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Pathways to Care: Gastrointestinal Health

Understanding Gastrointestinal Health

Whether you are focused on identifying the underlying cause of chronic health conditions or achieving ultimate health, there is no more important place to begin than in the gut.  Optimal gut health is at the foundation of true health.  Over two thousand years ago, Hippocrates made the statement, “All disease begins in the gut.”  Considering all the processed foods, toxins and environmental assaults on our gut today, this statement is even more true today than it was back then.

 Here is some surprising information about your digestive system:

  • If spread flat, your digestive system would cover a tennis court.
  • You have 10 times as many microbes in your gut as you have cells in your body. These microbes live in a symbiotic relationship with you and if all the microbes in your body died, you could not survive. These microbes live in colonies which make up the microbiome.
  • The bacteria in your digestive system help make vitamins, protect you against infection and control your metabolism.
  • Approximately 70% of your immune system is in the gut.
  • You have 100 times more DNA in your microbiome than in the cells of your body.
  • Your gut manufactures more neurotransmitters, like serotonin than are manufactured in the brain. In fact, 80 to 90 percent of serotonin is made in the gut and every brain neurotransmitter has been found in the gut.
  • You rely on your digestive system and gut microbes to digest, absorb, and utilize the food you eat, thus providing nourishment to all of your cells.
  • If you have digestive issues, you will most likely develop a diagnosable illness at some point.
  • Digestive problems contribute to a wide range of health issues, including arthritis, autoimmune disease, fibromyalgia, migraine headaches, depression, foggy thinking, autism, chronic fatigue and much more.

So what are some of the factors that lead to digestive problems?  These include things such as:

  • Chronic stress
  • Infections
  • Cigarette smoking
  • Medications
  • Environmental toxins
  • Lack of exercise
  • Lack of fiber
  • Poor food choices
  • Low stomach acid
  • Alcohol

Hopefully, it is now clear the gastrointestinal tract involves much more than simply digesting food.  In fact, it is a complex system with much more, and less obvious, functions.  Some of these functions include;

  • Immune: We mentioned over 70% of the immune system resides here. 
    • So when you think auto-immune disease, start by thinking about gut health.
  • Neurological: The enteric nervous system has more nerves than our spine and more neurotransmitters than our brains.
    • So think gut in neurological conditions like alcoholism, alzheimer’s, anxiety, chronic fatigue, dementia, fibromyalgia, neuropathies, and many more.
  • Endocrine: There are more than 16 known digestive hormones.  These include things like ghrelin, gastrin, secretin, and motolin.
    • Some endocrine disorders include hypothyroidism, osteoporosis, diabetes, etc.
  • Cardiovascular: Probiotic bacteria help normalize cholesterol and triglyceride levels. 
    • If you have difficulty with cholesterol and triglyceride levels despite a healthy diet and medication, it might be wise to consider the gut microbiome.
  • Metabolic: As previously stated, the commensal bacteria in the digestive system influence the body’s metabolism.
    • Many metabolic disorder like diabetes and dyslipidemia can be the result of malabsorption of vitamins and cofactors in enzyme production as a result of poor gut health. Also, if you have difficulty gaining or losing weight, you should always consider gut health.

You may have heard it said, “You are what you eat.”  While it is absolutely true that a healthy diet is critical to good health, the previous statement is not entirely accurate.  A more correct statement is, “You are not only what you eat, but also what you can absorb and make available to you cells.”  Yes, the healthiest diet in the world will be of little value if you are not digesting properly.

You must be able to digest foods, break them down into tiny particles, absorb the food, take it through the intestinal lining and into the bloodstream, and eliminate the waste products through the kidneys, bowels, lymph system and skin.  Health can break down at any one of these phases.

Now that you have a general understanding of the gastrointestinal tract, let’s move on to an overview of identifying issues.


If you are not able to digest and absorb your food, your cells will not get the nourishment they need to function properly.  As a result, many health issues begin because people are not fully digesting and/or absorbing food.

Here are some signs you may have poor gut health:

  • Digestive issues like bloating, gas, constipation and/or diarrhea
  • Food allergies and/or sensitivities
  • Mood swings and irritability
  • Anxiety
  • Depression
  • Skin issues like eczema, rosacea and psoriasis
  • Diabetes
  • Autoimmune disease
  • Recurrent infections
  • Problems with memory, concentration and ADHD


There can be several reasons for not fully digesting and absorbing food.  These include: 

  • Not chewing food properly and rushed eating
  • Hydrochloric acid insufficiency
  • Bile insufficiency
  • Enzyme insufficiency
  • Lack of dietary fiber (soluble and insoluble)
  • Choosing poor quality foods
  • Poor hydration (or drinking too much liquid with meals)
  • Toxins


As you previously learned, poor gastrointestinal health can lead to numerous health conditions. Here are some common warning signs of an unhealthy gut:

Autoimmune Disease

We previously discussed how 70% of the immune system is in the gut. 

