BeerDeCoded: Exploring the beer metagenome

Originally published as a F1000 Blog article

Jonathan Sobel shares his scientific quest to understand beer at a molecular level

A citizen science project carried out by the Hackuarium Association investigated the genome of various beers. The results of this work were published as as a Data Note on F1000Research. Jonthan Sobel explains what the thinking was behind this project and what they found. 

Beer is a fantastic beverage produced through a fermentation process and widely consumed around the world. It has inspired many generations of scientists and citizens. For instance, the famous student T-Test was initially developed for the beer industry, and has now become a popular statistical test for biologists. Again, James Joule was a brewer, who discovered the first law of thermodynamics with his brewing equipment. Many of us enjoy a good beer with our friends, and like to discover new ones.

Beer, an inspiration to generations

At Hackuarium, we chose beer to discuss the challenges and opportunities of DNA sequencing with fellow citizen scientists. The knowledge that we are acquiring could be of interest for breweries and microbreweries to develop new products.

Beer microorganisms

We wanted to detect different microorganisms in the beer ecosystem. Comparing different beers, allowed us to assess their similarities and their specificities, to see if there was a terroir – regional environmental factors that affect the properties of the final product – for beer, similarly to wine and cheese making. We thought this would trigger a discussion with a wider audience on the ethical issues regarding DNA sequencing data, while showing what we could learn about the product.

Creative solutions

Hackuarium, the bio-hacker space founded in 2014 by Luc Henry, was of paramount importance in the development of this project and bringing the team together. The team had experts from various backgrounds, including biologists, bioinformaticians, designers, a social community manager and business developer, met at the association.

By working in this association, we had greater freedom in choosing the direction of our project than in a company or in academia. We could virtually work on anything, providing that it was in agreement with our ethical charter and the law.

beerdecoded_JonathanSobel

When we set out on the project we had no money, so we had to find creative solutions to finance the project. In 2015, a kickstarter campaign led by Gianpaolo Rando provided us with the resources to generate a first dataset that we are now publishing as proof of concept in F1000Research.

The beer ecosystem

We produced a descriptive dataset of the fungal diversity referred to as the ITS region in 39 beers from 5 countries. Our preliminary analysis, revealed that the beer ecosystem is richer than expected in terms of fungal species.

In all the beers in our dataset, we found several Saccharomyces species, as well as  several species specific to one beer that could potentially represent their genetic identity, i.e., an internal fingerprint of authenticity.

Some ITS species could just be contaminants introduced during the beer making process, which could affect the final product quality, but that remains to be investigated.

Improving public understanding of sequencing

BeerDeCoded is an ambassador project about the DNA sequencing of a mass consumption product. Many have an idea about the beer production process or have a favourite beer, so using a familiar product makes it easier to communicate about molecular biology and sequencing techniques.

We are currently working with Berenice Batut from the Galaxy training network to train future generations of bioinformaticians with this dataset. We are also in discussion with other citizen science groups to export this project to other cities, to generate and gather more beer related data to expand our knowledge base.

Short Bio

Jonathan Sobel PhD pursued his master’s in a mucosal immunity lab at Lausanne university hospital, CHUV, where he studied the effect of lipoxin A4 on endometriosis at the protein level. Then, he did his Ph.D. in the computational systems biology lab at EPFL where he studied the interplay between metabolism and the circadian cycle in mouse liver, using next generation sequencing approaches. He joined the Regazzi lab at the university of Lausanne in 2017 as a post-doc in bioinformatics to study beta-cell maturation. Side to his academic work, Jonathan was involved in Hackuarium, a bio-hacker space in Renens, where he did science popularization.

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