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Heal Your Microbiome and Heal Your Brain

Updated: Mar 6

Struggling with depression, fatigue, anxiety, brain fog, poor memory, difficulty thinking, weight management, blood sugar issues, constipation, diarrhea, gas, bloating, food sensitivities/allergies? These are all signs that may indicate there is an imbalance in your microbiome. That’s right; scientific research is quickly establishing the incredibly important role of the microbiome in many aspects of health, including your mental health.

Microbiome: is a term that refers to the bacteria, fungi/yeast, viruses, protozoa, archaea, and parasites (collectively known as microbes) that live in and on our bodies.

Wait, the microbes in our gut have an impact on our brain?

Yes, that’s correct! This connection is termed the “microbiome-gut-brain-axis” or sometimes just the "gut-brain-axis." An internet or research database search for this term will give you tons of reading material on the subject. What the research is showing, is that these little critters that are living in our guts play a major role in regulating our immune system, controlling inflammation, providing nutrients (like B-vitamins), regulating body weight and metabolism, resisting infections, preventing leaky gut, and much more. Much of these issues have downstream effects on our brains (e.g. depression is quickly becoming known as a disorder of inflammation in the brain, which can be caused by inflammatory issues stemming from the gut).

To some this may sound like a stretch. It is a relatively new concept and research is continuing to uncover ways in which microbes are a part of us. For example, did you know that there are bacteria that live inside of our brains? Yup, they do. They are not harmful, in fact they are beneficial. What we are quickly learning, is that to be human means to be a whole lot more than just a bunch of human cells. Our microbes are as much of who we are as any other organ in our body. In fact, on a genetic level, the DNA of microbes in and on our bodies is 10 times greater than the DNA of human cells in our bodies. Hence, scientists now call the microbiome an important human organ!

To date, scientists have discovered thousands of different microbes that make up our microbiomes. Furthermore, every person has a unique microbiome, much like how we each have a unique finger print. This is important in thinking about how we can assess someone’s microbiome and how we can change it if necessary. But first…

What causes imbalances in the microbiome?

Stress, poor nutrition, poor digestion, gastrointestinal infections (diarrhea), medications (especially antibiotics and proton pump inhibitors), herbs, cleaning products, glyphosate based herbicides, head injuries… If you have history of exposure to any of these, there is a good chance you have developed an imbalance in your microbiome. There are many things that disrupt our microbes, which means there are also many ways to repair the microbiome.


How do I know for sure?

It is possible to conduct an analysis of someone’s fecal matter or urinary organic acids to find if there is a diverse group of many different kinds of bacteria (associated with good health) or find if there is any overgrowth of microbes that can cause diseases (e.g. C. difficile or candida). This is a useful starting point in determining if the microbiome is out of balance and which therapies will have an impact on your symptoms. I highly recommend speaking with your naturopathic physician about whether it makes sense to do some stool testing or pursuing other causes of your symptoms. A good doctor is instrumental in helping you navigate potential causes of your symptoms!

So what do I do once I know there is an imbalance?


Most would jump to the idea of using probiotics (microbes researched to improve health) as supplements or probiotic foods to improve the microbiome. This is a great idea and a great start. Health practitioners have been using probiotic foods for centuries to help cure gastrointestinal complaints. However, I generally recommend people take a step back and look at the conditions that have led to microbial imbalances.

If there has been a history of head injury than concurrent treatment of the brain and central nervous system (CNS) is essential, as this will help regulate your gut and thus change your microbiome. Have you recently had, or in your life had many course of antibiotics? Are you stressed out or burnt out? Have you had recent intestinal infections? Do you eat conventional foods that are sprayed with glyphosate herbicides? There are many things that affect the microbiome and mental health. I highly recommend speaking with a physician who understands these systems so that you can create a comprehensive plan for you as an individual.

Safe Therapies to Start With:

Getting your digestion back online:

This means getting yourself into a calm and relaxed state. Your autonomic nervous system is divided into sympathetic and parasympathetic brances. The resources your body allocates to one or the other is fixed. This means, if you are stressed, you are primarily in sympathetic dominance, and the parasympathetic that controls your digestive organs is functioning minimally. The solution? Get stress out of your life and use stress management techniques:

  • Deep breathing

  • Meditation

  • Gentle Exercise

  • Yoga

  • Tai Chi

  • Qi Gong

  • Singing

  • Laughing

  • Having fun

  • Mindfulness

  • Gratitude

  • Cold water plunges/showers


Many of the above mentioned techniques will increase vagal nerve activity, the major parasympathetic nerve that gets your digestion moving and improves the microbiome as a result.

Probiotic foods:

These are foods that have been fermented by healthy bacteria and fungi. They are always sour tasting as acids are a by-product of microbes digesting sugars and starches. These are great at regulating gut function, helping you digest foods for better nutrition, and build an environment that a healthy microbiome can thrive in. Here are some examples:

  • Kombucha

  • Kimchee

  • Sauerkraut

  • Pickles

  • Sour yogurt

  • Kavas

Prebiotic foods:

These are foods that contain carbohydrates/fibers that are researched to feed your gut microbes in a way to grow the beneficial ones and inhibit most bad ones. One of the most famous is called Inulin. This substance is found in foods such as:

  • chicory

  • agave

  • banana

  • plantain

  • burdock root

  • camas

  • dandelion

  • garlic

  • artichoke

  • jicama

  • onion

  • yacon

Many of these are common in grocery stores around the country and a good way to help build beneficial microbes in your gut. In general, more fiber in your diet is very supportive and adds many other prebiotics.

When in doubt, eat more vegetables!

Warning: Dietary fibers and probiotics must be added gradually, as too much too fast can lead to gas, bloating, abdominal pain, and rarely diarrhea (those microbes love this stuff). Consult your physician if there is any increase in these symptoms as this may be a sign of certain problematic microbial overgrowth.


Probiotic Supplements:

I will defer from recommending any probiotic supplements as this should be done individually once someone has been properly evaluated by a physician. While some would argue that probiotics are very safe, this is not the case for every probiotic for every person. Also, many people waste money on probiotics created by companies that do not confirm that there are still live bacteria in their product once you are taking it, or that the bacteria they put in it are actually the ones they say they are. Speak to a trusted professional about which companies, strains, and dose is appropriate for you.

Not sure where to start?

I have created a really amazing program called the Microbiome Reset. This masterclass teaches you exactly how to change your diet, lifestyle, and supplement to completely transform you microbiome and gut health to ultimately heal your brain and body. This program has achieved fantastic results and is transforming lives. If you would like to learn more check out my video by clicking HERE.

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Dr. Schull is a naturopathic physician who treats mental health conditions with a focus on depression, ADHD, and brain injury. He is certified as LENS (Low Energy Neurofeedback System) practitioner and integrates healing the many systems of the body related to mental dysfunction.


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© 2013-2020 by Derrick Schull, N.D.