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Human gut contains microorganisms such as bacteria, fungi, parasites and viruses; and microbiota refers to all of the special species that live with people. For many unhealthy microbiota; which may develop as a result of internal and external factors; the term ‘’dysbiosis’’ is used. The brain and gut may be connected with various ways including the metabolic processes of the enteric nervous system (ENS), the vagus nerve, the immune system, or the intestinal microorganisms. In the case of dysbiosis; the changes developing in these tracts may contribute to the development of many neurological diseases such as neurodegeneration, Alzheimer’s disease (AD), Parkinson’s disease (PD). Clarifying the relationship between gut-brain axis and neurodegeneration is crucial for development of treatment strategies such as prebiotics, probiotics and diet interventions and fecal transplantation.