Commonly referred to as "germs", pathogens are organisms which cause disease, e.g. certain bacteria, viruses, fungi or other microorganisms, like amoebas or flagellates. The term pathogen can also be used to refer to substances causing the disease. Not all microorganisms are pathogens; for instance there are many bacteria which reside on and in other organisms that do not cause disease; in fact, many are highly beneficial (e.g. gut microbes).

The manner of development of a disease. In other words, the way in which a certain trigger (for example a pathogen, an allergy or an intoxification) can lead to the developement of a disease's typical clinical signs.