Table 1.

Definition of terminology commonly used to describe microbial–host interactions in the context of host health and disease.

Term	Definition	Further reading
Commensal	A host-associated organism that does not induce host damage upon colonization	Casadevall and Pirofski, 2000
Disease	The health outcome of an organism where normal function is impaired after damage (often induced by a microbe(s)) has occurred.	Casadevall and Pirofski, 2003
Dysbiosis	A microbial community shift that has a negative impact on the host.	Petersen and Round, 2014
Holobiont	A host organism and the entirety of its microbial community, under normal conditions, and in the absence of disease.	Rosenberg et al., 2007
Koch’s postulates	A microorganism-centric methodology used to demonstrate a causal relationship between a pathogen and a disease. The postulates commonly cited are: the pathogen must be present in each case of the disease and absent from healthy individuals; and when isolated in pure culture and used to experimentally infect an individual, the pathogen must induce the disease.	Kaufmann and Schaible, 2005
Opportunistic pathogen	An organism that is capable of causing damage to a host under specific conditions, but may also exist as a commensal on the same host.	Casadevall and Pirofski, 2000
Polymicrobial infection	Disease as a result of the co-infection by multiple microorganisms	Hajishengallis and Lamont, 2016
Saprophyte	An organism that lives and proliferates on dead or already diseased hosts. Often a secondary invader or opportunist.	Willey et al., 2008
Virulence	A relative measure of a microorganism’s ability to induce disease on a host.	Méthot and Alizon, 2014
‘Dual role’ virulence factor	A microbial trait (molecule, protein, etc.) that has direct/indirect roles in both environmental survival/persistence and host disease progression.	Vezzulli et al., 2008