Probiotics and Gut Health: Is Your Probiotic Harming Your Gut?

Probiotics and Gut Health: Most people reach for probiotics as a way of promoting gut and whole-body health, but today we explore the reasons why you may want to do just the opposite. We discuss the latest science of the microbiome and how it relates to dysfunction and disease.

Why Gut Health Matters

Modern science has uncovered that approximately ¾ of your immune system resides in the intestinal tract (your gut). Your gut flora refers to the microbial diversity of your gut, which runs upwards of 500 species. Whether your gut promotes ‘good’ or ‘poor’ health relies heavily on this diversity, and if your microbiome is predominantly ‘good’ or ‘bad’ bacteria. [1]

The impact of gut health influences an array of bodily functions, including:

  • How your body extracts and absorbs nutrients and the general quality of your digestion
  • The way in which your genes express themselves
  • How your central nervous system signals (which impacts everything from energy, mood, and sleep)

Probiotics and Monoculturing Dysbiosis

Your gut microbiome is as diverse as the ecosystem of a dense jungle or underwater reef. The average gut contains 500 species of bacteria, but a genuinely thriving one should contain 20,000 to 30,000 different species existing symbiotically in your digestive tract. Different strains are working in various ways to promote digestion, hormonal health, gene expression, and more. [2]

These hundreds to thousands of species enter the gut via the things you ingest, and the environments you expose yourself to. The problem with consuming probiotic capsules, especially long term, is that out of the hundreds of thousands of possible strains, we’re ingesting three, five, maybe ten strains at a time. So whether or not each capsule contains 60 billion CFUs (copies) of the narrow strains, it is ultimately still only introducing a minimal spectrum of species into the gut. In time, the chronic exposure to such a restricted variety ends up creating a narrow dysbiosis in the gut.

Dysbiosis is simply an imbalance between the types of organisms present in a person’s natural microflora, especially that of the gut, thought to contribute to a range of conditions of ill health. [3] The key to a healthy gut is a diversity of the good stuff, and by chronically consuming such a narrow range of bacteria, an imbalance is created, and poor health may ensue.

Probiotics and Gut Health: How to Develop a Diverse Microbiome


One of the greatest things you can do to boost microbial diversity in your body is to get out into nature and breathe. You can take in spores into your body through your breath, and different landscapes in nature offer thousands of various latent spores ready to inoculate your body with good bacteria. [4]

Gardening or farming is one great way to supercharge your microbiome because playing in the dirt like that helps rustle up the dirt’s good bacteria. Walking barefoot in the forest is another, so is lying on the beach or swimming in the lake or ocean.

Probiotics and Gut Health: Appropriate and Prepared Ancestrally Foods

Understanding what foods do and don’t work for your microbiome is at its core bio-individual because your body’s dietary needs are your own. Dependent on factors like your ancestry, your current state of health, your activity and stress levels, and more: a diet that works for you may not work for someone else.

As a general rule, you want to opt for whole, organic foods. Tailoring from there will factor in things like food intolerances, and your lifestyle needs. Fermented foods are generally great (unless you’re dealing with severe SIBO, in which case you may need to heal before introducing too many ferments).

Wild fermented foods like sauerkraut, kefir, yogurt, kombucha, and kvass introduce an array of live food-based bacteria into your biome. They help balance out the good to the bad ratio in favor of the good stuff. [5]

Some foods are universally unfriendly to gut microbes, and should always be avoided. They include:

  • Refined vegetable oils (like canola, soybean, corn, or sunflower oil)
  • Refined sugars
  • Processed flours and grains
  • Pasteurized and homogenized dairy, especially when it is rendered ‘low-fat.’
  • Processed meats or grain-fed ruminant meat (grain-fed beef, highly processed meats like conventional salami, hot-dogs, etc., that contain artificial flavors, preservatives, and colors)

Rotate, Rotate, Rotate!

