BeerDeCoded: the open beer metagenome project

Introduction

Beer is probably the world’s oldest and most widely consumed alcoholic beverage on the planet, with a worldwide production of nearly 2 billion hectolitres (2·10E11 litres) annually [The Barth Report, Hops 2015/2016], and, as DNA sequencing becomes increasingly cheap, whole genome sequencing and metagenomic analyses are being explored as tools to better understand brewing in particular, and food fermentation in general¹. Complex microbial communities influence the wine- and cheesemaking process throughout^2,3. Indeed, microbial communities contribute to nutritional and aromatic properties, as well as shelf life of the products. In the case of wine, microorganisms are present in the soil, on the grapes, and in the fermenter, being carried over from the vine to the must to the wine, and there is increasing evidence for the existence of an important microbial contribution to the notion of “terroir”^4–7. One question that remains unanswered is whether there is such a thing as a “terroir” for beer.

Of particular interest is sour beer, such as lambic and gueuze, a beverage produced without the controlled addition of known yeast cultivates. Instead, the wort is exposed to ambient air, allowing naturally occurring bacteria and yeasts to start the fermentation and leading to a production that is difficult to standardize. To our knowledge, three initiatives are currently exploring the role of the beer microbiome in the brewing process and how it shapes the characteristics of the final product. Using metagenomic analyses, Kevin Verstrepen and colleagues at KU Leuven, Belgium, study the production of lambic, a traditional Belgian beer produced by spontaneous fermentation [VIB project 35]. Similarly, Matthew Bochman and colleagues 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^8,9. Similarly, researchers at the University of Washington, USA, have studied open-fermentation beer using chromosome conformation capture and discovered a novel interspecific hybrid yeast¹⁰.

To investigate the microbial composition of a collection of commercial beers, we initiated BeerDeCoded in the context of Hackuarium, a Swiss not-for-profit organisation that supports unconventional research projects 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 broaden 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 targeted metagenome analysis pipeline for beer samples that can be used in high schools, citizen science laboratories, craft breweries or industrial plants.

Methods

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).

The internal transcribed spacer regions (ITS) of fungal species¹⁴ were then amplified and, after quality control, 39 samples were sent for DNA sequencing. These 39 commercial beers originated from 5 different countries: 30 were from Switzerland, five from Belgium, two from Italy, one from France and one from Austria. We obtained an average library size of 600K reads (min 350K, max 2400K) per sample and a total of 88 fungal species were identified, including 52 unique occurrences. This high variety of wild yeasts in commercial beers was unexpected (Figure 1A), with some brews containing traces of up to more than 30 different fungal species (Figure 1B). Using hierarchical clustering, we built a proximity tree of the different beers (Figure 2).

Figure 1.

Barplot graph representing (A) the number of beers containing the species (n=36) occurring in at least two samples. Species (n=52) present in only one sample were excluded for clarity. (B) represents the number of fungal species identified in each of the 39 bottled beers.

Figure 2. Hierarchical clustering of the 39 beers included in this study, based on their fungal content.

Consistent with its widespread use for fermentation, brewer’s yeast (Saccharomyces cerevisiae) was detected in all beer samples, accounting for between 11% (Orval, an ale beer by Belgian Brasserie d’Orval) and 99% (Tempête, an ale from the Swiss brewery Docteur Gab’s) of all sequencing reads. In most samples, S. cerevisiae was present at very high levels (typically 90–97% of reads, Figure 3). More surprisingly, Saccharomyces mikatae, a species used in winemaking¹⁵ was also relatively abundant in all samples (0.5–5%). Interestingly, most brews were found to contain low to medium presence of multiple other yeast species, including Saccharomyces bayanus (used in winemaking and cider fermentation), Saccharomyces kudriavzevii and Saccharomyces pastorianus (used in lager manufacturing), Saccharomyces eubayanus (a probable parent of Saccharomyces pastorianus) and Brettanomyces bruxellensis (typically used for the production of the Belgian beer styles). B. bruxellensis represented 86% and 15% of the reads in the Orval and the “Chicha” experimental beer, respectively. Non-conventional, as well as wild yeast, such as Saccharomyces cariocanus and Saccharomyces paradoxus, two species closely related to Saccharomyces cerevisiae were also found. Another example is Kazachstania sp., a wild yeast of commonly found in brines. The presence of this species may be of interest, as it was previously reported that adding the parent Kazachstania servazzi to the brewing process 24 hours before the ale yeast contributed to the production of high level of esters, producing a strong fruity and floral aroma¹⁶.

