Why You Can’t Drug the Microbiome Into Compliance

pillsWe humans are always looking for quick and simple solutions to our problems. When we have the choice between a comfortable path, which is flat and easy to travel, and a path that is steeper and harder to travel, but that eventually gets us to a higher point than the comfortable one, we usually choose the former; in large part because we tend to value immediate benefits over future gains.

The pitfall of mainstream medicine

The aforementioned ideas and generalizations are part of the underlying premise that mainstream medicine rests upon.

When people go to their doctors with a problem, they don’t want a prescription that includes a list of diet and lifestyle changes; because making these changes tend to require work and effort, and the results may not be immediate. Rather, most patients want solutions that are quick and easy. This is part of the reason why pharmaceutical drugs of various kinds are an essential component of most conventional medical treatments and therapies.

It doesn’t get easier than popping a couple of pills in the morning.

This is truly the pitfall of mainstream medicine. Drugs have proven to be effective in the treatment of many acute, infectious diseases; however, when it comes to the chronic disorders and health problems that plague us in the modern world, their usefulness is markedly more limited. Prescription medicines rarely address the root causes of chronic disease; rather they just mask some of the symptoms of ill-health. For example, a drug may, temporarily, reduce your LDL cholesterol, but it won’t fix the underlying problems that caused the levels of this fatty substance to spike in the first place.

This brings us over to the microbiome. By now it’s well established in the scientific literature that the microbiome of the modern, industrialized man differs substantially from those harboured by hunter-gatherers and people living in non-industrialized settings (1, 2, 3). Moreover, it has become clear that a lot of people in contemporary, westernized nations carry a dysfunctional microbiota, lacking in diversity and stability, and that this is one of the reasons why chronic health disorders such as inflammatory bowel syndrome, major depression, and cardiovascular disease have increased rapidly in prevalence lately.

This begs the question: How can we fix this microbial mess?

Some writers, health practitioners, and nutritionists (including myself) have largely focused on diet and lifestyle, making the case that these are the key factors people should have in mind when they set out on the journey towards a healthier microbiota. However, others, in particular manufacturers and sellers of products aimed at manipulating the microbiota, place more emphasis on supplements and drugs.

Microbiome medicines

Over the past decade, microbiome research has taken off, and numerous newspaper articles, e-books, and blog posts covering topics related to gut health, microbes, fermented foods, and dietary fiber have appeared online. Given this, it was inevitable that large companies and other entities that are looking to make a buck got involved in the microbiome field.

As I see it, this is both a good and a bad thing. The good thing is that some, if not many, of the microbiome drugs and advanced probiotics that are coming down the pipeline may prove useful in the treatment of a range of health disorders. I’m not against using pharmaceutical drugs and supplements per se. If a company comes up with a product that does indeed work, I would not hesitate to use it or prescribe it to clients. Moreover, I’m looking forward to seeing the next generation of probiotic drugs and supplements hit the market, because these products may help us restore the diversity of our modern microbiomes to a level that is closer to the evolutionary norm for our species.

That said, I certainly don’t think it’s a good idea to rely exclusively on these modern inventions. The bad thing about filling up grocery stores, pharmacies, and health foods stores with foods and pills that contain a carefully selected mix of bacteria and/or fibers is that some people may be led to believe that as long as they use one or more of these products, their microbiome is in good shape. Perhaps needless to say, this is not the case…

Diet or drugs?

A second generation probiotic supplement may help you increase the diversity of your microbiota; however, it certainly won’t, by itself, provide you with a healthy, flourishing community of gut microbes. You can take as many pills as you want, it’s not going to result in the development of a healthy microbiota if you eat a low-fiber, processed diet, use drugs with antibiotic properties, and/or otherwise expose your body to stimuli that change the gut environment in such a way that a microbiome that conflicts with the human genome gets a chance to develop.

I think this is one of the really fascinating, but also disturbing, things about the microbiome. Pretty much everything we do affects the trillions of microorganisms that live in and on our body in some way. When we wash our hands with soap prior to a meal, the skin microbiota changes, when we take a cold shower, bacteria are “activated”, providing us with increased cold tolerance, and when we eat a meal, the community of microbes found in the gut changes as the food enters into the intestine and substrates become available for digestion.

A capsule containing a mix of bacteria or fiber can induce some changes in the microbiota; however, these alterations may be small compared to those that can be obtained through diet changes. A microbiota that is matched to a western, low-fiber diet will be resistant to change unless the diet is modified. Simply taking a microbiome drug may nudge the microbial community in the right direction, but it’s not going to result in a complete makeover.

Last words

In the past, we humans have made the mistake of thinking that we can solve our health problems by making and using new drugs. The problem with this strategy is that it rarely solves our problems; it just masks them. If the problems are indeed removed, other, often more severe, troubles tend to arise in their wake.

Let’s try to learn from these previous mistakes.
Let’s not make the mistake of thinking that we can drug our microbiomes into compliance.

Picture: Creative Commons picture by Laura Gilmore. Some rights reserved.


  1. Hi Eirik. You make some good points here. People seldom realize it, but the only thing that can heal the body is the body itself. All drugs are pretty much a Band-Aid that only addresses symptoms until normal healing can take place. Some drugs actually suppress the immune system and delay the healing response, which makes them a poor idea. That said, I do think a good probiotic can help with some issues such as IBS, as far as offering emergency relief, but it shouldn’t be considered a cure. A healthy microbiome (via proper diet and healthier lifestyle) set the stage for actual healing versus simply masking the problem.

  2. tedhutchinson says:

    Humans evolved near the Equator with access to full body UVB exposure throughout the day. UVB acts on 7 dehydroCHOLESTEROL near the skin surface to produce CHOLEcalciferol, Vitamin D3. So it fair to assume from dawn to dusk unlimited amounts of vitamin d3 were available to permeate through the body and we know modern humans living traditional lives near the equator typically have 25(OH)D levels near the 50ng/ml 125nmol/l mark.
    Effects of high doses of vitamin D3 on mucosa‑associated gut microbiome vary between regions of the human gastrointestinal tract
    http://link.springer.com/article/10.1007%2Fs00394-015-0966-2 free full text at link.
    Here they used the equivalent of a daily dose of 140 IU/kg bodyweight,for one month followed by a daily dose of 70 IU/kg bodyweight which brought participants to 55ng/ml 130nmol/l.
    They were looking that effect of daily cholecalciferol on both pathogenic and beneficial gut flora. Not surprisingly even over this short trial they could see movements towards the increase diversity and greater range of gut flora typically found in indigenous peoples.
    It may be that to achieve a paleo type gut flora we should attain and maintain paleo levels of 25(OH)D with paleo amounts of daily cholecalciferol. It is only at or above 50ng/ml 125nmol/l that significant measurable amounts of cholecalciferol are found in tissue (and human milk) and the presence of cholecalciferol not only maximizes it’s anti inflammatory potential but also impacts on endothelial barrier function.
    Dietary Vitamin D and Its Metabolites Non-Genomically Stabilize the Endothelium.

  3. Alessio says:

    Everything is just for business. Business over business above everything. Who really cares about your health? Sincerely, who?

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