Brewing Yeast Genetic Stability 

The rise of domesticated brewing yeast  

The modern brewing yeast is the result of millennia of selective breeding. The slow domestication process from spontaneous grain fermentations in neolithic pottery to modern stainless steel, in sterile mega-breweries has resulted in a species of yeast that is very different from its wild ancestors. The result of this domestication is that Saccharomyces cerevisiae has become well adapted to niche environments created by humans that do not exist in nature. Unlike wild yeast, the genome of S. cerevisiae is often quite ‘messy’. It’s the result of artificial selection and environmental pressures in human-made environments such as breweries. A common example of these adaptations is loss of functional PAD1 and FDC1 genes, which, in their functional form, are responsible for producing phenolic “POF” flavors in beer. Additionally, domesticated Saccharomyces species have developed unique mechanisms to rapidly metabolize complex carbohydrates such as maltotriose, a valuable energy source found in brewing wort that is not typically metabolized by wild yeasts. Other unique characteristics, such as an abnormal number of chromosomes, pervasive genetic homozygosity (genes are the same on each chromosome), and an inability to successfully mate and undergo meiotic rearrangement through sporulation, contribute to making domesticated S. cerevisiae so useful to us. 

Consistent beer through yeast genetic stability 

The utility of yeast domestication to modern brewers cannot be understated. These adaptations come at enormous biological costs, often making it very difficult for domesticated brewing yeast to sexually reproduce, further diminishing the capacity to adapt and evolve to different environmental conditions. This makes domesticated yeast less competitive in the wild, but extremely useful for a brewer as this genetic stability leads to consistent fermentation performance. 

In practice, “genetic stability” is the ability to minimize observable changes in fermentation performance and flavor during normal industrial use, despite slowly collecting mutations over long term use. This is a highly desirable trait of brewing yeasts and key to their ability to produce consistent and reliable results from batch to batch.  

Genetic drift is inevitable

While brewing yeasts are resistant to change, it is also important to understand that genetic mutations are inevitable. Every time a cell divides, there is a chance that an error occurs while replicating the DNA – resulting in some altered behavior of the new cell. When a yeast is propagated for use in brewing, the population increases by more than six orders of magnitude from just a few hundred cells per milliliter of wort to one billion cells per milliliter (or more!). When billions of cells are dividing, living, metabolizing, etc., mutations are not merely a possibility, but an inevitability. Fortunately, most mutations will not alter the desired behavior of the yeast. Occasionally, a mutation will occur in an important metabolic pathway that impacts the whole brewing process in unforeseen ways. When billions of cells are dividing, living, metabolizing, mutations are not merely a possibility, but an inevitability.

Genetic stability during yeast production 

As genetic drift is inevitable, what can we do to best ensure consistent yeast performance? Thankfully, a lot! As yeast producers, we carefully manage our culture collection to ensure the long term stability of our yeast strains through rigorous testing and documentation.  

Strain characterization

When a new strain is collected, or developed, it is subjected to a mating test to determine its ability to sporulate and mate. Documentation of mating capacity can provide valuable insight into the chances of rare mating events or spontaneous chromosomal rearrangements in the brewery. This also gives us an opportunity to explore novel strain development through hybridization. 

At present, there are two primary methods through which entirely novel strains may be developed: hybridization and bioengineering. Hybridization is a complex process which, if done incorrectly, may cause whole genome dysfunction – resulting in a genetically unstable organism that is completely unfit for brewing or other industrial applications. The same concepts apply to bioengineered yeast since genetic modifications may result in reduced fitness and introduce selective pressure against this modification. Careful selection and screening of offspring are required to ensure that the resulting organism can fully integrate any changes made to its genome, and successfully pass these traits onto subsequent generations without any loss of function. In our labs, we rigorously test novel traits in bioengineered yeast often exceeding 100 microbial generations – approximately equivalent to 25 repitches in a brewery.  

Yeast banking and storage

Banked yeast strains are stored long term in a dormant state at cryogenic temperatures of ≤ -150°C, which ensures that random mutations are kept to a minimum. These cryogenic yeast banks serve as a “doomsday” backup so that strains are never lost in case of a disaster. All cultures for commercial
production are derived from our culture bank and managed carefully to minimize the number of generations from the original banked culture and guarantee manufacturing consistency. Under these conditions, it is expected that major genomic changes will not occur. Nevertheless, our culture collection team performs routine genetic sequencing of our culture strains to monitor for rare genetic changes during storage. This can be achieved by initial whole genome sequencing when the culture is first submitted, and then routine sub-genome sequencing of important metabolic pathways. 

Yeast production quality control

During yeast production, when cell division is high, our production facilities keep an eye on key regions of the yeasts’ genome through genetic sequencing. By minimizing selective pressures during the propagation process, we ensure that Lallemand Brewing Premium dry yeast is genetically consistent from one production to the next, ready for use and subsequent re-pitching. 

Although genetic changes are inevitable in any biological system, we mitigate that risk through rigorous quality assurance. Through careful management of our yeast culture collection, we ensure that when a culture begins to drift in undesirable ways, we are able to provide a fresh culture with the desired, original genetic profile. 

Monitoring genetic drift in the brewery 

Despite the inherent stability of any yeast strain that we bring to market, genetic change is inevitable. The stresses of a normal beer fermentation will result in a very low level of genetic drift in the yeast culture. Most breweries are not equipped to sequence DNA or properly manage a yeast culture bank. So what can you do as a brewer to manage the normal risk of genetic drift in yeast? 

To ensure consistent high-quality beer, monitor the yeast for any changes in performance over time. Changes in fermentation kinetics, lag-phase, and attenuation may indicate that the yeast has a reduced ability to import and metabolize certain sugars. Small colonies on agar plates may indicate “petite mutations”, which results from mutations to the mitochondrial DNA.

Changes in sensory profile could indicate mutations to one of the many biochemical pathways involved in production or metabolism of esters, phenolics, fusel alcohols, sulfur compounds and diacetyl. It is important to monitor flocculation closely since the repeated harvesting of yeast from the cone or surface of the beer can change flocculation behavior. Harvesting from the cone will select for fast-settling cells, whereas top-cropping will select for cells that prefer to stay at the top of the tank. As always, test for wild yeast or bacteria contamination and check the yeast under the microscope to assess cell viability and morphology. Minimize your risk by limiting the number of re-pitch generations (5-8 max) and refresh your culture with a first-generation pitch if you have any doubt about yeast performance. By following yeast handling and re-pitching best practices, you will achieve consistently high-quality beer.