Rewilding: probiotics are not made for your gut

(#1 in Re-wilding blog series)

At least once per day I am asked, “which probiotic do you recommend?” by an acquaintance, friend or client who feels like their digestion or immune system “is just not right.” I take this as a good sign, that awareness of the enormous importance of gut health is rapidly growing. However, commonly the asker is left unsatisfied by my answer, “I don’t generally recommend probiotics for adults.” Unfortunately, there is no one panacea pill as the probiotic industry would like you to believe. Fortunately, there are other ways to recover your gut microbiome and health.

If you haven’t heard yet, your gut is home to a complex and dynamic community of microorganisms (see microbiome 101). These microbes and their end products have incredible sway over your health, as they influence nearly every aspect of your biology from your immune system and metabolism to your cognition and mental health. In fact, in 2017 the Cleveland Clinic named the microbiome the “next frontier in medicine” for the potential to “use the microbiome to prevent, diagnose and cure disease.”

And this is the reason I began researching the microbiome a decade ago. Yet, I have discovered through my research and practice, that most practitioners and patients alike are misguided in their approach to healing the ailing gut microbiome. This blog series titled “Re-wilding your Gut” describes both where we are going wrong, and a paradigm shift we can embrace to help our gut ecosystems recover and thrive.

So why then, would a gut microbiome researcher and specialist generally not recommend probiotics?

First and foremost, every gut microbiome is unique—more unique than even your fingerprint, because it is constantly changing with each choice you make during your day. Your entire life history—since before you were born—has led you to build this particular community of microorganisms. In a healthy adult gastrointestinal tract there should be a diverse community of microorganisms that contribute to nearly all of the body’s biological systems.

A healthy microbiome contains over 1000 different species of bacteria. Probiotics currently on the market are sourced from only 3-4 different genera—the ones that can easily be grown and stored—not the bacteria that will make your gut healthy and diverse like your hunter-gatherer ancestors. There is no one size fits all panacea: probiotic strains on the market simply will not restore your gut to a healthy, diverse state.

In order to restore and rebuild a depleted (or “dysbiotic”) microbiome, you must first understand who is in your gut, and what they are/not doing. Then I will show you how to selectively restore your indigenous microbial ecosystem, providing your body with the evolutionarily developed functions your body needs for optimal health. This blog series will help you better understand your gut microbiome and how you can restore its natural diversity and resilience.

But let’s get back to why probiotics on the market can’t and won’t work the magic that your gut requires. Imagine for a moment that your gut is a forest. When it is healthy, it is like a rainforest: the rich biodiversity has a complex and masterful ability to keep all species in balance. Blight may wipe out one kind of tree, but other seedlings emerge in their place with little impact on the overall ecosystem. Recovery is rapid and rich: the forest ecosystem incorporates the knowledge of each disease or stressor into its adaptive immune memory bank—making it even stronger as a whole.

Now let’s imagine a less-healthy gut is like a tree farm with only a few species of planted trees. If the soil lacks the integrity of diverse species, the entire farm can be devastated by one disease. The forest will take much longer to regrow, perhaps never achieving the biodiversity of a rainforest.

Our modern lifestyles, which represent a complete departure from our evolutionary history of millions of years, have radically altered our gut ecosystems. Our lifestyle, diet, sleep, medical care and environments have changed dramatically, resulting in a substantial loss of biodiversity and functionality of our gut microbiomes.1 2 This loss of important microbes leaves us vulnerable to chronic and infectious disease states. When we attempt to remedy our resulting ailments by supplementing with 3-4 genera of probiotics, we are effectively “monocropping,” or homogenizing our microbiome, not supporting the regrowth and resilience of our complex gut ecosystems.

Now, there exist important caveats to my “no probiotic” rule. For example, Lactobacillus and Bifidobacteria (the two main probiotic genera) are appropriate and important for pregnant and nursing mothers, infants, and young children, as these bacteria are indigenous species for infants, and critical for health, growth and development.3 Lactobacillus is also an indigenous species to a healthy vaginal microbiome, and utilizing specific strains can be extraordinarily beneficial for treating and preventing recurrent urinary tract infections (UTIs),4 5 yeast or candida,6 bacterial vaginosis (BV),7 Group-B Strep (GBS),8 and even preventing STDs9 (stay tuned for future blogs focusing on women’s vaginal health and probiotics). Finally, there are certain conditions in adults that may require a time-limited dose of specific strains of probiotics, but generally the adult human gut is not the place to be consistently introducing these specific species of bacteria.

There are other issues with probiotics for adults. For example, many probiotic strains do not survive transit through adult stomach acid to make it into the large intestine. Worse, the strains that do survive the stomach are not indigenous to the adult gut, and often cannot take up residence in your gut because your native microbes will inhibit their colonization.

There is however, evidence that certain strains albeit transitory, can influence host gene expression and immune function. This takes a careful understanding of a person’s current microbial profile, ailment and the selection of targeted strains to influence a specific outcome.

Finally, a recent Israeli study showed that treating the gut with probiotics after antibiotics actually delayed the normal recovery process of the gut microbiome in mice and humans, and particularly the administration of Lactobacillus (one of the most commonly used probiotic bacteria).10

My suggestion is, unless you have a specialist working with you to recommend a targeted probiotic for a specific health outcome, save your money: probiotics are not cheap and there are much more efficient ways of tending to the diversity of your micro-ecosystem.

I predict that in five years we will have probiotics containing “keystone species” that truly can make a difference for the adult gut. But what do we do NOW for our ailing digestive system? Don’t despair; you can reclaim your rightful diversity, and believe me, your body wants to. But this requires a paradigm shift in how we view and treat our bodies, and how we understand the diseases that ail us.

Stay tuned for the next article in my “Re-wilding” blog series…


  1. Schnorr, S. L. et al. Gut microbiome of the Hadza hunter-gatherers. Nat Commun 5, (2014). 
  2. Sonnenburg, E. D. et al. Diet-induced extinctions in the gut microbiota compound over generations. Nature 529, 212–215 (2016). 
  3. Sheets, G. M. “The Developmental Ecology of the Infant Gut Microbiome.” Emory University, 2017. ProQuest
  4. Beerepoot, M. A. J. et al. Lactobacilli vs antibiotics to prevent urinary tract infections: a randomized, double-blind, noninferiority trial in postmenopausal women. Arch. Intern. Med. 172, 704–712 (2012). 
  5. Hanson, L. Protective effects of breastfeeding against urinary tract infection. Acta Pædiatrica 93, 154–156 (2004). 
  6. Seta, F. D. et al. Lactobacillus plantarum P17630 for preventing Candida vaginitis recurrence: a retrospective comparative study. European Journal of Obstetrics and Gynecology and Reproductive Biology 182, 136–139 (2014). 
  7. Anukam, K. C. et al. Clinical study comparing probiotic Lactobacillus GR-1 and RC-14 with metronidazole vaginal gel to treat symptomatic bacterial vaginosis. Microbes Infect. 8, 2772–2776 (2006). 
  8. Ho, M. et al. Oral Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 to reduce Group B Streptococcus colonization in pregnant women: A randomized controlled trial. Taiwanese Journal of Obstetrics and Gynecology 55, 515–518 (2016). 
  9. Martin, H. L. et al. Vaginal Lactobacilli, Microbial Flora, and Risk of Human Immunodeficiency Virus Type 1 and Sexually Transmitted Disease Acquisition. J Infect Dis 180, 1863–1868 (1999). 
  10. Suez, Zmora and Zilberman-Schapira, et al. “Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT.” Cell 174, no. 6 (September 6, 2018): 1406-1423.e16.

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