Fermented Foods and Drinks FAQ: 10 Questions on Cultures, Safety and Shelf Life

Key terms used in this FAQ

People who make fermented foods and drinks ask the same practical questions: which culture to use, whether it survives, and how to tell when something has gone wrong. This fermented foods and drinks FAQ answers ten of them for US brands, formulators and curious makers, with the study or rule behind each point. The regulations themselves are covered in our US fermented food and drink regulations guide. This page is educational, not medical advice.

Table 1. Terms used in this FAQ

1. Do you need a starter culture, or can you use wild fermentation?

Both work; they trade control for tradition. Wild, or spontaneous, fermentation relies on microbes already on the ingredients and in the environment, so the microbial community, and the result, can vary from batch to batch. Adding a starter culture of known strains gives more repeatable acidification, flavour and timing.^[1]

For a commercial product the choice usually settles itself. If the label will state a live-culture count or name a strain, you need defined strains whose identity you can document and whose count you can measure. Our guide to microbes used in the food and beverage industry covers the main culture groups.

2. What is the difference between prebiotics, probiotics and postbiotics?

The International Scientific Association for Probiotics and Prebiotics (ISAPP) defines a probiotic as live microorganisms that, when administered in adequate amounts, confer a health benefit on the host.^[4] A prebiotic is a substrate that is selectively used by host microorganisms and confers a health benefit.^[5] A postbiotic is a preparation of inanimate microorganisms and/or their components that confers a health benefit.^[6]

A fermented food is not automatically a probiotic. ISAPP’s fermented-foods statement reserves the word probiotic for defined live strains with evidence of a health benefit.^[1] Any benefit wording on a label needs its own substantiation; see our article on probiotic claims in the EU and US.

Table 2. Prebiotic, probiotic and postbiotic compared

Source: FRL summary of the ISAPP definitions.^[4][5][6] For how live and inactivated cultures behave at warm storage temperatures, see probiotics vs postbiotics in shelf-stable foods.

3. Can fermented foods be made dairy-free, with oat or soy?

Yes. In a 2024 study, soy milk beverages fermented with Lactiplantibacillus plantarum and Lactobacillus acidophilus strains supported probiotic growth, and the counts stayed above 10⁶ CFU/mL in the acid-tolerance test.^[7] Oat bases also carry live cultures, but a 2024 comparison found that an oat matrix protected probiotic bacteria less well than milk during simulated digestion.^[8]

The base changes pH, protein and buffering, so the culture dose has to be confirmed in each one rather than carried over from a dairy recipe. Our probiotic ingredients in food guide covers strain and base choices.

4. Do probiotics survive stomach acid?

Some do; many lose most of their count. It depends on the strain and the food that carries it. In the 2024 milk and oat study, counts of both strains tested fell by several log units in the simulated gastric phase, in both matrices.^[8] The soy beverage strains above, by contrast, kept counts above 10⁶ CFU/mL at pH 2 and showed 84.6% to 89.6% survival after 3 hours in bile in laboratory tests.^[7]

Survival through digestion is a separate question from the count left in the pack at expiry. A product has to allow for both. Our live culture survival trial worked example shows how the in-pack count is planned and tested.

5. Do probiotics survive heat or pasteurisation?

Generally not. Heat treatment after fermentation kills most of the live microbes, so the food is still fermented but no longer a live-culture product.^[1] That is often deliberate: in our naturally flavoured kombucha lab note, the drink was mildly pasteurised for stability.

To keep live cultures and still control the product, heat-treat the base before fermentation, or add the cultures after the heat step, and then keep the product cold. If the cultures will not be live at the point of sale, the label should not suggest that they are.

6. Can you add probiotics to shelf-stable products?

It is one of the hardest briefs in probiotic formulation. Acidity, oxygen, moisture and warm storage all reduce viability, so most wet, acidic products lose live cultures quickly at room temperature.^[9] Shelf-stable formats rely on low moisture, robust strains tested in that exact format, and protection such as immobilisation in carriers or encapsulation.^[9]

If those cannot hold the count to expiry, the realistic choices are a refrigerated product, where cold chain and shelf life are designed together, or a postbiotic, which does not depend on live cells.^[6]

7. How can you tell if a fermented food has gone bad?

Look, smell and, for anything you sell, measure. Sourness, cloudiness, gentle fizz and a white sediment are normal in many ferments; a film of scum on the brine of fermenting vegetables is common and is skimmed off during curing.^[10] Fuzzy or coloured mould, a putrid smell, or vegetables that have turned soft or slippery with obvious spoilage mean the batch should be discarded.^[10]

Safety also depends on acidity and temperature. FDA describes refrigeration, acidification to pH 4.6 or below and water activity of 0.85 or below as barriers that slow or prevent pathogen growth.^[11] Only a pH reading confirms the acidity; when in doubt, throw it out (Figure 1).

