Probiotic Supplements: Are They Doing You More Harm Than Good?

SupplementsThe probiotic market has grown exponentially over the past few years. Pills and drinks containing probiotics – live microorganisms that, when administered in adequate amounts, confer a health benefit to the host – are no longer just niche products purchased by health aficionados, but rather something that “everyone” now seems to incorporate into their dietary regime.

This situation didn’t arise because there’s strong scientific evidence to show that probiotic supplements actually repair a damaged gut microbiota, but rather because the mainstream media, probiotic manufacturers, and some health practitioners and dietitians have made us believe that probiotic supplements permanently enhance our immune function, lift our mood and mental health, and increase our protection against a wide range of chronic diseases. In a not-so-distant future, a new generation of probiotic supplements that actually live up to this reputation may make their way onto the market. However, when it comes to most of the supplements on the market today, the story is somewhat different.

The probiotics you’re taking probably won’t stay around in your gut

Thanks to thousands of recent studies on the human microbiome, we’re now all aware of the fact that having a diverse, balanced community of microorganisms in our gut is key to good health. Taking a capsule containing some beneficial microorganisms may, on the surface, seem like a simple way to acquire this state.

There’s just one “small” catch: Many, if not most, of the microorganisms found in the probiotic supplements on the market today don’t permanently colonize the human gut. Moreover, most probiotic supplements only contain a handful of strains of Lactobacillus and/or Bifidobacterium. These organisms may confer some temporary health benefits as they pass through, but most of them won’t become permanent members of the gut.

That’s not to say that all probiotics are equally ineffective at colonizing the human intestine. For example, a 2014 study found that evoluntary exposure to a single, high dose of probiotic Escherichia coli resulted in prolonged colonisation (1). That said, in general, studies show that most probiotics don’t attach to intestinal cells and proceed to colonize the gut (2, 3, 4).

Here’s what a review paper titled “Probiotics: determinants of survival and growth in the gut” had to say about the matter:

Although it is believed that the maximum probiotic effect can be achieved if the organisms adhere to intestinal mucosal cells, there is no evidence that exogenously administered probiotics do adhere to the mucosal cells. Instead, they seem to pass into the feces without having adhered or multiplied. Thus, to obtain a continuous exogenous probiotic effect, the probiotic culture must be ingested continually. (2)

Since we know that a lot of people have a dysfunctional gut microbiota, and that probiotics can help inhibit pathogen colonization, stimulate the immune system, and carry out some of the same functions as a healthy gut microbiota during their journey through the gastrointestinal tract, it’s no surprise that many studies have shown that probiotic supplementation can improve our health and help reduce – at least temporarily – a range of disease symptoms (5, 6, 7). However, this doesn’t mean that those results are necessarily maintained after the probiotic supplement is discontinued, or that the supplement actually repairs a dysfunctional microbiota.

Today’s probiotic supplements don’t provide the range of microorganisms needed to build a diverse, healthy gut microbiota

We have to keep in mind that from the bacteria’s point of view, the human colon is an environment – one they are able to live in because the conditions there support their growth and reproduction. When we eat, we’re not only feeding our human self, but we’re also taking in indigestible (to the human host) compounds that pass into the large intestine.

Different types of microorganisms are involved in the breakdown of different types of fermentable substrates. If we don’t supply the bacteria the substrates they like to dine on, they won’t stick around.

Just like a zebra probably wouldn’t make it very long on the streets of Manhattan, a microbe that has evolved to live in milk may not do so well in the human gut. When we isolate specific strains of bacteria for use in probiotic supplements, we often forget that the organisms we pick don’t necessarily do well outside of their “natural” habitat.

This is where we get to the main problem with many probiotic supplements and fermented foods. Most of the microorganisms found in these products don’t produce enzymes that facilitate the breakdown of oligosaccharides and non-starch polysaccharides – which are the main forms of fermentable compounds that pass into the human large intestine. Rather, these organisms break down simple sugars, which are only available in the colonic environment after the polymers have been cleaved down to their smaller constituents.

As mentioned, some of the organisms in a typical probiotic supplement may find an available niche deep in the gut, but they certainly won’t fully repair a damaged gut ecosystem – or do much in terms of cleaving the beta 1,4-glycosidic bonds that exist in the cellulose we get through our diet. 

