Despite the common use of probiotics in bowel disorders, little is known about the mechanisms by which probiotics produce a beneficial effect. The clear identification of antigens and the immune cells that they interact with still remain to be discovered. The recent discovery of the anti-inflammatory effects of Bacteriodes fragilis has revealed a new concept of polysaccharide antigen presentation on antigen presenting cells. It has been found that polysaccharide A (PSA), produced by B. fragilis, interacts with antigen presenting cells and T-cells to modulate a potent anti-inflammatory response. The aim of this paper is to briefly summarize the mechanisms by which a specific probiotic organism, Lactobacilus rhamnosus GG, and the bacterium B. fragilis exert their beneficial effects while elucidating areas that need more study.