How Probiotics Could Damage Your Microbiome

capsulesNot so long ago I published a post entitled “Probiotic Supplements: Are They Doing You More Harm Than Good?” here on the blog. In that article I made the case that many, if not most, probiotic supplements likely do more harm than good. This notion goes against conventional wisdom in this area, which says that probiotic supplements boost the diversity of the gut microbiota and enhance gastrointestinal health.

Very recently, a new paper supporting many of the statements I made in my article on probiotics was published in the journal “Microbial Ecology in Health and Disease” (1). The authors of the paper, who are all experienced scientists that have spent several decades doing research on the human microbiome, make the case that it’s time we reconsider the view that probiotic lactic acid bacteria are unequivocally good…

Probiotic lactic acid bacteria – the fledgling cuckoos of the gut?

In today’s post I’m not going to take another in-depth look at the pros and cons of probiotic supplements. Rather, I wanted to focus on the scientific paper mentioned above. The authors of that article – entitled “Probiotic lactic acid bacteria – the fledgling cuckoos of the gut?” – had the following to say in their concluding remarks (Bold: My emphasis):

When they are members of a stable gut microbiota, lactic acid bacteria undoubtedly play an important role in maintaining good health. The mechanisms involved are apparently quite complex, involving immune modulation, production of peroxides, acid and bacteriocins, and also proteins that alter epithelial permeability and bind to intestinal receptors for pathogen (37). Their immunomodulating properties may, for example, be of fundamental importance in the development of mucosal and systemic immune tolerance (38). Therefore, if they for some reasons are outnumbered in the gut microbial ecosystem, resulting in disease conditions, it is a tempting strategy to replace them by oral administration of lactic acid bacteria produced in fermentation culture. The idea has proved to be good in the prevention of allergy and asthma (39), and it seems to be a very good idea to select strains of probiotic bacteria that will survive in the intestine and produce GABA (γ-aminobutyric acid) (40), an inhibitory neurotransmitter deficient in children suffering from ADHD (41). Lactic acid bacteria with strong bacteriocidal effects have been exploited in the eradication of methicillin-resistant Staphylococcus aureus infections (42). 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.

The warning of the author Edith Wharton (1862–1937) is apparently relevant also in our case: ‘Beware of monotony; it’s the mother of all the deadly sins’. (1)

This quote nicely summarizes the main points of the paper. As you can see, the article offers a more balanced perspective on the health effects of probiotics than most other scientific papers in this field. The researchers don’t just discuss the potential health benefits of probiotics, but also look into the potential negative health effects that may occur as a result of probiotic supplementation.

The dark side of probiotic supplements

The statements made by the authors of the paper above are consistent with the ones I made in my recent article on probiotic supplements…

Since probiotics can stimulate our immune system, inhibit the adhesion of pathogens to the gut mucosa, and carry out many of the same functions as a healthy adult gut microbiota, it’s not surprising that some studies have found that probiotic supplements improve symptoms of health disorders such as irritable bowel syndrome, chronic fatigue, and depression (2, 3, 4). The problem with these studies is that they only show us the immediate, short-term effects of probiotic supplementation; they don’t tell us much about the long-term effects.

It’s important to keep in mind that the ingestion of large quantities of one or a couple of strains of probiotic bacteria is a an evolutionarily novel behaviour. Some, if not many, probiotic supplements, in particular medical grade, high potency probiotic capsules, may actually do more harm than good, in the sense that they can destabilize the gut microbial community and/or block or undermine the development of a healthy gut microbiota. This is also true for industrially produced drinks and foods that contain a carefully selected mix of probiotics. These effects may occur, in part, because probiotics produce various bacteriocins – proteinaceous toxins produced by bacteria to inhibit the growth of similar or closely related bacterial strains.

Another obvious issue with the probiotic supplements on the market today is that they don’t contain the range of microorganisms needed to repair a dysfunctional gut microbiota. Most probiotic supplements only contain a handful of strains of lactic acid bacteria, typically belonging to the genus Bifidobacterium or Lactobacillus. Most of these bugs are unable to colonize the human gut (5, 6, 7), in large part because they are not adapted to live there. In other words, they are just transient members of the microbiota. Some exceptions do exist, however. For example, certain probiotic strains belonging to the species Escherichia coli have been shown to be able to set up shop in the human colon (8).

Several large companies are now in the process of developing new and more effective probiotic supplements, many of which may become available to the public in a not so distant future.

What does this mean for you?

Does this mean that you should stay away from all foods, drinks, and supplements containing “probiotics”? Not so fast… Not all probiotic products are created equal. There’s a big difference between a homemade jar of sauerkraut and a probiotic capsule. As I see it, the problem isn’t the probiotics per se, but rather the abnormal and evolutionarily novel composition of microorganisms that is found in many commercially available probiotic products.

Probiotic supplements and probiotic-enriched drinks typically contain only a handful of microbial strains, some of which are selected based on their ability to produce bacteriocins and antibiotics. This is in contrast to traditionally fermented foods such as kefir and sauerkraut, which harbor a diverse ecosystem of microbes. I’m a lot more optimistic when it comes to these types of products. That said, we know very little about how traditionally fermented foods affect the gut microbiota and gastrointestinal health. This may change in a not so distant future though, because I’m planning to carry out a randomized controlled trial on fermented foods and human health later this year.

So, to summarize: Probiotic supplements (the ones that are on the market today), as well as industrially produced foods and drinks containing just a couple of strains of probiotic bacteria, are unlikely to do you much good. In fact, some of these probiotic products may unfavorably affect your health. Just taking a probiotic capsule with breakfast every now and then is unlikely to do you much harm; however, regular consumption of high potency probiotic products certainly may. Some exceptions do exist, however. For example, probiotics belonging to the species E. coli (e.g., the strain E. coli Nissle 1917) have some unique characteristics. It should also be noted that traditionally fermented foods (e.g., fermented vegetables) have a very different microbial make-up than probiotic supplements and may offer a range of health benefits.


  1. Very informative. Thank you!

  2. Thank you for this article. It follows what I believe to be true, but had not the evidence to confirm until your article. Inliven superfood manufactured by Miessence, developed after more than 20 years research,is from an Australian company, is certified organic, contains the full spectrum of 13 lactobacillus bacteria plus 26 whole foods. Have you head of it? At you can investigate further and make your own assumptions.

    • Karen, I don’t presume to answer for Eirik, but I think this commercial product is exactly the kind of thing to avoid.
      Eirik, I look forward to seeing the outcome of your RCT.


  1. […] How Probiotics Could Damage Your Microbiome — Eirik Garnas […]

  2. […] bacteria, most of which are unable to colonize the human gut. Actually, some “dairy probiotics” may do more harm than good, in the sense that they could hinder the growth and survival of beneficial bacteria in the […]

  3. […] 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 kill […]

  4. […] not surprising that we a poorly adapted to such a practice. As I’ve pointed out before (e.g., here, here), the consumption of large quantities of fermented foods such as kimchi and sauerkraut on a […]

  5. […] microbes that are generally perceived as friendly, including various types of probiotics, can do us harm in certain situations. On the flip side, microbes that are generally perceived as bad can sometimes do us good. It all […]

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