The role of the intestinal microbiota in human health is gaining more attention since clear changes in the composition of the intestinal bacteria or environment are seen in patients with inflammatory bowel disease, allergy, autoimmune disease, and some lifestyle-related illnesses. A healthy gut environment is regulated by the exquisite balance of intestinal microbiota, metabolites, and the host's immune system. Imbalance of these factors in genetically susceptible persons may promote a disease state. Manipulation of the intestinal microbiota with prebiotics, which can selectively stimulate growth of beneficial bacteria, might help to maintain a healthy intestinal environment or improve diseased one. In this review, analytical methods for identification of intestinal bacteria and an update on the correlation of the intestinal microbiota with human health and disease were discussed by introducing our recent studies to determine the prebiotic effects of a fiber-rich food in animal model and on healthy people and patients with ulcerative colitis (UC).