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.