Modern Day Doctor | Ancient Wisdom

Naturopathic Gut Health Essentials


A healthy gut microbiome is essential to our overall well-being. More and more, research has established a strong connection between a healthy gut and our overall health. Our gut microbiome affects every organ in the body – it supports digestion, our immune system, our central nervous system, and hormone health. It also impacts brain function and mood. As the research continues, our understanding of the pivotal role our microbiome plays and its interconnectedness to all of our body systems becomes more apparent. Much has been revealed regarding the state of the gut microbiome and its effect on sickness and health, both physically and mentally, including autoimmune disorders. In naturopathic medicine, restoring gut health is often a first-line approach to healing most patient health complaints.

When approaching gut health, naturopathic doctors (ND) employ the 6 principles of naturopathic medicine to identify potential areas of imbalance and work with patients on healing and staying well:

  • First Do No Harm – Use the most natural, least invasive, and least toxic therapies.
  • Identify and Treat the Causes – look beyond symptoms to the underlying cause.
  • The Healing Power of Nature – Trust in the body’s inherent ability to heal itself.
  • Doctor as Teacher – Educate patients on the steps to achieve and maintain health.
  • Treat the Whole Person – View the body as an integrated whole in all its physical, psychological, and spiritual dimensions.
  • Prevention – Focus on overall health, wellness, and disease prevention.

Because the gut microbiome is interconnected to all body systems, uncovering and treating the root cause of someone’s illness or disease usually starts with a look at the patient’s gut health. NDs will use stool and blood testing to get a sense of the health of one’s gut.

  • Stool testing is done to identify the quality (and quantity) of bacteria and yeast. It’s also used to look for blood in the stool, as well as the presence of inflammation, digestive enzymes, parasites, pathological bacteria, and immune markers.
  • Blood tests help reveal food sensitivities/allergies, nutritional deficiencies, markers for celiac disease, liver function, as well as hormone balance, inflammatory indicators, and more.

The results of these tests will help your ND tailor an individualized treatment plan for you.

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The digestive tract (starting in the mouth and down through the anus) is inhabited by an intricate world of microorganisms — Bacteria, viruses, fungi, and other microbes live in the digestive tract and play a crucial role in a variety of body systems:


  • Food digestion, metabolism, and nutrient absorption.
  • Immune system regulation
  • Mental health, mood, and stress response

A healthy gut allows us to properly digest and metabolize food and absorb essential nutrients. Our immune system is regulated by a healthy gut because the microbes detect and defend against harmful pathogens that may cause infection or an inflammatory response. Our gut microbiome also affects our mental health, mood, and stress response through what is referred to as the gut-brain-axis – a network of nerves that runs like a two-way street between the gut and the brain and central nervous system. This two-way communication allows the brain to influence activity in the intestines and allows the gut to influence mood, cognition, and mental health. The gut-brain axis originated as a survival mechanism, keeping humans safe from things like poisonous plants, and also ensuring keen instincts from danger, dispersing energy when and where needed during times of heightened stress.


When the microbiome is out of balance, it can harm health. A compromised microbiome is known as “Dysbiosis”. Dysbiosis is when the microbes in the digestive tract are out of balance (too many “bad” microbes, too few good ones) and cause dysfunction. Research has linked Dysbiosis to several diseases and conditions – both physical and mental:

  • Digestive Issues (gas, bloating, constipation, diarrhea, poor digestion)
  • Autoimmune Disorders
  • Inflammation
  • Metabolic syndrome
  • Mental Health disorders (depression, anxiety, stress)

According to the National Institutes for Health (NIH), factors that negatively affect microbiome balance include:

  • Poor diet
  • Chronic alcohol use
  • Prolonged use of antibiotics
  • Prolonged use of other medications (including over-the-counter meds like antacids or ibuprofen)
  • Chronic stress
  • Long-term exposure to environmental toxins( i.e. glyphosate)

The good news is, with a little diligence, you can work with your ND to restore your gut health to a thriving ecosystem with simple changes to your diet and lifestyle.

Get started now with a 10-minute consultation. 


A balanced, anti-inflammatory diet, rich in nutrient-dense foods and fiber is crucial for keeping your microbiome healthy. The foods we eat contribute to the quality of microbes in the gut, but nutrition also has implications for the cell health of our digestive tract and inflammation and immunity.


