The Microbiome of Wine: How Yeasts and Bacteria Shape Every Sip

Jun 3

Written By Michele Edington (formerly Michele Gargiulo)

As someone who takes probiotics every day and is a sommelier, I’d just like to say, I’m a big fan of the chemistry of wine. Something a lot of people don’t think about at all, but before the grapes are crushed, before the cork is popped, before the swirl and the sip, there’s life.

It’s definitely not the kind you can see unless you have microscope vision (that would be an interesting super-power, wouldn’t it?), I’m talking about the quiet, invisible kingdom that clings to grape skins like stardust, that floats in the wind between rows of trellised green, or that lives in the pores of barrels and the cracks of old cellar stone.

A lot of people think that wine begins with harvest, but it actually begins with microbes; with wild yeasts, wandering bacteria, and microscopic ancestors older than the vines themselves. These little guys shape the soul of the wine long before the winemaker ever lays a hand on it.

I truly love to explore that hidden world and how life we can’t see can change everything we taste.

The Dust That Isn't Dust

If you’ve ever walked a vineyard in late summer, you might’ve seen it…that faint, silvery film on the skin of the grapes. You might’ve brushed it off, thinking it was dust. It’s the same thing that accumulates on blueberries, that whitish gray film you can brush off with your fingers.

It’s not dust, it’s wild yeast, and it’s sitting there patiently, waiting.

Well, I’m not truly sure about the patience of yeast to be honest, but it does cling to the skin and wait for the crush, the moment the sugar is released from the skins and they can finally feast. It reminds me of the line outside of a restaurant, with everyone waiting for the moment the doors unlock before they rush in, ready to order as fast as they can.

This yeast that clings to the skin (Saccharomyces cerevisiae, and its cousins) is not alone either, it brings company because who likes to be lonely: lactic acid bacteria, acetic acid bacteria, fungi, molds, even some native viruses join in. A living cloud of tiny tiny things is draped across every vine, every cluster, and every leaf in the vineyard.

Together, they all make up the microbiome of the vineyard…a world within the world, a chorus of single-celled composers writing symphonies into the wine. No two vineyards host the same community, because even row to row, grape to grape, the microbial makeup shifts. That difference, more than soil or sun or slope, might just be what we mean when we talk about terroir.

When the grapes are crushed, they bleed sugar, and the yeast wakes up hungry. This is fermentation yes, but it’s more than that, it’s a chemical concoction, a chaos of bubbling and bloom.

Yeast eats sugar and produces alcohol, and in the process it releases heat and some carbon dioxide. It grows, dies, then bursts open, leaving behind enzymes and esters and flavor.

There are two paths here that winemakers can take: wild fermentation is, where the native yeasts of the vineyard and the winery lead the charge…unpredictable, risky, magical. Or, inoculated fermentation, where cultured yeasts hand-selected and purchased, are added with intent, bringing consistency and control.

Some winemakers let wild yeasts start the job, then call in the cultured troops to finish, while others go fully native, embracing whatever path the microbes choose.

It’s a question of trust. Some wild yeasts die off before the job is fully finished, creating something called a stalled fermentation. Wild fermentations are gambles taken by those confident enough to be able to watch their elixirs and know when to intervene or let it run. If a fermentation stalls for too long other bacteria could move in and ruin your wine.

While there’s a lot of romance behind the wild fermentation (some even claim wines are too polished with inoculated yeasts versus wild ones), there’s also a monetary gamble others are not willing to take.

The Second Fermentation

Just when you think fermentation is over, something softer begins. Malolactic fermentation isn’t a fermentation in the strictest sense, it doesn’t use yeast at all, but is a bacterial transformation. It’s a mellowing out of the wine if you will, a smoothing of sharp corners. Here, lactic acid bacteria (chiefly Oenococcus oeni) convert tart, citrusy malic acid (think green apples) into soft, rounded lactic acid (think cream, butter, silk).

This is where that iconic buttery note in Chardonnay comes from, that plush, mouth-coating richness a lot of people out there seek when looking for a chardonnay. That sense of warmth, like a cashmere blanket wrapped around your tongue also imparts a lot of buttered-popcorn flavor, which is a personal preference.

Some wines undergo this transformation, while others don’t. It all depends on the winemaker’s intent, and the microbes' cooperation.

