(Deborah Jaffe for The Washington Post)

Humans and microbes go way back. The bacteria, yeast and viruses that live in and on and around us have incredible sway over the way we live. But when it comes to culinary pursuits, yeasts stand out as our most stalwart cooking companions: These tiny creatures consume sugar and produce gases and alcohol as waste, giving our breads the bubbles of air that make them fluffy and delicious and lending beer its foamy, boozy power.

According to research published Thursday in the journal Cell, humans have been domesticating the yeast used to make beer — breeding it for the properties that suit our needs — since the 16th century. That means we were breeding yeast for their beer-making qualities for over a century before scientists actually discovered microbes.

Humans started brewing beer thousands of years ago, probably in ancient Egypt. Without any knowledge of the microorganisms powering their breweries, it's no surprise that the first tipplers worked blind, brewing with whatever wild yeasts found their way into the brewing process. But according to genetic analysis of over 100 yeasts used by industrial brewers today, brewers started unknowingly breeding the best yeasts sometime around the 1500s.

"Brewers were smart enough to realize that if they used the sediment found at the end of the fermentation process, if you used it to inoculate a new batch, the fermentation will go much quicker," explained study author Kevin Verstrepen, a yeast geneticist at the University of Leuven and VIB in Belgium. "And when you take the sediment from a really nice beer, the new batch will for the most part turn out pretty nice."

They didn't know it, but these early brewers were selecting the fittest beer yeasts, which settle down into sediment after they stop producing gas. By putting them into a new batch of beer (a process known as back-slopping), the brewers were keeping their favorite strains of yeast warm and well-fed, encouraging them to reproduce.

"It was something between an art and a science, because they didn't know what microbes were but knew the sediment, whatever it was, was important," Verstrepen said. "So then you had this Darwinian selection, with the gut feeling of the brewers working hand in hand with nature."

According to the study's analysis of 157 different strains of yeast used to make beer, wine, spirits, sake, bread and bioethanol, this process has caused the yeast used in beer brewing to grow more distinct from feral cousins than microbes used for other commercial fermentation.

The flavors and aromas of beer all come down to chemistry. Reactions, a series from the American Chemical Society, takes a look at craft beer chemistry. (American Chemical Society)

The researchers identified two major lineages of beer yeast, one of which was domesticated from wild species slightly later than the first.

The beer yeasts showed clear signs of long-term human influence. They've become quite dependent on the beer-making process to survive. In fact, the researchers noted that many strains of beer yeast have lost the ability to reproduce sexually, which is key to survival in the wild — during times of trouble, yeast send sturdy spores out into the world in the hopes of finding somewhere to continue their genetic legacy.

Beer yeasts have lost the genes required for sex — and they've put their energy into beer instead. The researchers found many strains that had deleted the genes needed for sexual reproduction, but had multiple copies of the genes that allow them to grow on the sugars commonly found in vats of beer.

From an evolutionary standpoint, these yeast have found themselves a pretty cushy spot: All they have to do is help produce the kinds of beer humans like to drink, and they'll be kept alive for countless generations. For as long as humans are around to keep making beer, anyway.

"They were completely separated from wild yeasts," Verstrepen said. "They're just not breeding with them anymore."

The yeasts used for wine and sake had a lot more in common with their feral cousins. They showed signs of adapting to fermentation — genes that help them resist common pesticides or preservatives — but it was clear, based on their DNA sequences, that they continue to frequently mix with wild strains.

"We compare them to cats, while beer are really more like dogs," Verstrepen said with a laugh. "Beer is made all year, and so these yeasts are fed all year, they’re really quite spoiled, and they wouldn’t stand a chance outside."

But wine is only made during a brief period. For the rest of the year, the yeasts (which come in on the skin of the grapes they help ferment) have to survive in and around wineries without human aid. As a result, the yeasts in beer are ones we've trained to suit our needs, while the yeasts in wine stroll in whenever it suits them. Beer is our buddy, but wine is more of an exotic houseguest.

Verstrepen and his colleagues hope to use what they've learned to push yeast domestication even further.

"About half the team in my lab is now trying to make better beer yeast just by breeding. We're playing catch-up with all the cow and pig farmers, looking for parents with the best genes to make high-quality offspring," he said.

Luckily, yeast reproduces much more quickly than a cow or a pig — so they can make a lot of progress in a short period of time. Because they've created an extensive genetic family tree for desirable yeasts, the team can breed "parents" selectively and screen their "offspring" for promising genetic quirks.

"It brings us into an age of DNA-inspired breeding, which might sound a bit out there but has been used in the plant world for quite a while," Verstrepen said. "We're not making any genetically modified organisms. We're just speeding things up."

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