Heat is what kills the live cultures in fermented foods. Cooking, baking and pasteurization destroy most of the bacteria in yogurt, kefir, sauerkraut, kimchi and miso. Freezing is much gentler: many cultures survive frozen storage. Stomach acid kills some bacteria, and eating them with a meal helps more survive. Antibiotics disrupt your own gut bacteria, which usually recover over weeks. Here’s what the evidence shows for each.
Heat and Pasteurization
The lactic acid bacteria in yogurt, kefir and fermented vegetables don’t survive cooking temperatures. In US law, “pasteurized” dairy has been heated to at least 161°F (72°C) for 15 seconds, or an equivalent time and temperature such as 145°F (63°C) for 30 minutes (21 CFR 131.3) – conditions designed to destroy microbes. So any fermented food that’s heat-treated after fermentation – shelf-stable sauerkraut, most shelf-stable pickles and many bottled drinks – has no live cultures unless they’re added back afterwards.
Some bacteria are tougher. Natto’s Bacillus subtilis forms spores: boiling natto cut its live bacteria from about 5 billion to about 100,000 per gram – a huge drop, but not zero (Homma et al., 2006).
In practice:
- Miso soup: take the pot off the heat before stirring in the miso, and don’t boil it afterwards.
- Sauerkraut and kimchi: serve them cold on the side of hot food rather than simmering them in. Kimchi stew and kimchi fried rice are delicious, but they’re cooked.
- Baking: kefir pancakes and yogurt muffins lose their live cultures in the oven; the fermented dairy still adds flavor, acidity and tenderness.
Freezing
Freezing doesn’t sterilize fermented foods. In frozen yogurt stored at −20°C for 11 weeks, yogurt and probiotic cultures didn’t decline (Davidson et al., 2000). In probiotic ice cream at −29°C, L. acidophilus and B. bifidum fell from about 108 to 106–107 per ml over 17 weeks – fewer, but still many (Hekmat & McMahon, 1992). Results vary by strain and food, and texture suffers: frozen kefir and yogurt turn grainy (fine in smoothies), and frozen sauerkraut softens.
Stomach Acid
An empty stomach is very acidic, and it kills a share of swallowed bacteria. Food buffers it. In a lab model of the stomach and small intestine, probiotic bacteria survived best when given with a meal or 30 minutes before it, and poorly 30 minutes after; milk and oatmeal protected them better than apple juice or water (Tompkins et al., 2011). That’s a model, not people, but it supports eating fermented foods as part of a meal.
Antibiotics
Antibiotics kill gut bacteria along with the infection. In 12 healthy men given a 4-day course of three broad-spectrum antibiotics, the gut microbiome returned to near its original composition within about 1.5 months, although a few species were still missing after 6 months (Palleja et al., 2018).
- Probiotic supplements and diarrhea: in a Cochrane review of 33 trials in children, probiotics taken alongside antibiotics lowered antibiotic-associated diarrhea from 19% to 8% (Guo et al., 2019).
- But not always faster recovery: in one study, a multi-strain probiotic taken after antibiotics delayed the return of people’s own gut bacteria compared with no probiotic (Suez et al., 2018).
- Timing: follow your doctor’s or pharmacist’s advice on spacing supplements from antibiotic doses. Eating everyday fermented foods is fine, but don’t expect them to undo antibiotics quickly.
More in our guide to gut recovery after antibiotics.
What Doesn’t Kill Them
- Refrigeration slows bacteria down; it doesn’t kill them. That’s why raw, refrigerated sauerkraut and kefir keep their cultures.
- A little vinegar or lemon on top won’t sterilize a serving of kimchi. (But vegetables pickled in vinegar aren’t fermented foods in the first place (Marco et al., 2021) – see fermented vs pickled.)
- Salt at normal fermenting levels (about 2–3%) favors lactic acid bacteria rather than killing them.
If you make ferments at home and one won’t start, the usual suspects are too much salt, too cold a room, or chlorinated tap water; filtered or boiled-and-cooled water rules the last one out. See the troubleshooting guide. For what counts as a probiotic in the first place, see probiotics vs prebiotics.
