Early in the morning, silence still fills the hallways of the Faculty of Chemistry and Biology at the University of Santiago de Chile (Usach). At the far end stands Dr. Francisco Cubillos’s lab—a vibrant, bright space filled with flasks, test tubes, and cutting-edge biotechnology equipment where groundbreaking yeast genetics research takes place.
The small, somewhat cluttered lab was typical of a space where multiple research projects are conducted simultaneously. Of these, one involved yeasts that eventually turn into whiskey—a deep yellow variety stored in bottles resting on the shelves of the researcher’s office.
At the same time, this was the site where the Fondecyt Regular project “Genomic and transcriptional profiling of fermentative vigor in laboratory lager yeast hybrids” was undertaken, a study that sought to understand the origin and fermentative success of lager yeast—currently used in nearly 90% of the beer consumed worldwide—through the lens of yeast genetics and molecular biology.
While its exact origin remains debated, the earliest historical evidence of beer production traces back to ancient Mesopotamia. There, the Sumerians and Babylonians documented grain fermentation techniques, utilizing beer as a dietary staple and in sacred rituals dedicated to Ninkasi, the goddess of beer.
Despite its global spread, beer arrived in Chile in the 19th century through German brewing traditions. Crafted using the classic combination of water, malted barley, hops, and yeast—the same recipe used today.
Over a century later, Dr. Francisco Cubillos discovered that the wild genetic mother of lager yeast originates in the native forests of Chilean Patagonia: the cold-adapted species Saccharomyces eubayanus.
“In 2011, this wild yeast was first documented on the Argentine side of Patagonia, associated with native Nothofagus trees; we immediately investigated its distribution across Chilean Patagonia,” explains Dr. Francisco Cubillos. “We discovered that a major portion of these populations is concentrated in Chile, where we continue studying their unique genetic diversity to this day.”
In this context, the research team focused on the interspecies hybridization that created lager yeast (Saccharomyces pastorianus). Much like a mule resulting from a mare and a donkey, this hybrid emerged from crossing traditional ale yeast (Saccharomyces cerevisiae) with cold-tolerant wild yeast (Saccharomyces eubayanus), combining fermentative efficiency with low-temperature fermentation capabilities.
However, interspecies hybridization alone does not fully explain lager’s industrial dominance. For centuries, the precise genetic mechanisms allowing this hybrid yeast to master cold-temperature fermentation and sustain over 500 years of global brewing industry relevance remained an unsolved evolutionary mystery.
“What drives successful beer fermentation? How do human practices shape the selective breeding of specific yeast traits—and how do these characteristics adapt, gain, or lose function over time? These core questions guided our project,” explains Dr. Francisco Cubillos.
To reconstruct this lost evolutionary timeline, the team created novel laboratory yeast hybrids by crossing wild Patagonian strains with historical ale yeasts. Observing these hybrids in beer wort, researchers identified the key genetic adaptations that enabled lager yeast to survive, thrive, and, in the end, dominate global beer production.
“We initially assumed hybridization alone would guarantee superior fermentation efficiency, but many new hybrids performed no better than their parent strains. What truly drove their evolutionary success was the specific adaptive capacity of these yeast hybrids inside the beer wort,” explains Dr. Francisco Cubillos.
This adaptive behavior not only illuminated the evolutionary origins and success of lager yeast, but also revealed an incredible real-world opportunity: wild Patagonian yeast strains hidden in cold native forests hold vast potential far beyond basic evolutionary science, unlocking novel commercial applications for the global brewing industry.
Poco a poco, el proyecto empezó a dialogar con la idea de crear algo más, de aprovechar la biodiversidad presente y desarrollar nuevas aplicaciones biotecnológicas, en este caso, no solo para la industria cervecera, sino también para el mundo de los destilados y otros procesos fermentativos.
Little by little, the project evolved toward the idea of creating something else—harnessing the existing biodiversity to develop new biotechnological applications, in this case not only for the brewing industry but also for the world of distilled spirits and other fermentation processes.
“While we set out to answer fundamental questions about yeast origins and adaptation, we quickly uncovered immense applied biotechnology potential,” notes Dr. Francisco Cubillos. “Several novel yeast hybrids demonstrated exceptional performance in fermentation processes, opening direct commercial applications for the brewing industry and craft distilled spirits.”
Over four years, the Fondecyt Regular grant significantly expanded scientific understanding of Saccharomyces eubayanus and its pivotal role in lager yeast origins. Beyond advancing yeast genetics, the project trained undergraduate and graduate researchers, fostered international research collaborations, and yielded multiple scientific publications on native yeasts from Chilean Patagonia.
Ultimately, the team developed a novel yeast hybridization technique to engineer strains that adapt seamlessly to diverse wort compositions, paving the way for groundbreaking applications in craft beer production and whiskey distilling.
“Today, our laboratory possesses the advanced infrastructure to propagate these specialized yeast strains at scale for commercial beer and whiskey production,” says Dr. Francisco Cubillos. “Several of our yeast hybrids are already deployed in Swedish craft breweries and whiskey fermentation trials, yielding exceptional results that far exceeded our expectations.”
Beyond beer and microbiology, these wild strains highlight a vital strategic shift: how nations can convert native natural resources into cutting-edge scientific knowledge, applied technology, and sustainable economic development—moving beyond raw material exports toward a bio-based innovation economy.
Behind these yeasts lies not only a story about beer, fermentation, or microorganisms, but a much broader discussion: how a country that, since its origin, has lived off raw material export can transform native natural resources into knowledge, technology, and applied development.
As soft music drifts from the laboratory office, Dr. Cubillos reflects, perhaps, on years of groundbreaking field and lab work, students, and collaborators, concluding with a proud perspective:
“Our pristine environments offer a unique global advantage found nowhere else on Earth. By studying our native forests ourselves, we build homegrown applied science and technology transfer directly from our natural resources—allowing us to actively lead discovery and engage as equal global partners, rather than being mere spectators of our own biodiversity,” concludes Dr. Francisco Cubillos.