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Rifaximin increased fecal Bifidobacterium and decreased E. coli and Enterobacter in IBS1 patients. Although rectal mucosal bacteria and fecal fungi were not significantly altered in all patients after rifaximin intervention, rifaximin enhanced the connections among fecal bacteria, mucosal bacteria and fecal fungi in IBS1 patients. Compared with IBS0, we surprisingly found rifaximin ameliorated abdominal symptoms of IBS1 much better. Receiver operating curve analysis revealed patients whose fecal microbial dysbiosis indices (MDI) were hi