. Author manuscript; available in PMC: 2020 Jun 11.

Published in final edited form as: Curr Opin Microbiol. 2019 Nov 11;50:79–86. doi: 10.1016/j.mib.2019.09.010

Table 1.

Method	Technology	Target	Advantages	Disadvantages
High throughput sequencing (HTS)	Amplicon sequencing	Internal Transcribed Spacer 1 and 2 (ITS1/2)	Database availability; amplification of target sequences	Primary bias; amplification preference
		18S/26S rRNA genes	Database availability; amplification of target sequences	Primary bias; amplification preference
		Reverse transcribed rRNA	Decreased primer bias	Amplification preference
	Shotgun sequencing	Metagenome	No amplification preference	Low cost efficiency due to fungal DNA exiguity
	Shotgun sequencing	Meta-transcriptome	Identification of live organisms	Low cost efficiency; classification mostly reliable at phylum level
Culturomics	Culturing in selective media	Live organisms	Identification of live organisms	Potential to miss anaerobic or fastidious fungi (ex. anaerobic fungi from ruminant gut)
Mass spectrometry (MS)	Matrix Assisted Laser Desorption/ionization Time-Of-Flight (MALDI-TOF)	Protein	Fast process; strain-level identification	Limited and often proprietary databases