The review presents modern ideas about changes in the quantitative and qualitative composition of the human intestinal microbiome and their role in the development of stress-induced mental and neurological disorders, eating disorders, autism, etc. The dualism of the role of the commensal representatives of the microbiome, which have the ability to modulate metabolic and signaling reactions in conditionally healthy people and patients suffering from various neurological, psychoemotional and cognitive disorders associated with the development of neuroinflammation, is shown. The favorable and negative effects established by foreign researchers are associated with the presence of specific surface membrane proteins in the intestinal microbiota, the production of certain short-chain fatty acids, mucin degradation, changes in the intestinal barrier function, endotoxin production, as well as the synthesis of certain neurotransmitters. The prospects and difficulties of searching for new microbial biomarkers for predicting the development of stress-induced diseases, as well as for creating new microbial nutraceuticals and new-generation medicines based on living bacteria are considered.