Balancing our gut microbes can help our health

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By Christine Bowen / Special to The Herald

When our gut bugs are healthy and balanced, we are more likely to experience health in multiple other ways.

For the purpose of this article, I use the slang term “bugs,” but I am referring to mostly yeast, bacteria, and archaea — not actual bugs. The number of organisms in our intestines is estimated to be in the trillions, so the health and balance of these populations are vital to our health. Some of our gut bugs are deemed beneficial, others may be harmful and some can even be opportunistic. This mix of organisms with different actions is constantly shifting and changing. Often this is a good thing, but when the organisms shift and change in ways that can be harmful to our health, that’s what we call dysbiosis.

The foods we eat, the people and animals we contact, our stress levels and the medicines that we take are only some of the things that influence the diversity of our gut bugs. Dysbiosis can cause a negative domino effect of gut lining injury, increased inflammation, leaky gut, and can disrupt our immune system (remember, 70% of the body’s immune system is in the gut). These negative impacts can lead to other medical conditions starting or worsening.

There are two main types of dysbiosis. One is when our helpful bugs get depleted, and the other type is when potentially harmful organisms can overgrow and create problems from being overabundant. Whether too high or too low of colony counts, the impacts of our gut organisms can lead to poor health or chronic disease.

Some examples of medical conditions that can develop if dysbiosis isn’t identified or treated are autism (among many other factors), autoimmune diseases, inflammatory bowel disease (IBD), IBS, colon cancer, diabetes, asthma, allergies, mood imbalance and more.

What causes dysbiosis?

Medications: Antibiotics, proton pump inhibitors, metformin, NSAIDs (non-steroidal anti-inflammatory drugs), opioids, antipsychotics, laxatives, and oral steroids are some of the most common medications that contribute to dysbiosis.

Alcohol: Drinking two or more alcoholic beverages per day can deplete our gut health.

Chronic stress/anger: This is the single largest cause of changes in our gut microbes.

Poor sleep: Studies show that sleep disruption puts undue stress on the body and can negatively impact our gut health

Food: High protein, high fat, high sugar, low fiber, food chemicals such as additives and preservatives, lingering pesticides on produce, and food allergies/intolerances all increase dysbiosis.

No or low movement: Moving our bodies helps the microbiome stay in balance.

Infections: Current or past infections can have lasting impacts on the health of our gut microbes. Infections can even become chronic and continue to infect humans longer term if not detected and eradicated.

Overgrowth conditions: Potentially harmful organisms or even normal organisms can overgrow and create problems. The three common types of overgrowth conditions are small intestine bacterial overgrowth (SIBO, see my previous article on this at, intestinal methanogen overgrowth (IMO) and yeast overgrowth. Get tested for these conditions if you have gas, bloating, digestive changes, joint pain, brain fog, fatigue or rashes.

Steps for recovering from dysbiosis

Identify the level of dysbiosis, infections, or overgrowths in your gut using tests like stool testing to identify the organisms, urine tests to detect waste products from dysbiosis, or breath testing to look for archaea or bacterial overgrowth (IMO or SIBO) or stool, or blood testing to look for yeast overgrowth.


Nutritional changes: Specific nutritional changes may need to be made when working on shifting the gut bugs in a healthier direction. This may include identifying food allergies/intolerances.

Herbs or other more natural treatments targeted at removing harmful organisms are a good step for starting a plan for recovering from dysbiosis.

Restore the health of your microbiome

Once you have treated the gut imbalance, focus on rebuilding healthy gut bug colonies.

Eat more plants: Our gut bugs and intestinal cells really like fiber, especially from fruit and vegetables.

Eat more cultured/fermented foods: These foods are rich in probiotics (good or helpful bacteria. Food like yogurt (plain), kimchi, sauerkraut, pickles, kombucha, etc., can help with keeping a rich diversity of healthy gut bacteria.

Repair the intestinal lining with treatments like probiotics, glutamine, zinc carnosine, and herbs and nutrients that help to heal the gut.

Sleep: Improving our sleep can help with improving our gut health. Try going to bed an hour earlier, don’t look at your devices in bed, and try to wind down for sleep an hour before you need to be asleep. If you suspect that you have sleep apnea, get tested by a pulmonologist (lung/breathing doctor).

Peace: Since anger and stress make the single biggest shift in our gut bugs, this seems like a great place to find some helpful tools to manage stress. Walk barefoot in the grass. Stare at a lit candle and try to clear your mind. Talking to someone when you are having really high stress (friends, counselors, hotlines) can all be ways to help us navigate the stressful times in our lives. Consider calling 211 if you need help with resources.

Movement: Therapeutic movement does not have to mean exercising at a gym for an hour a day. Take the stairs an extra time (if that is possible for you), punch your fists in the air, and move in any way that feels good to you. Be in your body. Turn on your favorite music and move.

If you feel like your gut is out of balance or even if you have developed conditions like the ones mentioned above that can be connected to dysbiosis, please get help! It is very important to work with a knowledgeable digestive health provider who can help you get the testing and the treatments that you need and that are specific to the organisms that are overgrown or depleted in your gut, specifically. The right balance of helpful organisms can prevent the development or worsening of other medical conditions.

Dr. Christine Bowen of Everett is a licensed naturopathic doctor, keynote speaker, and author. In practice since 2005, Bowen specializes in holistic approaches for digestive health, autoimmunity, and complex cases. Go to for more information. Connect with her via Facebook drchristinebowen or Instagram @drchristinebowen.

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