Why the Microbiome is Important:

You’ve probably been hearing a lot about the “microbiome” lately, and it’s worth exploring since it’s a new paradigm that’s likely to change how medicine is practiced. For those of you not familiar with the microbiome, one definition is “the totality of microorganisms and their collective genetic material present in or on the human body or in another environment.”

I personally became interested in the microbiome when I was recently told by a doctor at a famous clinic that my health issue (mold toxicity) was due to my microbiome. He handed me a copy of an article by The Human Microbiome Project Consortium with no other explanation or treatment options offered. In a nutshell, we all have very different microbes in our body and things like genetics, diet and environment play a role in their diversity.

I had an idea of what the microbiome was but didn’t know what else I could do besides take probiotics and eat fermented foods. That’s why I was particularly interested in listening to the online Microbiome Medicine Summit in March 2016.

According to the summit host Dr. Raphael Kellman, author of The Microbiome Diet, new groundbreaking research about the microbiome is causing a revolution in medicine and will be the key to healing chronic disease. The body is made up of trillions of organisms and the bacteria outnumber your genes. In fact, nonhuman bacteria make up about 90 percent of your cells, and they communicate with our organs and genes. Conventional medicine is coming to to the realization that killing off all bacteria with antibiotics isn’t a great idea, as even the those deemed pathogenic have a purpose and the power to heal—it’s just when they get unbalanced they can become problematic.

Everyone’s microbiome is very unique, and understanding the microbiome of your gut, especially, is very important if you’re suffering from chronic disease. The bacteria housed there play a role in digestive health and have a role in sending messages from the gut to the brain and also regulate the immune system, 70 percent or more of which is housed in the intestines. In addition, the brain and gut have their own microbiomes that communicate with each other.

Summary of the Talks:

The 33 guest speakers talked about a variety of topics–everything from diet to the spiritual aspects of the microbiome. Of course, there was a lot of overlap and differences between speakers, and I didn’t get to hear every speaker; some I’d heard talk many times before and had read their books. I was especially interested the subject of diet and gut health, so that’s what I’ll mainly cover here. These were my main takeaways that may be of interest to you.

Dr. Mark Hyman, author of the book Eat Fat, Get Thin, talked about gut bacteria regulating everything, including your metabolism, and can change your weight independent of diet–it’s not about the calories we consume. He and many other speakers, such as Dave Asprey of Bulletproof, stressed the importance of eating an anti-inflammatory, low carbohydrate diet that’s high in healthy fats (e.g., fish oil, grassfed butter, and coconut oil).

Several doctors of functional medicine, such as Dr. Jill Carnahan, talked about the importance of testing for, and treating, possible fungal and bacterial gut infections, removing triggers such sugar, gluten (and other food sensitivities), environmental toxins, GMOs, and stress, which can adversely affect your gut microbiome, starving out bad bacteria with a low-carbohydrate and low-FODMAP diet, and replenishing by adding in enzymes, probiotics, prebiotic foods (e.g., asparagus, artichokes, garlic, etc.), and fermented foods. Also adding supplements that help heal the gut lining, such as zinc, l-glutamine, slippery elm, and marshmallow root.

While for most people, probiotics are beneficial, it was stressed by some speakers that you really need to know what the problem is before throwing supplements such as probiotics at your gut, because you can waste a lot of money and even potentially make the problem worse, especially in the case of something like small intestinal bacterial overgrowth (SIBO) or autoimmune disease. Dr. Leo Galland recommended the following strains: lactobacillus plantarum, which enhances Th1 immunity and helps with allergies, or bifidobacterium infantis, which downregulates the immune system; and brands containing soil-based organisms for things like gas and bloating. Targeted probiotics for specific conditions may become a future treatment method.

The same goes for fermented food. Fermentationist Summer Bock recommended starting slowly and even waiting for your gut to heal first; fermented foods such as sauerkraut contain histamine, which some people can’t handle.

Several doctors spoke about “leaky gut,” which is when the gut lining becomes impermeable and lets in toxins and food particles that can trigger an immune response and lead to allergies, autoimmune and other diseases, including brain problems. One was Dr. Natasha Campbell-McBride, author of the book and program The Gut and Psychology Syndrome and the GAPS diet. She spoke about the importance of healing the gut and advocated a strict grain-free, low-carbohydrate diet, including bone broths and fermented foods.

The thyroid was also discussed by several speakers as playing a role in gut problems and cellular energy production. If you have an unhealthy gut, you’re more likely to have a thyroid problem as a percentage of thyroid hormone is made in the gut. Having a full thyroid panel test was recommended.

Dentist Gerry Curatola talked about the importance of the microbiome of the mouth and didn’t recommend mouthwashes or even most toothpastes as they have ingredients that can adversely alter the mouth’s microbiome (use a Himalayan salt dissolved in water instead). Overuse of teeth whitening products can be harmful too. Again, when bacteria get out of balance, they are a problem. Thick plaque on your teeth means an imbalance of mouth microbiota. Gum disease is an inflammatory process that can cause disease in other parts of the body.

Dr. Joseph Mercola gave simple but important advice: get out in the sun, drink clean water, eat real food, move your body, get enough sleep, don’t eat 3+ hours before bed, and cut out sugar and gluten.

According to Dr. Larry Dossey, our thoughts can even affect our microbiomes, so being positive and reducing stress are important. Studies are showing the importance of believing in something larger than yourself.


I love summits like this one and always learn a lot, but at the same time, am often left a little overwhelmed with all the new information, ideas for books I want to read, and finding time to look at the speakers’ free gifts. It reinforced what I already believe about health: that we’re all unique so there’s no one-size-fits-all diet or treatment, and ultimately it’s how you live your life and what you put in your mouth that’s most important.

Always check with your health professional before trying new diets or supplements. Leave a comment if you found this information helpful or have a question.

xo, Kate


The Human Microbiome Project Consortium. (2012). Structure, Function and Diversity of the Healthy Human Microbiome. Nature, 486(7402), 207–214. http://doi.org/10.1038/nature11234. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564958/


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