Microbe new to science found in self-fermented beer

In May 2014, a group of scientists took a field trip to a small brewery in an old warehouse in Seattle, Washington. They were looking for some yeast to sequence—and to taste some beer, if it came down to it. Cody Morris, then brewmaster of Epic Ales, ushered them through the building, warning of a large hole in the floor. Then he brought the group over to one of the old wine casks in which Morris was brewing a “wild beer.”

“We opened it and it was alive,” says Maitreya Dunham, a geneticist at the University of Washington in Seattle who led the sudsy expedition. The liquid in the barrel was bubbling away vigorously. “It was definitely an actively fermenting mixture,” she says.

Whereas standard beers like Heineken or Sierra Nevada are produced by adding one type of yeast—usually a Saccharomyces species—wild brewers like Morris coax a community of bugs from the environment to settle in and ferment beer, an old Belgian tradition. But like many brewers making wild beers, Morris admitted he had no idea what microbes were living in the barrel staves that had inoculated his beer. Could the scientists figure it out?

The team accepted the challenge. Dunham and her colleagues collected a bit of the company's “Old Warehouse” beer into a plastic tube. If it was a mixture of microbes, it would be the perfect sample for a technique she and her colleagues were developing called Hi-C sequencing, which disentangles the genomic sequences of a community of microbe species using formaldehyde to link DNA fragments within the same cell. “The inference is that if two pieces of DNA are crosslinking to each other, they must have come from the same cell,” Dunham explains.

What she found got her excited. Using the Hi-C technique, the team identified a yeast belonging to the genus Pichia, which turned out to be a hybrid of a known species called P. membranifaciens and another Pichia species completely new to science, the team recently reported on the preprint server bioRxiv. (Such yeast hybrids are common in brewing; in fact, lager yeast was recently discovered to be a hybrid of two Saccharomyces species.) The scientists dubbed the new hybrid Pichia apotheca–Greek for “warehouse.”

The brew also contained Saccharomyces and yet another yeast genus, Brettanomyces, which is found in many wild beers and sold commercially. In addition, the mix contained Lactobacillus, Pediococcus, and Acetobacter bacteria, all known to imbue a sour character to a beer.

Dunham's team tried to brew a beer with P. apotheca alone, but that didn't work; the yeast produced little alcohol. That's not unusual; most yeasts found in mixed cultures won't brew a beer well on their own. But the hybrid may contribute to Old Warehouse's taste, the researchers write in their paper. Other Pichia species are known to spoil a beer, but the new hybrid seems to smell better, Dunham says. She's open to providing brewers with microbe isolates, if they want to experiment with them.

“This paper provides a proof-of-concept for using this method to study other spontaneously fermented beers,” says Ronn Friedlander, a co-founder of Aeronaut Brewing in Somerville, Massachusetts, who has a Ph.D. in bioengineering. What’s also striking, he says, is that the mixture Dunham and her team identified is very close to the “Roeselare” blend that commercial yeast provider Wyeast markets to brewers who want to inoculate a wild beer artificially. That mix contains a Belgian-style ale strain, Saccharomyces, two Brettanomyces strains, Lactobacillus, and Pediococcus, Friedlander says.

Perhaps wild beer fermentation is a more predictable process than once thought, Friedlander says. “This might point to specific niches that must be filled in a microbially stable, aging beer,” he says.

And that means brewers and scientists may be one step closer to unveiling the alchemy of spontaneous fermentation.