- The appreciation of the potential role of enteric flora in the pathogenesis of several gastrointestinal diseases has broadened the clinical use of rifaximin, which is now used for hepatic encephalopathy, small intestine bacterial overgrowth, inflammatory bowel disease, and Clostridium difficile infection. Theoretically, by reducing the total number of the gut bacteria, rifaximin could also be used to achieve intestinal decontamination in patients with liver cirrhosis and ascites, thus preventing spontaneous bacterial peritonitis.