8. Is home fermenting safe, and what about botulism?

Vegetable ferments made with a tested recipe, the right amount of salt and enough acidity are low risk: a minimum, uniform level of acid throughout the product is what stops botulinum bacteria growing, and cutting the salt in sauerkraut or fermented pickles is unsafe.^[12] CDC still lists improperly canned, preserved or fermented home foods among common botulism sources, and advises refrigerating homemade garlic or herb oils and discarding them after 4 days.^[13]

At commercial scale, a shelf-stable product needs a documented process: FDA’s decision flow uses pH 4.6, water activity 0.85 and whether the product is kept refrigerated to decide whether its low-acid or acidified food rules apply.^[2] See our US fermented food regulations guide.

9. Why do fermented drinks fizz, and can bottles explode?

Live yeasts and bacteria keep turning residual sugar into carbon dioxide and alcohol after bottling. In a sealed bottle the gas builds pressure: US home-preservation guidance warns that storing kombucha in airtight containers can let carbon dioxide build up to the point of explosion, and advises prompt refrigeration.^[14] Tea type, inoculum and surface area all shift a kombucha’s sugar and alcohol content.^[15]

Alcohol is a regulatory line as well as a quality one. A kombucha at 0.5% ABV or more at any time during production, at bottling or after bottling is an alcohol beverage regulated by TTB.^[3] Chill the product, control residual sugar and test alcohol through shelf life. Note too that one USDA study found no known probiotic bacteria in the kombucha it made.^[15] Labelling is covered in our kombucha labelling article.

10. What is the difference between kefir and yogurt?

In the US, yogurt is defined by its cultures: the federal standard names Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus.^[16] Kefir is made with kefir grains, a complex symbiotic mixture of bacteria and yeasts, and its composition changes with the milk, the grains, the fermentation time and temperature, and storage.^[17] The yeasts give kefir a tangier, sometimes lightly fizzy character.

Both are best kept cold if live cultures are part of the product. Our fermented kefir lab note shows how FRL approached a fortified, clean-label kefir.

For brands & formulators

If you are developing a fermented or probiotic food or drink for the US market, FRL’s Microbiome Solutions team helps you choose strains and bases, set the culture dose and plan the survival work. Our food product development team takes the recipe from bench to pilot.

We run or arrange shelf-life studies, culture counts, pH and alcohol testing through accredited partner laboratories, and our regulatory and scientific research team checks labels, claims and process requirements. FRL is based in Chennai, India, and works with brands in the US and elsewhere.

In this series

• Stanford’s fermented-food study explained: what the Wastyk et al. (2021) trial found on fermented foods and the gut microbiome.
• Fermented food scale-up: taking a fermentation from bench to plant.
• Formulating live-culture fermented foods: the pillar guide to strains, bases, dosing and stability.
• US fermented food and drink regulations: alcohol limits, labelling and claims.
• Live culture survival trial: fermented beverage worked example: trial design, filling dose and pH drift.
• Fermented foods and drinks FAQ: cultures, safety, fizz and shelf life. You are here.
• Service: Microbiome Solutions at Food Research Lab.

