The study of human microbiome has drawn the attention of many scientists worldwide, who have understood that this complex group of microorganisms play essential functions, such as preserving gut integrity, appropriate working of the immune system, vitamin production, etc. Additionally, the study of microbiome takes on dramatic importance when analysed from an evolutionary point of view. Humans are the result of integrating into their genome and their living together with millions of micro and macro-organisms (bacteria, fungus, helminths, virus) throughout their evolution, and have formed a superorganism with 2.1 microbial cells per each human cell. Social, technological and food consumption changes have caused a partial loss of the microbiome (epidemiological transitions), resulting in the occurrence of a number of allergic, inflammatory and neurodevelopmental diseases. By understanding the relationship between these diseases and the microbiome structure, an opportunity arises for intervention in the modulation of the microbial ecosystem and for compensating for the loss of microbiome, in order to change the course of the disease.