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The Importance of the Gut Microbiome and 5 Ways You Can Keep It Healthy

The Importance of the Gut Microbiome and 5 Ways You Can Keep It Healthy

There's a saying in naturopathic medicine to "treat the gut." We know how important it is to make sure digestion and elimination are happening effectively because gut health affects how the rest of the body functions. This is why NDs so often talk about beneficial bacteria, probiotics, fiber, and a healthy diet and why if you go to see one they will almost always ask you about your digestion.

There's been a lot of research lately about how the beneficial bacteria affect our overall health. The benefits don't just pertain to the digestive system, they are whole body benefits. In this post I'll discuss what the microbiome is, what it does for us and how to take care of it so it takes care of you.

What Is the Gut Microbiome?

The microbiome are all the bacteria, good and bad, that live on and in your body. You have many different species of bacteria that live on your skin and in your mouth, lungs, stomach, intestines, and bladder. They are everywhere and we have more bacteria than we have cells in our body!

The type of bacteria differ depending on where they're located and what the environment is like. For instance, you have bacteria in the stomach that can withstand the acidic environment and bacteria in the colon that don't need oxygen to thrive.

We get our bacteria from our mother when we're born. A baby's microbiome starts out mostly like mom's and gradually changes as they get older depending on what they eat, whether they are breastfed and what they encounter in their life. Babies born via C-section start out with bacteria mostly from the skin of those who deliver and care for them. Research is now showing that this initial bacterial exposure can put children at risk for or protect them against diseases later in life such as asthma, allergies, autoimmune disease and digestive diseases like Crohn's.

What Does It Do and Why Is It Important?

Now that you know what the microbiome is you may be wondering what it does for you. It does many different things from making nutrients, influencing the immune system, controlling weight, regulating mood and keeping bones strong and healthy.

  • Makes food for the intestinal cells - beneficial bacteria ferment fiber from the diet into short chain fatty acids that provide nutrition for the intestinal cells. This promotes good colon health and may prevent cancer. These fatty acids are also involved in regulating the immune cells and in maintaining good bone health.

  • Makes vitamins and nutrients for us - We don't have the enzymes needed to digest some plant-based carbohydrates we eat in our diets, but the bacteria do. They break down indigestible carbohydrates and make vitamins B12, K, and folic acid. They also make amino acids, which are building blocks for protein, that we are unable to make ourselves.

  • Keeps the immune system under control - when we're young our immune system has to be trained to attack harmful microbes and leave our own cells alone. Helpful bacteria assist in this training and in controlling our immune T-cells that regulate inflammation levels. This is why when our microbial balance is thrown off, immune issues like autoimmunity, allergies and asthma tend to develop. The microbiome also helps to reduce circulation of older immune cells that tend to cause damage and inflammation.

  • Controls weight - Studies have found that the microbiome differs in those who are overweight versus those who are lean. The bacteria present in obese individuals has the ability to extract more calories and energy from food, resulting in more fat storage and weight gain.

  • Regulates your mood and brain health - Mental health conditions like depression and anxiety, as well as learning, memory and cognitive function can be affected by the gut bacteria. Beneficial bacteria are also responsible for maintenance of nerve protecting immune cells. It's thought that the vagus nerve, which runs from the brain to the digestive system, is responsible for this gut-brain connection.

  • Defends against harmful pathogens - beneficial bacteria do this by crowding out harmful microbes and making antimicrobial compounds. They also help to maintain the protective gut barrier so pathogens can't get through and into our bloodstream. A strong intestinal barrier is important because it prevents a leaky gut from letting proteins through, which can trigger immune reactions.

How Can I Keep It Healthy?

  • More fiber - eating soluble and insoluble fiber provides the necessary fuel for the bacteria to produce short chain fatty acids. Good sources include whole grains like brown rice, wheat, oats, and quinoa, seeds like chia and flax and legumes. A diet high in whole fruits and vegetables is also a good idea. Your microbiome changes quickly, within days, once you alter your diet.

  • Stress management - the microbiome plays a role in the production of stress hormones like cortisol that come from the adrenals. Chronic stress can change the composition of your microbiome resulting in increased anxiety and depression. Stress management techniques like exercise, meditation, journaling, gratitude, counseling, adequate sleep, and botanical adaptogens are all good ways to keep your stress level low and your body healthy.

  • Eat prebiotics and probiotics - prebiotics help to feed the good bacteria. Good sources are artichokes, asparagus, bananas, eggplant, garlic, honey, jicama, leeks, legumes, onions and peas. Probiotics are foods that contain the beneficial bacteria themselves. Good sources of these are fermented foods like yogurt, kefir, sour cream, kimchi, kombucha, and miso.

  • Eat less fat and calories - having a lot of fat and calories in the diet promotes bacteria that can increase weight gain. While some fat is beneficial to your health, try not to overdo it on high fat, high calorie foods. Stick with nutrient dense, low-fat foods and keep carbohydrates at a reasonable amount too.

  • Use antibiotics sparingly - antibiotics can be useful in cases where someone is very sick, but they've been overused in the past for conditions where they aren't even effective. Now that we know more about the importance of the microbiome, it's important to use them only when needed to prevent killing off the beneficial bacteria and creating resistant bacterial strains. If you have to take one I recommend taking a probiotic as well and getting plenty of probiotic-rich foods in your diet.


Naturopathic medicine recognizes that taking care of digestive health is important for so many reasons. The beneficial bacteria that live on our skin and in our body do so much for us including making vitamins and amino acids, influencing immune system function, fighting harmful pathogens, controlling weight, regulating mood, and keeping bones strong. Ways to take care of the microbiome include eating fiber, managing stress, eating prebiotics and probiotics, eating low fat and low calorie diets and using antibiotics only when necessary.

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In Health,

Dr. Jamie


Thomas, S., Izard, J., Walsh, E., Batich, K., Chongsathidkiet, P., Clarke, G., … Prendergast, G. C. (2017). The Host Microbiome Regulates and Maintains Human Health: A Primer and Perspective for Non-Microbiologists. Cancer research, 77(8), 1783–1812. doi:10.1158/0008-5472.CAN-16-2929

Warner, Wendy. “Herbs and Strategies to Support Healthy Microbiome Function.” Gaia Professional Solutions Webinar, 17 Apr. 2019.

This website is not intended for the purpose of providing medical advice. All information, content, and material of this website is for informational purposes only and are not intended to serve as a substitute for the consultation, diagnosis, and/or medical treatment of a qualified physician or healthcare provider.


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