Table 1.

Summary of culture-independent methods for studying the mycobiome

Method	Procedure	Strength	Weakness
RFLP [10,60,61]	1. PCR of rDNA 2. Build the clone library 3. Digest with endonucleases 4. Run capillary electrophoresis	Allow comparisons of fungal abundance across groups	1. Considerable intraspecific variability 2. Not specific enough to differentiate fungi at the level of species 3. Unable to quantify the proportion of each type of fungi in the mycobiome
OFRG [62]	1. PCR of rDNA 2. Build the clone library 3. Hybridize with oligonucleotide probes
DGGE [14]	1. PCR of rDNA 2. Build the clone library 3. Run the denaturing gel electrophoresis 4. Analyze the patterns of the bands
In situ hybridization [14]	1. Process biopsy sample 2. Probe hybridization
Sanger sequencing [50]	1. PCR of rDNA 2. Build the clone library 3. Sanger sequencing	Specific enough to differentiate between species	High cost [63]
Pyrosequencing [18,64]	1. PCR of rDNA 2. Pyrosequencing		1. Homo-polymerization 2. Environmental contamination