Fermentation: How Microbes Transform Your Food

For most of human history, people fermented food without knowing why it worked. They knew that salted cabbage lasted through winter. That grape juice became wine. That dough left overnight rose better. The microbes doing all the work were invisible and unnamed.

We understand fermentation now. And that understanding makes you a better fermentation practitioner, whether you’re baking sourdough or making your first jar of kimchi.

What Fermentation Is

Fermentation, in the food science sense, is the metabolic process where microorganisms break down carbohydrates in the absence of oxygen and produce acids, alcohol, CO2, or some combination of these.

The word comes from the Latin “fervere,” meaning to boil. Early observers named it for the bubbling they saw when grape juice became wine, caused by CO2 escaping from the liquid.

Fermentation is sometimes defined more broadly in biochemistry (it includes any energy-generating metabolism without oxygen), but for food purposes, the key point is this: microbes eat carbohydrates and produce byproducts that change the food.

Those byproducts do three things:

1. Preserve the food (by lowering pH or producing alcohol)
2. Change the texture (by altering proteins and breaking down cell structures)
3. Create new flavors (through dozens of organic compounds the microbes produce)

The Two Main Types

Lactic Acid Fermentation

The most important type for most fermented foods. Lactic acid bacteria (LAB), primarily from the genus Lactobacillus but also Leuconostoc, Pediococcus, and others, consume sugars and produce lactic acid as their main byproduct.

Lactic acid is the compound that makes yogurt tangy, gives sourdough bread its characteristic sourness, makes sauerkraut and kimchi sharp, and preserves pickles. It’s an organic acid with a distinctive flavor: clean and sour, with less harshness than acetic acid (vinegar).

As LAB produce lactic acid, the pH of the food drops. A fresh cucumber might have a pH around 6.0. A properly fermented pickle can drop below pH 3.5. This acidic environment kills or inhibits most pathogenic bacteria, which is why fermentation preserves food so effectively.

LAB are salt-tolerant, which is why you use salt in vegetable ferments. The salt creates conditions that favor LAB while inhibiting competing bacteria that can’t handle salinity. You’re not sterilizing the environment. You’re selecting for the organisms you want.

Alcoholic Fermentation

Yeasts (primarily Saccharomyces cerevisiae) convert sugars into ethanol and CO2. This is the reaction that makes wine from grapes, beer from barley, and bread dough rise.

The CO2 is what leavens bread. Gluten (the protein network discussed in the gluten development article) traps CO2 bubbles, and as yeast produces more gas, the dough expands. The alcohol mostly evaporates during baking.

In wine and beer production, the ethanol is the goal. Ethanol is also a preservative. Above about 10-12%, it inhibits most bacterial growth, which is why wine doesn’t spoil quickly once fermentation is complete.

Sourdough bread uses both types of fermentation simultaneously. A sourdough starter contains wild yeasts that provide CO2 for leavening, and LAB (especially Lactobacillus sanfranciscensis, recently reclassified as Fructilactobacillus sanfranciscensis) that produce lactic and acetic acids for flavor and preservation.

Key Organisms

Lactobacillus species: The major players in dairy fermentation (yogurt, cheese, kefir), vegetable ferments (sauerkraut, kimchi, pickles), and sourdough. Different species and strains produce different flavor profiles. L. bulgaricus and Streptococcus thermophilus together make yogurt. L. plantarum is common in sauerkraut.

Saccharomyces cerevisiae: Baker’s yeast and brewer’s yeast are both strains of this species, selected over centuries for different properties. Baker’s yeast produces CO2 quickly and efficiently. Brewer’s strains are selected for alcohol tolerance and flavor compound production.

Acetobacter species: These bacteria convert ethanol into acetic acid (vinegar). They need oxygen to work, which is why vinegar fermentation is done in wide, shallow containers with lots of air exposure.

Aspergillus oryzae: The mold used to make koji, which is the foundation of miso, sake, soy sauce, and many other East Asian fermented products. Koji produces amylase and protease enzymes that break down starches and proteins, creating the deep, umami-rich flavor of these ferments.