The bacteria found in yoghurt for example don’t carry genes that code for enzymes that facilitate the breakdown of non-starch polysaccharides. Rather, these organisms are adapted to break down the lactose found in milk. In lactose-tolerant individuals, lactose is hydrolyzed in the small intestine by the brush-border enzyme lactase. Little, if any, lactose passes into the colon, where most of the microorganisms in the gut are found. In other words, in lactose-tolerant individuals, the conditions in the colon may not support the growth of the lactic acid bacteria found in yoghurt.

The bacteria found in products such as yoghurt can serve as a Band-Aid that covers up some of the symptoms of an unhealthy gut, in the sense that they modulate our immune system, inhibit pathogen colonization, and carry out some of the same functions as a healthy gut microbiota when they pass through. However, just like probiotic supplements, they won’t do much in terms of permanently repairing the gut microbiome.

Contrary to what supplement manufacturers want you to believe, there is no reason to take the same probiotic supplement day in and day out. If the bacteria actually set up shop in the gastrointestinal tract and/or contribute genetic material to the microbes that are already present, they do so shortly after you’ve started supplementing. In most instances, simply putting more of the same microbes into the system every day isn’t going to produce any significant additional benefits. 

Where supplements come up short

Probiotic capsules are in some ways analogous to vitamin and mineral supplements. Unlike real food, which is composed of a wide range of substances that form a biological network, a vitamin supplement contains just a couple of nutrients that don’t normally occur in isolation. There is a connection between the various nutrients in whole foods – a synergy that is lost when one or more of these constituents are removed.

The same thought process can be used to understand the difference between a probiotic supplement and a complex community of microorganisms, such as the one found in kefir grains, the human colon, or a jar of sauerkraut. In the human gut, bacteria don’t operate in isolation. Rather, there is a constant exchange of genetic material through horizontal gene transfer, communication through quorum sensing, and competition between species.

When the non-starch polysaccharides we eat pass into the large intestine, some microbes are involved in the first steps of the fermentation process, before others may take over as the polysaccharides have been cleaved down to their smaller constituents.

Diversity is key

This quote from a recent newspaper article, which includes an interview with one of my favorite researchers, Dr. Tore Midtvedt, summarizes some of the problems with the probiotic supplements that are on the market today:

“Giving probiotics to children is the largest biological experiment since Hitler’s experiments,” says professor Midtvedt.

He is very sceptical about probiotics, which is food containing live bacteria that are supposed to be good for intestinal flora, being given to children.

“Nobody knows which bacteria turn genes off and on during infancy.”

Research has been done showing that some types of probiotics can result in more rapid recovery from diarrhoea. But Midtvedt holds that there is a lack of research on the long-term effects. A Finnish study has shown less eczema after a short period of time, but more asthma in the long-term for children who received probiotics as infants.

The idea behind a faecal transplant is interwoven with the idea of intestinal flora as an ecosystem, where diversity is the most important thing. In healthy stools there are generally at least 1000 different bacteria, some have even called it super-probiotics. In comparison, industrially manufactured probiotics often contain from one to seven different bacteria – but with large quantities of each type of bacterium.

“That is the wrong philosophy. You’re supposed to have diversity,” Tore Midtvedt says. (8)

To date, no good, long-term studies have specifically looked at how a high intake of probiotics affects the stability and diversity of the human gut microbiota. In other words, there may be some unintended health effects associated with the use of probiotics that we are not currently aware of.

Could some probiotics block the development of a healthy adult gut microbiota?

Studies have shown that the intestinal microbiota of infants is very different from that of adults (9, 10). Bifidobacterium is a dominant bacterial genus in the infant gut microbiota (9). This isn’t surprising, as breast milk is high in lactic acid bacteria and contains prebiotic oligosaccharides that stimulate the growth of Bifidobacteria. In other words, breast milk selects for a very specific gut microbiota; one that helps support the growth and immune development of the child.

The organisms found in breast milk (and subsequently in the gut of the baby) help protect the newborn infant from bacterial and viral pathogens by lowering the pH in the colon through the fermentation of carbohydrates into short-chain fatty acids, inhibiting the adhesion of pathogens to the mucosal surface, and producing proteinaceous toxins (bacteriocins) that can kill or inhibit closely-related or non-related bacterial strains.

