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).