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Crohn’s disease is an immune-mediated disease which results from the persistence of a pro-inflammatory cytokine response to Mycobacterium avium subspecies paratuberculosis (MAP) and MAPs widespread presence in the food supply of industrialized nations. Over time, the destructive antigen/cytokine interaction overwhelms the regenerative capacity of the gastrointestinal mucosa. The resultant focal destruction of mucosal integrity creates a portal for invasion by the gastrointestinal microbiota; the second mechanism of pathogenicity for Crohn’s disease. Failure to effectively address polymicrobial submucosal infections has resulted in 25% of Crohn’s afflicted individuals requiring one or more operations within their lifetimes.