In recent years, Helicobacter pylori (H. pylori) has been identified by researchers as the cause of the majority of gastrointestinal ulcers. H. pylori is a bacterium that lives in the stomach and duodenum. It has a unique way of adapting to the usually harsh environment of the stomach. Gastric juice is composed of digestive enzymes and concentrated hydrochloric acid, which can readily digest food or kill microorganisms. Low levels of stomach acid increase the chance an organism's survival. It used to be thought that the stomach contained no bacteria and was actually sterile.

The stomach is protected from its own gastric juice by a thick layer of mucus that covers the stomach lining. H. pylori takes advantage of this protection by living in the mucus lining.

Once H. pylori is safe in the mucus, it is able to fight the stomach acid that does reach it with an enzyme it possesses called urease. Urease converts urea, of which there is an abundant supply in the stomach (from saliva and gastric juices), into bicarbonate and ammonia, which are strong bases. This creates a cloud of acid-neutralizing chemicals around the H. pylori, protecting it from the acid in the stomach. The breath test method of diagnosis relies on this reaction being present.

Contributing to the protection of H. pylori is the fact that the body's natural defenses cannot reach the bacterium in the mucus lining of the stomach. The immune system will respond to an H. pylori infection by sending white cells, killer T cells, and other infection fighting agents. However, these potential H. pylori eradicators cannot reach the infection, because they cannot easily get through the stomach lining. They do not, however, go away - the immune response just grows and grows. White cells die and spill their destructive compounds (superoxide radicals) on stomach lining cells. Extra nutrients are sent to reinforce the white cells, and the H. pylori can feed on this. Within a few days, gastritis and perhaps eventually a peptic ulcer results. It may not be H. pylori itself which causes peptic ulcer, but the body's response (inflammation of the stomach lining).

H. pylori is believed to be transmitted orally. Many researchers believe that H, pylori is transmitted orally by means of fecal matter through the ingestion of waste-tainted food or water. In addition, it is possible that H. pylori could be transmitted from the stomach to the mouth through gastro-esophageal reflux or belching, common symptoms of gastritis. The bacterium could then be transmitted through oral contact.

A 2002 trial demonstrated that a mixed probiotic acidophilus preparation failed to eradicate the H. pylori infection in the patients upon whom it was tried. [Digestion 2002;65(1):pp.16-20]