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Quick PCR Test Targets Beer Spoilers in Yeast Materials

A partnership between diagnostic company and yeast supplier strengthens QC programs to detect contaminants in yeast slurries.

By the time a brewer is able to test for contaminants in yeast slurries, the impact might already be felt in the flavor profile of the beer.
By the time a brewer is able to test for contaminants in yeast slurries, the impact might already be felt in the flavor profile of the beer.

It is relatively uncommon for craft brewers to produce their own yeast, instead sourcing this very sensitive process to third parties. The integrity of that yeast is essential to creating the right flavor profile for the beer. But by the time a brewer is likely to test for any contaminants that might be present in the yeast, it’s further down the line when the batch of beer has already been produced—at which point the brewmaster might find that the taste is off.

Traditional quality control test kits for the brewing industry are designed to detect potential spoilers in the finished product rather than in the yeast itself. But these are what the brewing industry has been using—the yeast suppliers as well as brewers producing their own yeast—to test for unwanted bacteria throughout the harvesting and yeast propagation processes.

This presents issues on several levels, including the time required and the inability to get the sensitivity needed in what is itself a living organism, notes Neva Parker, director of operations for White Labs, a San Diego-based manufacturer of liquid yeast cultures used primarily for fermentation in beer and other fermented beverages.

“There hasn’t been a lot of innovation in microbiology over the decades, particularly in craft beer microbiology. We have used very traditional microbiological techniques to detect contaminants,” Parker says, adding that the technology is very “old school,” with culture plates designed to detect very specific organisms. “We would make our product, we would test it multiple times for quality, and we would have to wait three to five days in order to release the product from a QC hold.”

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A few years ago, White Labs embarked on a collaborative development project with bioMérieux to develop a test geared specifically toward the yeast slurries themselves, which have a whole set of their own demands. “We really wanted to find a way that was not only more rapid but had a higher level of sensitivity when it came to detecting unwanted organisms in our cultures,” Parker says.

A difficult matrix to test

Though bioMérieux has a history of creating easy-to-use rapid assays for diagnostics in the beer and wine space, those tests were not focused specifically on yeast slurries. “We had a nice suite of several assays for different spoilage organisms in the brewing process. But it was very difficult for those brewers to test for the wide panels of organisms that could potentially be contaminating the yeast. It’s a very difficult matrix to work with,” says Adam Joelsson, senior director of assay development for bioMérieux. “There was a clear and evident need—with feedback from the market—for something compatible with yeast slurries.”

Because yeast has a very different matrix than finished beer, for example, bioMérieux needed to tap into outside expertise. “The natural thing to do was to reach out to the yeast manufacturers themselves,” Joelsson adds.

Before long, bioMĂ©rieux developed the partnership with White Labs and ultimately launched the Gene-Up Brewpro Yeast Slurry, a PCR test designed to detect contaminants in raw yeast materials and yeast propagations in order to ensure high-quality fermentations.

Diagnostic testing is an imperative part of White Labs’ quality control process. The yeast supplier partnered with bioMérieux to develop a test for specialized targets in raw materials and yeast slurries.Diagnostic testing is an imperative part of White Labs’ quality control process. The yeast supplier partnered with bioMérieux to develop a test for specialized targets in raw materials and yeast slurries.White Labs

Often used for testing yeast slurries are quality control tests designed to detect potential spoilers in finished beers. But the fact that there’s already a live organism in the yeast culture makes this problematic, Parker explains. “It’s really hard to test for other organisms when you’ve already got a huge population of one organism that you’re testing within,” she says.

“Some of these organisms are quite fastidious,” Joelsson adds. “They require specialized plates and enrichment broths to selectively grow them in this really difficult high-concentration background of yeast. To find one CFU of contaminating organism in there is quite a difficult task. Traditional agar-based or culture-based methods can do that, but it requires some significant expertise, and it takes quite a long time to get the results—five to 10 days for some of these yeasts.”

In quality control tests of finished beer products, the yeast level is so low, it’s not difficult to exclude it from the testing. But in tests of yeast itself, this becomes much trickier to parse out the unwanted yeasts and other bacteria. “It’s really hard to pick through all the different organisms and find the ones that you don’t want vs. the ones you do want,” Parker explains.

Fast results in a simple format

The goal of the collaboration, therefore, was to take that testing time down to two days and also provide testing in a simple-to-use format that gives a clear indication of contamination.

“It was a multi-year project to develop this. The goal was to have a really highly multiplexed panel against these various yeast and bacterial targets that may contaminate yeast and then subsequently contaminate the fermentation at a brewer,” Joelsson says.

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White Labs is focused heavily on the craft brew space. “Brewers really require strict quality control measures when it comes to the ingredients that they use, and one of those ingredients is yeast,” Parker says. “We really have to perform a pretty high level of quality control to ensure that our yeast cultures are free from contaminants—particularly contaminants that can spoil beer during fermentation.”

Though bioMérieux just released its Gene-Up Brewpro Yeast Slurry publicly this past fall, White Labs has been using it for a few years now, throughout the development process. “It’s been hugely helpful to us in that we can turn around our results faster—and they’re more reliable,” Parker says.

White Labs now gets the diagnostic results it’s looking for in one or two days. That’s considerably faster, but the reliability of those tests is a significant consideration as well. For the person recording the results, Parker says, traditional microbiology testing has a degree of subjectivity. The new rapid testing from bioMérieux, however, requires no interpretation of the results. “The results are the results,” she says.

Though the testing has been made easier for yeast producers, developing the test itself was not so easy. “It was difficult on many layers,” Joelsson says. “How do we design an environment where we select for the contaminating organisms so we can tease them out from the background, from a growth standpoint? The second challenge is: How do you treat that sample for PCR? There are potentially some inhibitory components—things that’ll impact the brightness of the system from a fluorescent standpoint. All of those things have to be conditioned to enable the most optimum PCR reaction.”

Testing for a single target is much easier, but bioMérieux designed this PCR test to target four or five contaminants in a single tube. “You need a good bioinformatics underpinning to ensure that your designs are inclusive of the important organisms but also exclude non-important organisms—things that might be there but won’t survive the brewing environment,” Joelsson explains. “Some of these organisms are very similar and some of them are very different from a genetic standpoint. So you really have to balance those designs in the best way for optimal performance of PCR.”

White Labs provided a range of expertise, including understanding the best conditions for growing contaminating organisms, as well as which contaminants were likely to impact the beer.

Brewers—especially those that cultivate their own yeast—might want to run these kinds of diagnostic tests themselves, although Parker notes the need for an advanced lab. But she points to the higher level of confidence that brewers can have in yeast suppliers using these tests. “It’s very sensitive, and you can really tell if there is even a low level of contamination in a product,” she says. “That translates to your flavor, and that’s really important to brewers. So that level of trust and confidence in our product is huge.”

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