A certain type of bacteria found in the small intestine (E. gallinarum) can travel to other organs and initiate the production of auto-antibodies and inflammation which both play a role in autoimmune disease.
A certain species called Enterococcus gallinarum, was found to spontaneously “translocate” outside of the gut to lymph nodes, the liver, and spleen in mice and was found in cultured liver cells of healthy people, and in livers of patients with autoimmune disease.
Most bacteria in the gut is in the large intestine near the colon and not small intestine. Typically, certain phyla and classes of bacteria that crop up on a low fiber diet and these bacteria possess flagella that allows move or “swim” up the intestines and penetrate the small intestine (where they are not supposed to be). This is often referred to as small intestine bacterial overgrowth.