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Beer sample preparation

The content of each beer sample was mixed to homogeneity by inversing the bottle several times. 50 mL were transferred into a conical tube and centrifuged (5000 rpm, 20 min, 4 °C) to collect cells and precipitable material. Pellets were resuspended with 1 mL TE buffer (Tris 10 mM, EDTA 1 mM, pH 8.0) and transferred into 1.5 mL tubes. The samples were centrifuged (10000 rpm, 10 min, 4 °C), the supernatant was removed and the pellet stored frozen (- 20°C) until future analyses. For DNA extraction, the ZR Fecal DNA MiniPrep kit (Zymo Research, Catalog No. D6010) was used with minor modifications.

Quatity control for DNA extraction

The absorbance of the extracted DNA was measured at 230, 260 and 280 nm using a Nanodrop instrument to ensure the DNA was free from protein and other contaminants.

PCR1: ITS amplification

To amplify yeast genomic DNA, we used the fungal hypervariable region ITS1 (internal transcribed spacer 1) as previously described \cite{Bokulich_2015} using the following primers:  BITS (5′–CTACCTGCGGARGGATCA–3′) and B58S3 (5′–GAGATCCRTTGYTRAAAGTT–3′). Typical PCR reactions contained 5–100 ng DNA template. Amplicon size (500nt) was verified using gel electrophoresis and with a fragment analyser. ITS amplicon were purified from free primers and primer dimers using AMPure XP beads following the manufacturer’s instructions (Beckman Coulter). Dual indices and Illumina sequencing adapters were attached using the Nextera XT Index Kit following manufacturer’s instructions (Illumina).

Sequencing

MiSeq sequencing was performed using the MiSeq v3 reagent kit protocol (Illumina). Briefly, the amplified DNA was quantified using a fluorimetric method based on dsDNA binding dyes (Qubit). Each DNA sample was diluted to 4 nM using 10 mM Tris pH 8.5 and 5 uL of diluted DNA from each library were pooled. In preparation for cluster generation and sequencing, 5 uL of the pooled final library was denatured with 5 uL of freshly diluted 0.2 N NaOH and combined with 30% PhiX control library to serve as an internal control for low-diversity libraries. After loading the samples on the MiSeq, paired 2x 300bp reads were generated and exported as FASTq files.

Bioinformatics Analysis

The curated set of ITS sequences from the  Refseq database (https://www.ncbi.nlm.nih.gov/refseq/targetedloci/) was used to build an ITS index for the Burrows-Wheeler Aligner (BWA) \cite{Li_2009}. The BWA was used to map the reads of each beer from the fastq files  to our ITS index. The bam files were sorted and indexed using samtools. Subsequently, the number of ITS per beer and per species were counted and only the species where we found more than 10 reads were kept.

Dataset content

The dataset contains the metagenetic profiles for 39 beers. The data was obtained using a targeted approach based on the phylogenetic typing with internal transcribed spacers (ITS) of ribosomal sequences.

Data and code statement

The raw data are stored in the SRA database in the bio project PRJNA388541

Author contributions

JS, LH and GR conceived the projects and communicated with the public. JS, NR and GR designed the experiments and carried out the research. JS, LH and GR wrote the manuscript.

Aknowledgements

The authors would like to thank Gabrielle Salanon for her help with sample extraction and analysis. Keith Harshman (Lausanne Genomic Technology Facility) for the access to the sequencing platform. Onecodex for the access to their metagenomic analysis tool. UniverCité and InArTiS for their support of the Hackuarium association and Rachel Aronoff for her critical review of the manuscript

Grant information

This project was funded by the 124 backers of the BeerDeCoded crowdfunding campaign that happened in June 2015. For a full list of backers, see [LINK]. These funders played a significant role in the data collection as they sent their beer samples for analysis. All backers from the crowdfunding campaign were given a chance to participate in the study design and analysis, decision to publish, or the preparation of the manuscript.
Copyright:  © 2017 Sobel J et al. This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Data associated with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).
Competing interests: GR is shareholder of SwissDeCode, a company selling to food manufacturers point-of-need DNA tests for food safety and compliance.