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The concept that the gut microbiota plays a major role in the development of pouchitis in ulcerative colitis patients after restorative proctocolectomy with ileal pouch-anal anastomosis, is widely accepted and supported by a widespread use of some antibiotics (metronidazole and/or ciprofloxacin, rifaximin) to treat this condition. A possible, safer therapeutic alternative is represented by probiotics. To date the controlled studies addressing the possible efficacy of probiotic agents in the treatment of active pouchitis are few and inconclusive. By contrast the prophylactic use of a probiotic mixture (VSL #3) appears to be able to prevent development of pouchitis. The most convincing results have been observed in the maintenance of remission, where the probiotic mixture has been found, in most of the performed controlled trials, significantly effective in preventing pouchitis recurrence.