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Fermentation: it’s the culture

Fermentation: it’s the culture header image
A story of the yeast that launched a thousand industries

As we celebrate Oregon's finest wine, beer, bread, and cheese we raise a toast to all the people who create this exceptional northwest cuisine.

But the unsung heroes of this great bounty are easily overlooked. Although they are swirling in and around us, we ignore the legions of yeasts, mold, and bacteria that have been harnessed to make some of our finest foods possible. If we think of microbes at all, we think of them in terms of dread and disease. Think again. Without microbes, and the orderly transmogrification that they create, we wouldn't have wine to raise in toast. (We wouldn't even have toast.)

Welcome to the world of fermentation. It's our culture.

Fermentation makes wine out of grapes, beer out of barley, and ethanol out of corn. Without fermentation, coffee and chocolate would be just a hill of beans.

Fermentation has helped people keep food on the table for millennia. Pickling and brewing changed the chemistry of food, making it last far beyond the normal sell-by date of its fresh ingredients. Hawaiians fermented taro to make poi; Koreans fermented cabbage to make kimchi; Europeans fermented milk to make cheese.

So, what is the difference between kosher dills and the cucumber rotting in the back of your refrigerator? The right microbes in the right environment. Fermentation microorganisms create alcohol and acid to inhibit the spoilage microorganisms, converting fresh food into storable pickles, sausages, and alcohol.

yeast petri dish
OSU graduate student Harper Hall checks a native yeast culture isolated from Willamette Valley grapes. Photo by Lynn Ketchum.

The hero of our fermentation story—the engine that helps create everything from bread to wine to biofuels—is a humble, hardworking fungus named Saccharomyces cerevisiae (SAK-a-row-MY-ceez sera-VAY-see-ay). Its name comes from saccharo (sugar), myces (fungus), cerevisiae (beer). It was with us at the dawn of civilization, one of our earliest domesticated companions.

Tom Shellhammer, a fermentation scientist at Oregon State University, explains how it might have happened: Ten thousand years ago, hunter-gatherers were collecting wild barley, perhaps storing it in a stone container. It rained; the container filled with water. The barley began to germinate, breaking down starch into sugars. Wild yeasts feasted on the sugars, converting them into alcohol and carbon dioxide, and fermenting the soggy grain into a mildly intoxicating bubbly brew. Happy surprise.

The discovery of beer encouraged people to grow barley and not simply to rely on what they could collect from the wild, according to Pat Hayes, who heads the barley breeding program at Oregon State. The result, he said, was that dawn of agriculture.

"The earliest agriculture was all about barley, and barley was all about beer," Hayes said. Soon enough, say a millennium or so, people found that they could bake the fermented grain mixture into a brick called bappir that could be soaked to make beer or sliced, awaiting the invention of jam.

It must have seemed like magic to transform barely digestible grains into breads and brews. Some of history's earliest writings refer to the production of beer. The hymn to Ninkasi, dating back nearly 4,000 years ago, served as both a prayer to the Sumerian goddess of fermentation and a way to remember the recipe for beer.

Last January, the Discovery Channel came to OSU in search of a recipe for the first ancient brew. OSU brewmaster Jeff Clawson brewed up a batch using raw barley, germinated barley, and dates.

How'd it taste? "Sweet; watery," Clawson said. "Let's say, we've come a long way in fermentation science."

OSU wine press
OSU food chemist James Osborne keeps an eye on fermentation to learn how yeast affects the flavor and aroma of wine. Photo by Lynn Ketchum.

And for a long time, yeasts invisibly went about their work turning juice to wine and bubbling mixtures of grain. Gods were worshipped. It wasn't until 1856 that Louis Pasteur recognized tiny dots of yeast as living organisms and fermentation as a living process within a community of microscopic life. Soon thereafter, industrious microbiologists began isolating particular yeasts, and fermentation became a calculated process rather than a divine event. Today, we make the distinction between pure fermentation, made with a cultured strain of yeast, and native fermentation, made with the community of microbes who live in the neighborhood.

