Naturopathic Approaches to Gut Health

“All disease begins in the gut.” – Hippocrates

One of the most common complaints that naturopathic doctors encounter revolves around digestion and digestive health. It is estimated that roughly 70 million Americans are affected by some type of digestive disorder, which includes everything from gas and bloating, constipation or diarrhea, to an actual named disease such as Crohn’s disease or ulcerative colitis. 1


Why is digestive health so important and why do NDs focus on it?

As the Hippocrates quote heading this article indicates, “All disease begins in the gut.”  This idea is echoed in naturopathic medical practice, as gastrointestinal (GI) function contributes to many other aspects of overall health.

A newer concept in mental and emotion health is the “gut/brain axis.”  It is acknowledged that there is an intricate communication mechanism between the digestive system and the brain. In fact, the gut is so highly innervated that it has its own dedicated nervous system, the enteric nervous system (ENS). The parasympathetic nervous system (PSNS) and ENS provide a feedback system to each other via the vagus nerve (a cranial nerve that innervates the heart, lungs, and almost the entire GI tract). 2 They are also connected through the limbic system (hypothalamus and amygdala), the area of the brain involved in memory and emotional response. 3

The vagus nerve begins in the brain stem and travels through the neck, down through the thoracic and abdominal regions, and particularly affects the organs of the digestive system.  During times of stress, anxiety, or depression for example, signals from the vagus nerve travel to the GI tract and can cause symptoms such as abdominal pain, constipation, and diarrhea. The feedback mechanism is such that these messages travel back up to the brain via the vagus nerve, possibly creating even more mental and emotional registration of symptoms. A similar effect occurs between the gut and limbic system in that signals from the brain impact digestive health and vice versa. 4 Additionally, many neurotransmitters directly act via the gut-brain axis, such as dopamine, epinephrine and norepinephrine. Large amounts of serotonin are actually produced in the gut. 5

The microbiome, which is a collection of micro-organisms found primarily in the large intestine, is critically important in optimal gut function, and overall health as well. The microbiome is an enormous population of bacteria that had previously been thought to outnumber our own body’s cells by as many as 10:1, though a recent study reports that the ratio is closer to 1:1 in most people. 6 That’s still a lot of bugs! The microbiome has been connected to several health conditions including depression and anxiety (7), lung conditions such as asthma and cystic fibrosis (8), impaired immune function (including autoimmunity and allergy) (9) , obesity (10), type 2 diabetes (11), Alzheimer’s Disease (12), Autistic Spectrum Disorders (13), and epilepsy.14

Finally, digestive health is tied to immune function, as nearly 70% of our entire immune system resides in the gut! 15 This intricate immune system consists of gut-associated lymphoid tissue (GALT) and is part of the larger mucosal-associated lymphoid tissue (MALT) which includes immune cells in the respiratory tract, oral passage, and genitourinary tract. These GALT areas of tissue, referred to as Peyer’s Patches, are found prominently throughout the intestinal tract and are critical in protecting us from pathogenic or opportunistic microbes (bacteria, fungi, protozoa, and viruses) and toxic material that may be in our food and water supply.

June 9, 2020
Megan Taylor, ND

GraduateNational University of Natural Medicine

"I often talk with my patients about how they can be good stewards of their digestive tract. It’s pretty straight forward (though not always easy) – eat plenty of plants (the brighter and more polyphenol rich, the better!), drink enough water (filtered, please), get daily de-stressing time and restful sleep, and avoid excessive snacking between meals and give your gut that nice long nighttime fast (it works hard, and needs breaks just like you!). If doing these things are difficult for you to implement or you have symptoms regardless, find a physician that can help you navigate appropriate testing and treatment. This is what we naturopathic physicians do best!"


Naturopathic Approach to Gut Health

Because NDs practice medicine by identifying the root cause of any condition, testing is usually required to determine underlying pathology responsible for issues in a patient’s health. If someone is suffering from digestive complaints, blood testing for food sensitivities and allergies, bacterial or yeast overgrowth via a stool test or even a breath test can be utilized to determine if there are organisms living in the small intestine (where there should not be) or other imbalances implicated in symptom expression.  Treatment is then individualized based on the results of the testing.  The following are digestive issues that are commonly treated by naturopathic doctors.



As described above, the microbiome is a collection of bacteria that resides in the large intestine of the digestive tract.  Unbalanced gut flora is one of the primary drivers of many digestive disorders. The problem can be either an overgrowth of unhealthy bacteria, or an undergrowth of beneficial bugs.  Frequently, an overgrowth of yeast is to blame, and the most common symptoms produced are gas, bloating, and diarrhea. Dysbiosis can be diagnosed via a stool test (large intestine imbalance) or a breath test for the small intestine. The naturopathic approach for treatment is a “weed and feed” process.  Either herbal or prescription antimicrobials (sometimes alternating with both) are given to kill the bad bacteria (the weeding), and then a probiotic is prescribed to re-populate the gut with good bacteria (the feeding). In this way, the good bacteria are able to crowd out the harmful microbes and proper digestive functioning can be re-established. Prebiotics may also be prescribed. These are substrates that the beneficial bacteria use to grow.

