Coexistence of humans with microorganisms is well known for a long time. Besides the association with infectious diseases, personal microbiota is important for human health, possibly for some non-infectious diseases. Colonization of the human body with appropriate microorganisms after delivery is essential for physiological immune system maturation and also has an influence on central nervous system development. The composition of the gut microbiota is affected by the mode of delivery, early life nutrition and last but not least by lifestyle and drug, especially antibiotics intake. A comparison of gut microbiomes between individuals living in different parts of the world showed a cardinal variation in its composition and basic enterotypes were defined. Interestingly, it has been found out that the different microbiota species composition covers the same, respectively similar metabolic pathways. It is suggested that gut microbiota composition and its dysbiosis may influence civilization diseases development, e. g. diabetes mellitus, obesity, asthma, inflammatory bowel disease, allergy, and autoimmune diseases.Key words: gut microbiota microbiome health immune system dysbiosis.