If you are going to take a probiotic, the key is rotation. Consuming one specific brand of probiotic (even if it has 5-10 strains in the formula) will ultimately lead to a narrowing of your gut microbial diversity. Knowing that the gut can/ should have over 500 strains, introducing such a narrow spectrum regularly and chronically will do nothing at best, and harm at worst.

When making a switch, opt for soil-based organisms first. These types of probiotics are the kind that does most of their functioning in soil. Spore-based probiotics, on the other hand, use the soil as a playground in which they move from host to host. Both are useful, but soil-based strains are highly bioavailable and compatible with human health. [6]

Lower Stress

Stress (and the cortisol released as a result), is a major destroyer of the gut microbiome. The connection between stress and gut health is a chicken and the egg situation: whereby stress influences the microbiome. An imbalanced microbiome causes inflammation and stress. [7]

Managing stress, in general, is essential to promoting whole-body health. Stress can be physical, chemical, or emotional– so be mindful of all the areas in your life that contribute to stress. As humans, we are very resilient and can take on a lot, but the problem lies in the low levels of chronic stress that take a toll on our body and mind day in and day out.

Sleep Quality

Finally, sleep is a non-negotiable for anyone wanting to cultivate a healthy microbiome. Sleep deprivation goes hand in hand with drastically lowered gut diversity. Adequate sleep is essential for rest and repair, and (being so intertwined with the immune system), it’s necessary to give your GI tract the time to rest adequately. [8]

Sleep quantity is essential, but even more important is the quality. Getting enough deep sleep requires good sleep hygiene. Some key things to increase deep sleep include a regular sleep/ wake cycle, gaining exposure to daylight as soon as you wake up, avoiding too much caffeine (especially afternoon), avoiding too much stimulation or any blue light 3+ hours before bed, and sleeping in a totally dark and technology-free space.

Probiotics and Gut Health: Summary

Your microbiome is an ecosystem that lives inside your body, filled with hundreds to thousands of different bacterial species. A wide scope of good bacteria is the foundation of good health since the majority of your immune system is found in the gut. Chronically consuming a narrow strain probiotics can lead to mono-cultured dysbiosis of the gut, and cause more harm than good. Increasing the diversity of your microbiome can be done by getting out in nature, consuming an array of fermented foods, cycling a soil-based probiotic, and getting high-quality sleep.


[1] Quigley, Eamonn M M. “Gut bacteria in health and disease.” Gastroenterology & hepatology vol. 9,9 (2013): 560-9.

[2] Bush, Zach. “Why Probiotics Don’t Always Work.” Zach Bush MD, Biomic Sciences,

[3] Principi, Nicola, et al. “Gut Dysbiosis and Irritable Bowel Syndrome: The Potential Role of Probiotics.” Journal of Infection, vol. 76, no. 2, 2018, pp. 111–120., doi:10.1016/j.jinf.2017.12.013.

[4] DeSalle, Rob, et al. Welcome to the Microbiome: Getting to Know the Trillions of Bacteria and Other Microbes in, on, and around You. Yale University Press, 2015.

[5] Taylor, Bryn C., et al. “Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome.” MSystems, vol. 5, no. 2, 2020, doi:10.1128/msystems.00901-19.

[6] Ursell, L. K., Metcalf, J. L., Parfrey, L. W. & Knight, R. 2012. Defining the human microbiome. Nutr Rev, 70 Suppl 1, S38-4

[7] Rea, Kieran, et al. “The Microbiome: A Key Regulator of Stress and Neuroinflammation.” Neurobiology of Stress, vol. 4, 2016, pp. 23–33., doi:10.1016/j.ynstr.2016.03.001.

[8] Smith, Robert P., et al. “Gut Microbiome Diversity Is Associated with Sleep Physiology in Humans.” Plos One, vol. 14, no. 10, 2019, doi:10.1371/journal.pone.0222394.



Leave a Reply

Your email address will not be published.