Table 1.

Term	Definition
Microbiota	The assemblage of all microorganisms present in a defined site or niche. Current usage often implies only bacteria.
Microbiome	The entire habitat, including the microbiota, their genomes (genes) and the surrounding site-specific conditions. Current usage often refers only to bacterial members of the ‘biome’.
Mycobiota Mycobiome	Variation on the above definitions referring specifically to fungi present in a habitat.
Metagenome Metagenomics	Collection of genomes and genes from the members of a microbiota, characterized by the process of ‘metagenomics’ (i.e. shotgun DNA sequencing) to obtain information on potential functions of the microbiota
Dysbiosis	Descriptive for imbalance in a microbiome, such as lack of homeostasis in microbial composition or functions
Diversity	Multiple types of measures exist. A calculated index or measure reflecting the types, numbers and distribution of microbiota present within a sample or site (oc-diversity) or between different samples or sites (β-diversity).