Abstract: Described are compositions and methods for treating inflammatory bowel diseases in a subject in need thereof. In certain aspects, the disclosure provides methods of treating a subject diagnosed with Irritable Bowel Disease (IBD), the method comprising administering to the subject an agent to reduce the number or pathogenic effects of a B. fragilis strain, wherein the subject is diagnosed with IBD by detecting the presence of the B. fragilis strain or a B. fragilis toxin in a biological sample of the patient.