Microorganisms in human life play a huge role: in particular, those that coexist with the host organism, inhabiting the skin, upper respiratory tract, external genitalia and especially the digestive tract. The intestinal microbiota, including bacteriome, mycobiome and virome, not only takes part in the digestion process, but also provides the synthesis of a number of vitamins. The intestinal microbiome also serves as the basis for a system of extensive bidirectional neuroendocrine pathways that connect microbiota with various regions of the central nervous system, the hypothalamic-pituitary-adrenal system, and the peripheral parts of the autonomic nervous system. This system of connections has got the name of gut-brain axis and has attracted close attention of scientists over the past two decades, since a targeted impact on the intestinal flora is potentially capable of changing the nature of nervous system regulatory influences on the whole body. It is especially important to study patterns of functioning of the gut-brain axis in patients with the nervous system pathology, namely neurodegenerative and demyelinating diseases. Methods for their treatment continue to improve, and perhaps the correction of the gut microbiotic composition will serve as an additional therapeutic approach. The review article describes current views on the role of the intestinal microbiota, provides the latest data on the composition of bacteriome, mycobiome, and virome in patients with relapsing-remitting multiple sclerosis.