Why Fermentation Preserves Food

Think of it as the microbes claiming territory. LAB and yeasts, given the right conditions, outcompete and chemically suppress other microorganisms.

pH reduction: Lactic acid drops the pH to levels where most pathogens can’t survive or reproduce. Clostridium botulinum (the organism that produces botulinum toxin) can’t grow below pH 4.6. A properly fermented vegetable that reaches pH 3.5 is far safer from botulism than a fresh vegetable would be.

Alcohol production: Ethanol above about 5% is hostile to most bacteria. Traditional fermented beverages were often safer to drink than the local water for this reason.

Competitive exclusion: LAB and Saccharomyces reproduce quickly and consume available sugars. They don’t just suppress pathogens chemically. They eat the food that pathogens would need to grow.

Bacteriocin production: Many LAB strains produce bacteriocins, natural antimicrobial proteins that directly kill competing bacteria. Nisin, produced by Lactococcus lactis, is one of the few bacteriocins approved as a food preservative (you’ll see it on some cheese labels).

Flavor Development

Fermentation produces flavors that don’t exist in the starting ingredients. This is what separates fermented foods from foods that are simply acidified with vinegar.

Organic acids: Lactic acid, acetic acid, and others contribute characteristic sour notes. The ratio of lactic to acetic acid strongly affects flavor. Lactic acid is milder and rounder. Acetic acid is sharper and more pungent. Temperature affects this ratio: cooler fermentation temperatures favor acetic acid production in sourdough, giving sharper sourness.

Esters: When acids react with alcohols during fermentation, they form esters: fruity, floral, solvent-like flavor compounds. The banana and apple notes in Belgian ales come from isoamyl acetate, an ester produced by yeast.

Amino acid breakdown products: Proteolysis (protein breakdown) during longer ferments produces amino acids that then further break down into aromatic compounds. The complex savory depth of aged cheese, miso, and soy sauce comes largely from this process.

CO2: Even in food where you don’t want obvious carbonation, CO2 produced during fermentation affects texture and mouthfeel. The slight effervescence of fresh kimchi and kombucha comes from dissolved CO2.

Fermentation vs Acidification

Not all sour foods are fermented. This distinction matters.

A quick pickle made by pouring hot vinegar over cucumbers and refrigerating them is acidified food, not fermented food. The pH drops because you added acid from outside, not because microbes produced it internally. The food is preserved and tastes tangy, but the biochemical complexity of true fermentation isn’t there.

True fermentation involves living organisms actively metabolizing within the food. This creates hundreds of flavor compounds, alters proteins and starches, and produces a fundamentally transformed product. Given enough time, the difference in flavor between a quick vinegar pickle and a naturally fermented pickle is significant.

This distinction also matters for the often-discussed gut health benefits of fermented foods. Live cultures in fermented foods may contribute to gut microbiome diversity in ways that acidified foods don’t.

Fermented Foods Around the World

Every food culture has fermented foods, because fermentation is what preserved food before refrigeration.

• Bread and beer: The oldest fermented foods with archaeological evidence, going back at least 14,000 years
• Yogurt and kefir: Dairy fermented by LAB, with origins in Central Asia
• Cheese: Uses LAB, sometimes mold (Penicillium for blue cheese, camembert), and rennet (enzyme from animal stomach lining)
• Sauerkraut and kimchi: Lacto-fermented vegetables. Kimchi adds garlic, ginger, and chili to a LAB base
• Miso: Fermented soybean paste using Aspergillus oryzae (koji). Fermentation can last from weeks to years
• Soy sauce: Similar koji-based process, then further bacterial fermentation
• Wine and beer: Classic alcoholic fermentation
• Sourdough: Dual fermentation with wild yeast and LAB
• Kombucha: Tea fermented by a SCOBY (symbiotic culture of bacteria and yeast)

The underlying chemistry is the same across all of these: microbes consuming carbohydrates, producing metabolic byproducts, transforming the food in ways that make it safer, longer-lasting, and more flavorful.