The human gut microbiota harbours over 100 trillion microorganisms that form the intestinal microbiota which is 10 times more than the number of all human cells in the organism. The development of the ecosystem of the intestinal microbiota begins with birth and established intestinal microflora during life is relatively stable, but susceptible to the influences of exogenous and endogenous factors (diet, use of medications, disease, ageing). The composition of the intestinal microbiota is unique for each person and it is difficult to define what the healthy microbiota is. The intestinal microbiota plays an important role in human health and disease. The importance of intestinal microbiota is manifested through their impacts on human physiology, metabolism, diet and immune function. Dysbiosis or disorder of intestinal microflora is a term describing the disruption of the natural balance of microorganisms in the digestive tract. The disorder may occur due to loss of beneficial micorbial organisms, expansion of pathobionts or potentially harmful microorganisms and loss of overall micorbial diversity. Disorders of gut microbiota are associated with a variety of conditions and syndromes, as well as diseases including inflammatory bowel disease, colorectal cancer, irritable bowel syndrome, allergic diseases, obesity, metabolic syndrome, celiac disease. Today, there is great interest in observing the relationship between diet and microbiota and impact of food interventions. In clinical practice is an increased use of nutritional components such as probiotics, prebiotics and synbiotics with the aim to restore balance in the compostion of microbiota. Probiotics are live microorganisms with a positive impact on the balance in the intestine, while prebiotics are degradable components of foods based on selective stimulation of favourable intestinal bacteria. To the probiotics and prebiotics are attributed a number of positive effects on human health. Also, other ways are today investigetd and applied such as intestinal manipulation with microbiome to restore the desired potential of our “bacterial alliance” for the prevention and/or treatment of diseases associated with disorders of the microbiota (such it is a faecal microbiota transplantation mesure).