This review will explore various aspects of the gastrointestinal microbiome and examine the recent scientific literature on the underlying mechanisms surrounding high-fat-diet (HFD)-induced alterations in gut microbiota and the subsequent development of obesity. Excessive consumption of HFDs has undoubtedly contributed to the obesity epidemic. However, the mechanisms responsible for this relationship are likely to be more complex than the simple concept of energy balance. Emerging literature has implicated HFD-induced alterations in gut microbiota in the obesity epidemic, from both an immunological and metabolic standpoint. These alterations have been associated with obesity and subsequent development of inflammatory-mediated chronic diseases such as irritable bowel disease, colorectal cancer, and certain autoimmune disorders. Potential mechanisms for this effect include: 1) changes in energy regulation and an improved capacity for energy harvest, 2) an increase in lipoprotein lipase (LPL) activity, and 3) enhanced gut permeability perpetuating metabolic endotoxemia and subsequent inflammation. This review will highlight the most important recent advances linking the gut microbiota, HFD-induced dysbiosis, and obesity, as well as explore potential mechanisms for this effect and the implications for chronic disease development. A better understanding of the mechanisms linking HFD to alterations in gut microbiota is necessary to allow for the regulation of dysbiosis and subsequent promotion of anti-obesity effects