In light of recent data, microorganisms are construed in the present monograph as living organisms that are capable of communication and advanced social organization, which conspicuously manifests itself in the formation of extracellular matrix-enclosed biofilms. Microbial communication signals, including quorum sensing pheromones, are of paramount importance both for interactions among microbial cells and the dialogue between them and the host organism. The monograph sums up the facts that demonstrate the complexity of the human organism-inhabiting microbial consortium comprising a wide variety of biofilm-forming eukaryotic, bacterial and archean cells. The microbiota is involved in maintaining microecological, metabolic, epigenetic, neuro-endocrine and immune homeostasis that normally stabilizes the brain-gut-microbiota axis. Microbially produced neuroactive chemicals include peptides, amino acids, amines, short-chain fatty acids, purines and gaseous substances that are used as nutrients, effectors, cofactors and signals by the host organism. In the present-day world, the human organism has to deal with a large number of environmental stress factors that overpower the organism's protective system and disrupt the functioning of symbiotic microbiota predominantly located in the gastro-intestinal (GI) tract. Homeostasis disruption may impede communication between microbial cells and the human organism and cause physical or mental health problems. The operation of the brain-gut-microbiota axis can be improved by useful microorganisms (probiotics) including psychobiotics that directly impact the human brain and behavior. In the authors' opinion, the lifelong epigenetic developmental program of the organism can be ameliorated and genetic and epigenetic disruptions in the human metagenome (comprising all nuclear, mitochondrial and microbial genes) can be prevented by supplementing the diet with traditional, organic and individualized functional food items that relieve the effects of various detrimental stress factors and agents. A reasonably designed lifestyle based on gut microbiota optimization will undoubtedly help human individuals live a decent healthy life and attain active longevity. Current research on the population organization, social behavior and intercellular communication of microorganisms is expected to promote the interdisciplinary dialogue between microbiology, cytology and ethology. In addition, the results of this research are of significant potential importance for medicine and biotechnology.