BeerDeCoded: the open beer metagenome project

Abstract

Next generation sequencing has radically changed research in the life sciences, in both academic and corporate laboratories. The potential impact is tremendous, yet a majority of citizens have little or no understanding of the technological and ethical aspects of this widespread adoption. We designed BeerDeCoded as a pretext to discuss the societal issues related to genomic and metagenomic data with fellow citizens, while advancing scientific knowledge of the most popular beverage of all. In the spirit of citizen science, sample collection and DNA extraction were carried out with the participation of non-scientists in the community laboratory of Hackuarium, a not-for-profit organisation that supports unconventional research and promotes the public understanding of science. The dataset presented herein contains the targeted metagenomic profile of 39 bottled beers from 5 countries, based on internal transcribed spacer (ITS) sequencing of fungal species. A preliminary analysis reveals the presence of a large diversity of wild yeast species in commercial brews. With this project, we demonstrate that coupling simple laboratory procedures that can be carried out in a non-professional environment with state-of-the-art sequencing technologies and targeted metagenomic analyses, can lead to the detection and identification of the microbial content in bottled beer.

Methods for detection and identification of beer-spoilage microbes

“…Ribosomal RNA genes contain slowly evolving regions that generally have low sequence polymorphisms that can be used for genus identification, but also contain fast-evolving regions which can be used as a species identifier ( Sambo et al, 2018 ). Specific regions or the entire length of the 16S rRNA gene are amplified via PCR with degenerate universal primers, then sequenced, commonly with the Next-Generation Sequencing (NGS) platform, Illumina MiSeq (Illumina, Inc., San Diego, CA) ( Britton et al, 2015 ; Sobel et al, 2017 ; Sambo et al, 2018 ; Callahan et al, 2019 ). While the sequencer may be affordable for some breweries ($99,000 new, quote from Illumina November 18, 2021), especially if purchasing preowned (~$25,000) ( LabX, n.d. ), with running costs at $18/sample ( Illumina, 2023 ) this method is yet to be affordable enough for routine use in most craft breweries.…”

Isolation and Characterization of Live Yeast Cells from Ancient Vessels as a Tool in Bio-Archaeology

“…4), while all the control isolated yeast strains produced spoiled aromas and flavors, also provides some support for the authenticity of the origin of the isolated yeast as descendants of the ancient fermenting yeast. As mentioned above, this support is weaker than the previous ones, because some wild yeast can also ferment beer and produced aromatic compounds (68, 69). Thus, there is a correlation between the source of isolation (putative beverage vessel or not), similar growth in wort compared to modern beer yeast strains, and the ability to produce drinkable beer.…”

“…In summary, these results exemplify the potential in the research of live microorganisms isolated from ancient vessels and their products. Nevertheless, it should be noted that aromatic beer can be produced also by wild yeasts (68) and even pathogenic yeasts such as C. parapsilosis (69), and thus beer production per se cannot support or reject the hypothesis that the isolated yeast are descendants of the fermenting yeast.…”

Citation needed? Wikipedia bibliometrics during the first wave of the COVID-19 pandemic

“…Viewed as such, Wikipedia’s citizen encyclopedists can play the same role communicating science that citizen scientists play in creating science. As previous citizen science projects have taught us [ 46 ], for that to work, citizens need scientists to provide the framework for non-expert contributions [ 47 , 48 ]. As this study indicates, a similar infrastructure can be seen to already exist on Wikipedia for encyclopedic (as opposed to scientific) work.…”