Status: Awaiting samples
The fungal composition of the flora of normal individuals has recently been termed the "mycobiome" and is a new area of exploration in humans. The mycobiome has been studied in various organs, including stool, primarily using DNA barcoding amplification. Overall, the number of fungal species that are thought to match the fungal resident is limited, potentially no more than 20 species. The concept of the core mycobiome- the resident yeasts that would be present in a majority of healthy individuals-has not been much studied, and the list of species belonging to this core mycobiome is still to be determined. We know that the mycobiome studies are sensitive to a large number of technical factors, starting with sample collection, storage and processing. In addition to culture methods, the detection of fungal species present in a biological sample relies primarily on next generation high-throughput sequencing methods. These methods are essentially metataxonomic (specific markers, i.e ITS) - amplification and sequencing of a barcoded DNA region - or shotgun metagenomic. The metataxonomy is highly dependent on the nature of the primer used to amplify the selected marker. The second is shotgun metagenomics - direct sequencing of the whole extracted DNA without amplification - which avoids any PCR bias. A major drawback of metagenomics is the lack of reliable quantification. Indeed, the number of ITS repeats varies between species and between isolates of the same species. In addition, the DNA sequence between different ITS repeats in the same individual may also vary, which may bias the interpretation of the data towards greater diversity. Finally, this approach is inherently biased during PCR amplification prior to sequencing, due to the preferential binding of so-called panfungal primers to certain sequences. Metagenomics appears to be better at quantifying the proportion of different fungal species, but this approach is less sensitive.
Submitted: 2022-10-06 14:24 · Last updated: 2023-01-24 09:22