Neurodegenerative diseases encompass a group of disorders with diverse etiologies characterized by the accumulation of neurotoxic substances that contribute to neuronal damage and brain degeneration. The integration of the microbiota-intestine-brain axis mechanism occurs via afferent and efferent pathways with the assistance of the vagus nerve and peripheral circulation. The gut microbiota produces pathogenic proteins and other harmful substances that can cross the blood-brain barrier and develop into even more pathogenic proteins when in contact with the bloodstream. The microbial metabolites most commonly associated with neurodegenerative diseases are butyrate and amyloid, although the precise role and mechanism of their relationship with the microbiota have yet to be fully elucidated. Additionally, in Parkinson's disease, the microbiome is directly linked to an increase in opportunistic pathogens, a decrease in beneficial anti-inflammatory species, and higher levels of carbohydrate metabolizers.