The vineyard often gets all the glory, but the winery is alive, too. The walls, the barrels, the tools, they all host microbial life, which is how a lot of transformations occur after harvest.

Oak barrels are especially porous on purpose, the winemakers like that they breathe. In the process of breathing though, they also absorb and become memory keepers. They sometimes hold onto yeast strains, passing them on to every batch that follows. Stainless steel tanks are cleaner, but never truly sterile. Microbes find homes in gaskets, in seams, or in forgotten corners that weren’t properly scrubbed clean by the intern the winery hired.

Over years, a winery develops a microbial fingerprint: just like a bakery’s sourdough starter or like your own skin.

This invisible ecology shapes the wine as much as any vine, it becomes part of its voice.

The Risky Business of Spoilage and the Beauty in Funk

Not every microbe is a friend as I touched on a little earlier. Some of these terrors are tricksters, and some are thieves. Acetic acid bacteria can turn wine to vinegar if oxygen sneaks in. Brettanomyces (or Brett) can bring leather, spice, barnyard, or just...dirty horse. (Check out A Sommelier’s Journey Through Alentejo Part 2 for one of the best wines I’ve ever had with Brett in it).

Some winemakers welcome Brett in small amounts, because it adds edge, wildness, complexity, while others see it as a flaw, an infection meant to be stomped out.

This is the razor’s edge the winemakers must walk: too much life, and the wine spoils, yet too little, and it loses its soul. Even sulfur compounds (used to preserve wine) can influence the microbial community, for better or worse.

It’s a constant negotiation between sterility and surrender, the science and letting go to let nature take over.

In the world of natural wine, the microbiome is the star of the show. No added yeast, filtering, with minimal sulfur, the goal is to allow the wine to become what it would’ve without help. Natural winemakers let the microbes lead and let the wine evolve in the bottle, change with the seasons, sometimes even sparkle when it wasn’t meant to.

These wines are alive in a way a lot of commercial wines aren’t. Sometimes they open up like poetry, while sometimes they smell like a wet goat. I’m not trying to over romanticize them either, there are some that really are tragically bad, while others or gorgeous. There was this one natural wine I found that was so good I bought three bottles of it to take home. At $30/bottle, I was frustrated to find two of them were already bad when I went to open them. That means I paid around $90 for one bottle. Not sure it was worth it to be honest with you.

Whether you love them or leave them, they’re undeniably alive.

Flavor Isn’t Just in the Fruit

What do you actually taste when you taste wine? Some people mention fruit or oak, maybe some minerality or herbs. You’re actually tasting metabolism: microbial transformation. You’re tasting esters, thiols, volatile acids, chemical whispers made by yeast and bacteria as they live and die.

Microbes bring esters → fruity, floral notes. They also bring thiols → grapefruit, passionfruit, sometimes cat pee (yep). Diacetyl → buttery richness. Phenols → smoke, spice, structure. Volatile compounds → both brilliance and flaws. These molecules don’t just appear in the grapes as they’re growing in the sun, no, they’re born in fermentation. They’re born in the chaos of life too small to see.

Recent research is showing what winemakers have always known in their bones: microbial life varies by place.

A vineyard in Burgundy has different yeasts than a vineyard in Sonoma. Even two sides of the same hill might host different bacterial tribes. This is microbial terroir. It means that wine made from the same grape, in the same vintage, but in two different regions will still taste different because of who’s living on the grapes. The life of the land becomes the life of the wine.

You think it ends at bottling? Ha, not quite. Some microbes (especially in unfiltered, natural wines) survive the bottle, they may sleep or stir occasionally, but they’re in there.

Sometimes they ferment a little more sugar or even shift the wine’s flavor. They might cause the wine to evolve months or even years after it’s sealed. Wine doesn’t die in the bottle, it just starts dreaming.

You don’t need to be a microbiologist to know these creatures. You’ve sipped a wine that smelled like peaches and wondered how. You’ve tasted one that was earthy, leathery, or primal and drank another one that changed in the glass minute by minute by minute.

That was the microbiome, the yeast and bacteria and age and light and time.

You’ve been talking to them this whole time, you just didn’t know their names.

The Microbiome of Wine: How Yeasts and Bacteria Shape Every Sip

The Dust That Isn't Dust

The Second Fermentation

The Risky Business of Spoilage and the Beauty in Funk

Flavor Isn’t Just in the Fruit

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