TABLE 1.

Commonly used terminology in microbiome studies

Microbiota	The whole collection of microorganisms within a specific location (e.g. the lung), includes bacteria, fungi and viruses
Microbiome	The genetic information and inferred physiochemical properties of the gene products of the microbiota. In most articles the term is used to mean the taxonomic classification of bacteria present in a sample and is used as such in this review
Bacteriome	The genetic information and inferred physiochemical properties of the gene products of the bacteria present in a specific location
Mycobiome	The genetic information and inferred physiochemical properties of the gene products of the fungi present in a specific location
Virome	The genetic information and inferred physiochemical properties of the gene products of the viruses present in a specific location
Metagenomics	Shotgun random sequencing of total DNA in a sample, including DNA from host and microbe origin, which is analysed, organised and identified using sequence databases and computational tools
16S rRNA gene	Component of the 30S small subunit of prokaryotic ribosomes. It is used in molecular studies owing to its extremely slow rate of evolution and the presence of both variable and constant regions
OTUs	Clusters of similar 16S rRNA gene sequences. Each OTU represents a taxonomic unit of a bacteria family or genus depending on the sequence similarity threshold. Identification to the species level is not usually possible
α-diversity	α-diversity is a measure of how diverse a sample is based on how many species there are (richness) and how abundant each species is (evenness) within that sample
β-diversity	β-diversity is used to show how different samples are from each other, based on differences in bacterial presence, abundance or a phylogenetic tree

rRNA: ribosomal RNA; OTUs: operational taxonomic units.