Probiotics & Prebiotics – Ingredient Safety

As requested by CRIS readership, this series looks at probiotics and prebiotics. This post looks at the ingredient safety around prebiotic and probiotic foods, focusing specifically on fermented foods.

What are probiotics and prebiotics? 

Prebiotics and probiotics can be foods, ingredients, supplements, products, and more that contain or support microorganisms, intended to be beneficial, that may impact our microbiome, with the goal of improving our overall health (1).

Typically, manufacturers design prebiotic and probiotic products to encourage beneficial bacterial growth that supports our microbiome.

Prebiotics are food, ingredients, supplements, and products that support the wanted beneficial bacteria in our microbiome by providing an ideal nutritional source for the bacteria.

Probiotics are food, ingredients, supplements, products, and more that contain desired beneficial bacteria. 

Are prebiotic foods and ingredients safe?

As discussed in our previous post, prebiotic foods primarily consist of the vegetables, fruits, and whole grains needed to support a healthy lifestyle. Unless you’re allergic to a specific food, they are perfectly safe and advisable to eat regularly, especially if you’re beginning to incorporate probiotic foods into your diet. 

The healthful microorganisms found in probiotic foods need prebiotic-rich veggies, fruits, and whole grains to thrive.

Are probiotic foods and ingredients safe?

For healthy adults, store-bought probiotic foods and ingredients are safe to consume and use in normal quantities. These will include foods like yogurt, sauerkraut, kimchi, kombucha, etc. 

For people with a weakened immune system, who are pregnant or nursing, or young children under the age of two, it’s best to talk with a state-licensed medical professional to ensure the foods are safe for you or your young children. 

The most significant risk with probiotic foods is the fermentation and/or pasteurization process. 

What is fermentation? 

Fermentation is a chemical process that, when done correctly, transforms ingredients into familiar foods and products that can introduce beneficial microorganisms into our system. Humans have used fermentation techniques for millennia to produce and preserve foods like yogurt, sauerkraut, kimchi, beer, sourdough bread, and more.

Chemical fermentation for products like yogurt, kombucha, vinegar, sourdough bread, and more often rely on introducing specific microorganisms and enzyme-rich cultures to begin the fermentation process. You may hear the terms SCOBY, mother vinegar, mother culture, or sourdough starter, to name a few. These are necessary to introduce the needed microorganisms to begin the fermentation process. 

Other fermentation processes do not require a starter rather, they rely on the naturally occurring microorganisms already present on the foods in combination with specific ingredients. Such is the case for sauerkraut and pickles.

What is the risk during fermentation? 

When done correctly, fermentation can be a safe way to transform ingredients into beneficial probiotic-rich foods that are healthy. 

When done improperly, foods will not ferment safely, and instead, you’ll introduce harmful bacteria that can cause adverse reactions to your health. 

There are many reasons adverse reactions can occur, but contamination with unwanted bacteria or microorganisms from improperly washed containers, improperly stored foods during the fermentation process, improperly washed instruments, and more are often the cause. 

Does pasteurization remove the risks associated with fermentation? 

Pasteurization will kill all bacteria and microorganisms indiscriminately, both those that are beneficial and harmful. So yes, it will remove any risk associated with fermentation, but it will also remove the beneficial probiotics for many foods. 

Pasteurization for commercial dairy products, like yogurt, is different because the manufacturers will pasteurize the milk to remove all microorganisms before fermentation. They will not pasteurize the final yogurt product to keep the beneficial microorganisms intact. The commercial fermentation process is highly controlled to ensure only beneficial microorganisms are introduced.

Should I consume unpasteurized, fermented products? 

If the product comes from a manufacturer you trust and it’s made properly, it’s safe for most healthy adults to consume unpasteurized, fermented products like sauerkraut, kimchi, and kombucha. 

However, for people with a weakened immune system, who are pregnant or nursing, or young children under the age of two, it’s best to talk with a state-licensed medical professional to ensure the foods are safe for you or your young children. 

Should I consume homemade unpasteurized, fermented products? 

There is more risk when consuming homemade fermented foods. If made properly, following health and safety protocols, they can be safe and nutritious for healthy adults. If made improperly, they can adversely impact your health. 

It’s essential to use your senses (taste, sight, smell, sound, etc.) to determine if a homemade fermented product is safe to consume. If something seems “off,” it’s best not to consume the product. 

Additionally, it’s important to know how the product was made. While modern crockery used to ferment foods are safe, vintage crockery may contain lead in the glaze, which can leech into the food or beverage, causing lead poisoning (1).

When in doubt, it’s best not to consume the product. 

Should I take probiotic supplements? 

It’s safe to take probiotic supplements if your health care provider recommends it (1,2).

As with all supplements, the quality of the supplement varies significantly between manufacturers. It’s important to go with a third-party laboratory-verified supplement to ensure you’re getting a supplement free from contamination that contains the advertised ingredients. It’s especially important for infant and children supplements as they’re more vulnerable to variations in product quality (1,2).

Many laboratories verify supplements, including NSF International, US Pharmacopeia, Consumer Lab, and more. Verified products will contain a label on the product informing you of the laboratory. 

If you take a probiotic supplement, it’s best to consume prebiotic vegetables, fruits, and whole grains to help support the beneficial microorganisms.

The good news.

Many beneficial probiotic foods can be consumed safely. You can even enjoy homemade probiotic foods if you follow health and safety protocols. 

If you have any more questions about probiotic and preboitioc foods and ingredients, please reach out to us on Twitter, send us an email, or submit your idea to us at

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