Microorganisms are everywhere - they inhabit various environments: from highest peaks to deepest seas, fertile soil, desert and among other things the human body. Microbial cells outnumber the host cells for one order of magnitude, so it is easy to conclude that these symbionts play an important role in our health. Microbiota interacts with the host in many ways, therefore, the composition of the microbiome can affect the balance of the entire system, and changes in microbial communities can exert significant effects on the health of the individual. The aim of this paper is to present the current knowledge of the human microbiota: its development, role in health and disease development. As human microbiome is insufficiently explored, the goal is also to assess the potential of the microbiota modulation as a new method of prevention and treatment, and to assess frequency of this method in clinical practice. For this purpose, scientific literature search was performed, including screening of publications and professional institutions, European Medicines Agency (EMA) website and other sources. A literature search identified the specific characteristics of the human microbiota and its role in the development of a healthy organism and development of diseases such as Crohn's disease and even mental disorders. The human body and microbiota are in symbiont relatonship, therefore, recently a hypothesis called "super-organism" was proposed, in which super-organism is composed of the human organism and microorganisms. Gastrointestinal microbiota fulfills an important metabolic and immunological role, and changes in its composition may affect the homeostasis and lead to the development of dysbiosis and microbiota associated diseases. Diseases in which the dysbiosis was observed include inflammatory bowel diseases, irritable colon syndrome, colorectal cancer, metabolic syndrome, obesity, allergic disease, and neurological disorders such as autism. The mere knowledge of the human microbiome is still scarce and more resources have to be invested for understanding of its role in the pathology of the disease in order to develop better treatment options and potential development of targeted therapies.