TABLE 1.

Summary of definitions

Microbiome	The combined genomes of all the microorganisms inhabiting a particular environment
Microbiota	Community of microorganisms in an environment
Metagenomics	The study of the whole genome of a community of microorganisms, allowing assessment of the functional potential of the microorganisms
RNA metatranscriptomics	The measurement of the total mRNA in a community, to allow representation of active gene expression at that time
Resistome	Collection of antibiotic resistance genes in a community
Metabolomics	Assessment of the metabolites of a given sample, allowing identification of metabolically active organisms
Proteomics	Assessment of proteins produced by the host and microbiota
Alpha diversity	The diversity of a sample, including the richness (number of species) or evenness (distribution of species)
Beta diversity	The measure of the similarity or dissimilarity of two communities