The smooth muscle of the gastrointestinal tract contracts and relaxes during digestion to move food from the stomach through the small intestine and to the colon (this process is known as peristalsis). This also helps move the bacteria from the small intestine into the colon, preventing them from multiplying to inappropriate levels. If the transport of food and bacteria in the small intestine is hindered, this can allow bacterial overgrowth in the small intestine and colonic bacteria to proliferate into the small intestine. Because peristalsis is controlled by the nervous system, muscular and neurological disorders can impact the function of the smooth muscles in the small intestine and lead to SIBO.

Diabetes, which can cause damage to gastrointestinal nerves, and scleroderma, which damages the muscles of the gastrointestinal tract, can both lead to SIBO. Partial obstruction of the small intestine can lead to SIBO as in the case of adhesions or scarring that occur as a result of surgery or as a result of Crohn’s disease. SIBO can also be caused by diverticulitis, in which the formation of small pouches in the small intestine which allow bacteria to proliferate.