Why You Should Think Twice Before Using Probiotics

probioticsI’ve talked a lot 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 today’s article, I’m not going to take another in-depth look at the pros and cons of probiotic supplementation. Rather, I wanted to talk a little about the science of probiotics, including a recent study that supports the statements I’ve been making here on the site.

Why you should be cautious when your interpret the results of studies on probiotics

I’ve pointed out many times here on the site in the past that the probiotic supplements that are on the market today aren’t capable of repairing a gut microbiota that lacks resilience and biodiversity. They don’t contain the broad range of microorganisms required to rebuild a microbiota that has been damaged by antibiotic use, consumption of an unhealthy diet, and/or other microbiota-disrupting behaviors.

The majority of them only contain a handful of strains of Lactobacillus and/or Bifidobacterium. These probiotics stimulate our immune system as they pass through us and may attack and knock out some pathogens, but most of them aren’t capable of colonizing the intestine: they quickly diminish in presence or disappear completely from the gut following cessation of supplementation (1, 2, 3). Even if they were adapted to thrive in the human body, they would only equip the system that is the human gut with a very small number of the many genes that are required for healthy digestion.

So, why then are probiotic supplements so popular? The main reason is probably that they have been hyped as being effective against a wide variety of ills. This reputation didn’t just grow out of nothing; science helped create it. Dozens of studies have found that probiotics are useful in the treatment of a variety of health conditions (e.g., 4, 5, 6). These studies have some serious limitations though. Perhaps the biggest one is that they fail to assess the long-term impact probiotics have upon the human microbiota and health; they only look at the immediate, short-term impacts. Typically, a group of patients are instructed to take one or two probiotic capsules each day for a set number of weeks and fill out a couple of forms along the way that include questions about symptom severity and health status. Sometimes, analyses of fecal matter and blood are also carried out in order to get a better understanding of how the probiotics work.

Most studies with this set-up have found that probiotic supplementation reduce the severity of the participants’ disease symptoms. A lot of people look at the results of these trials and jump to the conclusion that probiotics are highly beneficial supplements, which isn’t surprising, given that that’s exactly what the studies seem to show – at least upon first inspection. However, if we take a step back and bring in other pieces of evidence, as well as the knowledge we possess about biological systems, things no longer seem so clear cut…

The dark side of probiotics

Given that probiotics are capable of stimulating our immune system, produce compounds that are toxic to many pathogens, and carry out some of the same functions as a normal gut microbiota as they pass through the long tube that is the human intestine, it shouldn’t really come as a surprise that studies have found that probiotic supplementation positively affects a variety of health measures. What we have to keep in mind though, is that these effects are almost always temporary; not permanent. As soon as the probiotic products are discontinued, the observed effects tend to disappear.

Not only that, but it could actually be that the probiotics, via their actions in the gut, are causing some adverse health effects, in the sense that they may suppress and/or block the development of a healthy, resilient microbiota (7, 8). This is something I’ve talked a lot about here on the blog in the past, so I’m not going to repeat myself again here. What I would like to say though is that the fact that probiotics cause some effects that we perceive as beneficial doesn’t exclude the possibility that they are causing some harm as well.

Usually, the harmful effect – if there is any – is overshadowed by the immediate “beneficial” effects of the probiotics, which means that it’s rarely picked up in clinical trials. That doesn’t guarantee that it isn’t there though. Most studies on probiotics don’t include a follow-up period; hence, they fail to assess if the probiotics induce any lasting changes in the microbiota or health of the participants.

Fortunately, not all studies fail to pick up the not-so-great effects of probiotics. For example, very recently, an interesting animal study was published. Here’s what it found:

In rats fed on ‘junk’ diets, the probiotic medicine was able to significantly impact microbial composition in the gut and prevent memory loss. But for rats on a healthy diet, the probiotic did little to influence microbial composition and actually impaired memory function. (8)

These results are not surprising to me at all. In my previous articles on probiotics I’ve made the case that high-potency probiotic supplements – such as VSL#3, the supplement that was used in this study – can destabilize the gut microbiota. It’s a very unnatural behaviour for any animal – whether it be a human, rat, or any other organism – to take in large quantities of just one or a couple of strains of “probiotics” every day. This behavior is bound to cause some problems. The only people who may benefit from using high-potency probiotic supplements are those with severe, hard-to-treat gut illness or other conditions that require medical supervision. I wouldn’t recommend any “healthy” human to use a probiotic supplement such as VSL#3.

It’s important to point out that the study above was done in animals. By itself, it doesn’t prove that much. However, it does add to the evidence suggesting that probiotics are not as great as people have been led to believe.

