The Yeast Genome Project

With the recent boom in wild ales and sour beers, yeast is having a serious moment in the spotlight. But more experimentation with the precarious microorganisms means breweries risk greater exposure to cross-contamination and infection, and the standard tests aren’t always fast enough to prevent a single-celled disaster.

That’s why the folks at Avery Brewing Co. teamed up with the University of Colorado on a cutting-edge project: the genetic sequencing of yeast strains.

Thanks to a friend’s introduction, Dan Driscoll, Avery’s staff microbiologist, worked with Jim Huntley, the director of the Next Gen Sequencing Facility at the University of Colorado BioFrontier Institute, to create a more efficient way of identifying a yeast strain that’s been compromised. The faster a problem is found, the less likely a brewer will face the worst-case scenario—having to throw out an entire batch of infected beer. Right now, the standard test produces results in approximately 48 hours, while genetic sequencing takes just a few hours.

Huntley uses the same type of computers that sequenced DNA in the Human Genome Project to sequence the six brewer’s yeast strains Avery regularly uses. Huntley compared the process to ripping up a book into a million little pieces and then reassembling it using a complete book as a reference. “When we compare the DNA sequences of different strains, we look for differences in those sequences that we can use to distinguish strains,” he says. “It’s analogous to finding corrections, additions or deletions in subsequent versions of the same book.”

Once the yeast strains are sequenced, it will be easier (and cheaper) to develop methods to spot the differences in yeast strains. Because the cost of genetic sequencing has dropped dramatically, Huntley says he can see more breweries adapting to such a test for cross-contamination. Much like doctors in the near future may use genetic sequencing to diagnose patients, breweries may use genetic sequencing to identify cross-contamination in the tank—and salvage the beer before it’s too late.

Cross-contamination is just one of the challenges brewers face when dealing with yeast. A reused yeast culture’s genes can start to mutate over generations, which can change how the yeast behaves, says Driscoll. Improper handling of yeast, which results in off-flavors like chlorophenols (Band-Aid, medicinal), excessive acetaldehyde (green apple) or a metallic character, has opened up a conversation about the larger issues of quality control and proper sanitization.

“Some of these startup breweries are [operating on a] shoestring,” says Paul Gazta, director of the Brewers Association. “Many of these companies are not investing in methods to ensure quality and consistent beer from day one, and that is manifesting in some flawed beers entering the marketplace. This issue isn’t about whether someone prefers certain flavors and aromas like diacetyl or not. This issue is about beers with significant brewing, fermentation or packaging errors.”

Genetic sequencing may be the future of quality control, but right now, the go-to prevention—besides sanitizing—is a simple exercise in microbiology. Inside petri dishes filled with gelatinous media (agar media, or agar) are nutrients that cultivate certain bacteria or yeast strains. To test for microorganisms, such as wild yeast, brewers place a liquid sample (beer or wort) in the specific agar media; if a microorganism is present (like an unwanted yeast strain or harmful bacteria), it will grow into colonies of cells in the agar, showing whether or not a beer is contaminated.

Driscoll points out that these tests are quite subjective, only suggesting the possibility of contamination, whereas genetic sequencing will be “much more accurate.”

But agar-plate tests are still better than nothing. James Howat, head brewer and co-owner of four-month-old Former Future Brewing in Denver, says he and his co-owner (and wife) Sarah Howat, test each batch of beer and each new generation of yeast for wild yeast and bacterial contamination in their brewery lab. “It’s extremely low cost to do these kinds of tests,” says Howat, who has a background in microbiology. “Setting up a basic lab to do these tests should only cost around $1,000–$2,000.”

There’s also another, old-fashioned way breweries can catch yeast problems before they manifest, says Howat: Learn to recognize off flavors. “Everyone in the brewery should be able to taste a beer, whether just off the tank or off the bottling line, and know whether something is wrong.”

When the brewers at Boulder, Colo.’s Avery Brewing Co. finish with a batch of beer, they’ll empty out the tank, sanitize it and refill it with a new batch. But brewer’s yeast, or saccharomyces cerevisiae, knows how to linger at the party long after everyone else has left. If leftover yeast from the previous batch continues to make itself at home in the fermentor, it can start to compete with the original yeast that was pitched. That residual yeast strain can change how a beer tastes—for example, creating an IPA that tastes more like a Witbier—or worse, add some very unpleasant flavors. “It doesn’t happen often, but we want to make sure we can catch it if it does,” says Driscoll.

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