And we are finding novel uses to put those microbes to work. Industrial fermentation processes are manufacturing antibiotics, vitamins, plastics, and other chemicals that are too complex to be made synthetically but that microbes can produce for us. This global market is expected to exceed $48 billion by 2015, according to a 2010 report by Global Industry Analysts.

"With fermentation laboratories, a research brewery and winery, and a pilot processing plant, Oregon State is a national leader in meeting this future demand," said Sonny Ramaswamy, dean of OSU's College of Agricultural Sciences. "The college brings together a strong community of researchers, industry leaders, and talented students who are defining the future of fermentation science."

Fermentation itself is a community event that involves a parade of microbes, each cranking up the level of acid or alcohol as they pass through the process. In the case of our hero, S. cerevisiae, enzymes convert starch to simple sugars that the yeast consumes in the process of producing carbon dioxide and alcohol.

Basically, it's a bacchanal with S. cerevisiae gorging on sugar, reproducing like crazy, and pumping out a bubbly brew of alcohol and CO2. Yeast strains that are less tolerant of alcohol soon die off. But S. cerevisiae keeps the party going to the end, pumping out more alcohol and outlasting any questionable microbes that might have sneaked in from between the grape crushers' toes. At the end of the orgy, the alcohol level hits a point that overwhelms even our hero. The yeasts have consumed all the sugar, exhausted themselves, and settled, spent and undignified, to the bottom of the barrel.

It should be said that grapes and grains don't ferment at the drop of a hat. Plants have evolved mechanisms to fight off the effect of yeast and bacteria, to stay fresh long enough to ripen their seeds and entice someone to pluck them and distribute their next generation.

Consider barley. The sugar is bundled up in large molecules of starch that need to be broken down by enzymes before the yeast party begins. These enzymes, as it turns out, are on-call within the grain, ready to split apart the starch-containing endosperm when the seed is sprouted and the plant prepares to grow.

malting barley
OSU's new malter coaxes barley to start breaking down its starch to just the right stage for malting. Photo by Lynn Ketchum.
Tom Shellhammer
Tom Shellhammer shoulders much of the brewing research at OSU. Photo by Lynn Ketchum.

"The barley kernel is like a space ship with all that the plant needs to start growing; it's full of starch, like a concentrated energy capsule, and enzymes ready to kick-start roots, leaves, and photosynthesis," said Clawson. With OSU's new barley malter, Clawson can control germination to the point where enzymes just begin to break down the starch and he dries the sprouted grain to create malt. Then, he'll stew the malt to release fermentable sugars, filter it, add hops to taste, and bring in the yeast to get fermentation started.

S. cerevisiae is the yeast of choice for top fermented, British-style ales, where flocs of yeast attach to carbon dioxide and ride the bubbles to the top of the barrel. Top fermented ales ferment at higher temperatures than bottom fermented lagers and develop a different set of flavors, sometimes sweeter and more fruity.

Native fermentation is the preferred method to produce lambic beer, but not with just any yeast that comes drifting in the window. Brewers of lambic beer in Europe rely on a long heritage of feral cultures that cling to the dusty rafters of their breweries. "When they move a lambic brewhouse, they move the whole roof," explained Shellhammer, who works with brewers around the world and is the first American to serve as an examiner for the international Institute of Brewing and Distilling in London.

Bread and beer share many ingredients, including S. cerevisiae. Grains milled into flour with sticky gluten protein create an elastic dough that expands with tiny bubbles filled with carbon dioxide. Alcohol produced by the fermentation is evaporated during baking, which also kills the yeast. Today, most bakers rely on manufactured yeast, including strains of S. cerevisiae, some of them patented.

The exception is sourdough, which is cultured from a glob of fermenting dough saved from an earlier batch of bread. Andrew Ross, an OSU food chemist and self-described bread explorer, explains that sourdough calls in a large community of bacteria and wild yeasts, among them various Lactobacillus bacteria that add a lemony zing in the form of lactic and acetic acids. This marriage of yeast and bacteria lives happily, potentially ever after, in a bubbly fermenting starter that bread makers lovingly tend like members of the family.

