Macroorganism in combination with microbiota is considered as a “superorganism”. Microorganisms, belonging to the microbiota, are in dynamic equilibrium with a macroorganism. This balance is achieved through a molecular “language” of communication between prokaryotic and eukaryotic cells. Molecular communication between cells leads to positive and negative results. A large number of metabolites of microorganisms that carry the information load: autoinducers is revealed. Autoinducer affect on the immune systems, and variety of metabolic processes. This affects on practically all organs and systems of maсroorganism. Studied metabolites of aerococci affect on the immune system, regenerative cycles and other processes of macroorganism. The problem of informative communication between prokaryotes and eukaryotes provides new insights about vital functions of “superorganisms”.