An example of dysbiosis (microbiome imbalance) which has become better understood in recent years is small intestinal bacterial overgrowth (SIBO). SIBO occurs when bacteria inappropriately colonize the small intestine.  Because of defective motility of the gut, the bacteria migrate upward rather than staying in the colon where they belong. As with other forms of dysbiosis, the symptoms are abdominal pain, gas, bloating, constipation, and/or diarrhea. The treatment is also comprised of a weed and feed approach (remove offending bacteria and then replace with beneficial ones), with the addition of motility agents that prevent the bacteria from moving upward.


Dietary Considerations for Dysbiosis

Dietary considerations must be taken into account when balancing the microbiome to prevent and treat dysbiosis. Highly processed foods are associated with a less healthy microbiome, particularly a diet high in refined carbohydrates and low-quality fats. These foods have been shown to reduce the biodiversity of the microbiome, resulting in a host of health issues that may be related to the above conditions. A diet high in legumes, fruits, and vegetables are associated with a more diverse microbiome which keeps inflammation at bay and ensures a more properly functioning immune system. 16


Leaky Gut

Intestinal permeability, or leaky gut as it is commonly known, is a condition that affects the lining of the small intestine. When the intestinal wall comes into contact with inflammatory foods, toxins from food and water, or even metabolites from the above-mentioned bacteria and fungi, this can result in damage to the cells that line the gut. Connections between the cells are referred to as “tight junctions,” because its job is to create a sufficient barrier between the gut and the bloodstream. 17  This is necessary to prevent larger proteins from food and toxins from escaping out of the GI tract and entering the system. If these tight junctions are affected, and become “leaky” and proteins do escape, the immune system identifies them as outside invaders and will launch an immune response, resulting in food sensitivities, allergies, and autoimmunity. 18

Leaky gut is typically addressed by identifying and eliminating food sensitivities, healing the gut lining with supplements such as L-glutamine, and adding anti-inflammatory herbs and a whole foods diet low in processed fats and carbohydrates.


Inflammatory Bowel Disease

Inflammatory bowel disease (IBD), as its name suggests, is chronic inflammation of the gut. Generally speaking, the two most common forms of IBD are Crohn’s and ulcerative colitis UC) and are characterized by symptoms such as abdominal pain, diarrhea, rectal bleeding, and weight loss. 19

While the cause of IBD is not entirely known, research suggests that a genetic component may be present, combined with environmental factors, such as stress and lack of exercise, and of course, the state of the microbiome. 20 Research shows that a diet high in low quality fats, frequent meals of fast foods, high refined carbohydrate intake, and low fiber diets result in a dysbiosis that may exacerbate symptoms of IBS. Dietary recommendations include a low fat, high fiber, diet that excludes potential triggers such as dairy and refined grains. Foods high in vitamins A, D, E, folate, and beta carotene, as well as minerals zinc, selenium, manganese, and iron appear to be particularly helpful. 21


Gastroesophageal Reflux Disease (GERD)

Heartburn, and acid reflux are other names for GERD, which is an extremely common condition affecting approximately 20% of people in the United States. 22 GERD occurs when stomach acid moves upward from the stomach into the esophagus and results in symptoms of chest pain/burning, sour taste in the mouth, sore throat, chronic cough, and difficulty swallowing, and is usually worse at night when lying down. 23  GERD is caused by a laxity of the lower esophageal sphincter (LES), which allows the gastric juices to “reflux” up into the esophagus rather than remaining in the stomach where they belong. GERD is typically diagnosed by symptoms; however, an endoscopy may be ordered to assess for damage to the esophagus or to rule out more serious conditions. 24

Naturopathic treatments include finding and eliminating food sensitives, body work to tonify the LES, and supplements/ herbs that are soothing and healing to the upper digestive tract (see below).

June 9, 2020
Wm. Thor Conner, ND

GraduateNational University of Health Sciences

"Naturopathic doctors focus on making the delicately balanced system work the way it should – removing reactionary and irritating foods from the diet, balancing the flora, and encouraging digestion and motility. Just as importantly, we teach the patient to take charge of the process of healing and to alter lifestyle factors. We do not suppress the symptom to manage a disease. We will use drugs and surgery if it is necessary for the case, but as a last option."


