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Cited by 91Fermentation and Sensory AnalysisYeasts and Rust Fungi StudiesHorticultural and Viticultural Research

A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation

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Sternes, Peter R., Lee, Danna, Kutyna, Dariusz R., Borneman, Anthony R.·2017·GigaScience
DOI 10.1093/gigascience/gix040PMC PMC5570097

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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.

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  • Most yeast strains from wine were either within a Wine plus Dairy cluster (Wine-1) or a distinct cluster mainly constituted of Australian spontaneous wine fermentation samples (Wine-2).

    “Most yeast strains from wine were either within a Wine plus Dairy cluster (Wine-1) or a distinct cluster mainly constituted of Australian spontaneous wine fermentation samples (Wine-2). 74”

    From Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. (2024) · cites this paper as [74]

    The Laboratory ferments section describes changes in yeast species during Australian wine fermentation, but does not classify wine yeast strains into Wine-1 and Wine-2. Searches for “Wine-1,” “Wine-2,” dairy, and strain phylogeny found no passage in our copy addressing the claimed clusters; page numbers were not available. (LLM, conf=0.77)

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Cited by

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Authors
Sternes, P. R., Lee, D., Kutyna, D. R., & Borneman, A. R.
Affiliations
  • Queensland University of Technology (AU)
  • Uppsala University (SE)
  • Australian Wine Research Institute (AU)
  • The University of Adelaide (AU)
Corresponding author
Borneman, Anthony R.
ORCID
Venue
GigaScience
Publisher
Oxford University Press (OUP)
Published
2017-06-08
Volume
6
Issue
7
Pages
1-10
ISSN
2047-217X (ISSN-L)
DOI
10.1093/gigascience/gix040
PMC
PMC5570097
OpenAlex
W2951622419
Cited by
91
References
1
Citations by year
2026: 3 · 2025: 10 · 2024: 12 · 2023: 11 · 2022: 9 · 2021: 11 · 2020: 15 · 2019: 9 · 2018: 9 · 2017: 2
FWCI
10.77
Type
journal article
Language
en
Open access
Licence
Locations
  • GigaScience (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • QUT ePrints (Queensland University of Technology) (submittedVersion, cc-by)
  • Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion, cc-by)
Funders
Australian Government
Topics
  • Life Sciences › Agricultural and Biological Sciences › Food Science › Fermentation and Sensory Analysis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Yeasts and Rust Fungi Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Horticultural and Viticultural Research
Keywords
non-Saccharomyces yeasts, Metschnikowia, microbial community structure, grape must
MeSH terms
Fermentation, Saccharomyces cerevisiae, Wine, Metagenome, DNA Barcoding, Taxonomic

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