Table 1.

Most common definitions

Microbiota	the microbes (including bacteria, viruses, fungi, and protozoans) in a given population (103)
Microbiome	microbiota found in a particular habitat at a specific time and consists of the ecological community of commensal, symbiotic, and pathogenic microorganisms that share our body(103); “microbiome” and “microbiota” are often used interchangeably but they refer to different ecological principles.
Microbial community	microbes that interact functionally and metabolically (40)
Holobiont	the host organism together with its microbiome constitutes the “holobiont” (Greek, holos, whole/entire) and the totality of the genome is the “hologenome” (104)
16S ribosomal RNA gene	Characterization of the microbiome can be done by sequencing regions of a conserved gene, such as the hypervariable regions of the 16S ribosomal RNA gene (105). The gene comprises nine constant regions (C) and nine hypervariable regions (V1–V9). The variable regions enable sequence-specific discrimination between different bacteria. (106). 16S ribosomal RNA gene sequencing has been described to identify bacterial DNA in 95.7% of bronchoalveolar lavage (BAL) specimens compared with conventional culture techniques,which detected bacteria in 39.1% of BAL samples (107).
OTU	Operational taxonomic units: is an operational definition used to classify groups of closely related individuals