Fermentation Safety: When Good Bacteria Go Bad
Quick Answer
Homemade fermented foods like sauerkraut and kimchi are generally safe when made with adequate salt and kept properly submerged. The protective mechanism is acidification by lactic acid bacteria, which drops the pH enough to kill pathogens. Failure happens when salt is too low, contamination occurs, or anaerobic conditions aren't maintained.
The Science
Humans have been fermenting food for thousands of years without refrigerators, thermometers, or microbiology labs. Traditional fermented foods like sauerkraut, kimchi, yogurt, and kefir have excellent safety records. But “traditional practice” isn’t the same as “nothing can go wrong.” Understanding why fermentation works (and the specific ways it can fail) makes you a better and safer fermenter.
The Science of Competitive Exclusion
Lacto-fermentation is a race. The question is which microorganism wins.
When you salt vegetables and let them sit, you’re creating a selective environment. Lactic acid bacteria (LAB), primarily Lactobacillus, Leuconostoc, and Pediococcus species, are naturally present on raw vegetables. They’re relatively salt-tolerant. Many other bacteria and pathogens are not.
As LAB metabolize the sugars in vegetables, they produce lactic acid (and sometimes acetic acid and carbon dioxide). This acid drops the pH of the ferment. Within the first 1 to 3 days of fermentation, the pH typically falls from a starting point around 6 to below 4.6. At that point, Clostridium botulinum can no longer germinate, and most pathogens can’t survive.
The process is called competitive exclusion. The LAB don’t “fight” pathogens directly. They change the environment so rapidly, by dropping pH and consuming available oxygen, that pathogens can’t establish a foothold. By the time Salmonella or E. coli would have a chance to multiply, the acidity has already made the environment hostile to them.
This is why the first 48 to 72 hours are the most critical in fermentation. That’s the window before the pH drops enough to be protective. If something’s going to go wrong, it’s more likely to happen then.
Salt: Your Most Important Safety Variable
Salt is the mechanism that lets LAB win the race.
A concentration of 2 to 3 percent salt by weight of the vegetables (not volume) is the standard range for most vegetable ferments. At this concentration, harmful bacteria are suppressed while Lactobacillus and its relatives are not. Below about 1.5 percent, that selective pressure weakens. Above 3 percent, even the LAB slow down significantly, which also delays acidification.
Think of salt as a handicap system in the race. It slows down the competition so the LAB can get ahead. Remove the handicap and the race becomes unpredictable.
Two percent salt is calculated by weight: 20 grams of salt per kilogram of vegetables. The easiest approach is a kitchen scale. Volume measurements are less reliable because salt types vary in density. A tablespoon of kosher salt and a tablespoon of fine sea salt contain very different amounts of salt. For fermentation, weight is more accurate.
Use non-iodized salt. Iodine is added to table salt as a public health measure, but iodine is also antimicrobial. It suppresses LAB along with everything else.
Maintaining an Anaerobic Environment
Lactic acid bacteria are aerotolerant anaerobes. They work best without oxygen, but they can function in its presence. Many spoilage organisms, however, require oxygen. Keeping vegetables submerged below the brine serves a dual function: it keeps the ferment anaerobic, and it prevents the surface exposure that spoilage molds need.
Vegetables are buoyant. You need something to keep them under the brine. Weights made for fermentation jars work well. So does a folded cabbage leaf placed over the vegetables and held down by the jar shoulder. Any food-safe non-reactive weight will do.
If any vegetable surfaces are above the brine line and exposed to air for extended periods, that’s where surface molds can establish.
Recognizing Kahm Yeast vs. Actual Mold
Kahm yeast is one of the most common sources of confusion for new fermenters. It looks alarming but isn’t dangerous.
Kahm is a collective term for several wild yeast species that form white to off-white, flat, smooth films on the surface of ferments. It grows when oxygen reaches the brine surface and fermentable sugars are available. It won’t make you sick, but it can contribute musty or off-flavors if left unchecked.
To manage kahm: skim it off regularly, make sure your vegetables are fully submerged, and keep the jar covered. A little kahm doesn’t mean the ferment is ruined.
Actual mold is different. Mold is fuzzy and textured, not smooth and flat. If your ferment develops green, black, pink, or blue fuzzy growth, that’s mold. Unlike in hard cheeses, you can’t just cut the mold off a vegetable ferment. The brine has likely been contaminated throughout. Discard the batch.
| Appearance | What It Is | Action |
|---|---|---|
| Smooth white film | Kahm yeast | Skim, check submersion |
| Fuzzy colored growth (any color) | Mold | Discard batch |
| Bubbles in brine | CO₂ from fermentation | Normal, expected |
| Thick, slimy brine | Leuconostoc bacteria | Usually harmless but check smell |
What Can Actually Go Wrong
Fermentation failure follows a few predictable patterns.