Some of the microorganisms found in common probiotic supplements may elicit similar effects on our health and physiology as those that are found in breast milk. Among other things, they stimulate our immune system and inhibit the adhesion of pathogenic microorganisms to the intestinal mucus. It’s generally believed that the effects these microorganisms have on our health are unequivocally beneficial. However, this may not be the case.

While the influx of large numbers of probiotic lactic acid bacteria (through breast milk) is a good thing for a fragile infant with an undeveloped immune system, it’s may not be a good thing for an adult human. It’s possible that some probiotics could do more harm than good, in the sense that they may stimulate our immune system in evolutionarily novel ways and/or block the development of a healthy adult gut microbiota.

Simply taking a probiotic pill with breakfast every now and then is not going to have much of an impact on the microbial ecosystem deep in the gut. However, consumption of large amounts of probiotic-enriched drinks or the routine use of high potency, medical grade probiotics certainly will. The use of probiotics such as VSL#3 may be a good idea for those with chronic, hard-to-treat gut disease, acute illness, and/or a severely compromised immune system, but for the rest of the population, it’s most likely a very bad idea.

Lessons from our ancestors

Many of the microorganisms that we today classify as probiotics were probably not a part of our Paleolithic ancestors’ guts.

A recent study that investigated the phylogenetic diversity, taxonomic relative abundance, and short-chain fatty-acid (SCFA) profile of the microbiome of the Hadza hunter-ggatherers found that they have no Bifidobacteria in their guts (post-weaning) (11). This isn’t necessarily surprising, as the Hadza don’t consume milk or any other dairy products.

From an evolutionary perspective, probiotic-enriched milk and probiotic supplements are clearly novel additions to the human diet. Our Paleolithic ancestors didn’t consume capsules containing a carefully selected mix of bacteria, or drink strawberry-flavored yoghurt for breakfast. Rather, they got their “probiotics” from water, vegetables with clinging soil bacteria, raw animal intestines (yes, some hunter-gatherers have been known to consume the intestines of the animals they kill), other humans (through kissing and physical contact), and the rest of the natural milieu in which they lived.

These sources (e.g., plants, animals, soil) all harbour their own unique, complex microbiome. This is in stark contrast to the probiotic supplements you’ll find at your favorite health food store, which typically contain just a handful of Lactobacillus strains.

A common belief is that probiotic supplements with a high number of Colony-Forming Units (CFUs) are superior to low-potency probiotic supplements that contain less than 5 billion CFUs/dose. However, as I’ve discussed throughout the article, this isn’t necessarily the case.

The most important thing isn’t that the product has a high potency, but that the bacteria it contains are actually able to colonize our gut and/or otherwise produce any positive health effects. Our primal ancestors obviously didn’t take in billions of CFUs of just a couple of strains of bacteria every day.

As we live in an environment that is very different from that of our Paleo ancestors, we’re not necessarily best off emulating every aspect of their lifestyle. For example, I wouldn’t recommend that you go out in your backyard garden and pick some soil-covered plants to chew on. That said, as we all know, an evolutionary perspective on diet and health gives us many clues as to how we should live to optimize our health and longevity.

Key takeaways

Eating Greek yoghurt for breakfast or popping probiotic pills that contain a couple of Lactobacillus strains is not going to get us very far in terms of building a healthy, flourishing community of hundreds of species of gut microbes. Some high-potency probiotic supplements and probiotic-enriched foods may even do us more harm than good, in the sense that they could stimulate the adult immune system in evolutionarily novel ways and/or block the development of a robust adult gut microbiota. The focus should be on developing a healthy, diverse gut microbiota, not on pouring huge numbers of “probiotics” into the system every day.

This is not to say that all probiotic supplements are equally ineffective, or that nobody can benefit from probiotic supplementation. Probiotics can provide temporary immune support, help ward off infections, and shorten the recovery time from some acute illnesses (e.g., diarrhea). In other words, those with chronic, hard-to-treat gut disease, acute illness, and/or a severely compromised immune system may benefit from using probiotics. All I’m saying is that it’s a bad idea to rely on probiotic supplementation as a long-term solution for achieving good gut health.

