Stop Bombarding Your Gut With Probiotics

pills-capsulesOne of the biggest diet mistakes I’ve ever made was to take in large quantities of probiotics (in the form of fermented foods and supplements) on a daily basis. This behaviour harmed my microbiome and undermined my health.

Unlike what a lot of people seem to believe, probiotics – microorganisms that are believed to provide health benefits when consumed – are not harmless. Actually, in certain situations, they may cause a lot of damage. The term probiotics, which means pro life, is somewhat misleading, in the sense that probiotics don’t always promote life, sometimes they cause death. Some probiotics, including various types of lactic acid bacteria, produce powerful compounds (e.g., bacteriocins) that inhibit or kill other microbes. If you ingest large quantities of these critters on a regular basis, you may damage your gut microbiota and experience a range of adverse health effects.

Microbes are ruthless

We humans live in a bubble. Over the past 10.000-15.000 years, we’ve gradually separated ourselves from nature. We’ve lost touch with the natural world and it’s easy to forget that we, like all other organisms on this planet, are a part of complex, global ecosystem. All of the members of this system are fighting to survive; they compete among each other and adapt to their environment in order to avoid extinction.

Sometimes, the survival of one organism jeopardizes the survival of another. Some plant and animal species compete for the same resources and seek to exploit the same niches in their habitat. The ones that are best equipped to achieve this objective flourish, while those who don’t possess the traits that are required to win the competition wither or die out.

The same types of wars are fought within the invisible, microbial kingdom here on earth. Microbes are no different from larger organisms in that they too do whatever they can to survive. In many ways, the battle for existence that takes place in the microbial world is even more ruthless than the one that occurs among macroscopic life forms.

Microbes have been on this planet for a much longer time than we have. Over billions of years, they’ve evolved an ability to produce a long list of toxins, acids, and other compounds, some of which aid their survival by blocking the growth and survival of other, competing organisms.

You probably know that nasty bugs such as C. difficile and certain types of E. coli bacteria produce toxins that harm many other organisms. You may also be aware of the fact that it’s not we humans who designed antibiotics such as penicillin, but rather microbes. Penicillin was derived from fungi; it wasn’t created by humans in a lab.

What you may not know, though, is that it’s not just the stereotypical pathogens that produce toxins that damage other life forms – some microorganisms that are generally thought of as friendly do as well. For example, some types of probiotic lactobacilli have been shown to produce bacteriocins that inhibit or kill certain other types of bacteria (1). Not necessarily just closely related species, but also sometimes unrelated critters.

Unlike the toxins that are produced by pathogens such as C. difficile; the compounds that probiotics produce don’t have a direct, harmful effect upon the human body. If they had, the microbes couldn’t have been classified as probiotics. However, these probiotic-produced substances may inhibit the growth of certain commensal bacteria in the gut, thereby compromising the stability, diversity, and resilience of the gut microbiota.

This doesn’t mean that you should completely avoid probiotics – some are useful. What I’m trying to say is that we shouldn’t view probiotics as unequivocally good. Whether they enhance or undermine our health depends on several factors, in particular the current state of our gut microbiota and the quantity of probiotics consumed.

The consumption of large quantities of probiotics is an evolutionarily novel behavior that can disturb and destabilize the gut ecosystem

One of the first things I typically do when I set out to investigate a health-related topic is to look at the evolutionary evidence pertaining to the subject at hand. Evolution doesn’t necessarily provide us with clear-cut answers as to what we should eat and how we should live to achieve good health, but it does equip us with a guiding model that helps us to make sense of why the world is like it is and what types of behaviors and practices that different organisms are adapted for. It also helps us understand what types of foods we should include in our diet – and perhaps even importantly, which ones we should avoid.

It wasn’t until after the Agricultural Revolution that we humans started producing and consuming large quantities of fermented foods such as wine and yoghurt. Our Paleolithic forebears may have eaten smaller quantities of fruits and berries that had started to ferment, but they didn’t possess the tools or knowledge that are needed to make large batches of fermented foods via controlled fermentation. This notion is supported by anthropological research, including studies showing that contemporary hunter-gatherers primarily consume fresh food (2, 3, 4). It’s certainly possible that some of our late Paleolithic ancestors knew how to control the fermentation process and consumed fermented foods on a regular or semi-regular basis, but as a whole, I think it’s safe to say that fermented foods were not an important part of Paleolithic human diets.

Probiotic supplements and food products that are made using industrial starter cultures are obviously even more recent additions to the human diet. It’s only over the past few decades that these types of nutritional products have become widely available to the public. By itself, this doesn’t necessarily mean that we should completely avoid probiotic supplements and probiotic-enriched drinks; however, it does suggest that we should think twice before we choose to incorporate these products into our diet.

