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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
Control1_A shotgun870726  food metagenome Description:Shotgun sequencing of metagenomic DNA ...
Alternative accession-BioSample:SAMN04331397
Collection date:2014
...
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Control1_C shotgun870726  food metagenome Description:Shotgun sequencing of metagenomic DNA ...
Alternative accession-BioSample:SAMN04331398
Collection date:2014
...
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Control2_A shotgun870726  food metagenome Description:Shotgun sequencing of metagenomic DNA ...
Alternative accession-BioSample:SAMN04331399
Collection date:2014
...
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Control2_C shotgun870726  food metagenome Description:Shotgun sequencing of metagenomic DNA ...
Alternative accession-BioSample:SAMN04331400
Collection date:2014
...
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control_ferment1a870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331319
Collection date:2014
...
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control_ferment1b870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331320
Collection date:2014
...
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control_ferment1c870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331321
Collection date:2014
...
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control_ferment2a870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331322
Collection date:2014
...
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control_ferment2b870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331323
Collection date:2014
...
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control_ferment2c870726  food metagenome Description:ITS amplicon sequencing of metagenomic...
Alternative accession-BioSample:SAMN04331324
Collection date:2014
...
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Displaying 1-10 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 
OtherUNKNOWN51.62 MB2017-05-24
AlignmentsBAM2.31 GB2017-05-24
OtherUNKNOWN51.62 MB2017-05-24
Sequence assemblyFASTA221.6 KB2017-05-24
Sequence assemblyFASTA311.63 KB2017-05-24
AlignmentsBAM9.64 MB2017-05-24
AlignmentsBAM5.9 MB2017-05-24
OtherUNKNOWN51.62 MB2017-05-24
AlignmentsBAM2.03 GB2017-05-24
OtherUNKNOWN51.62 MB2017-05-24
Displaying 1-10 of 322 File(s).

History:

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