Balancing Our Gut Microbes Can Help Our Health

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

For the purposes of this article, I’m using the slang term “bugs”, but I’m mostly referring to yeasts, bacteria, and archaea – not real bugs. The number of organisms in our intestines is estimated to number in the trillions, so the health and balance of these populations is vital to our health. Some of our intestinal insects are considered beneficial, others can be harmful, and some can even be opportunistic. This mixture of organisms with different actions is constantly changing and evolving. That’s often a good thing, but when organisms move 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 come into contact with, our stress levels, and the medications we take are just some of the things that influence the diversity of our gut insects. Dysbiosis can cause a negative domino effect of gut lining damage, 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 the onset or aggravation of other medical conditions.

There are two main types of dysbiosis. One is when our helpful bugs run out, and the other type is when potentially harmful organisms can proliferate and create problems due to their overabundance. Whether the number of colonies is too high or too low, the impacts of our gut organisms can lead to poor health or chronic disease.

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

What causes dysbiosis?

Medications : Antibiotics, proton pump inhibitors, metformin, NSAIDs (nonsteroidal 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 a day can deplete our gut health.

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

Bad 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, persistent pesticides on produce, and food allergies/intolerances increase all dysbiosis.

No or weak movement: Moving our body helps the microbiome stay in balance.

Infections: Current or past infections can have lasting effects on the health of our gut microbes. Infections can even become chronic and continue to infect humans over the longer term if left undetected and eradicated.

Proliferation conditions: Potentially harmful organisms or even normal organisms can proliferate and create problems. The three common types of overgrowth conditions are small intestinal bacterial overgrowth (SIBO, see my previous post about this on, 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 to recover from dysbiosis

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


Nutritional changes: Specific nutritional changes may be needed when working on moving gut bugs in a healthier direction. This may include identification of food allergies/intolerances.

Herbs or other more natural treatments aimed at eliminating harmful organisms are a good step to start a dysbiosis recovery plan.

Restore the health of your microbiome

Once you have treated the intestinal imbalance, focus on rebuilding healthy colonies of intestinal insects.

Eat more plants: Our intestinal insects and our intestinal cells are very fond of fiber, especially that of fruits and vegetables.

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

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

Sleep: Improving our sleep can help improve our gut health. Try going to bed an hour earlier, don’t look at your devices in bed, and try to relax an hour before you need to fall asleep. If you suspect you have sleep apnea, get tested by a pulmonologist (a doctor who specializes in lungs and breathing).

Peace: Since anger and stress are the biggest change in our gut bugs, this seems like a great place to find some helpful stress management tools. Walk barefoot in the grass. Stare at a lit candle and try to clear your mind. Talking to someone when you are experiencing very high stress (friends, counselors, helplines) can be a way to help us through stressful times in our lives. Consider calling 211 if you need help with resources.

Movement: Therapeutic movement doesn’t have to mean exercising in a gym for an hour a day. Take the stairs one more time (if you can), punch your fists in the air, and move in whatever way feels good to you. Be in your body. Turn on your favorite music and get moving.

If you feel like your gut is out of balance or even if you have developed conditions like the ones mentioned above that may be linked to dysbiosis, get help! It’s very important to work with a knowledgeable digestive care provider who can help you get the tests and treatments you need that are specific to the organisms that are overgrown or depleted in your gut, in particular. The right balance of beneficial organisms can prevent the development or aggravation of other medical conditions.

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

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