Lactobacillus plays a role in making cheese, too. Raw milk is full of bacteria. Fresh from the cow, milk is warm and sweet, perfect conditions to convert milk sugar (lactose) into lactic acid. The bacteria form a kind of assembly line, each one exhausting itself in the production of lactic acid, lowering the pH for the next one in line, and incrementally transforming the milk.

cheese wheels
Aging cheese in cold storage at OSU's pilot cheese plant. Photo by Lynn Ketchum.

Cheesemakers such as OSU's dairy specialist Lisbeth Goddik stress the importance of controlling the assembly line of bacteria and the introduction of surface ripening molds and yeasts. She explains that cheese recipes call for precise measures of salt, milk solids, and water within a controlled temperature to ensure the survival of desired microbes and discourage those that would spoil the process.

Whether it's cheese or bread, wine or beer, most fermentation involves a series of yeasts and bacteria that succeed each other as they change the environment. They sort themselves out by, among other things, tolerating different levels of acid or alcohol. With so many microbial cooks in the kitchen, any number of things can go haywire. For winemaking, it's James Osborne's job to make sure they don't.

"Even if you do a careful job with your yeast during the alcoholic fermentation, you can still develop stinky sulfur compounds during aging," he said. He is investigating how wine's flavor and aroma is affected by yeast, both the purposeful inoculation of our cultured S. cerevisiae and the potluck of native fermentation with local yeasts.

The enthusiasm yeast displays in producing alcohol is also being harnessed toward making biofuel. Making wine may be a party for S. cerevisiae, but making fuel can be plain hard work. Especially the way Michael Penner is doing it. The easy way to make ethanol is from corn. Each corn kernel is a little packet of starch that can be treated with malt enzymes to release its fermentable sugars for the gorging pleasure of S. cerevisiae.

But Penner, another of OSU's team of fermentation scientists, wants to make fuel from waste material, not from food. So, he's looking at the stalk, not the kernel. In particular, he's looking at stalks of wheat straw, after the grain has been harvested. Penner's goal is to create a method to make biofuels, not from the stuff we would otherwise eat, but from the stuff we would otherwise throw away.

Straw is tough stuff, compared with the soft, starchy kernel of grain. It's loaded with lignocellulose, which helps keep its stems standing upright. To convert lignocellulose to ethanol requires that tightly packed cell walls must be broken down to allow yeast and enzymes access to the long sugar molecules they will ferment into ethanol. Penner explains that the holy grail of biofuels is to develop a strain of yeast that will generate the enzymes to break down the tough cell walls of straw at the same time it hydrolyzes the material into fermentable sugars.

"That can be a harsh process," Penner said, "and so far no single strain of yeast has been found that can withstand the process." Researchers around the world are searching for microorganisms to do the job, exploring inside the hay-churning stomachs of cattle and in the wood-digesting guts of termites. So far, the model microbe for this work is a fungus that produces cellulose-eating enzymes discovered during World War II by U.S. scientists in the Philippines when they noticed how rapidly it could rot the Army's tents.

researchers and wheat straw
Mike Penner and his research assistant, Tiraporn Junyusent, are on the trail of converting biomass to biofuel. Photo by Lynn Ketchum.

"We are just trying to speed up the carbon cycle, to create materials we can use to deconstruct plant matter and create a clean sugar platform for fermentation," Penner explained.

While S. cerevisiae awaits Penner's sugar platform, Alan Bakalinsky notes that this yeast has become the lab rat for discovering the physiology of adaptation.

"This organism's love affair with sugar exposes it to great stress," said Bakalinsky, an OSU fermentation scientist with an evident fondness for the life of yeasts. "While S. cerevisiae is one of the most alcohol-tolerant organism on earth, it must also tolerate wild swings in osmotic pressure, and eventually it creates an environment that is too extreme for its own survival."

Bakalinsky, Penner, and others are working to push forward what we understand about S. cerevisiae and the world of fermentation. It's a community of scientists studying a community of "great little bugs." Next time you enjoy a slab of Oregon Gruyère on crusty sourdough, with a good northwest microbrew or a glass of Pinot noir, thank the microbes. Without fermentation,it would be just so much rot.