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  4. The Science Behind Probiotic Foods and the Microbiome

The Science Behind Probiotic Foods and the Microbiome

Learn how probiotic foods can support gut health and immunity, and what science really says about their benefits.

4 MIN READ — 03/11/2025

Probiotic foods are widely believed to strengthen gut health, boost the immune system, and even support emotional well-being. But is this true? Here, we’ll provide you with all the essential information about probiotic foods and explain why opinions on them are often mixed.

Table of Contents

  • 01.

    What Are Probiotic Foods?

  • 02.

    What Health Benefits Do Probiotics Offer?

  • 03.

    Why Can’t Food Manufacturers Promote Probiotics’ Benefits?

  • 04.

    How Do Probiotics Work in the Gut and Why Are They Important for Gut Health?

  • 05.

    Probiotics vs. Prebiotics: Differences and Shared Benefits

  • 06.

    The Best Foods With Probiotics

  • 07.

    Who Should Be Cautious About Consuming Probiotic Foods?

At a Glance

  • 01.

    Probiotics are live microorganisms that can support gut health and the immune system.

  • 02.

    They’re found in foods like yoghurt, kefir, fermented vegetables, and cheese, promoting a balanced gut microbiome.

  • 03.

    While probiotics are believed to benefit the gut, the European Food Safety Authority (EFSA) only partially recognises their effects.

What Are Probiotic Foods?

Simply put, probiotic foods are those that contain probiotics. These are live microorganisms that naturally form part of the gut microbiome. They include certain yeasts and lactic acid bacteria, particularly various Lactobacillus strains and the highly effective Bifidobacteria. So, probiotic foods contain microorganisms that also reside in our gut.

What Health Benefits Do Probiotics Offer?

Probiotics help keep your gut in balance. Although there is no definitive scientific proof that probiotic foods directly improve gut health, it’s clear that beneficial microorganisms play an important role in the gut. As part of the helpful bacteria in the gut, probiotics contribute to gut function once they arrive in the intestines.

A balanced gut microbiome supports the immune system by helping it fend off threats, thus boosting immunity. Additionally, beneficial gut bacteria play a crucial role in healthy digestion.

Why Can’t Food Manufacturers Promote Probiotics’ Benefits?

The European Food Safety Authority (EFSA) has not found sufficient scientific evidence to support claims that probiotic foods have direct health benefits. As a result, it has not approved most probiotic products for inclusion on the list of authorised health claims. So far, EFSA has only recognised the benefits of three specific lactic acid bacteria strains.

One of the reasons for scepticism is that not all beneficial microorganisms in food survive the journey to the gut. Only yeasts and bacteria that are resistant to stomach acid can make it through and exert their positive effects.

How Do Probiotics Work in the Gut and Why Are They Important for Gut Health?

Among the trillions of microorganisms in our gut, there are both beneficial and harmful ones. The good bacteria ensure that harmful ones don’t dominate. This balance means the gut microbiome has a significant impact on the body, promoting healthy digestion and supporting the immune system.

When you consume foods containing stomach-acid-resistant probiotics, you introduce more beneficial yeasts and bacteria into your gut. This increases the proportion of helpful microorganisms and helps them keep harmful ones in check. Key probiotic strains include Bifidobacteria and Lactobacillus.

Probiotics vs. Prebiotics: Differences and Shared Benefits

When discussing probiotics, the term "prebiotics" often comes up. There’s a connection between them, but also a key difference. Prebiotics aren’t microorganisms. Instead, they serve as food for gut bacteria or support them in other ways.

Prebiotics are a type of fibre, the non-digestible parts of food. They pass through the digestive system to the gut, where they promote the growth of probiotics. Vegetables like salsify, garlic, chicory, and onions are typical prebiotic-rich foods. Some foods contain both prebiotics and probiotics, offering a synergy known as synbiotics.

The Best Foods With Probiotics

Lactic acid bacteria, particularly Bifidobacteria, are the most common probiotics, found mainly in fermented dairy products, fermented vegetables, and drinks. While probiotics occur naturally in these foods, the food industry also adds them to certain products.

Here are some probiotic-rich foods:

  • Kefir
  • Yoghurt
  • Skyr
  • Ayran
  • Cultured milk
  • Buttermilk
  • Cheeses like Harzer, Cheddar, Parmesan, Mozzarella, Bergkäse, Gouda, and Gruyère
  • Sauerkraut
  • Apple cider vinegar
  • Lactic-fermented beetroot, carrots, and beans
  • Lactic-fermented cucumbers and pickles
  • Fermented soybeans (Tempeh)
  • Miso paste made from fermented soybeans
  • Fresh kombucha tea
  • Kvass (fermented bread drink)
  • Water kefir
  • Lassi
  • Kimchi (fermented vegetables)

Fresh yoghurt is especially high in lactic acid bacteria, so it’s a good idea to make your own. You can choose different yoghurt cultures, including ones with high probiotic content. With cheese, the older and more mature it is, the richer it is in lactic acid bacteria. Living microorganisms are only present in non-pasteurised foods. Make sure your pickles are lactic-fermented, not pickled in vinegar, as vinegar destroys the lactic acid bacteria, just like pasteurisation.

