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Fundamentals

Yeast and Bacteria: Your Flavor Partners in the Distillery

When it comes to microbes, the choices you make will shape the expression of your final spirit. Here are some key considerations.

Gabe Toth May 16, 2025 - 8 min read

Yeast and Bacteria: Your Flavor Partners in the Distillery Primary Image

Photo: Courtesy Imperial Yeast

The microbes you invite into your brewhouse and distillery are essential partners in the quest to make great spirits.

These tiny accomplices create many of the flavors and precursors that find their way into the finished product and, as a distiller, your options for using them to develop fermentation character are virtually endless.

The primary by-products of fermentation are roughly a 50/50 mix of carbon dioxide and ethanol by weight. Those components account for about 99 percent of the total fermentation activity, while the remaining 1 percent of by-products is a wide variety of tiny but important flavor-active compounds.

That remaining 1 percent can make up the difference between the gnarliest open-fermented whiskey and the most refined light lager. Yeast can produce hundreds of flavor and aroma compounds, including numerous esters, organic acids, aldehydes, phenols, and higher alcohols.

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The yeast catalog is thick with options—too many to detail here. However, we can make some generalizations about various groups of strains, and the choices you make here are among the first steps to shaping the character of your final spirit.

Select Your Yeast(s)

Many of the commercially available yeast strains for fermenting beverages fall into three broad families:

  • Distillers’ yeast strains are often optimized for yield based on a certain substrate—grain, fruit, or sugar—though flavor development is not a null factor.
  • Wine yeast strains have evolved via selection to ferment fruit—generally but not exclusively grapes—with a variety of profiles that reflect wine’s broad array of flavors.
  • Brewers’ yeast strains are arguably even more diverse in their flavor profiles, from clean lager strains and low-ester American and English ale strains to the wide range of esters and phenols from Belgian and German ale yeasts to the next-generation, genetically engineered yeasts designed to ramp up certain flavors (more about that below).

Beyond these broad groups, there are other unique opportunities such as sake yeast, Lactobacillus bacteria, acid-producing yeast strains, and other controlled or uncontrolled acidifying agents.

The choices you make regarding fermentation parameters multiply the variables when it comes to flavor profile. Within different groups of yeasts, there are a variety of strains that offer different flavor profiles. Even working with a single strain can create variability, depending on your chosen fermentation parameters—including mash schedule, fermentation temperature, nutrient levels, oxygenation, and potential interactions with microbes that are copitched or otherwise take hold in the fermentation.

Open fermentation reduces hydrostatic pressure, allowing yeast to be more expressive, whereas higher pressure—from taller, narrower tanks or pressurized fermentation—reduces that yeast-driven profile. And Belgian yeasts, in particular, are known for being happier in a large window of fermentation temperatures.

Variables abound.

Know Your Cast of Characters

Even among distillers, there are those who would argue that creating a clean fermentation profile with a desirable, appealing flavor and aroma makes a great spirit—a distiller’s beer more reminiscent of actual beer.

Other distillers would argue that a funky fermentation packed with certain unpalatable compounds will age out into a lovely, estery final product.

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They’re both right.

Distillers who favor an ugly, unenjoyable profile for aged spirits understand, at least to some degree, that they’re providing the ingredients for a stew that needs years to cook. Fundamentally, the fruity esters that round out the profile of many spirits are the products of a combination of an alcohol and an acid.

A fermentation high in fusel alcohols and organic acids is fertile ground for esterification, though not all fusels and acids are desirable, or desirable at high levels. A spirit with a variety of trace fusel alcohols—isoamyl alcohol, propanol, isobutyl alcohol, and others—and organic acids—including lactic, acetic, succinic, propionic, butyric, and isovaleric—creates a heady broth that can mature into an ester-rich spirit with great complexity if given the time.

Butyric acid is one dramatic example: It has sensory notes of rancidity, baby vomit, or baby diaper. However, as it sits in contact with ethyl alcohol—perhaps aging for years in a barrel—it can combine with ethanol, or esterify, into ethyl butyrate, which offers notes of tropical fruit, particularly pineapple.

Bacteria and even some yeasts can contribute organic acids to a fermentation. The most common are acetic acid and milder lactic acid. Acetic acid is the primary note in vinegar; it is generally produced by Acetobacter, which requires oxygen to thrive and esterifies into ethyl acetate, which brings a fruity note at low levels but is solventy at higher levels. As a chemical marker, it can indicate maturation because of its abundance in aged spirits.

Both fermentation and spirit maturation can produce aldehydes, notably acetaldehyde, whose green-apple note is generally considered undesirable in beer. The compound is also a known carcinogen. In spirits, however, acetaldehyde can catalyze into ethyl acetate—producing the same ester as the combination of ethanol and acetic acid, but via an alternate pathway.

A variety of bacteria and some yeast strains can produce lactic acid. Lachancea thermotolerans is a widely distributed natural yeast that produces lactic acid as a by-product of fermentation; there are now engineered Saccharomyces strains that can do the same. Lactic acid esterifies with ethanol into ethyl lactate, lending a fruity, lightly buttery note to spirits.

Another group of yeast by-products is known as ketones. The common beer off-flavor diacetyl is probably the best-known of these compounds. Most commonly associated with certain types of yeast or beer infections, diacetyl is recognizable for its butterscotch or buttered-popcorn note. It can be a pleasant accent to a whiskey at lower levels but is considered a flaw at higher levels. Diacetyl is difficult to remove via distillation because its evaporation point overlaps with ethanol.

Fermentation also can produce phenols, such 4-vinyl-guaiacol and its clove-like notes. That phenol relies on the precursor ferulic acid, which you can optimize with a particular mashing regimen—once again illustrating the wide variability of options. However, most phenolic notes in spirits evolve through cask aging.

Yeast can also produce sulfur compounds—lager yeast, in particular, is known to produce hydrogen sulfide and dimethyl sulfide during fermentation, and extended lagering times allow these compounds to dissipate from the beer. There are even yeasts that have been engineered to unlock a particular class of sulfur compounds, thiols, which produce tropical-fruit flavors and aromas. However, these are not a good option for the distiller—copper contact during distillation is intended to bind up sulfur compounds. Undesirable sulfur compounds such as dimethyl sulfide (rotten egg) are also some of the first compounds to volatilize out of a barrel during maturation.

Choose Your Partners

Clearly, there are enough variables that any distiller could spend lifetimes exploring how to produce the “best” flavor profile.

To take an example from beer: A skillful brewer can shift a German hefeweizen yeast profile from banana to bubblegum to clove by manipulating the mash regimen, fermentation temperature, oxygenation, and nutrient levels—and that’s with one strain. As distillers facing the full catalog of yeasts, fermentation media, and fermentation profiles, we could be forgiven for being temporarily paralyzed by the countless options.

Fermentation isn’t the only place where distillers can impact the creation of congeners—those flavor compounds such as esters, phenols, aldehydes, and others. However, it’s a primary driver of what ends up in the spirit, and each choice can have a significant impact on the final product.

Gabe Toth, M.Sc., is an accomplished distiller, brewer, and industry writer who focuses on the beer and spirits worlds. He holds brewing and distilling certificates from the Institute of Brewing & Distilling and a master’s from the Rochester Institute of Technology, where his graduate studies centered on supply-chain localization and sustainability.

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