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Do Probiotic Supplements Stick Around In the Gut?

People assume that taking probiotics results in the beneficial probiotic bacteria colonizing and living in the gut (or sinuses when using L. sakei). It is common to hear the phrase "take probiotics to repopulate the gut" or "improve the gut microbes". The human gut microbiota (human gut microbiome) refers to all the microbes that reside inside the gut (hundreds of species). Probiotics are live bacteria, that when taken or administered, result in a health benefit. But what does the evidence say?

First, it is important to realize that currently supplements and foods contain only a small variety of probiotic species, with some Lactobacillus and Bifidobacterium species among the most common. But they are not the most common bacteria found in the gut. And very important bacteria such as Faecalibacterium prausnitzii (a reduction of which is associated with a number of diseases) are not available at all in supplements. One problem is the F. prausnitzii are "oxygen sensitive" and they die within minutes upon exposure to air, a big problem when trying to produce supplements.

The evidence from the last 4 years  of L. sakei use for sinusitis treatment is that for some reason, the L. sakei is not sticking around long-term and permanently colonizing in the sinuses. My family's experiences and the experience of other people contacting me is that every time a person becomes sick with a cold or sore throat, it once again results in sinusitis, and then another treatment with a L. sakei product is needed to treat the sinusitis, even though less is needed over time. And of course this has been a surprise and a big disappointment. [See Dec. 2020 update below.]

The same appears to be true for probiotics (whether added to a food or in a supplement) that are taken for other reasons, including intestinal health. Study after study, and a review article, finds that the beneficial bacteria do not colonize in the gut even if there are health benefits from the probiotics. That is, there may be definite health benefits from the bacteria, but within days of stopping the probiotic (whether in a food or a supplement) it is no longer found in the gut. Researchers know this because they can see what bacteria are in the gut by analyzing (using modern genetic sequencing tests) what is in the fecal matter (the stool).

However, the one exception to all of the above is a fecal microbiota transplant (FMT) - which is transfer of fecal matter from one person to another. There the transplanted microbes of the donor do colonize the recipient's gut, referred to as "engraftment of microbes". Some researchers found that viruses in the fecal matter helped with the engraftment. So it looks like more than just some bacterial strains are involved. Another thing to remember is that study after study finds that dietary changes result in microbial changes in the gut, and these changes can occur very quickly.

[Dec. 2020 update: A few recent studies are now suggesting that if a person takes or uses a bacterial species that naturally occurs in the body and is depleted, than it may stick around for a while - this is colonization, even if only short-term. We also find this occurring with L. sakei - while we may need to use it now and then, this is occurring less frequently over time, and we need to use a much smaller amount when needed. Colonization! Overall, there has been major improvement of our sinuses over time - and yes, they feel great.]

From Gut Microbiota News Watch: Learning what happens between a probiotic input and a health output

What scientists know is that probiotics in healthy individuals are associated with a number of benefits. Meta-analyses of randomized, controlled trials show that probiotics help prevent upper respiratory tract infections, urinary tract infections, allergy, and cardiovascular disease risk in adults. But between the input and the output, what happens? A common assumption is that probiotics work by influencing the gut microbe community, leading to an increase in the diversity of bacterial species in the gut ecosystem and measurable excretion in the stool.

But this theory doesn’t seem to be true, according to a recently published systematic review by Kristensen and colleagues in Genome Medicine. Authors of the review analyzed seven studies and found no evidence that probiotics have the ability to change fecal microbiota composition. So even though individuals in the different studies were ingesting live bacterial species, the bacteria didn’t stick around to increase the diversity of the gut fecal microbiota.

Do probiotics alter the fecal composition of healthy adults? The answer seems to be no,” says Dr. Mary Ellen Sanders, Executive Science Officer for the International Scientific Association for Probiotics and Prebiotics (ISAPP)....Dr. Dan Merenstein, Research Division Director and Associate Professor of Family Medicine at Georgetown University Medical Center in Washington, DC (USA), agrees. “Initially when probiotics were studied, some people expected to see permanent colonization. We now realize that is unlikely to occur,” he says. “This study shows that the probiotics tested to date do not result in overarching bacterial community structure changes in healthy subjects. But clinical effects are clearly demonstrated for probiotics, and likely some are mediated by microbiome changes.

At issue, then, is not what probiotics do for healthy individuals, but exactly how they work: the so-called ‘mechanism’. Sanders, who described some alternative mechanisms in her BMC Medicine commentary about the Kristensen review, points out a logical error in news stories worldwide that covered the article: the assumption that if probiotics fail to change the microbiota composition, they fail to have any health effects. Sanders emphasizes that probiotics might work in many possible ways. “Probiotics may act through changing the function of the resident microbes, not their composition. They may interact with host immune cells,” she says. “They may inhibit opportunistic pathogens that are not dominant members of the microbiota. They may promote microbiota stability… .” 

14 thoughts on “Do Probiotic Supplements Stick Around In the Gut?

  1. Dan

    I'm confused. Some bacteria must be commensal or colonize or else we'd lose those trillions of bacteria that make up the gut. Perhaps some of these studies results were due to relatively low doses used?