According to Thomas T. MacDonald, Professor of Immunology and Dean for Research at Barts and the London School of Medicine, “The gut immune system has the challenge of responding to the pathogens while remaining unresponsive to food antigens and the commensal flora.  In the developed world this ability appears to be breaking down, with chronic inflammatory diseases of the gut commonplace in the apparent absence of overt infections.”

In other words, the job of the immune system is to determine what is you and what is not you.  The reason 70% of the immune system is located in the digestive system is because an enormous amount of food that we ingest contains foreign material that needs to be sorted.  If you consider the fact that our modern diet of processed foods is high in chemicals and preservatives, all of which are foreign material, you can see why the immune system can become overactive and confused.  When this happens (as in autoimmune disease) the immune system has lost the ability to distinguish foreign invader from self.

Mental Health

The intestinal wall contains 500 million neurons which make up our enteric nervous system and produces 30 different neurotransmitters.  This system is responsible for balancing our mood, reducing stress and anxiety and keeping our overall mental health in check.

In several studies with mice, researchers were able to alter the mice’s behavior by changing their gut bacteria.  Additionally, intestinal bacteria can influence processes in the brain through the gut-brain axis. (1)

The moral of the story is that your gut absolutely affects your brain, so if you are struggling with stress, anxiety, brain fog, mental fatigue or depression the first thing you should do is check your gut.

Type 2 Diabetes

Researchers have shown an association between type 2 diabetes and changes in the gut microbiota.  A 2015 study identified dysbiosis (overgrowth of bad bacteria) associated with both pre diabetes and type 2 diabetes suggesting early treatment of gastrointestinal dysbiosis could impact the development of type 2 diabetes. (2)

When studying the gut bacteria of people with and without type 2 diabetes, it was found that those with type 2 diabetes had high levels of bad bacteria that did not support gut health.

Immune System

It is now known that a prerequisite to developing an autoimmune condition is the development of Leaky Gut Syndrome (LGS).  LGS is a particularly harmful condition in which your intestinal wall becomes damaged and permeable to deadly toxins that leak out of the intestines into the bloodstream.  When this happens, your immune system recognizes these as foreign invaders and begins to fight them.  As this continually happens, your immune system becomes overworked and you become more susceptible to infection.  Additionally, the immune system loses the ability to distinguish self from foreign invader and can start to attack your organs and tissues.

Skin Conditions

It seems like we are seeing skin conditions like acne, rosacea, psoriasis and dermatitis increasing in frequency.  It is important to understand these are symptoms of something else going on inside our body.  Multiple studies published in the Journal of Dermatology have linked gastrointestinal symptoms to the development of skin issues.  In fact, there are now numerous studies linking psoriasis to gastrointestinal health, including celiac disease, ulcerative colitis, IBD and gluten intolerance. (3)


It has been shown that people at a healthy weight have more balanced and diverse bacteria in their gut than overweight or obese people.    Recent studies found the firmicutes species of bacteria are more prevalent in obese individuals, whereas bacteroidetes was almost 90 percent lower in obese subjects.

Human studies showed that both the diversity of the microbiota and the Bacteroidetes/Firmicutes ratio are decreased in obese individuals.  These “obese microbiota” seem to be able to increase dietary energy harvest and favor weight gain and fat deposition. (4)

Acid Reflux (GERD)

GERD is caused by stomach acid or bile refluxing or backing up into the esophagus.  The lower esophageal sphincter (LES) should normally close and prevent acid from backing up into the esophagus.  While the idea that acid reflux is caused by too much stomach acid is still popular, anyone familiar with current scientific literature is aware GERD is not a disease of excess stomach acid.  In fact, if the LES is working properly, it would not matter how much acid is in the stomach. 

While suppressing acid will reduce the symptoms of GERD, it does nothing to address the underlying problem.  Therefore, it makes sense to focus on the underlying cause and avoid the host of side effects associated with chronic acid suppression.  (More on the side effects of acid suppression in another article).

It is now well accepted that GERD (and failure of the LES to close properly) is caused by increased intra-abdominal pressure.  Acid reflux occurs when pressure causes gastric distention, or stomach bloating, to push the stomach contents, including acid, through the LES and into the esophagus.  This is what leads to recommendations regarding overeating, obesity, bending over or lying down after eating, consuming spicy or fatty foods and alcohol come in, as they all relax or put pressure on the LES.

There can be a number of causes of increased intra-abdominal pressure.  One major cause is carbohydrate malabsorption, leading to bacterial overgrowth, which ultimately causes fermentation of foods in the intestines resulting in gas and increased intra-abdominal pressure.  Other causes of poor digestion or malabsorption, which can produce the same results include:

  • Enzyme deficiencies
  • Nutrient deficiencies
  • SIBO (small intestine bacterial overgrowth)
  • Too little stomach acid

Finally, other and somewhat related causes of GERD include:

  • Food allergies
  • Pylori infection
  • Candida overgrowth
  • Stress (which can cause improper digestion)

As you can see, there are many potential causes of GERD.  Unfortunately, while the chronic use of acid suppressing drugs may relieve symptoms, they do nothing to resolve the underlying cause.  In fact, they contribute to poor digestion and bacterial overgrowth, again contributing to increased intra-abdominal pressure.  And worse they lead to a host of other long term side effects including nutrient depletions, leaky gut syndrome and potentially auto-immune disorders.

