Distinctive domestication of farmhouse beer yeasts preserved pre-industrial genetic and phenotypic diversity

Since its inception over 10,000 years ago, beer brewing has transformed from a domestic activity based on uncontrolled spontaneous fermentations into a highly optimized industrial process that uses pure single-strain starter cultures of Saccharomyces yeasts. Along with the storage of frozen yeast stocks, this shift halted the domestication process of beer yeasts and led to a massive loss of beer yeast biodiversity. However, a few traditional farmhouse brewers in Northern and Eastern Europe still rely on artisanal fermentation methods, using mixed cultures of yeasts that are passed on from one fermentation to the next. We genetically and phenotypically analyzed 1,760 isolates from 44 traditional European farmhouse ale yeast cultures from Norway, Latvia, Lithuania, and Russia. We find that farmhouse cultures harbor remarkable genetic diversity, from near-monocultures to intricate communities of over 30 different S. cerevisiae variants. Farmhouse yeast genomes exhibit clear geographic structuring but also reveal signs of admixture alongside lineage-specific genomic features, such as a horizontally transferred gene cluster in Baltic strains. Large-scale phenotyping reveals that farmhouse yeasts harbor domestication signatures that are distinct from those of industrial beer yeasts, including maintenance of a sexual cycle, higher stress tolerance, and more diverse flavor profiles. Together, our study reveals the complex structure and diversity of farmhouse cultures and provides a reservoir of new yeast strains that can propel the next wave of beer innovation.