The gut microbiota regulates the function and health of the human gut. Preliminary evidence suggests its impact on multiple human systems including the nervous and immune systems. A major area of research has been the directional relationship between intestinal microbiota and the central nervous system (CNS), called the microbiota-gut-brain axis. It is hypothesized that the intestinal microbiota affects brain activity and behavior via endocrine, neural, and immune pathways. An alteration in the composition of the gut microbiome has been linked to a variety of neurodevelopmental and neurodegenerative disorders. The connection between gut microbiome and several CNS disorders indicates that the focus of research in the future should be on the bacterial and biochemical targets. Through this review, we outline the established knowledge regarding the gut microbiome and gut-brain axis. In addition to gut microbiome in neurological and psychiatry diseases, we have briefly discussed microbial metabolites affecting the blood-brain barrier (BBB), immune dysregulation, modification of autonomic sensorimotor connections, and hypothalamus-pituitary-adrenal axis.