Comparison of meta-barcoding and shotgun metagenomic analysis of fungi associated with spontaneous wine fermentation. food metagenome

Wine is a complex beverage, comprised of thousands of metabolites that are produced through the action of yeasts and bacteria in fermenting grape must. To ensure a robust and reliable fermentation, most commercial wines are produced via inoculation with large amounts of the major wine yeast, Saccharomyces cerevisiae. However, there is a growing trend towards the use of uninoculated or “wild” fermentations, in which the yeasts and bacteria that are naturally associated with the vineyard or winery perform the fermentation. The varied metabolic contributions of the numerous non-Saccharomyces species in this microbial community are thought to impart complexity and desirable taste and aroma attributes to wild ferments when compared to their inoculated counterparts.In order the map the microflora of spontaneous fermentation, metagenomic techniques were used to characterise and monitor the progression of fungal species in several wild fermentations. Both amplicon-based ITS phylotyping and shotgun metagenomics were used to assess community structure, in addition to the isolation, sequencing and de novo assembly of the first reference genomes for several dominant wine-associated species.