The microbiome co-evolved with its human host over a long time and became essential for many processes. Bacteria play a role in maintaining human health as they digest food, produce vitamins and participate in the regulation of metabolism. By influencing the cytokine balance along with the composition and activity of leukocytes, they constantly interact with the immune system, affecting innate and adaptive immune homeostasis. A growing number of studies indicate that the microbiome in the human intestine may have an impact on the functions of the central nervous system (CNS), through identified pathways called the gut–brain axis. Recent data show that the human microbiome ecosystem interferes with the brain’s development, central signaling systems and behavior. It has been proposed that disruption in the human microbiome may affect the course of psychiatric disorders. The aim of this review is to summarize the recognized pathways of the gut–brain axis that have been thoroughly studied in animal models and to evaluate the role of the dialogue between the microbiota and the central nervous system in schizophrenia, bipolar disorder and depression.