Table 1.

Terminology and Nomenclature of the CF Microbiota^a

Term	Definition
Ecological
Microbiota	The entire collection of microbial organisms at a particular site.
Microbiome	Defined as a characteristic microbial community occupying a reasonably well-defined habitat that has distinct physicochemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theater of activity.
Mycome	Collective genomes and gene products of fungi within and on humans.
Virome	Collective genomes and gene products of viruses within and on humans.
Diversity	General term used to describe the number of different species of microbes present and their distribution within an ecosystem.
Dysbiosis	Imbalance of ecological homeostasis and loss of diversity in microbial communities often associated with disease states or acute antibacterial therapies. Characterized by altered bacterial landscapes, pathogen domination, and colonization resistance.
Metagenome	Collection of genomes within members of the microbiota (ie, what functional genes are present—but cannot determine who or what is active).
Transcriptome	High-throughput process to identify and quantify microbial genes expressed by the microbiota (ie, who is active and expressing genes).
Metabolome	Analysis of the complete set of metabolites present in a population (ie, what end-products, such as short-chain fatty acids, are present).
Resistome	Collection of all genes from pathogenic and commensal organisms associated with antibiotic resistance.
Multi-omics	Assimilation of data from various “omics” technologies, such as microbiomic, metagenomic, transcriptomic, and metabolomic.
Factors shaping the microbiome
Immigration	The movement of microbes into a new environment. For example, in CF, this may be seen in the context of lower airways that includes aspiration, subclinical microaspiration, and inhalation of microbes leading to direct dispersal across airway mucosa.
Elimination	The movement of microbes out of an environment. For example, in CF, this may be seen in the context of lower airways done through adjunctive airways clearance measures, antimicrobial therapies, cough, and host immune defenses.
Relative reproduction	Bacterial growth influenced by regional growth conditions, including (i) environmental (ie, nutrient availability, temperature, pH, and oxygen tension), (ii) host (ie, concentration and activation of inflammatory cells), and (iii) bacterial (ie, local microbial composition/competition).
Methodology
16S Ribosomal RNA (rRNA/rDNA) gene	Amplification and sequencing of part of the 16SrRNA gene (SSU rRNA gene), typically including ≥1 hypervariable region(s) that can provide taxonomic resolution of the community structure.
Shotgun sequencing	Direct sequencing and analysis of total DNA extracted from a sample. This approach provides information on all genes present and can provide genome scale information on the more abundant community members.
Culture-independent	Analysis of the microbiome based on nucleic acid extracted directly from a sample (eg, 16S rRNA gene profiling, metagenomics, metatranscriptomics).
Culture-enriched metagenomics	Coupling culture enrichment methods with shotgun metagenomic approaches to improve the resolution of community analysis.
Operational taxonomic unit (OTU)	Clusters of similar sequence variants of the 16S rRNA gene used to identify taxa. 97% similarity is commonly used as a species-specific cutoff.
Amplicon sequence variant (ASV)	Alternative to OTUs. Infers the biological sequences prior to the introduction of amplification and sequencing errors. ASVs offer higher sensitivity to biological variation, as a change in one nucleotide in the 16S rRNA gene of a bacterial strain can indicate large variations within the rest of the genome relative to OTU.
Analysis
Abundance	Total number of bacteria within a sample.
Relative abundance	Proportion of the microbiome made up of specific bacteria (ie, more dominant bacteria have higher relative abundances). Often denoted as a percentage or proportion (0-1).
Absolute abundance	Actual abundance of a taxon in a unit volume of an ecosystem (ie, a measure of bioburden).
Alpha-diversity	A measure of the composition of microbial community (single sample) based on richness (number of species) and may include measures of evenness (different abundances of community members). Common alpha-diversity measurements include observed species, Chao 1, Shannon Diversity Index, and/or Simpson’s Index.
Beta-diversity	A measure of the differences in community composition inclusive of taxonomy between samples (eg, longitudinal within a subject, or between subjects). The measures can be based on the presence/absence (unweighted) or different abundances of community members(weighted) and some measures incorporate phylogenetic relatedness within a community. Common beta-diversity metrics include Weighted- and Unweighted-Unifrac, Aitchison Distance, and Bray Curtis Dissimilarity).
Core microbiome	Group that contains species that affect a large proportion of individuals with high relative abundance.
Satellite microbiome	Group that contains species that are present in low relative abundance and at limited locations. Often detected infrequently, may be transient.
Pulmotype	Partitioning of airway bacterial communities into distinct types across patients.

^aAdapted from references [5–10].