1. Marco, M. L., Sanders, M. E., Gänzle, M., Arrieta, M. C., Cotter, P. D., De Vuyst, L., Hill, C., Holzapfel, W., et al. (2021). The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nature Reviews Gastroenterology & Hepatology, 18(3), 196–208. https://doi.org/10.1038/s41575-020-00390-5 (cited for the definition of fermented foods, spontaneous vs starter-culture fermentation, heat treatment after fermentation and the distinction between fermented foods and probiotics).
2. U.S. Food and Drug Administration. (n.d.). LACF/AF: Precursor questions and flow. https://www.fda.gov/media/89861/download (cited for how pH 4.6, water activity 0.85 and refrigerated distribution decide whether 21 CFR Part 113 or 114 applies).
3. Alcohol and Tobacco Tax and Trade Bureau. (n.d.). Kombucha. https://www.ttb.gov/regulated-commodities/beverage-alcohol/kombucha (cited for the 0.5% alcohol by volume threshold at any time during production, at bottling or after bottling).
4. Hill, C., Guarner, F., Reid, G., Gibson, G. R., Merenstein, D. J., Pot, B., Morelli, L., Canani, R. B., et al. (2014). The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nature Reviews Gastroenterology & Hepatology, 11(8), 506–514. https://doi.org/10.1038/nrgastro.2014.66 (cited for the definition of a probiotic).
5. Gibson, G. R., Hutkins, R., Sanders, M. E., Prescott, S. L., Reimer, R. A., Salminen, S. J., Scott, K., Stanton, C., et al. (2017). Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nature Reviews Gastroenterology & Hepatology, 14(8), 491–502. https://doi.org/10.1038/nrgastro.2017.75 (cited for the definition of a prebiotic).
6. Salminen, S., Collado, M. C., Endo, A., Hill, C., Lebeer, S., Quigley, E. M. M., Sanders, M. E., Shamir, R., et al. (2021). The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics. Nature Reviews Gastroenterology & Hepatology, 18(9), 649–667. https://doi.org/10.1038/s41575-021-00440-6 (cited for the definition of a postbiotic).
7. Rana, A., Taneja, N. K., Raposo, A., Alarifi, S. N., Teixeira-Lemos, E., Lima, M. J., Gonçalves, J. C., & Dhewa, T. (2024). Exploring prebiotic properties and its probiotic potential of new formulations of soy milk-derived beverages. Frontiers in Microbiology, 15, 1404907. https://doi.org/10.3389/fmicb.2024.1404907 (cited for probiotic growth and acid and bile tolerance in fermented soy beverages).
8. Pawlos, M., Szajnar, K., & Znamirowska-Piotrowska, A. (2024). Probiotic milk and oat beverages with increased protein content: Survival of probiotic bacteria under simulated in vitro digestion conditions. Nutrients, 16(21), 3673. https://doi.org/10.3390/nu16213673 (cited for probiotic survival in milk and oat beverages during simulated digestion).
9. Terpou, A., Papadaki, A., Lappa, I., Kachrimanidou, V., Bosnea, L., & Kopsahelis, N. (2019). Probiotics in food systems: Significance and emerging strategies towards improved viability and delivery of enhanced beneficial value. Nutrients, 11(7), 1591. https://doi.org/10.3390/nu11071591 (cited for causes of viability loss in foods and protective strategies such as immobilisation and carriers).
10. National Center for Home Food Preservation. (n.d.). Causes and possible solutions for problems with fermented pickles. University of Georgia. https://nchfp.uga.edu/how/ferment/general-information-on-fermenting/causes-and-possible-solutions-for-problems-with-fermented-pickles/ (cited for normal white sediment and scum, and not eating soft or slippery pickles when spoilage is evident).
11. U.S. Food and Drug Administration. (1997). Guidance on labeling of foods that need refrigeration by consumers. https://www.fda.gov/media/134845/download (cited for refrigeration, acidification to pH 4.6 or below and water activity of 0.85 or below as barriers to microbial growth).
12. National Center for Home Food Preservation. (n.d.). General information on fermenting. University of Georgia (adapted from USDA, Complete Guide to Home Canning, 2015). https://nchfp.uga.edu/how/ferment/general-information-on-fermenting/general-information-on-fermenting/ (cited for acidity, salt and tested recipes as safety controls against botulinum bacteria).
13. Centers for Disease Control and Prevention. (n.d.). Preventing botulism. https://www.cdc.gov/botulism/prevention/index.html (cited for improperly fermented home foods as a botulism source and refrigerating homemade garlic or herb oils and discarding them after 4 days).
14. National Center for Home Food Preservation. (n.d.). Kombucha tea. University of Georgia. https://nchfp.uga.edu/how/ferment/recipes/kombucha-tea/ (cited for prompt refrigeration and the risk of carbon dioxide build-up and bursting in airtight containers).
15. Chaluvadi, S., Hotchkiss, A. T., Smith, B., McVaugh, B., White, A. K., Guron, G. K., Renye, J. A., Jr., & Yam, K. L. (2024). Key kombucha process parameters for optimal bioactive compounds and flavor quality. Fermentation, 10(12), 605. https://doi.org/10.3390/fermentation10120605 (cited for process parameters affecting sugar and alcohol content in kombucha and the finding that no known probiotic bacteria were identified).
16. U.S. Food and Drug Administration. (n.d.). 21 CFR 131.200: Yogurt. Electronic Code of Federal Regulations. https://www.ecfr.gov/current/title-21/chapter-I/subchapter-B/part-131/subpart-B/section-131.200 (cited for the yogurt cultures Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus).
17. Rosa, D., Dias, M., Grześkowiak, Ł., Reis, S., Conceição, L., & Peluzio, M. (2017). Milk kefir: Nutritional, microbiological and health benefits. Nutrition Research Reviews, 30(1), 82–96. https://doi.org/10.1017/S0954422416000275 (cited for kefir grains as a complex symbiotic mixture of bacteria and yeasts and the factors that change kefir composition).