They live in fiber within the lumen, so low fiber diets also decrease the good guys. Studies in human's show that increased bile salts have relation to colon cancer. If good guys are killed this increases pH, which allows yeast to grow. Aldehydes also decrease the mucous layer, which contains the antibodies of the intestinal immune system. End result is leaking of abnormal things into the blood.
Food allergies cause inflammation of intestinal cells, also causing leaking.
Leaking toxic stuff from the intestine is taken care of by the bloods' immune system. But over time, that immune system gets depleted too. If liver can't deal with the toxic overload, it flushes it back into the blood. Connective tissue acts like a filter and traps the toxins so they can't create major organ damage. But the body still recognizes these as foreign substances and so tries to destroy them, creating inflammation.