We do not live alone in nature. Living in an ocean of microorganisms we enter into relations with them; some are parasitic, but most of them are harmless and establish symbiotic mutualism with us. Microorganisms that fix on our body or inside it form the so-called microbiome. The numbers of microbial cells that establish relationships with our body is 10 times higher than the number of own cells that build our own organism. The global genome of the microbiome is about 100 times larger than the own genome. These two genomes are associated and form the so-called hologenome, which has importance for the existence and evolution of the human species. The microorganisms of the microbiome are looking for their environments of life on and in the interior of our organism. It is about what we call somatic ecosystems. Forming smaller or larger ecosystems, the microorganisms are interested in the health of the host. As a result of the relationships of symbiotic mutualism, the microbiome took over some functions of the organisms fulfilling them totally or partially. In this situation, the organism becomes dependent on microbiome or in such an extent that it cannot survive in its absence. Symbiotic mutualism relationships were established between organisms and microbiome in the process of evolution. According to the theory of hologenomic evolution, elaborated by Richard Jefferson (1980), the Human evolution itself was influenced by the microbiome. The microbiome protects us against the aggression of pathogenous agents and can be used as a weapon against them.