Several different parasitic, commensal, and opportunistic protozoa can be found in the human intestinal tract. We define an organism as parasitic if it can cause disease (note that it will not necessarily cause illness in everyone all of the time). An organism is commensal if it lives in the intestines but does not typically cause any harm or disease. An opportunist is one that is not typically disease causing, but under certain conditions (such as the host having a suppressed immune system), it can do harm.
Although protozoa (also known as protista) are single-celled organisms, they are unlike bacteria because they are eukaryotes (having a nucleus) and bacteria are prokaryotes (no nucleus). Therefore, protozoa represent a different challenge both to our immune systems, and to their diagnosis. They are larger and more complex than bacteria, and our immune responses are thus different than responses to bacteria which can be phagocytosed as well as initiate various innate and adaptive responses. As far as diagnosis, parasites can't be cultured in clinical laboratories, thus diagnosis depends on finding the individual infective organisms.
