Metabolic syndrome is a disease affecting 25% of North America’s population causing strain on the medical systems. With diet and exercise, genetics, environment, and the gut microbiota all being targeted as potential causes of the disease, there is a lack of consensus on the exact aetiology and pathophysiology. With improved methods in bioinformatic sequencing of faecal bacterial DNA in recent years, our research indicates that a dysbiosis in the gut microbiome is both necessary and sufficient in causing immunological changes in the host in order for the development of metabolic syndrome, T1Ds, and T2Ds. Specifically, our data indicates these shifts in microbiota occur prior to the onset of disease, and produce the disease regardless of diet and genetics. The findings in the current study indicate that future research towards manipulating the gut microbiota to prevent disease, as well as using the faecal bacteria as a screening tool should be pursued.