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Probiotics are not harmless. Actually, in certain situations, they may cause a lot of damage. The term probiotics—which comes from Latin, meaning “pro life”—is somewhat misleading, because probiotics don’t always promote life—sometimes, they cause death. Certain probiotics, including various types of lactic acid bacteria, produce powerful compounds (like bacteriocins), toxins that inhibit or kill other microbes. If you regularly ingest large quantities of these critters, you may be damaging your gut microbiota, which can initiate a range of adverse health effects.

Microbes Are Ruthless

We humans live in a bubble. Over the past 10,000 to 15,000 years, we’ve gradually separated ourselves from nature. Having lost touch with the natural world, it’s easy for us to forget that we, like all other organisms on this planet, are a part of a complex, global ecosystem. All of the members of this system are fighting to survive—competing among each other and adapting 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 not possessing the traits required to win the competition wither and die out.

The same types of wars are fought within the invisible, microbial kingdom here on Earth. Microbes are no different than other organisms; 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 conflicts polarizing larger organisms.

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 an extensive inventory of toxins, acids and other compounds, some of which aid their survival by blocking the growth and profusion of 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 was not we humans who designed antibiotics such as penicillin, this was achieved by microbes. Penicillin was derived from fungi—it wasn’t created from scratch in a lab.

What you may not know, however, is that it’s not just the stereotypical pathogens that produce life-damaging toxins, some microorganisms that are generally thought of as friendly do equal harm. For example, some types of probiotic lactobacilli have been shown to produce bacteriocins that inhibit or kill certain other types of bacteria.1 Not only harming closely related species, but also unrelated critters.

Unlike the toxins that are produced by pathogens such as C. difficile, the toxins that probiotics produce don’t have a direct, harmful effect on the human body. If they had, the microbes couldn’t have been classified as probiotics. However, the compounds that these probiotics produce may inhibit the growth of some types of beneficial gut bacteria, thereby compromising the stability, diversity, and resilience of the gut microbiota.1

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 your gut microbiota and the quantity of probiotics consumed.

Probiotic Overconsumption

The consumption of large quantities of probiotics is an evolutionarily novel behavior that can disturb and destabilize the gut ecosystem. It wasn’t until after the Agricultural Revolution that we humans started producing and consuming large quantities of fermented foods, such as wine and yogurt. Our Paleolithic forebears may have indeed eaten small quantities of fruits and berries that had started to ferment, but, being unfamiliar with controlled fermentation, they didn’t have the tools or knowledge to make large batches of fermented foods. This notion is supported by anthropological research, including studies showing that contemporary hunter-gatherers primarily consume fresh food.2, 3, 5

It’s certainly possible that some of our late Paleolithic ancestors knew how to control the fermentation process and consumed fermented foods with some regularity, but as a whole, I think it’s safe to say that fermented foods were not an essential part of Paleolithic human diets.

Probiotic supplements and food products made using industrial starter cultures are obviously even more recent augmentations of the human diet. It’s only over the past few decades that these types of nutritional products have become widely available to the public. On its own, 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 choosing to incorporate these products into our regular 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.2, 4, 6-8

Any time the environment of an ecosystem changes, the ecosystem will also 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. The influx of large numbers of one or more organisms represents an environmental change. In some instances, these new organisms may perturb the homeostasis of the existing community. For example, if you put a lot of large predators into a rainforest, the ecosystem in that area will likely change dramatically. The invasive creatures may seek to exploit niches that are already occupied by the system’s original inhabitants, and, in their effort to proliferate, the predators may attack, kill, and perhaps wipe out completely the other animal species.

Though obviously different from larger organisms, microbes also adhere to the laws of evolution. When new microbes are inserted into an ecosystem, things are bound to happen. The immigrants may produce certain foreign compounds 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 this new milieu, others, however, may simply pass through. Unfortunately, many probiotics do not linger around for long, entering and exiting the human gut relatively quickly, because they aren’t capable of colonizing the intestine.

Key Takeaways

Taking a good probiotic supplement 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 your biome is degraded and dysbiotic.

Keep in mind: The goal is not to flood the gut with probiotics, but rather to bring in new, beneficial bugs that are capable of growing in the gut.


1. A. Berstad, J. Raa, T. Midtvedt, and J. Valeur. ‘Probiotic Lactic Acid Bacteria – the Fledgling Cuckoos of the Gut?’ Microb Ecol Health Dis 27 (2016): 31557.

2. Pedro Carrera-Bastos, Maelan Fontes-Villalba, James H O’Keefe, Staffan Lindeberg, and Loren Cordain. ‘The Western Diet and Lifestyle and Diseases of Civilization.’ DovePress (2011).

3. L. Cordain, S. B. Eaton, A. Sebastian, N. Mann, S. Lindeberg, B. A. Watkins, J. H. O’Keefe, and J. Brand-Miller. ‘Origins and Evolution of the Western Diet: Health Implications for the 21st Century.’ Am J Clin Nutr 81 (2005): 341-54.

4. G. L. Hold. ‘Western Lifestyle: A ‘Master’ Manipulator of the Intestinal Microbiota?’ Gut 63 (2014): 5-6.

5. D. Lieberman. The Story of the Human Body: Evolution, Health, and Disease (Vintage, 2014).

6. Staffan Lindeberg. Food and Western Disease: Health and Nutrition from an Evolutionary Perspective (Wiley-Blackwell, 2011).

7. I. A. Myles, ‘Fast Food Fever: Reviewing the Impacts of the Western Diet on Immunity,’ Nutr J 13 (2014): 61.

8. B. Ruiz-Nunez, L. Pruimboom, D. A. Dijck-Brouwer, and F. A. Muskiet, ‘Lifestyle and Nutritional Imbalances Associated with Western Diseases: Causes and Consequences of Chronic Systemic Low-Grade Inflammation in an Evolutionary Context.’ J Nutr Biochem 24 (2013): 1183-201.