Supporting data for "A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation"

Dataset type: Metagenomic
Data released on May 30, 2017

Borneman AR; Kutyna DR; Lee D; Sternes PR (2017): Supporting data for "A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation" GigaScience Database. http://dx.doi.org/10.5524/100309

DOI10.5524/100309

Wine is a complex beverage, comprising hundreds of metabolites 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 commercial strains 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 and winery perform the fermentation. In doing so, 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 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 several wild fermentations. Both amplicon-based ribosomal DNA internal transcribed spacer (ITS) phylotyping (meta-barcoding) and shotgun metagenomics were used to assess community structure. While providing a sensitive and highly accurate means of characterizing the wine microbiome, the shotgun metagenomic data also uncovered a significant over-abundance bias in the ITS phylotyping abundance estimations for the common non-Saccharomyces wine yeast genus Metschnikowia.

Additional details

Read the peer-reviewed publication(s):

Sternes, P. R., Lee, D., Kutyna, D. R., & Borneman, A. R. (2017). A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation. GigaScience, 6(7). doi:10.1093/gigascience/gix040

Accessions (data included in GigaDB):

BioProject: PRJNA305659





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Y3_D2-C870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331381
Collection date:2014
...
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Y3_D3-A870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331382
Collection date:2014
...
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Y3D3_A shotgun870726  food metagenome Description:Shotgun sequencing of metagenomic DNA ...
Alternative accession-BioSample:SAMN04331415
Collection date:2014
...
+
Y3_D3-B870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331383
Collection date:2014
...
+
Y3D3_B shotgun870726  food metagenome Description:Shotgun sequencing of metagenomic DNA ...
Alternative accession-BioSample:SAMN04331416
Collection date:2014
...
+
Y3_D3-C870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331384
Collection date:2014
...
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Displaying 81-86 of 86 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Sequence assemblyFASTA10.69 KB2017-05-24
Sequence assemblyFASTA28.98 KB2017-05-24
Sequence assemblyFASTA6.36 KB2017-05-24
BLASTUNKNOWN23.19 MB2017-05-24
BLASTUNKNOWN362.4 KB2017-05-24
Sequence assemblyFASTA41.15 KB2017-05-24
Sequence assemblyFASTA3.97 KB2017-05-24
Sequence assemblyFASTA4.67 KB2017-05-24
Sequence assemblyFASTA5.75 KB2017-05-24
Sequence assemblyFASTA12.65 KB2017-05-24
Displaying 91-100 of 322 File(s).
Date Action
May 30, 2017 Dataset publish
October 2, 2017 Manuscript Link added : 10.1093/gigascience/gix040