Normal bowel flora may play a role in inflammatory bowel disease (Crohn's disease and ulcerative colitis). An article appearing in the Scandinavian Journal of Gastroenterology (2001;36(Suppl 234):29-40) discussed the role of bowel flora and intestinal permeability in this disease. The intestinal tract is a long tube that goes from the mouth to the anus. The food you eat and everything inside the intestinal tract is still technically outside of the body. The cells lining the intestine form a barrier that selects what gets inside of the body and what stays outside of the body. If these cells fail to act as an effective barrier, too much intestinal permeability become a problem (sometimes called "leaky gut"). This article states that increased intestinal permeability leads to a lack of tolerance to the bacteria that normally exist in the bowel. There is evidence of the immune system working against the bacteria that exist in the bowel, perhaps even overreacting. Also, the makeup of the bacteria is different in these patients. 

In patients with inflammatory bowel disease, the bacteria tend to invade the mucosa (lining of the intestine). Research appearing in Gastroenterology (January 2002;122(1):44-54) compared colonoscopic biopsies in 305 patients with 40 normal controls. Patients with inflammatory bowel disease had much higher concentrations of bacteria invading the intestinal lining than did the healthy subjects. A normal, healthy intestinal lining has the ability to act as a barrier to bowel bacteria; this ability has been compromised in patients with inflammatory bowel disease. 

The  Scandinavian Journal of Gastroenterology article mentions that taking probiotics is sometimes helpful; patients with Crohn's disease tend to have less Bifidobacteria, and more Bacteroides, Eubacteria and Peptostreptococcus. Probiotics are supplements composed of living bacteria that, when taken, can be beneficial to the digestive tract. Generally these are lactic acid bacteria, like Lactobacilli, Bifidobacteria (the species found to be in short supply in patients with Crohn's disease), and Streptococci. These bacteria can release antibiotic-like substances, reduce the pH in the intestine, improve the absorption of nutrients and help stimulate the immune system. 

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