In my previous article here on Darwinian-Medicine.com, I made the case that certain current implementations of the probiotic concept are pernicious. That post is the last in what has now become a fairly sizeable list of articles I’ve written about the potential downsides of probiotic supplementation; all of which are built on a similar line of reasoning. My arguments have mostly been theoretical in nature and based on my understanding of human-microbe interactions, ecosystem dynamics, and the nature of probiotics. I’ve also talked about my own experience with probiotic supplementation and the ideas and thoughts of some leading microbiome researchers.

I haven’t been able to produce compelling evidence derived from experimental studies though, for the simple reason that there’s very little research to go on in that area. The vast majority of studies that have been conducted to date have focused almost exclusively on the potential benefits of using probiotics, while largely ignoring the potential downsides. However, new research, which I came across shortly after I’d published my last piece on probiotics here on the site, doesn’t conform to this pattern. It sheds light on the dark side of probiotics and supports the statements I’ve been making regarding probiotics’ ability to undermine the development and maintenance of a healthy gut microbiota.

Probiotic supplementation may undermine, rather than stimulate, microbiome restoration processes

The research, conducted by a group of Israeli investigators, was published late last year and consists of two studies, both of which highlight a need for a more in-depth evaluation of the potential dangers of so-called probiotics (1, 2). Of the two studies, the one that examined the impact of probiotic supplementation on post-antibiotic microbiome reconstitution is the most relevant to the things I’ve talked about here on the site.

It’s well established that the use of antibiotics, in particular broad-spectrum ones, is detrimental in the context of gut microbiota diversity and resilience. Antibiotics may wipe out keystone species and imbalance the ecosystem, potentially giving pathogens a field day. In turn, this sets the stage for inflammation and illness.

The dysbiotic state that is produced by long-term antibiotic use is representative of gut dysbiosis in general, in the sense that a similar pattern of disturbances is present across the board with respects to microbiome disruption and can occur as a result of other imprudent practices, such as the consumption of a highly processed, sugary diet. This general pattern of microbiota depletion and instability is inherent to a number of disease states and causally involved in many disease processes; hence, it goes without saying that it’s important to elucidate what constitutes the best approach for transforming this pestiferous condition into an amicable one.

Probiotic supplements have long been thought to be beneficial in this respect; however, this new study questions the soundness of this assumption. It found that the gut microbiomes of people who were given a multi-strain probiotic following antibiotic use didn’t recover as quickly as the microbial communities of individuals who were either given nothing or subjected to autologous fecal microbiome transplantation. And it wasn’t just a small difference. The researchers found that the probiotics kept the intestinal mucosal microbial communities of the participants from recovering for up to 6 months. In contrast, the participants whose guts were left to their own devices largely recovered within a few short weeks. Not surprisingly, those who were given an infusion of their own fecal microbiota, collected prior to the antibiotic intervention, recovered even more rapidly. For them, it only took a couple of days to regain a sense of normalcy.

Here’s how the researchers summarized their findings:

Compared to spontaneous post-antibiotic recovery, probiotics induced a markedly delayed and persistently incomplete indigenous stool/mucosal microbiome reconstitution and host transcriptome recovery toward homeostatic configuration, while aFMT [autologous fecal microbiome transplantation] induced a rapid and near-complete recovery within days of administration. In vitro, Lactobacillus-secreted soluble factors contributed to probiotics-induced microbiome inhibition. Collectively, potential post-antibiotic probiotic benefits may be offset by a compromised gut mucosal recovery, highlighting a need of developing aFMT or personalized probiotic approaches achieving mucosal protection without compromising microbiome recolonization in the antibiotics-perturbed host. (1)

The results of this new research support the idea that probiotic supplementation is inadvisable in many cases

The findings of the above study support the statements I’ve put out regarding the potential complications that may arise as a result of probiotic supplementation. They fit nicely with the Band-Aid and crutch analogies I’ve been making, both of which center on the idea that probiotics can cover up some of the symptoms of a distorted, fragile gut ecosystem by providing some of the same functions as a normal, healthy gut microbiota, but that they are unlikely to bring about a rectification of the ecosystem in question. Not only that, but they may undermine repair processes by inhibiting diversification and stabilization of the ecosystem.

In lacto-fermented foods such as yogurt and kimchi, lactic acid bacteria shape their local environment in such a way that it becomes inhospitable to a number of other microbes, including acid-intolerant fungi. An excessive intake of such bacteria may give rise to a similar, albeit less rigid, situation in the gut.

Furthermore, the study verifies that probiotic lactic acid bacteria produce compounds that hinder the growth of various types of microbes that are commonly found in human intestines, some of which may be essential for maintaining a healthy gut. Lactic acid bacteria are an important part of normal, healthy gut microbiotas and can help keep pathogens at bay; however, that doesn’t necessarily mean that it’s smart to consistently bombard one’s gut with a handful of selected strains of such bacteria. It just becomes too much of a good thing. This principle is applicable pretty much across the board in life. Some sun exposure is good for you, but if you lay out on the beach in the middle of a sunny day for many hours, chances are you’ll get burned.

The key point is that more isn’t necessarily better when it comes to probiotics. This is true irrespective of whether they come in the form of probiotic supplements or fermented foods. Such products can deliver some potentially useful bugs to one’s gut; however, if they are overused, they may undermine, rather than enhance, the stability and diversity of one’s gut microbiota. This is particularly true if one consistently brings large numbers of probiotics into one’s gut for a long period of time.

Finally, the study shows that probiotic colonization is enhanced post-antibiotic use. This is exactly what one would expect based on what we know to be true about the dynamics of living systems and is consistent with what I’ve been saying here on the site, in the sense that I’ve repeatedly suggested that people who harbor a dysbiotic, fragile gut microbiota are affected to a greater extent by probiotic supplementation than people who harbor a resilient, diverse microbiota. In the disorganized guts of the former, more niches are open for exploitation and there’s less competition, which helps explain why probiotics have an easier time setting up shop there and exerting a marked influence. This is obviously relevant to discussions about probiotic supplementation, as the people who are generally drawn to probiotics are individuals who suffer from gut problems.

Primary takeaway

The evolutionarily novel practise of consistently infusing large numbers of a handful of isolated microbial strains into one’s gut may hinder, rather than support, the development and maintenance of a healthy gut microbiota. The impact of such microbial infusion is particularly potent in cases where the microbial communities that are being targeted are imbalanced and feeble, for example as a result of long-term exposure to broad-spectrum antibiotics. Instead of taking a particular probiotic supplement day in and day out or trying to get as many probiotics into one’s gut as possible, it’s generally better for people who harbor a damaged gut microbiota to work on gradually incorporating a small number of a diversity of microbes derived from many different sources, such as for example healthy humans, fermented vegetables, and fresh fruits and vegetables, into their guts. Certain types of probiotic supplements may also be of some small value in this respect; however, using the same supplement for long periods of time is likely to do more harm than good.