Fiber is probably the most important nutrient for digestive health since fiber is the food for the microbes in your gut. The microbes that make up the microbiome need to eat good food to thrive. Research shows that high-fiber foods, like vegetables, fruit, legumes, and whole grains keep the bacteria in your gut healthy and diverse for optimal functioning of your microbiome. Fiber is also essential for keeping your digestion running smoothly. The bulk of the fiber aids in eliminating waste, preventing constipation, and normalizing bowel movements. Fiber slows down digestion, helping to keep blood sugar stable by slowing the absorption of glucose into the bloodstream.


When fibrous foods are digested, the fiber becomes food for the microbes in your gut. When the microbes feast on the fiber, they release short-chain fatty acids (SCFAs), which play an important role in gut inflammation and repair. They also synthesize Vitamin K2 which is essential for bone ossification to fend off osteoporosis. Some of these SCFAs are butyrate, propionate, and acetate. According to NIH, SCFAs are beneficial to gut health in several important ways:


  • Repair the lining of the digestive tract,
  • Regulate the immune system and
  • Inflammatory response
  • Regulate blood pressure
  • Stabilize blood sugar

Omega-3 fatty acids and Omega-6 fatty acids are important to have in your daily diet as they will help keep your microbiome functioning properly. Sources of fatty acids can be found in nuts, seeds, oils, soybeans, fish, meat, poultry, and eggs.


In addition to fiber, the gut needs other essential vitamins and minerals to support gut health. According to research, these nutrients were beneficial to creating an optimal environment in the gut:


  • Vitamin D is well-known for supporting immune function. It improves the diversity of gut microbes while also decreasing inflammatory markers in the blood. Sources of vitamin D include fatty fish, like salmon, fortified dairy products, mushrooms, and sunlight.


  • Vitamin A is essential for immune function, just like vitamin D. It helps keep mucous membranes healthy, including that of the intestinal tract. A compromised intestinal lining will cause a leaky gut, which then causes food allergies and immunity issues. Foods rich in vitamin A include leafy greens, orange and yellow fruits and vegetables (sweet potatoes, carrots, squashes, cantaloupe), liver, eggs, and milk.


  • B Vitamins help regulate digestion by increasing the quality of the microbes in the gut, decreasing inflammation, and. B vitamins can be found in meat, liver, fish, eggs, dairy, leafy greens, legumes, whole grains, citrus fruits, and avocados.


  • Vitamin C also helps protect the lining of the gut and the immune system. It’s also high in antioxidants, which protect against inflammation. Good sources of vitamin C include citrus fruits (oranges, grapefruit, lemon, lime), strawberries, bell peppers, broccoli, and potatoes.


  • Vitamin E is an antioxidant that helps protect the cells that are part of the gut lining. Studies show that vitamin E slows the aging process and increases healthy microbes in the gut. Vitamin E can be obtained from nuts, seeds, avocados, and green leafy vegetables.


  • Minerals like magnesium, iron, zinc, and calcium are all important for immune function, production of red blood cells, and muscle function, which have implications on the health of the digestive tract. These minerals have also been shown to positively affect the quality of microbes in the gut. Good sources of magnesium include nuts, seeds, leafy greens, and whole grains. Foods rich in zinc include meat, shellfish, legumes, nuts, and seeds. Find iron in meat, fish, legumes, and leafy green. Good sources of calcium include dairy and leafy greens.

The best way to make sure you get the right nutrients for optimal gut health is to eat an anti-inflammatory diet that includes a variety of fruits, vegetables, legumes, whole grains, meats, and eggs.


The use of herbs is a powerful way to support digestion and treat a compromised microbiome. Herbs can act as a “prebiotic”, which means they provide fuel for the microbes in your gut. Poor diet, stress, and medications are all factors that can kill off these microbes and upset the balance of the flora in the gut. Herbs are a common naturopathic treatment that helps to restore balance, repair the gut lining, soothe discomfort, and get digestion moving again.


Common herbs used in naturopathy for gut health include turmeric, peppermint, ginger, slippery elm, aloe vera, and marshmallow root, among others:


  • Turmeric is well-known for its anti-inflammatory benefits. It is also a powerful antioxidant and anti-cancer. Research shows that turmeric is effective in restoring gut lining and reducing inflammation. It’s being studied for its promise in the treatment of irritable bowel syndrome.


