Beer is probably the world's oldest and most widely consumed alcoholic drink on the planet, with a total production of around 2.5 billion hectolitres (2.5·10E11 litres). While a continuous process of market consolidation has led to 5 companies controlling more than half of global production, there has been an explosion of local craft beer industries in Europe and North America over the past years. As DNA sequencing becomes increasingly cheap, whole genome sequencing and metagenomic analyses are being explored as a resource to better understand the brewing process, winemaking and food fermentation in general \cite{De_Filippis_2016}. Microbial communities contribute to nutritional and aromatic properties and shelf life of the products. Wine is a notorious example of such a product, where a complex microbial community composed of yeast and bacteria influences the winemaking process throughout \cite{Liu_2015}. There is also increasing evidence for the existence of a strong microbial contribution to the notion of “terroir” in wine \cite{Bokulich_2016,Bokulich_2013,Pinto_2015,Belda_2017}. These microorganisms are present in the vineyard soil, on the fruits, and in the fermentation process, being carried over from the grapes to the must to the wine. One question that remains unanswered is whether thre is such a thing as a “terroir” for beer?
Of particular interest are sour beer, such as lambic and gueuze. These beverages are produced without the addition of known yeast cultivates. Instead, the wort is exposed to ambiant air, allowing naturally occurring bacteria and yeasts to start the fermentation. This process faces high variability and difficulties to standardisation. To our knowledge, three initiatives are currently exploring the role of the beer microbiome on the brewing process and also on characteristics of the final product. Using metagenomic analyses, Kevin Verstrepen and coworkers at KU Leuven, Belgium, study the production of lambic, a traditional Belgian beer produced by spontaneous fermentation [
VIB project 35] . Similarly, Matthew Bochman and coworkers at Indiana University, USA, have recently published preliminary results showing how the microbial community evolved over the fermentation process, together with the relative abundance of the organic acids that give sour beer its characteristic taste
\cite{Bochman_2017} and
\cite{Osburn_2017} . Finally, at the University of Washington, USA, have discovered a novel interspecific hybrid yeast in an open-fermentation beer sample using chromosome conformation capture
\cite{Smukowski_Heil_2017}.
To investigate the microbial composition of a collection a commercial beers, we initiated
BeerDeCoded in the context of
Hackuarium, a Swiss not-for-profit organisation that supports unconventional research ideas and promotes the public understanding of science. Members of the Hackuarium, community are interested in participatory biology and want to promote interdisciplinary citizen research and innovation outside traditional institutions, using low-cost, simple and accessible technologies. The goal of the BeerDeCoded project is not only to extend the scientific knowledge about beer, but also to improve the public understanding of issues related to personal genomics, food technology, and their role in society. With the release of this first data set, we built the proof of concept for a beer targeted metagenome analysis pipeline that can be used in high schools, citizen science laboratories, craft breweries or industrial plants.
Results
Over the month of June 2015, a total of 124 individuals contributed over 10,000 Euros to a
crowdfunding campaign that provided financial resources for the first stage of the BeerDeCoded project. Reaching out to the public through this campaign also enabled crowdsourcing a collection of 120 beer samples from 20 countries. We have subsequently demonstrated that it is possible to extract DNA directly from bottled beer using low cost methodologies, typically available to citizen scientists (see Methods). After amplification and quality control, 39 samples were sent for DNA sequencing. Among these 39 beers we had 30 beers from Switzerland, 5 beers from Belgium, 2 beers from Italy, 1 from France and 1 from Austria.