Supplements for Gut Health

Because digestive complaints are so incredibly prevalent in our society, naturopathic doctors have lots of treatment options to help re-establish gut health! Here are a few of our favorites:

  • L-Glutamine – this amino acid acts as a primary fuel source for the cells of the GI tract and can heal leaky gut.
  • Digestive Enzymes – taken orally, digestive enzymes help breakdown our meals to ensure proper digestive function and takes stress off of the pancreas and gall bladder.
  • De-glycyrrhizinated Licorice (DGL) – is made from licorice root (not the candy!) and is used to sooth inflamed tissues from GERD and to treat gastric and intestinal ulcers.
  • Slippery Elm – another soothing herb, as its name implies, the bark of this tree develops a “slippery” consistency when brewed into a tea. Useful in treating GERD and ulcers.
  • Peppermint – made as a tea, tincture or soft gel to swallow, this common herb is great for dispelling gas and reducing abdominal bloating – too much can lead to GERD – so it is best monitored by an ND.
  • Chamomile – not only is chamomile very relaxing to the nervous system, but it acts as a gentle bitter herb to stimulate digestive enzyme production. Very helpful for indigestion and constipation.
  • Curcumin – the active component of turmeric, this compound is a powerful anti-inflammatory that can effectively treat IBD and leaky gut.
  • Berberine – this chemical constituent of Goldenseal and Oregon Grape root is a broad spectrum, antimicrobial used to kill harmful bacteria and yeast.

Naturopathic doctors are specifically and thoroughly trained to assess and treat a wide range of digestive disorders in cases where conventional medicine often fails.


Hear from a few naturopathic doctors about how they help patients with GI complaints

June 9, 2020
Megan Taylor, ND

GraduateNational University of Natural Medicine

"Naturopathic physicians view the health of the gastrointestinal tract as foundational for overall health and wellness. We often have many more tools that our conventional colleagues for approaching functional gastrointestinal disorders (IBS, dyspepsia, abdominal pain, constipation, etc.), and are a perfect complement providing adjunctive care for many of the pathologic diagnoses, including inflammatory bowel disease, hepatic and biliary conditions, and malignancies of the GI tract. As with naturopathic medicine as a whole, we think about the “whole person” and provide strategies guided by this perspective, as opposed to a singular focus of GI-based interventions for GI conditions, as can happen more so in conventional medicine. I think this is our greatest strength and is why patients keep seeking us out for care."

June 9, 2020
Crane Holmes, ND

GraduateNational University of Natural Medicine

"Growing up, my aunt battled ulcerative colitis. I didn’t need to understand pathophysiology to see chronic GI illness play a mental, emotional and physical toll on patients and families that cannot be addressed by surgeries and medications alone. I enjoy treating every patient as unique and utilizing all of my tools as a naturopathic doctor to find an individual treatment to address all of parts of health."

June 9, 2020
Marisol Teijeiro, ND

GraduateCanadian College of Naturopathic Medicine

"I truly believe that the greatest wealth is gut health. Our gut is where life begins, it is where we take in the outside world and use it for our inside world. It is how we digest, absorb, and eliminate – the three most vital functions to living well. We must be able to take in nutrients and use them to survive. It is ALWAYS the first thing I focus on when patients come to me because without a healthy gut, nothing in the body will get the nutrients it needs to function optimally."

June 9, 2020
Lela Altman, ND, LAc

GraduateBastyr University

"Gut health is so important because what is happening in the digestive system can have a large effect on all other systems; from skin to mood. I feel that gut health is the basis for overall health. An example of this is the fact that significant amounts of neurotransmitters such as serotonin are also made in the gut (in addition to the brain) which may help explain the gut-brain connection."

June 9, 2020
Poonam Patel, BSc, ND

GraduateCanadian College of Naturopathic Medicine

"I often use specific probiotics that have been studied to treat particular GI conditions, control symptoms, and reset the gut balance. Additionally, I frequently emphasize fermented foods, such as sauerkraut, kimchi, pickled foods, etc., to promote gut health with my patients, in order to create an environment that facilitates and sustains the optimal health of the microbiome."

June 9, 2020
Wm. Thor Conner, ND

GraduateNational University of Health Sciences

"Pre-digesting the food is important. That sounds gross, but it’s just cooking, cutting and fermenting to make it ready to be absorbed quicker and more efficiently when it gets to the gut. For example, lightly steamed broccoli is easier to digest than raw, yogurt is easier to digest than milk, and think about the difference cooking makes to a potato or chicken. Fermented foods like sauerkraut are great to add to a healthy diet. The fermentation process unlocks a lot of extra nutrients and confer a decent dose of probiotic bacteria and prebiotic food for the bacteria. A good amount of mixed fiber from food sources and supplements will keep things moving, and don’t forget to drink enough water."

If you want to explore a deep healing relationship with a naturopathic physician or are curious about what they do before applying to ND school, click here for a directory of NDs in the US and Canada.




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