    I found this study VERY interesting:

    Especially this quote: "The pollen season induced a reduction in Bifidobacterium, Clostridium and Bacteroides..."

    So, the trigger, be it pollen, food allergen, infection, stress, etc., may cause a reduction in the species needed to deal with said trigger.

    Also, people weren't taking these probiotics, but had a certain level which went down when pollen season arrived. That suggests those species had colonized the gut doesn't it?

    They go on to say that supplementing didn't help raise the lowered numbers, but DID help alleviate allergy symptoms. So perhaps the doses were too low to raise the counts?

    1. Sima

      The issue is that probiotic strains taken as a supplement do not stay around after you take them - within a week of stopping probiotic supplements they are no longer detected in the stool. Each bacterial species has many strains (L. sakei has over 200 strains) and the laboratory strains can be easily measured in stool samples precisely because they are different from the strains already in the gut. The species already living in the gut can be nurtured and fed by foods we eat, but affected in a negative way by allergies, viruses, food poisoning, poor diet, anything that causes inflammation. etc.
      There are theories, but researchers don't really know how the ingested probiotics do their positive effects on the person ingesting them. One could say that the ingested probiotics are giving a "helping hand" to the person ingesting them.

      Thanks for the link. Looking at the study results, the few positive effects were pretty minor, and the probiotic group actually had an increase in eye allergy symptoms. And both groups continued taking antihistamines during the study. They also discuss how each allergy study is trying out different bacterial species.
      It looks like they are on the right track, but other combinations or species may be better. See the recent post on a new study of probiotics for seasonal allergies.

      1. Dan

        Certainly some strains taken as supplements don't stay around for long, but how can there be any in the gut in the first place if some didn't colonize?

        Thanks for pointing out the details in that study. I didn't even realize the full paper was available. Talk about flawed. Acidophilus is a well-known histamine producing strain. No wonder the eye symptoms got worse.

        I'll check out your link...thanks. 🙂

        1. Sima

          The fact that ingesting a few species of bacteria in a supplement NOT colonizing in the gut has been a big surprise to researchers. Right now eating foods that feed and nurture existing bacteria - encouraging the growth through diet and lifestyle changes (such as exercising, not smoking) - is the best method to change your gut bacteria and other microbes. This is why microbiologists eat healthy foods, especially fruits, vegetables, nuts, etc, and typically don't take probiotic supplements.

  2. Russ

    Could it be because of our highly sanitised environment and life style? With antibiotics in the meat products we consume or the bug killing hand soaps that we use in the bathroom for example.

    1. Dan

      Yup. There are studies that show the link between 'too much' sanitation, and the increase in IBS, Crohn's, colitis, etc...

  3. Marisa De More

    The fecal implant research is interesting but scary ... what if it comes with a load of stuff the recipient doesn't want, such as latent viruses or other nasties? I also read somewhere that fecal implants only last around 18 months before the new colonies died off too.

    I don't mean to be crude here, but I wonder if anyone has tried pushing a probiotic capsule up their bottom to see if it colonizes the gut better that way, instead of via the mouth? Just a thought ...!

    1. Sima

      Yes, your concerns are the main concerns about fecal microbiota transplants (FMT) - what viruses, etc are also being transplanted?
      Research shows that the transplanted microbes can stick around for years, and change the microbial community of the recipient. (here and here). Stay tuned for longer studies.

      It shouldn't make any difference how one gets the probiotics in capsules - they survive the stomach's acidity, go through the intestines, and eventually are excreted (they are measured in feces with modern genetic sequencing).
      The probiotics sold in the marketplace only have a few species and they're not even the main ones in the gut. The really important beneficial ones such as Faecalibacterium prausnitzii are currently not yet available because it can't live more than a few minutes with exposure to air.

    1. Sima

      Don't know - but one would expect it to be part of the stool transplant.
      Faecalibacterium prausnitzii only lives a few minutes when exposed to oxygen, which is why it isn't in any supplement.
      But research finds that when people start eating a diet rich in whole grains, fruits, vegetables, seeds, nuts, legumes (real foods high in fiber), and cut back on highly processed food (Western diet) that the levels of this beneficial bacteria in the gut really increase.
      Also, when people increase their physical activity levels and/or exercise to at least 2 1/2 hours per week.

  4. Marcia

    I suppose you've heard this, but as of 2021, there's now a supplement available that contains f. prausnitzii. I tried it once early this year -- SUPER pricey -- but it did help decrease my belly fat during the two months I took it. No doubt it would help if I'd fed it the right probiotic foods. Belly stopped shrinking within a couple weeks of stopping... 🙁

    1. Sima

      Surprised to hear that one is available.
      The problem with F.prausnitzii is that it dies after only a few minutes of exposure to air.
      Some researchers feel that even some dead probiotic species have benefits, but they may be different than live probiotic effects.
      An easy way to increase F. prausnitzii amounts in your gut is by increasing fiber rich foods such as fruits, vegetables, whole grains, seeds, legumes, and nuts.


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