  • Peppermint has many powerful properties that make it particularly useful in treating GI issues. Research shows it is anti-inflammatory, antioxidant, and antimicrobial. It strengthens the immune system and is a natural anesthetic. It is also antispasmodic, which means it helps calm muscle contractions. If you suffer from bloating, cramping, and flatulence, peppermint can relax the bowel muscles, helping aid in digestion.


  • Ginger is well-known for being supportive of the healing of digestive issues. It is often used to combat nausea and is known for its antispasmodic and anti-inflammatory properties. It is effective in soothing irritated digestive tract and helps calm bloating, gas, and abdominal pain that comes with it. Ginger can help ease constipation by increasing motility. Research has shown the use of ginger to also help increase the variety of microbes in the gut.


  • Slippery Elm is often used for its healing effect on the mucous lining of the gut. It forms a protective layer along the digestive tract, which makes for fertile ground for microbes to flourish. Slippery elm also has anti-inflammatory effects, which soothe an irritated digestive tract.


  • Aloe Vera has similar effects as slippery elm in that it soothes, protects, and restores the mucous lining of the digestive tract. It’s incredibly hydrating and can restore water balance to the microbiome, which is conducive to good digestion.


  • Marshmallow Root is another herb that helps to restore the gut lining because of its mucilage properties that coat and protect as it moves through the digestive tract. These properties also help ease heartburn, which makes marshmallow root a good alternative to antacids, which can wreck your gut lining.

Herbs have been used for thousands of years to treat illness. The benefits of using herbs to treat digestive conditions are often a welcome alternative to conventional treatments. Herbs like peppermint, ginger, and turmeric have been proven to be powerful allies in the restoration and repair of the gut. However, herbal medicine is not for everyone. If you are curious about how herbs can work for you, work with a trained practitioner who can prescribe the right remedies specifically for you and your condition.


Fermented foods, like pickles, sauerkraut, yogurt, kefir, kimchi, and kombucha, offer prime health benefits to the microbiome. The notion of fermenting foods is age-old and stands the test of time, but recent studies show the live and active cultures present in these foods help populate the gut with the microbes necessary for a balanced microbiome and good digestion. These live and active cultures are known as “probiotics”.


Probiotics are live bacteria and yeasts that make up the flora in a healthy gut. They naturally occur in fermented foods, like yogurt, pickles or sauerkraut. They can also be obtained through nutritional supplements. Without probiotics, the ecosystem of the microbiome can’t thrive, which then causes digestive and other health issues. Someone with digestive health issues or autoimmune gut health issues likely doesn’t have the proper balance of microbes and is often treated with probiotic foods and supplements to help restore the balance of flora in the gut. There are many different strains of probiotics, each has a specific function. Your naturopath is trained to help identify the right strain of probiotics for your specific digestive issue to help you heal.


Probiotics need to be eaten too and rely on fiber from the foods we eat for their food. This is known as “prebiotics”. Prebiotics are as important for digestive health as probiotics. Eating a fiber-rich diet, high in fruits, vegetables, legumes, nuts, and seeds is a natural way to nourish the flora in your gut by offering them probiotic fuel. Studies show that taking probiotics and prebiotics together has a positive impact on health, hormones, and weight as a result of restoring digestive health.


To get the benefit of probiotics from fermented foods, and prebiotic fiber add little bits to your daily foot routine each day. For instance:


  • Pickles (probiotic) to your salad with chickpeas (prebiotic) at lunch
  • Sauerkraut (probiotic) atop your potato (prebiotic) as a side to protein at dinner
  • Kimchi (probiotic) as a fish topping or to a stir fry (prebiotic)
  • Yogurt or kefir (probiotics) with ground flax and blueberries (prebiotic) as a snack or breakfast


Our diets directly influence the health of our gut microbiome. Research has made it clear that the gut microbiome is shaped by what we consume. Our microbiome is a living ecosystem. What we consume determines if it’s a thriving environment or not, depending on what we take in.


