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How to Heal Your Gut using Functional Medicine

A staggering 60 to 70 million Americans suffer from gut dysfunction.

Many people with gut dysfunction don’t seek medical help, preferring to deal with symptoms of bloating, gas, heartburn, diarrhea, constipation, and nausea on their own. Others simply wait for the symptoms to pass without considering what these signs might reveal about their health.

Gut dysfunction includes many common gut disorders such as irritable bowel syndrome (IBS), dysbiosis, parasites, small intestinal bacterial overgrowth (SIBO), etc. These disorders not only affect the quality of your life but can lead to more severe health problems in the future.

A comprehensive stool study and food allergy and sensitivity panel reveal many clues about your overall health. The doctors at Boulder Holistic Functional Medicine in Boulder, CO use the results of these tests to heal your gut using a holistic approach.

Functional medicine digs for the root cause of your digestive issues. Keep reading to learn more about how to heal your gut using functional medicine.

Healing Your Gut: The Microbiome’s Role

To heal the gut, you need to start with the microbiome. Your gut houses your microbiome – an incredibly diverse variety of beneficial bacteria that holds the key to brain health, mood stability, a strong immune system, and so much more. A healthy gut microbiome consists of 39 trillion bacteria cells – more bacteria cells than human cells!

The diversity of these beneficial bacteria is critical for optimal health because each strain of beneficial bacteria in the gut has a distinct health benefit. One strain controls your mood, one your metabolism and weight, another affects allergies, etc. We don’t yet know which strain has to do with which medical condition, but we do know that you want a wide diversity of bacteria in your gut for optimal health.

Experts are slowly learning what each bacterial strain can do. For example, one strain may have something to do with your metabolism, another with mood, another with atopy or allergies, and yet another with immune function.

When it comes to immunity, the microbiome is our biggest immuno-modulator. It increases beneficial immune signaling and decreases immune dysfunction – such as allergies, inflammation, and auto-immunity.

In the preceding sections, we will look at leaky gut, acid reflux, and small intestinal bacterial overgrowth (SIBO). These common gut dysfunctions appear when your gut is thrown out of balance. The dysfunction could result from an illness, medical treatment, food intolerance or allergy, or a myriad of other reasons.

In the functional medicine approach to healing gut dysfunction, you focus on getting as many strains of good bacteria permanently colonized as possible to optimize your health. Whatever the source, Dr. Fox at Boulder Holistic Functional Medicine in Boulder Colorado can use a functional medicine approach to root out the cause of your digestive issues. Keep reading to learn more about how to heal your gut using functional medicine.

A Little Gut Anatomy

Your gastrointestinal tract is one long tube that starts in your mouth and ends where your stool comes out.  The food you eat gets broken down in your mouth, passes into the esophagus, and then into the stomach. The hydrochloric acid in your stomach breaks down your meal from macro to micromolecular substances that can then be broken down further into microscopic molecules that your body can take in as food.

From there, food passes into the small intestine which is responsible for absorbing nutrients into the body as fuel. A healthy small intestinal lining has microvilli where the receptors are located to absorb nutrients.

The small intestine is about 20 feet long and is intricately folded into itself to fit in your abdominal cavity. When spread out, the surface area of the small intestinal wall is almost the size of a tennis court!

Once the food enters the small intestine, a signal is sent to your pancreas to release its digestive enzymes. These enzymes break down your proteins, fats, and carbohydrates into small enough particles that they can bind to a receptor on the small intestinal wall.

Bile is released from the gallbladder which breaks down fats and emulsifies them in a way that they can then be absorbed into the body. Bile also carries systemic toxins into the GI tract in order to detox and get them out of the body via the stool.

Once the food is sufficiently broken down and nutrients absorbed, your food ends up in the large intestine or colon. The colon is responsible for pulling the water out of the indigestible food. The microbiome is located in your colon so it can assist in food breakdown, create essential vitamins, and train the immune system to recognize potential threats.

