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Table 1 Summary of culture-independent methods for studying the mycobiome

From: The human mycobiome in health and disease

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