A diet high in refined carbohydrates, gluten, highly processed foods, and unhealthy fats is highly inflammatory and will cause a breakdown in the microbiome by killing off healthy flora and destroying the gut lining. This disruption will cause inflammation, leaky gut, acid reflux, and a host of other ailments. The benefits of going gluten-free, even if you do not have serious allergies to gluten, like celiac, have been shown to have a positive impact on gut health; this could be due to a reduction in the consumption of glyphosate.


To keep a diverse microbiome and a strong intestinal lining, eating foods like fruits, vegetables, legumes, and other fiber-rich foods will feed the microbes the foods that keep them healthy, keeping inflammation at bay and ensuring that your immune and central nervous systems are functioning smoothly.


Naturopathic dietary recommendations for a healthy gut include a routine of fresh, whole foods:


  • Fibrous foods, like fruits, vegetables, legumes, nuts, and whole grains, for the fiber helps feed the microbes in the gut. If you have trouble digesting raw vegetables then try roasting or steaming.


  • Fermented foods, like sauerkraut, kimchi, yogurt, and kefir are especially helpful for restoring the healthy flora in the microbiome because they contain live and active cultures, which is a way to get in some good, healthy bacteria (probiotics) into your gut.


  • Proteins, like beef, chicken, fish, and eggs keep microbial balance. Protein also keeps the digestive muscles strong and functional, and the digestive lining and mucosal layer intact, optimizing nutrient absorption.


  • Healthy fats like avocado and olive oil keep the lining intact and pliable.


  • Gluten-free diet.  This doesn’t mean swapping gluten cookies for non-gluten cookies.  This means to eat whole grains like quinoa.

Foods to avoid for optimal gut function include:

  • Low-quality fats
  • Sugar
  • Highly refined carbohydrates
  • Gluten
  • Alcohol
  • Caffeine
  • Animal foods with antibiotics
  • Overusing antibiotics and medications
  • Wheat, other grains, fruits, and vegetables that have glyphosate.

This means staying away from fast food, and junk foods, like chips and candies, sodas, and sugary cereals. According to research, all of the foods and food items above destroy the gut lining, deplete the healthy microbes in your gut, and lead to inflammation and conditions like irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD), GERD and acid reflux, metabolic disease, food allergies, and cancers.


Some people can’t tolerate certain healthy foods, like certain types of vegetables, fruits, or grains. If you have food sensitivities or if you have digestive issues after eating even fruits and vegetables, your ND may have to do an elimination diet to inform you of what foods are working for you or making you sick. An elimination diet is when you remove common food categories to cause allergies or discomfort like bloating and gas, then slowly add them back in to discover if you have an intolerance.


A low FODMAP diet is a type of elimination diet. FODMAP stands for Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols. These are a certain class of carbohydrates that can be difficult for some people to digest. Typically high FODMAP foods include, but are not limited to:

  • Dairy
  • Legumes
  • Wheat
  • Onions
  • Garlic
  • Apples

If you have an intolerance to these foods, eating them will only irritate and inflame your digestive tract, which will compromise its function.

Diet is not the only lifestyle factor that can influence gut health. Other lifestyle factors that have implications for gut health include:

  • Stress. According to NIH, chronic stress and mental health disorders like depression can wear down your gut lining. When stress is high for prolonged periods, the constant release of stress hormones, like cortisol, damages the gut lining and leads to leaky gut syndrome. Once this happens, not only is the diversity of your gut bacteria compromised, but bacteria can get into the bloodstream and cause inflammation and immune issues.


  • Sleep Quality. Sleep and gut health are linked in similar ways, as poor sleep causes the adrenals to release the stress hormone cortisol. If you have chronic sleep issues, you likely have chronically high cortisol, which will wreak havoc on your gut health. While there is a clear link between poor sleep quality and poor gut health, it’s not clear if poor sleep is causing digestive issues, or if the digestive issues are causing poor sleep, research is ongoing.


  • Physical activity. Exercise benefits the digestive system in various ways. It increases motility (helps things move along), enhances circulation, and increases muscle strength of the digestive tract. Exercise helps metabolize food so it can be sourced out for energy quicker, and exercise helps boost sleep quality, which is key for rest and repair of the digestive system.


