There is increasing scientific evidence highlighting the critical role of the composition and function of the gut microbiota in many physiological and immunological processes. Disturbances in the composition of the microbiota typically detected in healthy individuals have been linked to many conditions ranging from allergy and necrotizing enterocolitis to obesity. The microbial colonization that takes place during infancy may be related to the occurrence of later disease through microbial programming. Although the gut microbiota can become altered due to exposure to environmental factors during the whole human lifespan, the most intense development occurs during the first years of life, when shortly after birth, the infant’s gut is rapidly colonized by multiple microbes. In adulthood, the microbiota is less plastic and thus more resistant to changes.