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 gut dysfunction specialists 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!

Email Us

Have a question? Need to schedule an appointment? Send us an email. We'll get back to you right away.

Get Directions

2355 Canyon Blvd
Suite 102
Boulder, CO 80302

Phone Icon

Call Us

Need an appointment, prescription refill or have questions? Call us from 9:30am to 4:00pm.

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.

Read more from the Boulder Holistic blog:

Castor Oil: Your New Go-To For Detoxification & Flawless Skin

In a world inundated with remedies, castor oil is one that has stood the test of time. Boulder Holistic Functional Medicine highly recommends this natural remedy for detoxification and flawless skin. Castor oil has a history rooted in traditional medicine and enhanced by modern science. Ever heard of a castor oil pack? The topical application of …

Read More »
Sirtuins & Aging - two happy women launching after a workout

Sirtuins: Your New Best Friends in the Fight Against Aging

Sirtuins are one of the seven “longevity genes” found inside your cells. These tiny enzymes are essential for regulating cell cycles and protecting your DNA. They also play a major role in cellular processes that control inflammation and metabolism. From deep within your cell, sirtuins influence…

Read More »

Revolutionizing Gut Health: The Truth About SIBO And SIFO

In the intricate world of gut health, two often misunderstood conditions stand out: Small Intestinal Bacterial Overgrowth (SIBO) and Small Intestinal Fungal Overgrowth (SIFO). SIBO and SIFO not only sound similar, they have similar symptoms including bloating, gas, and abdominal pain.

Read More »

Unleashing Mitochondria Function: The Power Within

When you were in school, you probably learned about the mitochondria as the powerhouse of the cell. Every cell in your body, from your brain to your heart, has mitochondria. They convert energy from our food into a form that our body can use as energy to move, speak, think, and grow.
But what happens when your mitochondria don’t work properly? And how do you keep your mitochondria …

Read More »

Sleep: Causes of Poor Sleep & Natural Remedies For a Better Night Sleep

Do you fall asleep easily only to lie in bed wide awake at 3 a.m.? Or maybe it’s easy to fall asleep but you wake up exhausted? Do you dread bedtime because you have such a hard time sleeping? Nobody wants to stay awake in the middle of the night, mind racing through scenarios that may never come to pass. But good sleep is more than a desire – You need to sleep. Not only because sleep supports healthy digestion and detoxification, but because the world …

Read More »

Low Dose Naltrexone (LDN): A Game-Changer for Autoimmune Disease & Chronic Illness

The functional medicine providers at Boulder Holistic Functional Medicine make it a point to stay up-to-date on the latest advancements in alternative treatments. Low Dose Naltrexone (LDN) is one that is increasingly popular among holistic medicine practitioners because studies have shown it has significant benefits for those suffering from autoimmune diseases and chronic …

Read More »

Exploring Hair Loss in Women: Causes, Treatments, and How to Manage It

Hair loss in women is more common than you might think. Women both young and old may have clumps of hair come out in the shower or see areas of thinning in the front or top of their head. Societal standards of beauty often center on healthy hair and skin. So now female hair loss comes with emotional strain on top of worries about potential health problems. Not to mention that stress about your looks and health can lead to high levels of cortisol, which can lead to …

Read More »
Intermittent Fasting - Boulder Holistic Functional Medicine (stacked rocks)

Unlock the Power of Intermittent Fasting: Pros, Cons, and Secrets Revealed

Fasting is an ancient therapeutic technique that dates back to the 5th century BCE. Back then, fasting mainly was a religious practice, but it was also used to treat certain illnesses. It took the advances of modern science to reveal the many benefits of fasting for your health. Intermittent fasting is the most recent trend in fasting, a practice …

Read More »
Lyme Disease Boulder Holistic Functional Medicine 1 Hero

What Causes Lyme Disease? The Top 5 Reasons Lyme Disease Remains Chronic

Over 300,000 Americans are diagnosed and treated for Lyme disease every year. Despite growing awareness of Lyme disease’s prevalence, the tick-borne illness often goes unnoticed. Even properly diagnosed, Lyme disease can remain in your system for years and severely affect your quality of life. The doctors at Boulder Holistic Functional Medicine in Boulder, Colorado are Lyme disease specialists who …

