 The human gastrointestinal tract is home to an extremely numerous and diverse collection of microbes communities, collectively termed the intestinal microbiota. This amazingly complex and poorly understood group of communities has an enormous impact on humans. Indeed, microbiota is considered to play a number of key roles in the maintenance of host health, including aiding digestion of otherwise indigestible dietary compounds, synthesis of vitamins and other beneficial metabolites, immune system regulation and enhanced resistance against colonization by pathogenic microorganisms. Conversely, the intestinal microbiota is also a potent source of antigens and potentially harmful compounds. Schematically, humans can be considered to exist in a state of natural balance with their microbial inhabitants. A shift in the balance of microbiota composition such that it may become deleterious to host health is termed dysbiosis. Dysbiosis of the gut microbiota has been implicated in numerous disorders, ranging from intestinal such as inflammatory bowel diseases and colorectal cancer to disorders with more systemic effects such as diabetes, obesity, insulin resistance and steatohepatitis. The link between the microbes in the human gut and the development of obesity, cardiovascular disease and metabolic syndromes, such as type 2 diabetes, is becoming clearer but, because of the complexity of the microbial community, the functional connections are less well understood. 