clinical disturbances related to antibiotic therapy were decisive for demonstrating the beneficial effects of the endogenous microbiota and establishing the beneficial effects of biotherapeutic agents, known as probiotics. Most areas of gastroenterology (cryptogenic inflammatory bowel disease, irritable bowel syndrome, lymphomas, etc.), but also those in medicine overall (obesity for example), are affected by this new approach and are showing very significant progress. This article summarizes the historical steps of these discoveries and reviews what the "modern" clinician should know in this very dynamic area in regard to research and practical consequences.