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), 1–10. doi:10.1093/gigascience/gix040

Accessions (data included in GigaDB):

BioProject: PRJNA305659





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Y2D1_B shotgun870726  food metagenome Description:Shotgun sequencing of metagenomic DNA ...
Alternative accession-BioSample:SAMN04331410
Collection date:2014
...
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Y2_D1-C870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331366
Collection date:2014
...
+
Y2_D2-A870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331367
Collection date:2014
...
+
Y2_D2-B870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331368
Collection date:2014
...
+
Y2_D2-C870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331369
Collection date:2014
...
+
Y2_D3-A870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331370
Collection date:2014
...
+
Y2D3_A shotgun870726  food metagenome Description:Shotgun sequencing of metagenomic DNA ...
Alternative accession-BioSample:SAMN04331411
Collection date:2014
...
+
Y2_D3-B870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331371
Collection date:2014
...
+
Y2D3_B shotgun870726  food metagenome Description:Shotgun sequencing of metagenomic DNA ...
Alternative accession-BioSample:SAMN04331412
Collection date:2014
...
+
Y2_D3-C870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331372
Collection date:2014
...
+
Displaying 61-70 of 86 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Sequence assemblyFASTA5.76 KB2017-05-24
Sequence assemblyFASTA19.93 KB2017-05-24
Sequence assemblyFASTA3.61 KB2017-05-24
Sequence assemblyFASTA13.23 KB2017-05-24
Sequence assemblyFASTA3.47 KB2017-05-24
Sequence assemblyFASTA7.22 KB2017-05-24
Sequence assemblyFASTA14.21 KB2017-05-24
Sequence assemblyFASTA5.78 KB2017-05-24
Sequence assemblyFASTA13.56 KB2017-05-24
Sequence assemblyFASTA7.41 KB2017-05-24
Displaying 61-70 of 322 File(s).
Date Action
May 30, 2017 Dataset publish
October 2, 2017 Manuscript Link added : 10.1093/gigascience/gix040