Read More »
Herbal Remedies

Methylation and Mental Health: Why We Should Pay Attention to Our DNA

Methylation and Mental Health: Why We Should Pay Attention to Our DNA – You might not know it, but a crucial bodily process is often overlooked when it comes to mental health. Methylation and mental health are naturally intertwined, and supporting methylation could revolutionize mental health care. Mental health disorders …

Read More »
Joint Inflamation

Inflammation May Be Aging You Faster Than You Think

Inflammation May Be Aging You Faster Than You Think :: Inflammation may be aging you faster than you think and if you want to live a long, healthy, active life – decreasing your inflammation is critical. Inflammation is a natural, healthy part of the healing process. However, sometimes this inflammatory response is …

Read More »
Menopause on spell out blocks

The 3 Stages of Menopause: The Importance of Teaching Women About Menopause

When we educate ourselves about menopause, we are more capable of understanding and supporting the women in our lives who will inevitably experience menopause. If you’re a man and don’t think this article pertains to you – I urge you to read on. All of us are affected by menopause. We either go through it ourselves or watch our mothers, grandmothers, wives, and lovers experience

Read More »

The Functional Medicine Approach for Improving Your Mental Health

Mental health conditions like anxiety, depression, ADD, ADHD, and PTSD are on the rise. One in five children and adults will experience any of these mental afflictions in a given year. Functional medicine offers a unique approach to mental health support. Instead of treating the symptoms, it treats the root cause of mental health. What we get wrong about mental health is looking at the …

Read More »
Membrane Power Shake Drink Duo with Blueberries

Revitalize Your Body and Mind with Membrane Supportive Power Shake

We all know what happens if we don’t change the oil in our cars, but what about the oil in our bodies? Every cell membrane in our bodies is made up of a phospholipid bi-layer and maybe even more importantly, every mitochondrion in our cells also is made up of the lipid bilayer. So what happens to the fats in our membranes over time? Exposure to …

Read More »
French press is best when making coffee enema

Benefits of Coffee Enema

The health benefits of coffee enemas may include relief from symptoms of Lyme disease, multiple chemical sensitivities, and heavy metal toxicity. There are very few toxicity-related reactions that couldn’t be stopped or tremendously reduced with a coffee enema. Coffee enema is great …

Read More »

Mold Toxicity Symptoms & Treatment

Most people have some experience with mold, but what does toxic mold look like? The black gunk in a window frame, the moldy smell in a damp basement, or the fuzz on food left in the fridge for too long.
Not all molds are inherently harmful. Some strains of mold …

Read More »

Bioidentical Hormones: What Women Need to Know

We are hormonal beings. Hormones are powerful and connected to every part of your body in a beautiful, delicate balance. They control many of the body’s essential functions including your mood, energy level, survival instinct, libido, anxiety, and sleep.

Read More »

Limbic Retraining for Chronic Illness

What is the limbic system and how does the limbic system function? The limbic system is the part of the brain involved in our behavioral and emotional response. Often referred to as our animal brain, the limbic system is dramatically affected by illness. It responds to illness like a smoke alarm responds to smoke or fire. It activates and stays activated until …

Read More »

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…

Read More »
What causes Thyroid problems?

What Causes Thyroid Problems?

According to recent estimates, about 10 million Americans suffer from an underactive thyroid. This condition, called hypothyroidism, causes several tell-tale symptoms, including fatigue, brain fog, hair loss, constipation, low mood, and temperature intolerance. What causes low thyroid? These symptoms are related to inadequate or imbalanced thyroid hormones, including high reverse T3.

Read More »

August Summer Heat Hydration Special

The heat is ON and it’s a great time to revitalize, hydrate and boost your immune system to get the most out of the last few weeks of summer before school starts. Medical grade nutritional IV’s have been found by many to help get your energy and vitality back after COVID.

Read More »

The leaves are back, the kids are out of school, it smells like flowers, summer in Colorado is here!

Boulder Holistic has an exciting announcement! Our Registered Nurse extraordinaire, Ame, is back! She will be in clinic 2-4 days per week including some Saturdays and we are offering Nutritional IV’s, blood draws, PRP (more info to come), urine and throat checks, ionic foot baths, etc. on those days. Please call the office at 303-390-1245 or email us at to schedule.

