We are all aware of the impact of “Probiotics” on human health. Recently DNA sequencing of the Human Microbiome has revealed not only an overgrowth of “normal” flora, but a lack of certain anti-inflammatory species may be an underlying cause of auto-immune diseases such as Chrohn’s disease and Ulcerative colitis. Years of low level exposure to anti-biotics, pesticides and herbicides as well as low or “wrong” fiber diet can create a dysfunctional Microbiome. We will discuss ways to normalize the human flora and the dramatic results that can be seen in many patients. Consumption of certain fiber sources increases some and lowers other microbial populations. Poor bile flow, excessive dissacharide intake, food allergies and hormone replacement therapy can significantly alter gut homeostasis.