Common Gut Dysfunctions

As you can see, the digestion of food relies on many functions working smoothly and cohesively. When even one part of the system is disrupted, you may experience symptoms of gut dysfunction.

In this article, we will focus on what causes leaky gut, GERD, SIBO, and parasites.

1. Leaky Gut (Increased Intestinal Permeability)

Your gut lining is naturally semi-permeable to allow water and nutrients to flow from the digestive system into the bloodstream. If the small intestinal lining gets too porous, dysfunction is the result.

Leaky gut, or increased intestinal permeability, can be caused by antibiotics, steroids, NSAIDs (like Advil), infections, and food allergies. You may not know that you have a leaky gut since it is usually asymptomatic.

As the small intestinal lining becomes more permeable, substances are free to move between your small intestinal cells and encounter your immune system before they are properly broken down.

The danger of having a leaky gut is that it creates an environment for autoimmune disorders, food sensitivities, and allergies as the body mistakes the strange substances in the bloodstream for harmful pathogens. This is called molecular mimicry.


Gastroesophageal reflux disease (GERD) is often referred to as acid reflux. This is when hydrochloric acid splashes out of the stomach into the esophagus, causing a burning feeling in the upper chest and throat.

GERD is partially the result of a lax lower esophageal sphincter. One reason why your sphincter may become lax is a type of medication called a proton pump inhibitor. These medications block your stomach’s ability to create hydrochloric acid. Hydrochloric acid is one of the triggers for the lower esophageal sphincter to close tightly.

The signal for the stomach to secrete its protective layer comes from the acid itself. So, when the production of acid is blocked, the parietal cells stop secreting their protective layer.

If you have chronic acid reflux, proton pump inhibitors may only prolong the issue. At Boulder Holistic, we use mucilaginous herbs like marshmallows, licorice, and slippery elm to line the lower esophagus and stomach and decrease inflammation. Adaptogenic herbs also help retrain the parietal cells to secrete their own protective mucous layer.

A lack of stomach acid, or hypochlorhydria, is the cause of many gut dysfunctions. Without stomach acid, your body is not able to break down food properly or absorb essential vitamins and nutrients. Over time, a lack of stomach acid can result in indigestion, malnutrition, and bacterial overgrowth.


You may know that when you take antibiotics, you flush the system of both good and bad bacteria. The antibiotics don’t distinguish between the two.

Small intestine bacterial overgrowth or SIBO is when bad bacteria and other harmful substances take over the walls of the small intestine. These substances create a biofilm to protect it from your immune system and to keep it from being flushed from the body during digestion. SIBO is characterized by chronic gas, bloating, constipation, and/or diarrhea.

Small intestine fungal overgrowth (SIFO) is a similar issue that results from an overgrowth of yeast or mold.

When Dr. Fox at Boulder Holistic treats SIBO/SIFO, she uses a unique approach through immunomodulation to help heal your SIBO/SIFO for good!

4. Parasites

Parasites are more common than you might think and difficult to find. They don’t always show up on stool studies because they reproduce on a certain cycle and are only detectable during reproduction.

Some signs that your gut dysfunction might be related to a parasite include vomiting, diarrhea, abdominal pain, gas bloating, nausea, and even constipation.

If Dr. Fox has treated your gut dysfunction symptoms without any visible results, she may consider a parasite cleanse protocol to rule out any undiscovered parasites in your gut.

Diagnosing Gut Dysfunction

But first, your doctor needs a clear picture of your overall gut health. Your functional medicine doctor at Boulder Holistic will use both a stool study and a food panel to uncover the root cause behind your gut dysfunction.

The Stool Study

A comprehensive stool study provides a wealth of information to your functional medicine provider. It reveals where your gastrointestinal (GI) tract might be imbalanced using different markers that your doctor uses to diagnose and treat your gut dysfunction.

