The set of bacteria, viruses and fungi that live on human bodies, is called in all microbiota and its genes are called microbial. Microbial, because of its products, its response to the environment and its reciprocal response to other systems is considered as one of the organs of the body. Sometimes, it is also called the second genome of human beings and the microbial genes that form microbial are more than 1% of human beings' genes and in bowel there are more than three million bacterial genes. One of the most important parts of body that its microbial has attracted the attention of scientists very much is the microbial of alimentary canal. A set of unicellular organisms in our bowel, called intestinal microbial appears as the important index of health. Errors and mistakes in a suitable microbial colonization in the early life causes food sensitivity, allergic responses, type 1 diabetes and other disorders of autoimmune. The important role of the intestinal microbiota in weight adjustment is through harvest and appetite control. Intestinal microbiota has an important role in the pathology of various infl ammatory bowel diseases and also developing colorectal, gastric and prostate cancers and cardio metabolic disorders.