Table 1.

Challenges in next-generation sequencing of the mycobiome.

Stage	Challenges
Sample processing	Contamination DNA degradation with lysis of the fungal cell walls Variation in the DNA yield and quality between different commercial kits and extraction methods
Targeted amplicon sequencing	Primer bias Amplification bias Target accuracy Data reproducibility
Shotgun metagenomic sequencing	Low overall fungal abundance relative to bacteria High levels of host DNA impedes fungal detection High costs Data reproducibility
Bioinformatics analyses	Lack of consensus on best practices Limited established bioinformatics pipelines Poorly curated fungal reference databases Large numbers of unidentified taxa Poor species-level resolution