The Bactrim itself can wreak enough damage to the intestinal flora as to create ongoing inflammation throughout the body for years to come. Many autoimmune problems are now considered to start in the intestinal tract. IBS is associated with a folic acid deficiency in the body. Bactrim will induce further folic acid deficiencies. Folic acid deficiencies can create many tissue changes through disruption and alteration of DNA in the cells.