Table 1.

Glossary of Key Terms in GI Microbial Ecology

Term	Definition
Biogeography	The study of patterns of biodiversity along spatial, temporal, and environmental scales
Commensalism	Relationship in which one partner benefits without detriment to the other
Conventionalized	Animals derived germ-free and later colonized with a microbiota harvested from conventionally raised donors
Conventionally raised	Animals raised under standard conditions in the presence of a normal microbiota
Germ-free	Animals raised in the absence of all microorganisms; also called axenic
Gnotobiotic	Animal or environment in which all microorganisms are excluded or known
Habitat	Physical location or “address” occupied by an organism within an ecosystem
Metabolomics	Identification and quantification of host and microbial metabolites in a particular host compartment
Metagenomics	Culture-independent measure of the gene content and physiologic potential of a microbial community
Microbiome	Collective genomes within a microbiota
Microbiota	Collective community of microorganisms within a habitat
Mutualism	Relationship in which both partners benefit; also called symbiosis
Niche	Function or “profession” of an organism within an ecosystem
Pathogenesis	Relationship in which one partner benefits to the detriment of the other; also called parasitism
Pattern	The variation of biodiversity within an ecosystem
Phylotype	Group of SSU rRNA gene sequences with ≥97%–99% sequence identity
Scale	The spatial, temporal, or environmental ranges within which variation in an ecosystem is perceived