Figure 3. Heatmap of the number of reads per ITS per beer (in log 10 read counts).

Only ITS with more than 10 reads and present in at least two beers are shown.

The beer in which we measured the highest ITS diversity was Waldbier 2014 “Black Pine”, an Austrian beer brewed using pine cones collected in local forests, with 38 fungal species. Two other beers contained more than 20 fungal species: La Nébuleuse Cumbres Rijkrallpa (a sour/wild ale beer made with cranberries and the fermented corn “Chicha”) and Chimay Red Cap, a Belgian trappist beer. Fungal DNA from 52 species was unique for specific beers. For instance, Chimay Red Cap, was the only beer containing traces of Ganoderma sp., a fungus rich in terpenoids well known for its bitter taste¹⁷. A fungus naturally present in the kernels of cereals and used in organic agriculture as natural herbicide, Alternaria sp., was found in 15 of the 39 samples, suggesting that microorganisms, or their DNA, could be carried over from the ingredients to the final product.

Discussion and future perspectives

While a continuous process of market consolidation has lead to 5 companies controlling more than half of global beer production, there has been an explosion of craft industries over the past years, especially in Europe and North America. In 1978 there were 89 large industrial breweries in the USA. In 2016, there were 5,301, among them 3,132 small, independent microbreweries (American Brewers Association). There is a parallel with Hackuarium, an independent “craft” science initiative that has branched out from large institutional research institutes and provides an environment that allows scientists to explore topics that are rarely found in academia or industry. What is truly unique is the participation of individuals with no formal science training, and therefore the strong focus on citizen science and communication. With the BeerDeCoded project, we explored the potential of crowdfunding and crowdsourcing in engaging members of the general public in the production of scientific knowledge. We demonstrated that it is possible to execute complex molecular analyses on everyday products using limited resources and technical support from research institutions, and no financial support from traditional funding sources. The resulting dataset contains the ITS profile of 39 bottled beers from five different countries, revealing the low abundance but widespread presence of wild fungal species. Further analyses could go as far as shedding light on the so-called biological “dark matter” of the beer ecosystem^18,19.

With the costs of DNA sequencing falling dramatically, and with the emergence of portable and user-friendly instrumentation, we believe that it is a favorable time to expand the application of DNA analysis to novel fields, including food and beverage. This industry is starting to explore the potential of genome sequencing to understand the contribution of various species to product characteristics. The sequencing of the full genome of 157 brewing yeast strains was, for example, recently reported²⁰. Metagenomic analyses could also have important implications for the optimization and batch-to-batch reproducibility of the various fermentation processes, as well as quality control, traceability and authentication of the products. One hypothesis that could be investigated further in the future is whether the presence of a specific fungal species can be diagnostic for a unique geographic area. In our data set, the non Saccharomyces yeast that contributes to wine aroma through the production of volatile compounds, Wickerhamomyces anomalus, was found exclusively in five of the brews manufactured in Switzerland. The limited sample size, however, does not allow us to draw a statistically significant conclusion, and it remains to be seen if W. anomalus is present in beers from other locations as well. Due to inherent limitations of DNA sequencing, it is difficult to anticipate whether the microbes identified are likely to be having an impact on the fermentation process. However, based on the identification of strains present in brews with desired characteristics, controlled experiments in which the microbial composition of the brew is altered could allow us to investigate if the presence of specific microorganisms affects flavour²¹. The origin of each yeast species could also be investigated; i.e. whether they come with the ingredients or from the environment at the production site. Techniques to sample airborne DNA exist²². Furthermore, other protocols could also be used to catalogue plant DNA²³, such as malt and hop varieties, and to map the bacterial diversity.

In order to standardize and simplify our pipeline, and facilitate the contribution of new data and their further analysis by individuals not involved in this initial study, we are in the process of developing a BeerDeCoded repository and a Galaxy instance²⁴. This tool will enable any citizen scientist to carry out beer metagenomics and reproduce our analysis. In the meantime, we encourage researchers from other laboratories, microbreweries and citizen laboratories to further explore our data set, and invite them to consider contributing additional data in the future.

Data availability

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. All methods, quality control, processed tables, metadata and code are accessible at: https://github.com/beerdecoded/Beer_ITS_analysis. The raw data are stored in the SRA database in the bio project PRJNA388541