If we consider how many bacteria inhabit our organism , it is easy to conclude that they play an important role in its development and functions. The bacteria are involved in the metabolic, physiological and immunological functions, so disorder of the microbiota composition leads to disruption of these functions, or to the development of various diseases . Probiotics have shown beneficial effects in numerous studies, on some children's diseases . These are mostly diseases of the gastrointestinal system, such as necrotizing enterocolitis, irritable bowel syndrome , and acute gastroenteritis. There are also many childhood diseases for which studies have shown the possible role of microbiota in the development, but there is lack of quality studies to prove the efficacy of probiotics in the prevention of these diseases. Some of them are the allergic diseases, such as atopic dermatitis and asthma, metabolic, such as obesity, autoimmune, such as diabetes mellitus type 1 and neurodevelopmental diseases such as autism. Our knowledge about the functions of microbiota is rapidly progressing, and a lot of new diseases for whose development dysbiosis of bacteria may be a trigger, are discovered. New technologies have enabled us to determine the amount of bacteria in our bodies , as well as to recognize most of the bacterial species that we can found in the human body. Also, using new techniques to characterize the microbiota we can determine the functional capacity of bacteria. However , although our knowledge is making rapid progress, there are still many gaps in knowing the functional capacity of the microbiome, which need to be filled.