Who Should Be Cautious About Consuming Probiotic Foods?

While probiotics offer many benefits, they’re not suitable for everyone. There is still insufficient evidence on how they affect people with ulcerative colitis. Those with weakened immune systems should consume probiotic foods in moderation. People with acute pancreatitis or other serious abdominal inflammations, as well as those suffering from a stomach flu (gastroenteritis), should avoid probiotics altogether. In these cases, it’s important to consult a doctor before consuming probiotic foods.

Article Sources

Verbraucherzentrale: Lebensmittel mit speziellen Bakterienkulturen (früher: "Probiotika"), 2024
https://www.verbraucherzentrale.de/wissen/lebensmittel/kennzeichnung-und-inhaltsstoffe/lebensmittel-mit-speziellen-bakterienkulturen-frueher-probiotika-13937

Deutsche Gesellschaft für Ernährung (DGE): Ernährung und Mikrobiom, 2021
https://www.dge.de/presse/meldungen/2021/ernaehrung-und-mikrobiom-1/

Bundeszentrum für Ernährung: Milch: Einkauf – Das Milcherzeugnis-Sortiment, 2023
https://www.bzfe.de/lebensmittel/vom-acker-bis-zum-teller/milch/milch-einkauf/

Bundeszentrum für Ernährung: Präbiotika, Probiotika, Postbiotika – Was ist der Unterschied? 2023
https://www.bzfe.de/service/news/aktuelle-meldungen/news-archiv/meldungen-2023/maerz/praebiotika-probiotika-postbiotika/

Europäische Behörde für Lebensmittelsicherheit: Die EFSA veröffentlicht erte Reihe von Gutachten zu gesundheitsbezogenen Angaben über "allgemeine Funktionen", 2009
https://www.efsa.europa.eu/de/press/news/091001

Hamza Ait Seddik, Farida Bendali, Frédérique Gancel u. a.: Lactobacillus plantarum and Its Probiotic and Food Potentialities, in: Springer Link, 2017
https://link.springer.com/article/10.1007/s12602-017-9264-z

Anna Zawistowska-Rojek und Stefan Tyski: Are Probiotic Really Safe for Humans?, in: Sciendo, 2018

Colin Hill, Francisco Guarner, Gregor Reid u. a.: The International Scientific Association for Probiotics and Prebiotics consensus statement on the Scope and appropriate use of the term probiotic, in: Nature Reviers Gatroenterology & hepatology, 2014
https://www.nature.com/articles/nrgastro.2014.66

Seon-Kyun Kim, Robin B. Guevarra, You-Tae Kim u. a.: Role of Probiotics in Human Gut Microbiome 0150 Associated Deseases, in: Journal of Microbiology and Biotechnology, 2019
https://www.jmb.or.kr/journal/view.html?doi=10.4014/jmb.1906.06064

V. Gupta, R. Garg: Probiotics, in: ScienceDirect, 2009
https://www.sciencedirect.com/science/article/pii/S0255085721016273?via%3Dihub

S C. Bischoff, K. Köchling: Pro- und Präbiotika, in: Thieme Aktuelle Ernährungsmedizin, 2012
https://www.thieme-connect.com/products/ejournals/abstract/10.1055/s-0032-1305309

E. Eugster, F. Götze, D. Heine: Das Potenzial fermentierter Lebensmittel für eine gesunde und nachhaltige Ernährung, in: Agrar Forschung Schweiz, 2023
https://www.agrarforschungschweiz.ch/2023/07/das-potenzial-fermentierter-lebensmittel-fuer-eine-gesunde-und-nachhaltige-ernaehrung/

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b. In a double-blind, randomised, placebo-controlled 2-week cross-over clinical trial assessing microbiome shifts in 20 active adults ages 19-37.
c. In a double-blind, randomised, placebo-controlled 2-week cross-over clinical trial assessing microbiome shifts of 24 healthy adults with occasional GI distress ages 26-59.
d. In a double-blind, randomised, placebo-controlled cross-over clinical trial assessing bioavailability in 16 healthy adults ages 18-42 over the course of 8 hours.
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(1) Immune system: With vitamins A, C, B6 and B12 as well as folate, zinc, copper and selenium, AG1 contributes to the normal function of the immune system. Vitamin C contributes to maintain the normal function of the immune system during and after intense physical exercise. 200 mg Vitamin C taken daily in addition to the recommended daily dose (80 mg) contributes to the normal function of the immune system during and after intensive physical activity.

(2) Energy levels: Vitamins C, B6, B12, riboflavin, niacin, pantothenic acid and magnesium contribute to normal energy-yielding metabolism and to the reduction of tiredness and fatigue. Magnesium contributes to electrolyte balance. Biotin, zinc and chromium contribute to normal macronutrient metabolism.

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(4) Focus; Mental performance; Psychological function; Nervous system: With pantothenic acid, AG1 contributes to normal mental performance. Zinc contributes to normal cognitive function. With vitamins C, B6, B12, B1, B3 and B7 AG1 contributes to normal psychological function and to normal functioning of the nervous system. Calcium contributes to normal neurotransmission.

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