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Treating Clostridium difficile with fecal microbial transplantation. A healthy digestive system is home to thousands of bacteria. The intestinal tract includes the stomach, small intestine, and large intestine, which is also known as the colon. In most cases these microbes are harmless or even beneficial to a healthy individual. However, conditions that require treatment with antibiotics can kill off many of the good bacteria in the colon, allowing the bad bacteria, called clostridium difficile to take over. Toxins released by Clostridium difficile can damage the lining of the colon, a condition known as Clostridium difficile colitis. Clostridium difficile infection can lead to life threatening complications. Such as toxic megacolon, where the colon becomes dangerously enlarged. Clostridium difficile is normally treated with a course of antibiotics. But a recurrent infection occurring between 20% to 60% of patients after an initial episode. The standard treatment for a recurrent infect