Abstract
While metabarcoding is commonly used to describe prokaryotes in the microbiome of many environments, methods for describing micro-eukaryote diversity is lacking and requires better methodology and standardisation. One reason is that the universal fungal barcode, the Internal Transcribed Spacer (ITS) region, displays considerable size variation among yeasts and other micro-eukaryotes. There are also several repeats leading to sequencing errors or termination. Additionally, the ITS databases are far from complete, especially for Ascomycota that are commonly found in food. Other rDNA barcodes have been used but often do not harbor enough polymorphism to identify taxa at the Species level. In food, microbiota are usually composed of a reduced number of species compared to wild environments. Identifying micro-eukaryotes at the Species level, and potentially strain level, is therefore necessary.