  • Hydration. Hydration is paramount to a properly functioning digestive system. Research shows that without adequate hydration, digestion and absorption of nutrients suffer, there is an impairment of secretions of fluids that line the digestive tract, and waste elimination is hampered, causing constipation. Saliva can’t be formed without proper hydration (remember– digestion starts in your mouth, for which saliva is key). Drinking water and eating a nutrient-rich diet all contribute to good hydration.

Our digestive system is built to filter and eliminate toxins and waste from the body. Consistently consuming nutrient-dense foods, staying hydrated, and getting decent movement all aid in the body’s natural detoxification processes, and promote liver and adrenal function.


Naturopathic medicine believes in the body’s innate ability to heal itself and treat the root cause of illness rather than. However, certain cases can benefit from more deliberate detoxification measures. When a person’s digestion is not working properly and health issues arise as a result, your naturopath may help free up congestions using detox and cleansing methods, such as an elimination diet or low FODMAP diet, herbs, teas, and colon cleanses. Simple detox strategies that support the digestive system include:


  • Elimination diet
  • Regular Movement/exercise
  • Proper Hydration
  • Herbal Therapy
  • Nutritional Supplementation, such as probiotics.
  • Fasting
  • Colon hydrotherapy – flushing the colon with fluids to remove waste
  • Saunas
  • Gut Health Restoration

Studies show that it is common in naturopathic medicine to utilize research-backed detoxification therapies. 

You may benefit from a more structured detox plan if you’ve had recurring digestive distress, such as gas, bloating, diarrhea, constipation, or acid reflux. When you’ve tried changing your diet and made lifestyle changes to get in more movement and manage stress and sleep, but have not seen changes to your symptoms, talk with your naturopath about what steps you could take next. Naturopaths understand that each person is unique in what is causing their digestive issues. They can help you come up with a customized plan that makes the most sense for you.


Common health problems associated with poor gut health include bloating, constipation, and IBS and IBD. A naturopathic approach to these digestive issues includes looking for what is causing them in the first place, such as:

  • Food intolerances
  • Stress
  • Hormone imbalance
  • Dysbiosis (an imbalance of microbes and flora in the gut)
  • Leaky gut syndrome (a deteriorated lining of the digestive tract)

Naturopathic approaches to the treatment of common gut disorders are gaining popularity and being studied for their efficacy.

If you suffer from chronic diarrhea, constipation (or flip-flop between the two), or experience bloating and gas regularly, or if you have an autoimmune disorder, seek professional help to uncover what is causing your issues and get a personalized plan. Your naturopath is trained to investigate digestive health issues and will be adept at customizing a plan to treat and restore your gut health based on your symptoms, health history, and lifestyle.


Since beginning this journey as a mold-literate doctor, I have started to see themes in patient cases.  Right now, the most common theme is with my patients who have GI issues.  The most typical concern is gas and bloating, but there have also been issues with constipation, diarrhea, abdominal pain, and nausea. Some of them have been diagnosed with SIBO.  The common link between them is this; they get better but don’t fully heal while doing all the right things. 

These folks have done stool tests, SIBO tests, H Pylori tests, parasite tests, and even food sensitivity tests.  They remove foods that trigger inflammation.  They try probiotics, enzymes, or even antimicrobials depending on stool testing.  And they get better but not completely better. Then we test for mold and viola, there it is, the root cause trigger lurking in the background.

Some things that definitely make us consider mold testing with GI Symptoms are:

  • Sinus congestion
  • Postnasal Drip
  • Headaches
  • Brain Fog
  • Sleep issues
  • Severe fatigue

Click here to get started with a free 10-minute consultation to see if mold might be the cause of your gut issues.


Naturopathic medicine provides an approach to gut health that is personalized, integrative, and holistic. Adopting a balanced diet by learning which foods are right for you specifically, along with management of other lifestyle practices, like consistent exercise, stress, and sleep regulation are the first steps to restoring the gut. When your microbiome is revitalized and functioning well, you will absorb nutrients and get your immune system on track again so that you can experience health without the burden of a dysbiotic gut. Your hormones will stabilize, your energy levels will increase, and your clarity of mind will improve because the gut-brain axis will be free from congestion and will flow freely again. Potentially any autoimmune issues will go into remission after a leaky gut has been healed. Naturopathic practices for gut health will lead you to overall wellness and lasting health.

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