The MetaHIT project is part of a global effort to identify, characterize and quantify the microbial communities within the human gut. With over 100 trillion micro-organisms, the gut microbiota outnumbers the cells in the human body ten-fold. The microbiome is not only the primary interface between food and the gut epithelium, it also modulates the body’s main pool of immune cells and second largest neural network. Not surprisingly, perturbation of the gut microbiome has been associated with nearly every chronic disease, from cancer to dementia. Professor Dusco Ehrlich describes the MetaHIT project whose goal is to construct a reference gene catalog of gut microbes. Ehrlich uses this as a springboard for examining microbial status in health and disease. He outlines a fascinating body of evidence that uncovers imbalances in the constellation of bacteria in disorders such as obesity and ulcerative colitis. These new findings will pave the way for personalized medicine, allowing patients to be stratified and treated according to profile of their gut microbiota.