Diet plays a pivotal role in the overall health of an individual. Not only does it help carry out and regulate certain physiological functions, but it also can determine the composition of the gut microbiome. While the microorganisms that make up the gut microbiome vary between individuals and can be dependent on different environmental factors, there has been evidence to suggest that the type of bacteria that colonize the gut can correlate to better overall health. When the GI microbiome is upset or suddenly changes it results in gut dysbiosis, a condition that correlates to the presence of certain diseases and can worsen clinical symptoms. Diseases linked to gut health range from metabolic disorders, inflammatory bowel diseases, and even disorders of the brain. Many of these diseases are linked to the connection between the brain and the gut, known as the brain-gut axis. This bidirectional communication helps in the digestion of food, intestinal function, and is responsible for GI response to emotion as well as the emotional response to GI upset. By exploiting the interaction between microbiome health and nutrition, diet can be used to alleviate disease symptoms, protect against developing certain conditions, and better maintain overall health. This review will examine the effects of gut dysbiosis, nutrition on the microbiome, the presence of disease linked to disruption of normal microflora, and the way that altering diet can mitigate symptoms or prevent disease.