Table 1.

Terminology used in human and animal microbiome research presented in order of experimental and analytical workflow.

General Terms	Microbiome	The totality of human (or other host) body's micro-organisms (including bacteria, viruses, fungi, archaea, protozoa), their genomes and molecular products, and the surrounding environmental conditions.
	Microbiota	The assemblage of microorganisms present in a defined environment (e.g. human lung microbiota)
	“Meta-omics”:	The total content of a community of microbiota in terms of:
	Metagenome	- genomic DNA
	Metatranscriptome	- transcribed RNA
	Metaproteome	- entire protein complement
	Metabolome	- metabolite pool
	Commensal microbiota	Microbes that provide benefits to the (human) host without being affected by it
	Symbiotic microbiota	Microbes in a mutually beneficial relationship with the (human) host
	Dysbiosis	A condition in which the normal structure and function of the microbiome has been disturbed and which is considered to be detrimental for the host
Experimental Analysis Terms	Culture-independent techniques	Molecular techniques that analyze the DNA (or other biologic material) directly from a sample rather than from individually cultured microbes
	Marker	A DNA sequence that identifies the genome that contains it
	Amplicon sequencing	Amplification (with PCR) and sequencing of specific markers
	16s rRNA	(or 16S rDNA) 16S ribosomal subunit gene, unique to prokaryotic cells, with highly preserved sequence and hypervariable regions, which are amplified and used as markers for bacterial identification
	Whole Metagenome Shotgun sequencing	Sequencing of short, random DNA/RNA fragments in an undirected whole-genome fashion
Bioinformatic Analysis Terms	Operational Taxonomic Units (OTUs)	A common classification used for the amplicon sequences, which are clustered based on a similarity threshold (e.g.>97%) as a proxy for species-level taxonomic assignment.
	Abundance	Prevalence of a particular taxonomic group in a microbial community
	Diversity	Taxonomic distribution within a community, including both the number of distinct taxa and their relative distribution
	Richness	Number of taxonomic groups in a microbial community
	Evenness	Relative abundance of different taxonomic groups
	Dominance	Emergence of a single, overtly abundant taxonomic group
	Alpha-diversity	Within-sample taxonomic diversity (including richness and evenness) as a summary statistic of a single population
	Beta-diversity	Between-sample taxonomic diversity describing absolute or relative taxonomic overlap between samples
	Community structure	Taxonomic composition of a microbial community
	Functional metagenomics	Computational or experimental analysis of a microbial community with respect to the molecular activities of its composite genome
Interventional Studies Terms	Germ-free animal	Host animal containing no microorganisms
	Gnotobiotic animal	Host animal containing artificially transferred humanized microbiota
	Prebiotic	A nutrient promoting the growth of symbiotic or commensal microbes
	Probiotic	A live microbe introduced in the host with the intention to preserve or restore symbiosis
	Symbiotics	Combination of both prebiotics and probiotics

Abbreviations: PCR: polymerase chain reaction