Modern scientific research has shown that virtually every time we deviate from the dietary path that was carved out for our species by evolutionary forces over millions of years, bad things happen. Our microbiota configuration changes, our genome expresses itself in an abnormal way, and we become inflamed (3, 4, 5, 6).

A large influx of probiotics represents an evolutionarily novel stimulus for the human gut microbiota. No studies have specifically looked at how high-potency probiotics affect the stability and diversity of the human microbiota. That said, there is little doubt in my mind that a daily intake of large quantities of probiotics can disturb and destabilize the microbial ecosystem that is found deep in the human gut. This notion is based on everything I’ve read about microbial systems and ecology, as well as my own personal experience.

If new organisms are put into an ecosystem, the dynamics of that ecosystem are going to change. This is true regardless of whether the ecosystem in question is found in the human gut, a rainforest, a lake, or any other milieu. For example, if you put a lot of large predators into a rainforest, the ecosystem in that area will likely change. The creatures that are inserted into the system may seek to exploit niches that are already occupied by other organisms and they may attack, kill, and perhaps cause an extinction of other animal species.

Microbial systems are obviously different from those that are made up of larger organisms; however, they too adhere to the laws of evolution. When new microbes are inserted into an ecosystem, things are bound to happen. The immigrants may produce certain compounds that are not normally present in large quantities in the environment, and could, on their way through the system, “push” other bacteria aside (1). Some of the immigrants may be able to set up shop in the milieu in which they’ve now entered; however, others may simply pass through. Unfortunately, many probiotics simply pass through the human gut, they aren’t capable of colonizing the intestine.

Key takeaways

Taking a good probiotic supplement (there aren’t many of them out there) on a semi-regular basis or adding some fermented vegetables to your dinner plate every now and then is unlikely to do you much harm. Most likely, it will do you good. A daily intake of large quantities of probiotics, on the other hand, can – and most likely will – do you a lot of harm. This is particularly true if you consume mostly industrially produced probiotic products.

The amount of probiotics that you can handle without experiencing adverse health effects largely depends on the state of your gut microbiota. If you harbor a diverse, stable microbiota, you are more resilient than if you harbor a degraded, dysbiotic biome.

I know I’ve said it before, but I think it’s worth repeating: The goal is not to flood the gut with probiotics, but rather to push the microbiota in a “healthy” direction and bring in new, beneficial bugs that are capable of growing in the gut. I’m very skeptical of the recommendation made by probiotic manufacturers to take a probiotic pill every day, indefinitely.


  1. It may well be that keeping 25(OH)D around the level typically measured in indigenous peoples living outdoor lives enables your body to move the microbiota in a healthy direction, Reducing pathogenic gram negative bacteria while enabling the range and number of beneficial species.
    Effects of high doses of vitamin D3 on mucosa-associated gut microbiome

  2. I started taking sauerkraut last year in large amounts and ended up with diarrhea within a week. After that I was so scared that I didn’t try probiotics after that until now. I have prepared a new lot two days back and going to try it in within a week’s time, this time in small quantities though.

    • Hi Shimi,

      It’s not uncommon to experience fatigue, bloating, diarrhea, etc. the first couple of days of consuming fermented vegetables. People with a dysbiotic microbiota seem to be particularly prone to develop these issues. Fermented vegetables are potent stuff – they contain a lot of bacteria.

      I’m currently conducting a clinical trial on sauerkraut and irritable bowel syndrome ( One of the purposes of that study is to see how individuals with a dysbiotic microbiota responds to regular consumption of sauerkraut.

      More isn’t necessarily better, at least when it comes to fermented vegetables. I think you’re making a wise choice in reducing the quantity the second time around.

      Check out my recent article on this topic for more tips.

  3. Hi. Do you believe the gut microbiome can be destroyed after mulitple rounds of antibiotics? And can we re-establish a good a range of bugs post antibiotics and HOW SO? Thank you.

    • Absolutely. Several courses of antibiotics can destroy the microbiome.

      If you look around here on the site you’ll see that I’ve talked about many different strategies that can help repair a damaged microbiota. The fastest way to populate the gut with a broad range of microorganisms is to perform a microbiota transplant.

      • Hi. Do you have info on your site regards SIBO? Can’t do fecal transplants with sibo unfortunately and with sibo ALL practioners want to do is go in all guns blazing and destroy gut bacteria.. 🙁

        • I suspect that SIBO is far less common than people make it out to be. I think many of the problems people attribute to SIBO are either partly or largely caused by a dysbiotic colonic microbiota. An overgrowth of bacteria in the small intestine may be a contributing factor, but I think it’s unlikely to be the main problem in most cases.

