"Our bodies are our gardens.  Our wills are our gardeners."  ~William Shakespeare

Our blog article this week is on the importance of the microbiome.  Let us start by defining it.  What is a microbiome?

The word microbiome means “small… life.”  It denotes all the good probiotic bacteria and fungus that lives within the lumen of our digestive tract.  If you have ever visited our office, you would have learned about the profound importance of the health of the microbiome.  If you have not had the opportunity to follow a natural health restoration program at our office, I hope someday you decide to.  It will change your life.


Considerable research these days has been very insightful into the ways in which the probiotic microbes in our gut impact our health.  Without their ability to break down the foods we eat, it would be very difficult for us to obtain the nutrition we require on a daily basis.  We humans and these probiotic bacteria and fungi live together symbiotically… we give them a nice place to live and they in turn feed us and fight off invaders.  When we do not have a microbiome that exists in harmony we do not feel well with such symptoms as constipation, diarrhea, malabsorption, weak bones and teeth, fatigue, and even mental disorders.  It behooves us to tend our microbial garden because when we do not, we suffer.

Humans are naturally meant to be colonized by probiotic microflora beginning on the first day of life.  In fact, a baby’s first meal is when he/she becomes inoculated with Mom’s flora on the trip through the birth canal.  This is why I am strongly opposed to giving expectant mothers antibiotics prior to giving birth.  Drugs such as Amoxicillin decimate the mother’s microbiome which the baby will inherit.  When the baby is born by Caesarean section, the baby will accumulate hospital flora to build the microbiome. The majority of breastmilk is composed of oligosaccharides that are prebiotic food.  You heard that right- most of the nourishment a baby gets is not used by the baby, it’s used by the flora!

On every visit, starting with the first, I routinely check the vitality of the microbiome living within each person’s gut.  In all honesty, roughly 95% of new patients have a microbiome that has flatlined to completely nonfunctional.  Even more shockingly, many have been nonfunctional for many years in spite of efforts to repair it.  Over the past decade I have seen a large number of patients bring in various brands of probiotics they have consumed but never succeeded in fixing their health challenges.

The same is true for health practitioners who do not fully comprehend this issue.  I once met a natural doctor at a seminar who also does muscle testing and he told me that he thought probiotics were a scam because they always test poorly regardless of the company who made it.  Interesting viewpoint!  The question is why?  Why would bodies reject microbiome support when we know they need the help?

Now, when I say that a patient’s microbiome is nonfunctional, I am NOT saying the gut is sterile.  Quite the opposite, in fact.  The human gut will always become populated by some type of microorganisms.  The difference is, do the bugs work for the betterment of you (probiotic) or do they work for the betterment of themselves (pathogenic)?  In the interest of good health, you want to maximize the beneficial flora and minimize the pathogenic flora.

The answer to this puzzle is surprisingly very simple.  When the probiotic bacteria and fungus cannot colonize, supplements and fermented foods go in one end (the mouth) and out the other end (the anus).  No one likes to flush their money down the toilet!  I have seen clinically without exception the reason probiotic flora cannot colonize is because the person has a suppressive poisonous chemical that is stuck in the lower gut and kills the good flora on contact.  If I may use an analogy, think of it like planting a flower garden in your yard- when the soil is poisoned it will not matter how many flowers you plant, they could never bloom!  Thus, no matter how many probiotics you swallow, they will never populate and grow.

Here are some examples of the most common chemicals I have found that cripple the microbiome from reconstituting:

  • Roundup, a pesticide made by Monsanto (now owned by German-based Bayer Pharmaceuticals) is the number one selling pesticide in America. Bayer just settled for over $12 billion a series of lawsuits related to Roundup causing lymph cancer.
  • Dicamba, also made by Monsanto/Bayer was banned just this year.
  • Chlordane, an organochlorine pesticide still used for killing termites was banned in 1983 but persists in our environment.
  • 2,4-Dichlorophenoxyacetic Acid (also known as 2,4-D) frequently sold as Ortho Weed-B-Gon.
  • Neonicotinoid pesticides such as Acetamaprid, Imidacloprid, Dinotefuran, Clothianidin, and Thiamethoxam. Incidentally, neonicotinoids are strongly suspected of killing our honeybees through Colony Collapse Disorder.
  • Anhydrous Ammonia, a common fertilizer used in the agricultural industry, can reside in the gut for many years.
  • Antibiotics from prescription usage and from eating meat where the livestock was given heavy doses of those same drugs. The vast majority of antibiotic use in this country is actually on livestock, not on humans.
  • And there are many more!

As you can see from the above examples, Big Ag is responsible for the problem the vast majority of the time.  When these chemicals persist in the gut, the terrain is inhospitable to friendly microorganisms.  The solution is to detoxify these harmful substances from the body using liquid herbs such as Eleuthero, Eyebright, and Horsetail.  In my experience there is simply no other way to do it.  When the toxins are dealt with, you can at last incorporate a good probiotic that will colonize and grow.  Best of all, you will lower the possibility of uncomfortable reactions that can occur when you start changing the dynamics of your flora.

I should also mention that I NEVER fight candida (yeast) directly.  Candida is in fact a normal part of a human flora- it is not your enemy!  The human body will allow candida to grow to take the edge off a bigger problem such as heavy metal toxicity or plastic poisoning.  When you eliminate the toxic metal or chemical and restore the balance to the ecosystem, the candida overgrowth clears all by itself.

When a person’s microbiome is restored, health begins to come back in a big way.  The friendly flora help us by kicking out the pathogens, breaking down our food so we can get things like vitamins and minerals, feeding us beneficial fats such as butyrate, interfacing with our immune system via the gut lymphatic organs, detoxifying poisons, and helping to repair damaged tissue.  When the microbiome is functional and diverse, you should not have to spend money on probiotics, ever.  You can maintain it by eating lacto-fermented foods such as yogurt, kefir, beet kvass, kombucha or sauerkraut.

I am a big fan of a website called the American Gut Project and I highly recommend you subscribe to their newsletter.  They have lots of interesting info if you wish to learn more about how a microbiome is important and what you can do to cultivate the best of the best.  I also have a great video on the microbiome located under the videos tab on our website.

Until next time, take care of that microbiome!

Daniel J. McDonald, DC

Updated 10/19/20