Some markers show whether or not you have enough hydrochloric acid in the stomach to break down your food from macro to micro-molecular size. Others show your enzyme levels which indicate how well your body digests food so that your body can absorb them into the system as nutrients. The study also has markers for bile acids that are necessary to emulsify the fats in your diet and take them into the body as food.

More significantly, the stool study shows the diversity – or lack thereof – of your microbiome. It gives your doctor a sense of the levels of beneficial bacteria but also shows areas that need improvement.

Unhealthy overgrowths of yeast, parasites, or disease-causing bacteria indicate a need for a gut reset. Your doctor will also look for markers that point to a more serious problem such as colon cancer, Crohn’s disease, or colitis – all of which require a colonoscopy to rule out.

All of the information in your stool study makes it easier to get rid of the bad stuff and replace it with the good stuff – healing your gut!

Boulder Holistic uses GI effects (Genova diagnostic) or GI Map for your stool study. However, there are many other great options out there.

The Food Panel

A food panel reveals your food sensitivities and allergies. Both food allergies and sensitivities can cause inflammation, IBS, bloating, and many other uncomfortable gut disorders.

An alternative to a food panel is to try an elimination diet. During an elimination diet, you remove all inflammatory foods for six weeks. Common inflammatory foods include dairy, eggs, gluten, soy, corn, refined sugars, nuts, and legumes.

Once you’ve successfully removed all of these items from your diet for six weeks, you add one back in at a time for five days in a large quantity to elicit a response if you have one, as a diagnostic procedure.

Another common test – separate from a food panel – is the DQ2 and DQ8 genetic test that shows your susceptibility to celiac disease.

Boulder Holistic recommends IgG, IgA, and IgE testing for food sensitivities and allergies. However, there are many other great options out there.

How Boulder Holistic Treats Common Gut Dysfunctions

The functional medicine approach uses the information from the stool test and the food panel to find the cause of your gut dysfunction. Both tests reveal a lot about your health and give your doctor an idea of where they should start treatment.

Each type of gut dysfunction requires a unique approach. Here is how Boulder Holistic treats two of the most common gut dysfunctions: irritable bowel syndrome (IBS) and dysbiosis.

Irritable Bowel Syndrome (IBS)

Irritable Bowel Syndrome is a term used to describe chronic gut dysfunction. You might experience diarrhea, constipation, bloating, gas, or all of the above.

Essentially, an IBS diagnosis indicates that something is irritating the GI tract but the cause is still unknown. Functional medicine searches out the cause using the food panel, stool study, and other studies to better identify what is agitating your GI tract.

Gut Dysbiosis

Gut dysbiosis is an imbalance in the gut flora. The imbalance might be caused by antibiotics, illness, a parasite, or any number of unforeseen life circumstances. But the bottom line is that bad bacteria take over all available space in the colon where the good bacteria were before.

Even if you take a probiotic, the bad bacteria will prevent the good bacteria from sticking or permanently colonizing. To rebalance the gut, you need to kill off any pathogenic or bad bacteria. The stool sample is used to find bad bacteria as well as the best herbs to remove them from the colon.

As you kill off the bad bacteria, you add the good bacteria back in. You want to expose the gut to as many different beneficial bacteria as possible during this process. As you do that, the good bacteria stay in the colon, hopefully permanently colonizing, and the gut begins to heal.

Make an Appointment at Boulder Holistic Functional Medicine

Boulder Holistic is a functional medicine practice in Boulder, CO, that uses integrative medicine to address gut dysfunction. Their experienced doctors search out the root cause of your unique symptoms to heal your gut naturally.

Contact our office to schedule an appointment or ask questions about what Boulder Holistic can do for you!

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Dr. Terri Rebibo Fox

Dr. Terri Fox is a holistic, integrative, functional medicine doctor in Boulder, Colorado. She works on your behalf as a medical detective searching for the underlying dysfunction, instead of just treating your symptoms. She has expertise in fatigue, bio-identical hormones, sleep disorders, gastro-intestinal dysfunction, and Chronic Inflammatory Response Syndrome from mold toxicity and Lyme disease.