A pathogen or infectious agent – in colloquial terms, a germ — is a microbe or microorganism such as a virus, bacterium, prion, or fungus that causes disease in its animal or plant host. There are several substrates including pathways whereby 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.

The body contains many natural orders of defense against some of the common pathogens (such as Pneumocystis) in the form of the human immune system and by some “helpful” bacteria present in the human body’s normal flora. However, if the immune system or “good” bacteria is damaged in any way (such as by chemotherapy, human immunodeficiency virus (HIV), or antibiotics being taken to kill other pathogens), pathogenic bacteria that were being held at bay can proliferate and cause harm to the host. Such cases are called opportunistic infection.