          • I swear that’s my thoughts too! But at no point have been offered a stool test at the coat of $500+ until recently. My gut feeling has always been it’s in my colon.. but if tour practioners don’t believe you how do you treat it!!! *sigh*

  4. Did I miss the study that showed adverse health effects by taking probiotics? I can only find the ones that praise probiotics. That’s weird.

    • Hi Sam,

      I highly recommend that you read this article:
      It’s written by a group of very experienced scientists. Among the authors is Dr. Tore Midtvedt, a guy who’s been doing research on the microbiome for about half a century (!!) and is responsible for developing the microbiota culture ACHIM.

      Here’s a quote from the paper:

      … But use of probiotics may have its downsides. Strains of lactobacilli producing bacteriocins and other antimicrobial substances may have an ‘antibiotic-like’ effect for short duration, but at the same time they may eradicate their closest relatives and pave the way for a dysbiotic gut microbiota, resulting in other health problems. Furthermore, we do not know what might be the implications of overwhelming the complex gut microbiota by introducing very high numbers of one or a few alien bacterial species.

      A very important thing I’d like to point out is that studies only tell us so much.
      In my opinion it’s a huge mistake to base our understanding of medicine/health/nutrition exclusively on RCTs, meta-analyses, etc. If we don’t have a conceptual biological/evolutionary framework in place before we delve into the depths of PubMed, it’s extremely likely that we get lost and end up coming to inaccurate or wrong conclusions.

      As you point out, a long list of studies have shown that probiotic supplements improve markers of inflammation, alleviate symptoms of irritable bowel syndrome, and confer several other beneficial health effects. If we just look at the results of these studies, without considering any other pieces of evidence, we’ll likely conclude that probiotic supplements are highly beneficial.

      However, if we first establish which mechanisms that are involved and consider the role probiotics have played in the human diet throughout our evolution, we’ll likely come to a different conclusion. Since it’s well established that commonly used probiotic strains such as Lactobacillus infantis and Bifidobacterium breve can stimulate our immune system, tighten intestinal junctions, and carry out some of the same functions as a healthy, established gut microbiota, it’s no surprise that studies show that probiotic supplements induce positive health effects.

      What we have to ask ourselves is: Are the probiotics inducing some permanent beneficial effects, or are they merely masking the symptoms of an unhealthy gut? May it be that they are actually doing more harm than good, in the sense that they impede the development of a normal, healthy gut microbiota (e.g., by producing bacteriocins)? The RCTs on probiotics don’t help much in terms of answering these questions. If we then go on to consider the issue from an evolutionary perspective, we’ll see that it’s very unnatural for a human being to ingest large numbers of just one or a couple of strains of microorganisms every day.

      This is not to say that probiotic supplements are never useful. All I’m trying to say is that simply looking at the results and conclusions of the RCTs and meta-analyses in this area doesn’t get us very far. To really be able to make some headway we also have to bring in other pieces of evidence, and perhaps more importantly, we have to do some logical thinking based on what we know about biology and evolution.

  5. I find that small amounts of fermented vegetables (sauerkraut, kimchi, etc.) benefit me more than any supplemental probiotics. I eat the fermented foods in very small portions–an eighth of a cup or so–and not every day. Most of the “expert” advice on this subject recommends more than what will set well with my system, so I’m careful not to overdo it. Glad to see you agree.

  6. Dear Erik,
    As one of the leading manufacturers of probiotics, using our own bacterial strains and inhouse research team. I would like to give you an insight into the latest research results and scientific studies. Our experience with therapists and scientists is consistently positive. In many cases, it is enough to take only bacteria and there is still a lot of uncertainty about supplementary therapies.

    Best regards,
    Martin Hess
    On behalf of
    Albert Hesse
    Nursing Practitioner / Ceo Tisso Naturprodukte GmbH,
    Contact Email: for further info.

    • Hi Martin,

      I have nothing against probiotics per se. I advocate the use of fermented vegetables and certain types of probiotic supplements here on the blog.

      Here are the key points I’m trying to get across:
      – The probiotic supplements that are available on the market today don’t contain the broad range of microorganisms that are needed to repair a damaged gut microbiota. Most of them only contain a handful of strains of lactic acid bacteria – the majority of which don’t seem to colonize the gut. Several large companies are now in the process of developing more advanced probiotics.

      – Probiotic lactic acid bacteria seem to carry out some of the same functions (e.g., modulate the immune system, inhibition of pathogens) as a healthy microbiota on their way through the system (which is part of the reason why RCTs have shown probiotics to be therapeutic in a variety of disorders), but they don’t replace a normal, colonic microbiota. They mask some of the symptoms of an unhealthy gut (while you take them), but they generally disappear from the system shortly after the supplement is discontinued.

