Flagellate protozoans such as Giardia and Trichomonas are commonly found in the intestinal tract of reptiles, and the jury is still out as to their pathogenic impact. Serious infections can cause diarrhea, mucous and/or bloody stool, and anorexia, so they should be treated. Most infections if caught early respond well to the medication Flagyl, which is really a type of antibiotic.