Rather than going to the health food store to buy a probiotic supplement that contains a carefully selected mix of 5 or 10 microorganisms, you’re probably better of focusing on boosting your intake of fiber-rich foods, exchanging bacteria with healthy friends and family members, eating more raw, minimally cleaned fruits and vegetables, spending more time in natural environments, and reducing your use of cosmetic products, lotions, cleaning detergents, and other products that contain a wide range of potentially harmful substances.

Now I want to hear from you: Whar are your thoughts on the effectiveness of probiotic supplements? Do you use them yourself? If so, do you feel they have improved your health?


Picture: Picture source. License.
Note: A previous version of this article of mine was published in Paleo Magazine, the first, and only print magazine dedicated to the Paleo lifestyle and ancestral health. You can subscribe to Paleo Magazine here!


  1. Alessio says:

    Ehi dude, this is definetly the best article I’ve read about the issue so far, thank you!
    You perfectly hit my concern about probiotics. As pointed out, it’s about what kind of buddies are supposed to live in a Sapiens’ gut. We co-evolved with our microbiome and physical features, genome, gene expression and microbiome are interrelated in a multivariate complex function, and any oversimplification that is going to take aside one or more variables is getting flawed. We are a midway between a carnivore and a vegetarian animal, thus one could expect to find a microbiome somewhere between a cat and a chimp. We also don’t have to forget that we primarly evolved as scavengers, and a good hint about the potential benefits about fermented fish and meat comes from some traditional cultures around the world that included them in their diet. If a particular bacteria may help you to breakdown a compound, it doesn’t necessarily mean that it’s supposed to live in your gut and it says little about long term health.

    • Thanks, Alessio!

      It seems like rarely a day goes by when I don’t read about the many health benefits of taking probiotic supplements. Far less attention is given to the potential downsides and limitations of using these supplements for improving gut health.

  2. Re -“From an evolutionary perspective, probiotic-enriched milk and probiotic supplements are clearly novel additions to the human diet.”

    On the one hand – ” a microbe that has evolved to live in milk may not do so well in the (adult) human gut.”

    But, on the other hand – “The same thought process can be used to understand the difference between a probiotic supplement and a complex community of microorganisms, such as the one found in kefir grains, the human colon, or a jar of sauerkraut.”

    Kefir is essentially a probiotic enriched milk product. I’m unclear if your opinion is that is that you rank highly, as with fermented veggies. I know I’m just asking your opinion, but you are very well read.

    • Hi Newbie!

      Kefir is in a somewhat different category than other fermented dairy products in the sense that it contains a broader spectrum of microorganisms. However, the same limitations apply to kefir as to other fermented dairy products.

      Keep in mind, it’s primarily non-starch polysaccharides and oligosaccharides that escape digestion by human enzymes in the small intestine and make their way into the large intestine. Kefir – and other fermented dairy products – doesn’t provide the range of microbes that are needed to break down these substrates and establish a gut community that is well-matched with the diet.

      I want to make it clear though that no studies to my knowledhe have investigated how kefir impacts the gut microbiota over the long-term. While kefir certainly won’t supply you with a diverse, flourishing community of bacteria, it may be that kefir can positively modulate the existing populations of microbes in some way.

      I know this is probably not what you want to hear, but my belief is that fermented dairy products (including kefir) are not very effective for the treatment of a damaged gut microbiota.

      Hope this helps!

  3. What do you think about soil based probiotics?

    • Hi James!

      I know soil-based probiotic supplements have received quite a bit of positive press within the ancestral health community. I’ve looked at the studies in this area, particularly those on Prescript Assist, tried some soil-based probiotics myself, and given this topic some thought.

      I don’t think the soil-based probiotics on the market today are going to provide much benefits in terms of permanently increasing the biodiversity of the gut microbiota or treating gut dysbiosis. You are probably much better off focusing on the things I regularly mention in my articles on the human microbiome (e.g., fiber-rich foods, FMT, raw vegetables).

      That being said, taking some soil-based probiotics for a couple of days or a week to see if you notice some benefits is unlikely to do any harm.

  4. Would fecal transplants prove more effective for providing proper gut microbiota?

    • Hi Steve!

