I wonder what are the possible sources of endotoxins and gut inflammation. I know that starch can be either a direct source (small particles that penetrate through the intestinal wall) or indirect (feeds on bad bacteria). But what about incompletely digested fat or proteins? For example, hypothyroidism makes it more likely that the food is not digested thoroughly in the stomach due to insufficient acid produced (I believe), so I wonder what happens to the fat when eating say a large portion of cheese, and if incomplete digestion could explain some symptoms.