Antibiotics too, can increase the risk of IBD. While antibiotics kill bacteria that make you sick, they also affect the gut’s protective mucus layer, since the medicine can’t differentiate between the two. This mucus acts as a barrier between the immune system, and the trillions of bacteria living in the intestines. According to doctors, antibiotics damage the cells that produce this mucus, making it easier for bacteria to penetrate the gut lining and trigger inflammation