Insufficient salt is the most common error. Too little salt and the selective pressure on LAB is weak. Before enough acid forms to protect the ferment, pathogens have a chance to grow. This is unlikely to cause dramatic illness (most pathogens are outcompeted even without much salt) but it can lead to spoilage and unpredictable fermentation.
Adding fats or oils creates risk. Fat creates pockets of oxygen-free space within the ferment that aren’t acidified by the surrounding brine. If those oil pockets trap vegetables at a pH above 4.6, you have anaerobic, neutral-pH conditions: exactly what C. botulinum needs. Traditional fermented vegetables don’t include oil for this reason. The canning science article covers why anaerobic, low-acid conditions are such a consistent risk factor.
Wrong temperature affects fermentation speed. The optimal range for most vegetable ferments is 65 to 75°F (18 to 24°C). Warmer temperatures speed up fermentation but favor undesirable bacteria and can produce off-flavors. Cooler temperatures slow fermentation and extend the vulnerable early window. Very cold fermentation (below 50°F) can stop it almost entirely.
Contamination with non-food materials is obvious but worth stating. Use food-safe containers. Avoid containers that previously held non-food substances.
Kombucha: specific risks with a more complex system
Kombucha involves a symbiotic culture of bacteria and yeast (SCOBY) that ferments sweetened tea. It shares the general safety principles of lacto-fermentation (acidification provides protection) but has some specific risks worth understanding.
SCOBY contamination: Unlike vegetable ferments, where LAB are naturally present on the vegetables, kombucha depends on a specific SCOBY culture. Contaminated SCOBYs can harbor mold or introduce problematic organisms. A healthy SCOBY is tan to brown, consistent in texture, and smells like vinegar and yeast. Fuzzy mold growth on a SCOBY means discard it and start with a fresh culture.
Alcohol content: Kombucha naturally produces alcohol as a byproduct of yeast fermentation. Commercial kombucha is kept below 0.5% ABV. Home batches, especially those fermented longer or at warmer temperatures, can reach 1 to 3% ABV or higher. This is relevant for anyone avoiding alcohol for medical, religious, or personal reasons.
Second fermentation pressure: Bottling kombucha with added fruit or sugar for carbonation produces CO₂. In sealed bottles, this builds pressure. Bottles can burst if over-carbonated. Use bottles designed for carbonated beverages, and burp them during second fermentation. Glass bottles that weren’t made for carbonation are a genuine explosion risk.
pH monitoring: Commercial pH strips or a pH meter are useful for kombucha. A finished kombucha should be at or below pH 3.0 to 3.5. If pH stays above 4.0 after a week of fermentation, something is wrong with the culture or the conditions.
How Fermented Food Compares to Commercial Products
Commercial sauerkraut, kimchi, and pickles are made using the same organisms and the same biological principles as homemade versions. The differences are:
- Commercial producers test pH and microbial counts
- Temperature is controlled more precisely
- Inoculation with specific starter cultures (sometimes) rather than relying entirely on wild bacteria
- Production is designed for consistent, reproducible outcomes
This doesn’t mean commercial products are safer in any dramatic sense. Traditional fermentation has a very strong safety record. It means that commercial products have documented quality control, and home fermentation relies on understanding the principles and monitoring for signs of failure.
The evidence from thousands of years of traditional food preparation is consistent: properly made lacto-fermented vegetables, dairy, and beverages are safe. The safety comes from the biology. LAB create an environment that kills pathogens. Understanding that mechanism lets you recognize when you’ve created those conditions and when something’s going wrong.
For more on the biochemistry of fermentation and what happens to flavor and texture during the process, see fermentation basics.
What This Means for You
Use 2 to 3 percent salt by weight of the vegetables. Keep everything submerged below the brine. Ferment at room temperature (65-75°F) and watch for the pH to drop below 4.6 within the first few days. White filmy yeast (kahm) is harmless. Fuzzy colored mold is not. Discard that batch.
References
- Mokoena MP. (2017). Lactic Acid Bacteria and Their Bacteriocins: Classification, Biosynthesis and Applications against Uropathogens: A Mini-Review. Molecules. 22(8):1255.
- Di Cagno R, Coda R, De Angelis M, Gobbetti M. (2013). Exploitation of vegetables and fruits through lactic acid fermentation. Food Microbiology. 33(1):1-10.
- USDA Agricultural Research Service. Processed, Acidified, and Fermented Vegetable Products.
- Leroy F, De Vuyst L. (2004). Lactic acid bacteria as functional starter cultures for the food fermentation industry. Trends in Food Science and Technology. 15(2):67-78.
- Muhialdin BJ, Kadum H, Farouk AE. (2022). Metabolomics profiling and biological activities of fermented bitter gourd using lactic acid bacteria. Food Chemistry. 371:131073.
- National Center for Home Food Preservation. Fermented and Pickled Foods. University of Georgia.