An overview of the improvement in the health of obese/T2DM patients treated by modulating their GM using prebiotics supplementation in a regular diet. Administration of prebiotics has the potential to modulate GM composition in patients suffering from T2DM and obesity and can be used as a therapeutic approach to cure the adverse effects of metabolic diseases. The daily intake of prebiotics in a designed diet has a major influence on GM by decreasing gut permeability, bacterial translocation, and reducing LPS-induced inflammation. However, this diet increases SCFAs and bifidogenecity in the gut, leading to lower TC levels, lipogenesis, LDL triglycerides, and adiposity, eventually resulting in lower risk of cardiovascular diseases.