Probiotics, Fermented Foods or Dietary Microbes?

Bringing clarity to the beneficial microbes categories

Photo acquired from iStock

There is a lot of confusion between the terms probiotics, fermented foods, and dietary microbes, and what they imply. Magazines, the internet, and product labels are mixed up. Even the probiotics and food industries seem to get disoriented at times. Here is a recap for better use of the terminology.

1. Probiotics

The World Health Organization's definition of probiotics is widely recognized and used as a reference across the globe. It states:

“Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host.”

Although there is a consensus on this definition, it does not have legal value and remains too broad to discriminate and identify probiotics: what are adequate amounts? And what qualifies as a health benefit?

In 2020, an expert paper established criteria to define when a microorganism qualifies as a probiotic:

  • it must be characterized (whole genome sequencing and identified to the strain level)
  • it has to be safe for the intended use
  • the health benefit must be shown in at least 1 positive human study or the strain must belong to a species with a recognized benefit shared across that species
  • the product must deliver the viable efficacious dose until the end of its shelf life

Despite the excellent applicability of these criteria, proposed together with standards, references, and methods, the European Commission still considers that “probiotic” is a health claim, and has not approved any health claim dossier beyond the traditional yogurt cultures in the past 12 years. For this reason, in most of the European Union, “probiotic” does not appear on products labels even if the above criteria are met.

Certain countries established local guidelines for the use of the term probiotic. For example, in Italy, as long as the strain pertains to the Qualified Presumption of Safety list and is included at a dose of at least 1 billion live cells per daily dose for at least one strain, the food or supplement can label probiotic and even use the claim “promotes the intestinal flora balance”.

In the USA on the other hand the use of the word probiotic is broadly authorized and used — sometimes abusively.

Take-home message:

There is a harmonized definition for probiotic, but there is no harmonized interpretation and legal frame to label probiotic. However, you can navigate the shelves keeping in mind the key principles: a probiotic needs to be alive, safe, proven beneficial, and delivered in sufficient amounts to bring about the benefits.

2. Fermented foods

In 2021, the International Scientific Association for Probiotics and Prebiotics (ISAPP) published a consensus statement on the definition of fermented foods:

“Fermented foods are foods made through desired microbial growth and enzymatic conversions of food components.”

Fermented foods have been staples of human diets for centuries and represent a tremendous diversity of foodstuffs, with over 5000 types currently consumed globally.

The statement article provides more clarifications: fermented foods don't require the presence or viability of microbes in the food at the moment of ingestion. In many cases, as for bread, the foodstuff is cooked, and thus the bacteria or yeasts are killed before eating time.

The question of benefits is important: although the definition of fermented foods does not imply a health benefit, literature has reported that diets rich in fermented foods can enhance health, longevity, and quality of life. Nonetheless, there is a scarcity of well-designed placebo-controlled trials for specific fermented foods, and when there are studies, they point to an important heterogeneity of benefits even for the same category of fermented foods, as shown by a recent study on kefir. Professor Paul Cotter, a specialist in fermented foods’ characterization, says you may have only 1 in 50 different commercial milk kefirs actually delivering health benefits.

Take-home message:

Fermented foods consequently don’t equate to probiotics: if the microbes in these foods are not well characterized, not proven beneficial for human health, or not alive, they don’t qualify as probiotics.

3. Dietary microbes

Generation after generation, and especially after the last transformations of our food system into industrial production, leading to sanitized processed foods and diets, we have lost bacterial diversity. Crucially, there appears to be a correlation between this biodiversity loss and the rise in non-communicable diseases.

We, humans and animals, have co-evolved with bacteria. We established metabolic and immunological crosstalks, we delegated some key functions to our microbiota. Now that the microorganisms' numbers, diversity, and functions are receding, scientists agree on one marker of good microbiota health and resilience: diversity.

For this reason, experts such as Professor Bruno Pot propose that nutritional guidelines should integrate the physiological and nutritional importance of eating live microbes. He proposes the following definition:

“Dietary microbes are live microorganisms ingested as part of the normal diet.”

Dietary microbes, like fermented foods, can be largely uncharacterized. But in contrast to fermented foods, they require to be alive at the time of consumption.

The objective of proposing this terminology is to advocate for the establishment of national and international recommendations for daily intake of live microbes, similarly to the existing recommendation of dietary fiber, since they have proven at least as important for human health.

According to Bruno Pot, there is a long and winding road ahead of us, and we’ll probably need to wait for 5 to 10 years for such a recommendation to become official.

Take-home message:

Dietary microbes could become a new category to label foods with live microbes, supporting people’s food choices toward gut microbiota biodiversity. However, probiotics from food supplements would not, according to this definition, be considered dietary microbes, while certain fermented foods would be sources of dietary microbes, such as non-pasteurized yogurt, kefir, kombucha, kimchi, etc.


The living realm is a continuum, and we humans with our limited cognitive capabilities feel the need to create categories to apprehend concepts, even if these categories’ boundaries are arbitrary. The confusion caused in the field of beneficial microbes is that probiotics can be used in fermented foods, fermented foods can contain probiotics and dietary microbes, probiotics are live microbes but not necessarily in foods… There is interpenetration and porosity of one category into another.

Critically, the term “beneficial” must rely on science, and science can be conducted in many different ways, with many scales of confidence. There can be benefits that are not known or clear yet in fermented foods and dietary microbes, but it makes sense for authorities to protect consumers from claims such as “probiotic” in these cases when the healthfulness is just a non-demonstrated hint or applies to the neighboring product on the shelf, not the one you’re picking.

In a nutshell, no, homemade kombucha is not swarming with probiotics — not as we define them today, not with the little that we know about SCOBY communities, or at least not yet.

You just read another post from In Fitness And In Health: a health and fitness community dedicated to sharing knowledge, lessons, and suggestions to living happier, healthier lives.

If you’d like to join our newsletter and receive more stories like this one, tap here.



Get the Medium app

A button that says 'Download on the App Store', and if clicked it will lead you to the iOS App store
A button that says 'Get it on, Google Play', and if clicked it will lead you to the Google Play store
Nina Vinot

Nina Vinot

My Education is in Biology, Agronomy and Nutrition My Career is in Health-Promoting Bacteria My Passion is to Benefit Life, Happiness and the Planet