      – There’s no point in taking the same probiotic supplement day in and day out, indefinitely. If the probiotics in questions contribute genetic diversity to the gut microbiota and/or modulate the microbiota in some other way, they do so shortly after you’ve started supplementing.

      – The practise of taking in large numbers of one or a couple of strains of probiotic organisms on a daily basis is an evolutionarily novel behaviour that may block the development of a normal, diverse human gut microbiota.

      – The studies that are out there on probiotics today have several limitations, chief of which is that the vast majority of them don’t have a follow-up period. If you do a well-designed study on your probiotic supplement and find that the probiotic is capable of inducing lasting (i.e., not disappearing after the supplement is discontinued), positive changes in the microbiota and health status of the participants, then I would be more than happy to take a look at the study, and if I find it convincing, speak favorably about your supplement.

      Read my previous articles on this topic for a more thorough explanation of these things.

  7. Erik
    I’ve been battling c.diff for years. I had a fmt 3 yrs ago but my symptoms persisted. Then I had severe bowel yeast which showed up in every stool test as “many yeasts”.most of the candida literature out there tell patient’s stool testing doesn’t work that a urine test Oat. Is #1 for diagnosing yeast overgrowth in bowels? I’m confused by this? I had thick whitish amounts of yeast coming out of my Rectum for years in my stool. I begged my gi drs to run tests. It wasn’t until I was quarantined in hospital with c.diff that I noticed all of my stool tests; Ova&parasites, stool.culture, wbc and c.diff tests show yeast present or many yeast. I went on Diflucan for 12 weeks and the discharge went away.
    Unfortunately I’m still very sick. I have severe low bowel pain and I believe I still have cdiff. I never had diarehea with cdiff only constipation or softer stool with lots of mucous. I just had an environmental swab test done in my home for c.difficile. 3 areas showed contamination . A and B toxin with several ribotypes. My bathroom sink, my broom and my shoes.
    So IM Waiting On A Stool test. Although half the time c.diff stool tests fail. I did an experiment 3 years ago.i used the same stool but had 2 seperate stool c.difficile was positive and the other negative.
    I’ve taken sach. Boulardi but im.very hesitant to take other probiotics. My colon is so inflamed.
    I’m looking for another perform a fmt. Mabye a weeks worth to try to get this virulent infection out of me.
    Would you recommend taking any probiotics. Do you think sach.boulardi is useful?
    thank you

    • Hi Danielle,

      I’m sorry to hear about your situation.

      It sounds like you harbor a severely dysbiotic gut microbiota.

      I think fermented vegetables may help you out. The lactic acid bacteria present in sauerkraut, kimchi, and other similar fermented vegetables produce substances that are toxic to various types of gut pathogens. These foods won’t populate your gut with the wide diversity of microbes that are needed to build a healthy, diverse gut microbiota, but they stimulate your immune system, contribute some genetic diversity to the microbiota, and help reduce the pathogen load in the gut.

      I also recommend the probiotic Mutaflor, which you can read about here. S. boulardi supplements are probably not going to do you much good.

      These products plus a healthy diet should help you get better. However, you may also have to do one or more microbiota transplants to really make some headway.
      You’ll likely experience some gastrointestinal distress when you first start consuming fermented veggies and using Mutaflor, but these problems will probably subside after a while.

      Keep in mind, all of this is general advice. I don’t feel comfortable giving you any more suggestions without knowing more about your current health condition, medical history, etc. It sounds like your health condition is very poor at the moment and you need help from a nutritionist/clinician. You can contact me through the e-mail form here on the blog if you need more help and is interested in online coaching. I may be able to take you on as client and help you get through this.


  1. […] recently, I published an article here on the blog entitled “Stop Bombarding Your Gut With Probiotics“. In that article I stated that one of the biggest diet mistakes I have ever made was to take […]

  2. […] can bring a lot of potentially beneficial microbes into the lower gut. The bad thing is that (excessive) consumption of fermented vegetables may destabilize the gut microbiota, hindering the development of a stable, resilient […]

  3. […] about probiotics here on the site in the past. In my earlier articles on this topic (e.g., here, here), I’ve made the case that many probiotic products likely do more harm than good. In […]

  4. […] As I’ve pointed out in many of my previous articles on probiotics and fermented foods (e.g., this one, this one), I think that’s unwise. Regular consumption of large quantities of fermented foods […]

  5. […] lactic acid-producing probiotics, may, via their impact on the microbiota of the gut, actually cause more harm than good over the long term, in the sense that they can disturb the gut ecosystem, suppressing the growth and functions of some […]

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