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Data released on May 30, 2017

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

Sternes, P, R; Borneman, A, R; Kutyna, D, R; Lee, D (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 RIS BibTeX Text

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.

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Accessions (data included in GigaDB):

BioProject: PRJNA305659

Metagenomic

http://gigadb.org/images/data/cropped/100309.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Y1_D3-C870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331357
Collection date:2014
...
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Y1_D4-A870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331358
Collection date:2014
...
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Y1_D4-B870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331359
Collection date:2014
...
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Y1_D4-C870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331360
Collection date:2014
...
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Y2_D0-A870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331361
Collection date:2014
...
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Y2_D0-B870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331362
Collection date:2014
...
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Y2_D0-C870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331363
Collection date:2014
...
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Y2_D1-A870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331364
Collection date:2014
...
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Y2D1_A shotgun870726  food metagenome Description:Shotgun sequencing of metagenomic DNA ...
Alternative accession-BioSample:SAMN04331409
Collection date:2014
...
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Y2_D1-B870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331365
Collection date:2014
...
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Displaying 51-60 of 86 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
Tabular dataTEXT549.77 KB2017-05-24
Tabular dataTEXT343.62 KB2017-05-24
OtherFASTA741.38 MB2017-05-24
file_typeUNKNOWN52.95 MB2017-05-24
file_typeFASTA332.73 KB2017-05-24
Tabular dataTEXT124.07 KB2017-05-24
file_typeUNKNOWN82.72 MB2017-05-24
Sequence assemblyFASTA10.76 KB2017-05-24
Sequence assemblyFASTA21.01 KB2017-05-24
Sequence assemblyFASTA4.86 KB2017-05-24
Displaying 1-10 of 322 File(s).

History:

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