Abstract
Wine is a complex beverage, comprising hundreds of metabolites produced through the action of yeasts and bacteria in fermenting grape must. Commercially, there is now a growing trend away from using wine yeast (Saccharomyces) starter cultures, toward the historic practice of uninoculated or “wild” fermentation, where the yeasts and bacteria associated with the grapes and/or winery perform the fermentation. It is the varied metabolic contributions of these numerous non-Saccharomyces species that are thought to impart complexity and desirable taste and aroma attributes to wild ferments in comparison to their inoculated counterparts. To map the microflora of spontaneous fermentation, metagenomic techniques were employed to characterize and monitor the progression of fungal species in 5 different wild fermentations. Both amplicon-based ribosomal DNA internal transcribed spacer (ITS) phylotyping and shotgun metagenomics were used to assess community structure across different stages of fermentation. While providing a sensitive and highly accurate means of characterizing the wine microbiome, the shotgun metagenomic data also uncovered a significant overabundance bias in the ITS phylotyping abundance estimations for the common non-Saccharomyces wine yeast genus Metschnikowia. By identifying biases such as that observed for Metschnikowia, abundance measurements from future ITS phylotyping datasets can be corrected to provide more accurate species representation. Ultimately, as more shotgun metagenomic and single-strain de novo assemblies for key wine species become available, the accuracy of both ITS-amplicon and shotgun studies will greatly increase, providing a powerful methodology for deciphering the influence of the microbial community on the wine flavor and aroma.
Highlights
Wine is a complex beverage, comprising thousands of metabolites that are produced through the action of yeasts and bacteria in fermenting grape must
There is a growing trend away from using wine yeast (Saccharomyces) starter cultures, toward the historic practice of uninoculated or “wild” fermentation, where the yeasts and bacteria associated with the grapes and/or winery perform the fermentation
In the very early stages of fermentation, aerobic and apiculate yeasts and yeast-like fungi from genera such as Aureobasidium, Rhodotorula, Pichia, Candida, Hanseniaspora and Metschnikowia, which reside on the surface of intact grape berries or winery equipment, represent the majority of the microbiota [1]
Summary
Wine is a complex beverage, comprising thousands of metabolites that are produced through the action of yeasts and bacteria in fermenting grape must. Recent advances in cultureindependent methods for species analysis, such as ampliconbased phylotyping ( known as meta-barcoding) and metagenomics provide a high-throughput means to analyze large numbers of microbiological samples at great depth [8] These techniques are being adapted for the study of wine fermentation, and several amplicon-based studies have been conducted to investigate vineyard and wine microbiomes [9,10,11,12,13,14]. To map the microflora of spontaneous fermentation, both amplicon-based ITS phylotyping (meta-barcoding) and shotgun metagenomics were used to assess community structure, while comparing the biases inherent in PCR-based phylotyping relative to the unbiased shotgun metagenomic sequencing These data provide key insights into the species participating in wild wine fermentation, while highlighting the at least 1 significant bias in the ITS analysis of wine yeasts. The datasets supporting the results of this article are available in the GigaDB repository [17]
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