      FMT is in a completely different category than probiotic supplements. In contrast to probiotic supplements (which typically just provide a handful of strains of lactic acid bacteria), FMT contains a complex, diverse ecosystem of microorganisms.

  5. Hi Eirik. Thanks for an informative article. I and others in my family have found probiotics to be quite helpful for short-duration issues. Otherwise, I agree that they aren’t necessary on a regular basis. Some probiotics are definitely better than others, but all of them are more of a temporary fix than a cure.

  6. I have taken probiotic supplements off and on, on the advise from my functional medicine doctor (a brand they recommend and you can buy in their office). I never really noticed any benefit. I read another article just recently about probiotics not really providing any benefit and I tried to relay that information to the nutritionist in my doctor’s office and she didn’t even want to hear it and said something about the studies show blah, blah, blah. It’s so nice to read other views.

  7. Very interesting read! I’ve spent a ton of money on probiotics over the years and have really only seen improvements at the start. Over time I’ve become more and more bloated and developed Sibo. The lactate producing strains make my stomach burn and soil based strains made my constipation worse! But I kept experimenting with them because everyone recommends it! But now I’m starting to think they’ve done me more harm than good… Still finding it hard to let go. I even had FMT, but ubiome testing showed that even there wasn’t a lot of colonisation of ‘new’ strains. Have you come across equilibrium probiotics by Generalbiotics that has 150 strains, apparently in ideal proportions? I’m very tempted to try that.

    • Hi Layla.

      I checked out the website of Generalbiotics right now. It looks very unprofessional to me, and I get the distinct impression that the whole thing is a scam. There are no probiotics on the market today that contain 150 strains.

      I talked to one of the leading researchers in the microbiome field a couple of weeks ago. He is – as me – very skeptical of probiotics. However, he mentioned one probiotic strain (E. coli nissle, which is found in products such as Mutaflor) that might be worth taking. I’ve previously talked about that specific probiotic here on the site.

      Have you tried homemade fermented vegetables?

      • Hi Eirik,
        Thanks for the reply. Interesting to hear that microbiome researchers are skeptical of probiotics.
        I heard about Generalbiotics from Dr. Grace Liu’s ( podcast and thought it sounded good as I normally trust her opinion…Are you familiar with her work?
        I heard of Mutaflor as it’s popular in Germany – does Symbioflor 2 contain the same strain?
        Yes, I eat homemade Sauerkraut, kefir and yoghurt daily…

        • Yes, I’m familiar with her work. She seems like a very nice lady, but I’m very skeptical of many of her statements and opinions regarding the microbiome. From what I’ve gathered, she seems to promote the use of many probiotic supplements (most probiotic supplements do very little, and many probably do more harm than good), advocate the use of fiber supplements (IMO, it’s better to just stick with real food), focus a lot on the types of microbial strains and species that we should have in our guts (I think it’s more important to focus on the genetic repertoire of the microbiota), and promote the use of supplements containing antimicrobial herbs (In most instances, these types of supplements are probably doing a lot more harm than good).

          One caveat: I haven’t checked out her latest work, so it might be that she has recently adjusted her opinion on some of these issues.

          Again, I have absolutely nothing against her personally. All I’m saying is that I think you shouldn’t rely on her as your no.1 source of information about the microbiome. The blog of Dr. Art Ayers is much better in my opinion.

          • No, I don’t think Dr Grace has changed her opinion recently. Thanks for sharing your viewpoint as well, it’s always great to get different opinions. I’ll check out Dr Ayers blog as well, thanks for that!

          • Josh Finlay says:

            Grace doesn’t advocate for “hardcore” antimicrobials anymore. I have heard her say that taking broard spectrum things liek berberine or oregano oil is plain dangerous.

            There is a good book called the gut health protocol in which the author highlights what the research shows to be the most selective antimicrobials on the market. Namely cinamon oil, capryli acid and garlic. Worth a read


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  8. […] the microbiota and inhibit the development of a healthy, diverse microbial ecosystem in the gut (6, 7). These effects may be attributed to the production of bacteriocins – toxins that could […]

  9. […] Actually, as I’ve stated in my articles on this topic, I think most probiotic supplements do more harm than good. This is particularly true for high-potency, medical grade probiotics containing lactic acid […]

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