Read More »

Mask-acne… it’s a thing

Masks are now the new hot accessories but wearing a mask for hours a day can block the pores of your skin and put you at risk of developing acne. As healthcare providers, we know the best way to treat acne is to prevent it before it happens.

So, since mask wearing is not likely to go away for a while, it seems important to figure out how to best protect our faces and stop the pimples that masks can cause.

Read More »

Reversing Insulin Resistance

Insulin resistance is a hot topic in the health and functional medicine world. Our fast passed, high stress and inactive lifestyles put many people at risk for this undesirable condition. Luckily, insulin resistance is not only preventable, but may be reversible by making healthy diet and lifestyle changes now!

Read More »

The Latest COVID-19 Updates from Boulder Holistic

On Friday November 20th 2020, Boulder and Denver counties entered the “new red” COVID restriction levels. So what does that mean for us at Boulder Holistic?

Due to the current risk of COVID-19 infection, we are trying to do our part in slowing the spread of the coronavirus by limiting the number of face-to-face appointments per state order. We are booking appointments with our doctors via telemedicine through zoom or over the phone over the next few weeks in order to best comply with the new restrictions.

Read More »

Using Your Supplements Wisely: How to Best Protect and Heal from COVID-19

As fall turns to winter, the number of coronavirus cases in our state and the country continues to grow. Thankfully, over the past months doctors and researchers have learned more about the virus and how to best approach prevention and treatment.

Functional medicine thrives when it comes to understanding root causes of illness and how to support proper immune function. The research has shown that a step-wise approach to the coronavirus may be the best medicine.

Read More »

Fall and COVID-19

Autumn is my favorite season…it must be the Midwesterner in me. I absolutely love watching the leaves change, feeling the crispness in the air and diving headfirst into my fuzzy sweaters.

As the nights get colder, my family and I are enjoying our back yard, social distanced dinner gatherings seated near our propane fire pit, wrapped in cozy blankets. One thing quarantine has gifted me is a deep appreciation for the connections I share with close friends and family.

Read More »

Heal The Vagus Nerve and Improve Your Health

Heal The Vagus Nerve and Improve Your Health

Optimum Vagus nerve function or vagal tone is a hot topic in current research, especially as it relates to the treatment and management of chronic illness.

As practitioners, we are just now beginning to understand how important supporting this nerve is to maintaining health.

So what exactly is the Vagus nerve?

Read More »

Melatonin: Why this sleep-inducing hormone is a surprise hero in COVID-19

Many of us are familiar with the use of melatonin for better sleep, but did you know that melatonin might also be helpful in managing some of the symptoms of a COVID-19 infection?

Over the past few months, we have learned more and more about this new virus. Much of what we know about those individuals who become very sick from COVID-19 is the devastating effects this virus has on the lungs and respiratory system. Many of those who become hospitalized with coronavirus end up there because the inflammation in the lungs is so great that they are no longer able to get enough oxygen on their own.

Read More »

We Are Here For You!

Boulder Holistic is dedicated to providing the best possible service to you and your family during this crucial time. We are excited to announce that we will be re-opening for IV therapy and blood draws on Wednesday and Friday through the month of June.

Read More »

Allergies in the time of COVID-19

There’s bad news and there is good news this allergy season.

Many of the symptoms of seasonal allergies can be mistaken for signs and symptoms of other upper respiratory infections including COVID-19. Many symptoms include runny nose, stuffy nose, red eyes, scratchy throat, cough, tight chest and sneezing.

Read More »

Up The Nose

COVID Prevention AND great for allergy season too!
One great way to help prevent the seeding of a virus into upper respiratory tract is by sinus rinsing. Sinus rinse and prevent viral infection, improve allergies and neurodetoxification!

Read More »

What the Heck is EMF?

What Exactly is EMF? Electromagnetic Fields (EMF) are a form of non-ionizing radiation (their frequency is somewhere between microwaves and radio waves). This radiation is

Read More »

Tired of feeling so tired?

Spent. Haggard. Beat. There’s no end to the words we can use to describe being tired, especially in today’s hyperspeed cyber world. My personal favorite?

Read More »