These are not "flukes", but, they are often associated with intestinal disorders.
It could be one of two things: microscopic pathogens which are encapsulated by actions of the immune system (many chemical processes go on within the bowel) or it could be the waste product of a larger parasitic helminth.
Either way, the body will react to these antigens in a way that attempts to render the offending protein incapable of causing further harm to the body.
The material should be pulverized and sent to a university lab for analysis. They don't really need to know the source. You will be asking to identify toxins.