Table 1.

Definitions and abbreviations related to NGS-based methods, such as metagenomic analysis, for studying the mycobiome

ASV	Amplicon Sequence Variant: individual DNA sequences produced by targeted NGS after elimination of poor-quality sequences and use of a sequencing error correction algorithm (e.g., DADA2). All ASV are then assigned to a taxonomic identification. ASVs are an alternative to OTUs
Alpha-diversity	An estimate of the diversity of a given sample taking into account richness and evenness. Simpson and Shannon indexes are common alpha-diversity indexes
Beta-diversity	An estimate of the difference in community composition between different samples (e.g., two anatomical sites, two individuals, etc.). It can be evaluated through principal component or coordinate analysis (PCA/PCoA)
Core mycobiome	Taxa, genera or species present in the majority (generally > 50%) of individuals in the same group with a relative abundance > 0.1%
Fungal dysbiosis	Imbalance in the composition of the mycobiota compared with the steady state (eubiosis) detected in healthy subjects
Evenness	Evaluation of the distribution of species/taxa/OTUs/ASVs present in a sample, taking into account the relative abundance of the different groups
Shannon or Simpson diversity indexes	Indexes measuring the alpha-diversity of a community's composition, taking into account both richness and evenness
OTU	Operational Taxonomic Unit: cluster of sequences obtained from targeted-amplicon NGS using a pipeline (e.g., VSEARCH) that clusters sequences with a high percentage of similarity (> 97%). The OTUs are then assigned to a taxonomic identification (or taxon)
Richness	Evaluation of the number of species, taxa, OTUs or ASVs present in a sample, without taking into account the relative abundance between the different groups
Shotgun metagenomics (SMg)	Global metagenomics: study of all components of microbiome (bacterial, viral, fungal and other eukaryotes) at once using a nontargeted approach