Typically the term is used to describe an infectious agent such as a virus, bacterium, prion, fungus, viroid, or parasite that causes disease in its host. The host may be an animal, a plant, a fungus, or even another microorganism.here are several substrates including pathways where the pathogens can invade a host. The principal pathways have different episodic time frames, but soil contamination has the longest or most persistent potential for harboring a pathogen.