The cause of IBS/IBD is considered unknown, but the inflammation is suggested to be due to small intestine bacterial overgrowth (SIBO), according to research published in JAMA in 2004 (1). Normally bacteria reside in the large intestine, but little if any is found in the small intestine (1).
A few years earlier in 2000, California researchers found that in IBS patients SIBO could be discovered using a simple breath test (2). When given treatment of antibiotics almost half of patients showed IBS symptoms were eliminated (2). Other studies did not show the same results (3) so more research is necessary.
Based on this research, nutritionists and doctors have often used antibiotics to treat IBS and then followed up with using probiotics and prebiotics to replenish healthy gut flora.
1. University Of Southern California (2004, September 3). Bacteria May Be The Cause Of Irritable Bowel Syndrome. ScienceDaily. Available at: http://www.sciencedaily.com/releases/2004/09/040903093237.htm