As I see it, most (not all) of the probiotics that are on the market today work like a Band-Aid. They mask some of the symptoms of an unhealthy gut, but they don’t heal the festering wound they cover. Sometimes, they may actually make the wound more severe, but since they do such a good job of covering it up, the symptoms of the damage don’t necessarily show, at least not until the Band-Aid is removed (i.e., probiotic supplementation is discontinued).

Last words

Make no mistake, I truly believe that medicines and supplements containing microorganisms can be very useful in the treatment of a wide variety of health problems. Probiotics may one day be routinely used in the treatment of everything from cancer to diabetes to depression. The point I’m trying to make with this article is not that the probiotic concept is without merit. Rather, the point I’m trying to make is that it’s immature, and at the moment, flawed. Perhaps the biggest problem with today’s probiotics is that they don’t contain the many different types of microbes that are needed to repair a damaged gut microbiota; most only contain a couple of lactic acid bacteria.

Another thing I would like to mention is that I’m very skeptical of the idea that it’s a wise to take probiotics every day, indefinitely, which is what a lot of probiotics manufacturers and sellers advice us to do. If the probiotics in question actually set up shop in our intestine, they do so shortly after we start supplementing. In most cases it’s unnecessary – and maybe even harmful – to continue supplementation for long periods of time.

Again, I’m not waging a war on the probiotic concept here. All I’m saying is that at the moment, probiotics don’t live up to their reputation. There aren’t many probiotic supplements on the market today that I like. Hopefully, in a not so distant future, that will change.

Picture: Creative commons picture by jaqueline. Some rights reserved.


  1. I’m with you on this. Especially as someone who has histamine intolerance so anything fermented causes me problems.

    When you read some cases where people still don’t improve even after fecal transplants, it makes one wonder what use weak oral probiotics are. I think probiotic transplants is the only way this field will make any progress, and even then I expect the results will be limited.

  2. MacManiac says:

    Do you have any comments on the Russian Yogurt called Kefir? Apparently, some population groups have used it for generations with positive effects. Also, I have seen several studies suggesting that the Appendix may have a role as a safe harbour for the microbiome to be reseeded from. Any comment?

    • Hi MacManiac,

      As I said to Anthony, I’ve been planning to write an article on kefir. I hope to get around to it soon.

      As for the appendix, I’ve always questioned the long-standing dogma that it’s a redundant organ. As you point out, it seems to play an important role in microbiome reseeding. People who’ve removed their appendix are probably more susceptible to develop longstanding health problems following food poisoning and other events that disrupt the microbioal community of the gut, due to the fact that they haven’t got a reservoir of commensal bacteria.

  3. Hi, How about Kefir? I have been preparing my own daily for about a month and my gut finally feels good in the morning. Do you think I’m doing more harm than good? I know taking a break occasionally is advised and is what was traditionally done, but now I wonder if I’m taking too much (a glass per day)

    • Hi Anthony.

      I’ve been planning to write an article on kefir for some time. I hope to get around to doing so soon.

      Quick question for you: Do you still feel great when you stop drinking kefir, or do the beneficial effects quickly disappear?

  4. alec trivass says:

    hi erik
    read with interest, as usual. you mention that some strains are beneficial. which would you advise?
    also, are there any foodstuffs that would encourage good gut bugs?
    i know we inherit our initial supply of bacteria from our mothers, presumably thru breast milk when the young digestive system is less likely to destroy imbibed bacteria.
    in order for newly ingested bacteria to survive the stomach and small intestine, should medication be taken to suppress the digestive juices prior to ingestion?

    • Hi Alec,

      You may consider trying Mutaflor. It contains the bacterium E. coli Nissle 1917. Check out this article for more information.

      Pretty much all fruits and vegetables contain fermentable fibers. My recommendation would be to eat a species-appropriate diet that’s rich in several different types of plant foods. Make sure to include some onions, leeks, jerusalem artichoke, and/or other foods rich in inulin-type fructans.

      I would recommend against using medications that suppress stomach acid production. The only exception would be if you’re using some type of special medicine containing microbes and have been advised by your physician to take stomach acid suppressants.

  5. Hi, I found this very interesting and wondered if you had any advice for my situation. My one year old was on antibiotics and my doctor told me to give him probiotics for a while atterwards. As soon as I gave them to him his guts very very explosive and have never been the same since and he is in constant discomfort and very gassy. Do you have an ideas on how to repair his micro biome or is there nothing I can do?

    • Hi Claire,

      People (including children) who have a dysbiotic microbiota often experience gastrointestinal distress following the consumption of probiotics. My advice would be to slowly incorporate small quantities of homemade fermented foods into your son’s diet. Also, make sure he’s eating healthy and is exposed to bacteria associated with healthy humans, plants, and environments.

      Check out my articles on microbiome restoration (e.g., this one, this one) for tips on how you can improve the state of your son’s microbiota.

      Don’t give him probiotic supplements.

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