Table 1.

List of Definitions

Term	List of Definitions
Microbiome	The collection of all genomes of microorganisms from a defined environment, such as the human intestine.
Microbiota	The collection of all microorganisms in a defined environment, such as the human intestine. Virome: The collection of all viruses in a defined environment, such as the human intestine.
Mycobiome	The collection of all fungi in a defined environment, such as the human intestine.
Resistome:	The collection of all antimicrobial resistance genomes derived from microorganisms from a defined environment, such as the human intestine.
Ecosystem	The complex of a community of organisms and its environment functioning as an ecological unit.
Ecology	The totality or pattern of relations between organisms and their environment.
Commensal microbiome	Often referred to as an ensemble of microorganisms that reside in close proximity and in mutualistic relation with the host. However, the more correct term describing the resident microbiota in the intestines may be “Amphibiont” organisms that may have a pathogenic (detrimental), commensal (neutral), or symbiotic relationship (beneficial) with the host. We therefore use the term, “resident microbiota” in this review to describe the aggregate (pathogenic, commensal, symbiotic) endogenous microbiota in the intestine.
Pathobionts	Potentially pathogenic microorganisms residing in the microbiota.
Dysbiosis	A perturbation that departs from an otherwise balanced ecology to prolong, exacerbate, or induce a detrimental health effect.
Prebiotics	Nutritional substrates that promote the growth of microbes that confer a health benefit on the host.
Probiotics	A live microorganism that, when administered in adequate amounts, confer a health benefit on the host.
Synbiotics	Formulations consisting of a combination of pre- and probiotics.
Fecal Microbiota Transplantation (FMT)	The introduction of a liquid filtrate of stools from a healthy donor into the gastrointestinal tract of an ill patient.
Selective Decontamination of the Digestive Tract (SDD)	Use of daily antibiotics with the aim of preventing hospital-acquired infections while preserving the anaerobic microbiota.