Since GERD and the use of acid suppressing medications is so prevalent in our society we will cover much more on this topic, including how to identify the cause and steps to healing in a future article.

Constipation or Diarrhea

If you have a healthy and balanced gut, your elimination should be smooth and easy.  Believe it or not, your bowel movements tell you a great deal about your overall health.

Maintaining a healthy gut is the only way you can regulate your elimination.  If you struggle with diarrhea, constipation, IBS (Irritable Bowel Syndrome), Chron’s disease, Ulcerative Colitis or any other digestive disorder you need to address gut health.  Yes, there can be genetic and auto-immune components involved, but remember that both genes and auto-immune can be influenced by lifestyle and diet.

Root Cause Healing

As previously stated, functional medicine is focused on finding the underlying mechanisms of disease rather than focusing on treating symptoms.  This means there is no cookie cutter approach.  For instance, two people with the same diagnosis may need completely different therapies.   As an example, migraine headaches, fibromyalgia, and irritable bowel syndrome may be different diagnoses, but they may all be caused by leaky gut syndrome or food intolerances.

In the case of digestive issues, we want to look at six potential areas of imbalances.  These include: 

  • Digestion/absorption
  • Gut microbiota
  • Intestinal permeability
  • Immune function
  • Inflammation
  • Enteric nervous system

Once imbalances are identified in one or more of these areas, functional medicine practitioners work to bring these areas back into balance.  In doing this, the practitioner frequently utilizes what is known as the 4 R program, which includes:


Remove: This critical first step involves the removal of anything that can be damaging your gut.  This includes processed foods, poor quality fats and oils, foods you may be allergic or intolerant to, infections, parasites, heavy metals and stress. It is recommended to follow an allergy elimination diet to identify possible food allergies and intolerances.  Additionally, remove alcohol, caffeine, refined sugars and foods containing chemical additives.  Avoid the use of antibiotics, antacids and anti-inflammatory drugs.  Depending on the severity of digestive issues, it may even be necessary to temporarily remove any foods that are difficult to digest to allow the gut time to heal.

Replace: Next, replace what may be missing.  Frequently people suffering from digestive issues are deficient in digestive enzymes and stomach acid.  Both of these are critical to properly digesting food and feeding beneficial bacteria.  Lab tests, including fat absorption tests and gastric tests can help determine what factors need to be replaced.  You should work with your health care practitioner to determine which tests are needed, and what supplements may support healing.  Commonly used supplements to improve digestion include digestive enzymes (including protease, lipase, amylase, and pepsin) and hydrochloric acid (betaine).

Restore: Our intestinal tract is host to over 500 different types of bacteria. In fact, you have more bacteria in your gut than cells in your body.  In a healthy gut the ratio of good bacteria to bad bacteria is approximately 80:20. This ratio can easily get out of balance with poor diet, use of antibiotics, environmental stress, and other factors.

This step involves restoring a healthy gut flora through the use of probiotics.  In    addition to supplementing with good quality probiotics, it is important to focus on a healthy diet to feed the good bacteria. This includes incorporating fermented foods and foods containing resistant starch.

Repair: The final step involves healing the damaged intestinal mucosa.  This is an important step because a damaged intestinal lining leads to a condition called Leaky Gut Syndrome (LGS).  In LGS, the intestinal lining allows substances such as large undigested food particles, pathogenic organisms and other chemical toxins to pass through the intestinal barrier and into the blood stream.  Once in the blood stream, these substances are recognized as “foreign invaders” by the body and can trigger an autoimmune response, resulting in many chronic health conditions like IBS, Crohn’s disease, ADHD, migraine headaches, chronic fatigue syndrome, and eczema just to name a few. 

There are a number of supplements that are beneficial in healing the intestinal tract. The preferred supplement is L-glutamine, as it is the preferred food source of the cells of the small intestine.  Other beneficial supplements include quercetin, gamma linoleic acid (GLA), licorice root (DGL), aloe, marshmallow root, turmeric, and omega-3 fatty acids.

In more severe cases, following a short term diet like the Specific Carbohydrate   Diet is often beneficial.

While the steps mentioned above can be followed by almost anyone, the   specifics of each step should be tailored to the individual.  For this reason, it is recommended you work with a practitioner who is familiar with the protocol, especially if you suffer from a more serious digestive disorder.

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  1. Intestinal Cesk Fysiol. 2015;64(1):23-34.  Microbiota and the brain: multilevel interactions in health and disease.
  2. J Diabetes Obes. 2015 Dec 26;2(3):1-7. Composition, Diversity and Abundance of Gut Microbiome in Prediabetes and type 2 Diabetes.
  3. Br J Dermatol.  2016 Mar 9. Doi: 10.1111/bjd.14528.  Association between psoriasis and inflammatory bowel disease-a Danish nationwide cohort study.
  4. Dig Dis. 2016;34(3):221-9.doi: 10.1159/000443356. Epub 2016 Mar 30.  The Gut Bacteria-Driven Obesity Development.