In my last newsletter, I spoke about how we had hoped that when we had the human genome completely mapped out, then we would have all the answers to how our genes affected our health.  And while the Human Genome Project has provided unprecedented information, as is often the case, we learned that there is always more to learn.  Two areas that were shown to be huge influences on health beyond just our genes were Epigenetics and the Microbiome.  I talked about Epigenetics last time and will talk about the Microbiome this week.  And, again, these are areas of much continuing research and offer hope for new disease treatment.  These two are also exciting because unlike our genes, these two areas are places we can intervene and make positive changes for ourselves, and even potentially for our descendants.

The Microbiome refers to all the microscopic creatures that live in or on our body.  The predominant type of organism that makes up of our Microbiome is the single cell bacteria that live in our guts and on our skin.  But it goes beyond just bacteria – yeasts, protozoa, fungi, parasites such as worms and flukes, and even viruses all make up our total Microbiome.  Estimates show that there are at least as many cells from other creatures in and on our body as there are our own cells.  Some studies have proposed that there is even up to 10x more of their cells than our own.

Before you get too freaked out thinking about this, many of these creatures are quite helpful and without them, we may not be able to live.  For example, we cannot make our own Vitamin K which is needed for our blood to clot.  Most of our Vitamin K comes from bacteria in our gut synthesizing it.  Beneficial bacteria in our gut also prevents us from being overrun with yeast which is always around us.  This is why many times when you have to take antibiotics, you may get a yeast infection afterward – the good bacteria have been killed off allowing the yeast to take root and begin to multiply.

Scientists started a Human Microbiome Project in 2008 with the hope of completely mapping out which bacteria and other microscopic creatures were associated with health and which were associated with disease. It was a 5-year project, but as the number of studies being published in this field in recent years, it appears as if it only just scratched the surface.

There is truly fascinating information about how the Microbiome affects our health and I would encourage you to look more into it.  What inspired me to write on this topic was a recent study linking the Microbiome to depression and despair (  In mice studies they found that microbes of the Lachnospiraceae and Ruminococcaceae families generate metabolites that can travel through the bloodstream and reach the brain leading to behavioral changes similar to despair.  When these bacteria were treated with an antibiotic cocktail, the behavioral changes reversed and the mice were normal.

Other studies have linked imbalances in the Microbiome to acne, allergies, asthma, anxiety, autism, autoimmune diseases, cancer, cavities, Crohn’s disease/colitis, diabetes, eczema, gastric ulcers, malnutrition, obesity, and others.  Mainstream conventional medicine treatments based on treating the Microbiome are only being investigated at this point; they have yet to develop definitive treatment plans at this point, but research continues.

Thankfully, Naturopathic Doctors have been treating the gut for over a century. It seems doing our best to maintain as much diversity in our bacterial Microbiome is our best defense.  Especially, trying to maintain levels of beneficial bacteria like Lactobacillus acidophilus, Bifidobacterium, and others is seen as protective for many diseases.  Some tips for this include:

  • Increasing fermented foods like sauerkraut, yogurt/kefir (there are dairy free versions for people with allergies), kimchi, kombucha tea, and live culture pickled vegetables
  • Taking a regular probiotic supplement that is refrigerated.  We sell a high quality one on our website here.
  • Avoiding antibiotics unless it is truly a life-threatening emergency.  We tend to overuse antibiotics in medicine today without considering the consequences.  Antibiotics always wipe out beneficial bacteria in addition to the bacteria we are targeting.
  • Eating more organic fruits and vegetables which naturally contain soil based organisms that can contribute to our Microbiome diversity
  • Increasing fiber in our diet with more beans, whole grains, fruits, and vegetables – fiber can provide a food source for many beneficial bacteria.

If you suspect you may have an imbalance in your Microbiome (and I could argue that almost everyone eating a Western diet or who has taken antibiotics in their life probably has some level of dysfunction), there are a couple things to do.

  1. Consider testing your microbiome.  I have run the Comprehensive Stool Analysis test many times on patients with long-standing digestive symptoms.   This test will show levels of beneficial and non-beneficial bacteria.  It also tests for yeast levels and will look for parasites.  If there are harmful species it tells us specifically what prescriptions and natural substances we can use to clear them from our body. It also gives information about overall digestion and inflammation in the gut.  I don’t think I have ever run this test without learning something new that can be addressed for the betterment of health.  It can be especially useful if someone developed symptoms after antibiotics or after travelling. Want to learn more about the test? Browse here.
  2. Look into a diet that supports the Microbiome.  The one I recommend the most is the GAPS (Gut And Psychology Syndrome) diet.  It was first laid out by Natasha Campbell-Mcbride in the early 2000s book by the same name.  She found that by treating people with diet – she saw dramatic improvements in depression, anxiety, learning disabilities, and even schizophrenia, bipolar disorder, and autism symptoms.  The basis of her diet was 4 things:
    1. Regular fermented foods
    2. Avoidance of grains
    3. Increased intake of Bone broth soups and stews
    4. Increased intake of healthy fats like coconut oil, grass fed butter, and organic animal fats

A great resource for this diet is the ¨Heal Your Gut Cookbook¨ on

Like Epigenetics, research into the Microbiome is fascinating and on-going.  It is another confirmation that medicine needs to be individualized – we are not all alike.  What works well for one person, may not work at all for someone else.  Naturopathic physicians specialize in working in this sphere of individualized medicine.  Schedule an appointment today with one of our talented doctors if you would like to explore how these topics can be put into your life for the betterment of your health.


Jeremiah Stevens

Dr Jeremiah M Stevens is a licensed Naturopathic Physician and co-founder of Consult A For more information or to schedule go to