GI Tract Function & Health – Where It All Begins

Part I: Understanding Digestion

“Death begins in the bowels”

- Hippocrates, 3rd Century BC

“All disease starts in the bowels”

- Élie Metchnikoff, circa 1908

“It all starts in the gut”

- Alessio Fasano MD, Chief, Pediatric Gastroenterology at Massachusetts General Hospital

You may find it hard to believe that gut function is so crucial to our health. Yet every ancient healing tradition believed this, and current medical research is confirming this age old wisdom. Whether it is Traditional Chinese Medicine, Ayurveda, Ancient Greece, or now medicine at the top university in the county - your health status, your vitality, all begin in your digestive system. And it makes sense as well: you really are what you eat.

What I’d like to do in this series is take a Functional Medicine approach to gastroenterology. In part one, I will discuss the basic systems at work in your GI tract during digestion of foods. In part two, we will talk about what happens when things go wrong. Finally, in part three, we will discuss ways to correct these irregularities and heal the gut.

But first, I would like to start with a patient’s story.

June was 67 years old when she first came to my clinic. She had been suffering from chronic diarrhea for years and consequently knew where every bathroom was located in any store or any place that she would visit. Her bowel movements had so affected her health that now she rarely would leave her home for fear of soiling herself. While performing her initial evaluation, I heard a typical patient history. This all started in her 20’s and had slowly worsened over time. She had endured multiple colonoscopies and CAT scans, but they all were normal. Her main symptoms were bloating after eating anything followed by a liquidly bowel movement in 30–45 minutes. But she also had systemic symptoms; hand and joint stiffness, muscle pains, recurrent allergies and respiratory tract infection. Theses clued me into the fact that her condition included her entire body and was being mediated through her gut. After our initial evaluation showing multiple nutritional deficiencies, I also performed a functional bowel assessment; my assessment showed significant inflammation in her GI tract as well as bacterial and fungal overgrowth.

At her follow-up visit, I recommended an elimination diet to remove any potential inflammatory foods and replace her nutrient deficiencies. We also started an anti-inflammatory regimen for her bowels and antimicrobial herbs to diminish the load of bacteria and yeast. It was a rough start. In fact, her symptoms initially worsened before she started to see some positive results. The first thing she noticed was she was less stiff getting out of bed and her hands hurt less in the morning. She also noticed that during the current allergy season, her allergies were less severe, and she didn’t end up needing any antibiotics. It took about 3 months for her bowels to respond to the changing treatments, but at month four she started to notice a decrease in her bowel movements with no undigested food in her stool. When we had our fourth visit, she was happy to inform me that she was having only two bowel movements daily, and they were normal. Her story was a gentle reminder to me that though her major complaint was diarrhea; her actual issues were systemic, and the diarrhea was only a symptom of the immune system inflammation that was going on in her digestive tract.

And June is not an isolated patient…

43% of Americans have intermittent digestive issues

14% of Americans have acute or chronic digestive issues

35% of doctor visits in our country are for digestive concerns

But that’s not all. The digestive tract is responsible for absorption of vitamins and minerals and from the chart below, it becomes easy to appreciate the fact that most of us have multiple nutritional deficiencies. The deficiencies can further impact our gut health and lead to body-wide effects.

Percent of U.S. Population NOT Meeting the Dietary Reference Intake (DRI) for Specific Nutrients

Understanding Digestion

So, what actually happens during the process of digestion? How does that piece of salmon turn into the small amino acids and fatty acids needed at the cellular level for nutrition? The process of digestion consists of five major steps:

  1. Mechanical - chewing food into smaller particles
  2. Digestion - using chemicals secreted by the GI tract to further break down food
  3. Absorption - the translation of this digested food across the lining of your gut into your blood and lymph tissues
  4. Assimilation - the incorporation of these nutritive particles into the cells of your body
  5. Excretion - removing the leftover waste product

Let’s review these five processes in a little more detail.



First during the mechanical phase, food is turned from large pieces of food into a bolus or round ball of food. This is the first defense in our GI tract against bad food. If it smells bad, it won’t even enter you mouth, if it tastes bad you will spit it out. The food bolus is mixed with digestive enzymes during chewing that begin the digestive process of carbohydrates and antibacterial enzymes and proteins (called immunoglobulins) are mixed in the food. Magnesium, potassium and calcium are secreted to help in the digestive process as well as to protect the enamel of the teeth during this process. Ideally, each bit of food would be chewed between 20–30 times to ensure it is ready for the next step in the digestive process. Once this is complete, the brain senses this, transfers the ball of food to the back of the throat; then, an automatic system kicks in to transport the food ball to the entrance of the stomach.



It is a little confusing to start the discussion of food digestion when food enters your stomach because the process starts when food is being chewed in the mouth. This process just speeds up when the food bolus mixes with stomach acid and digestive enzymes. The stomach acid takes protein and food digestion to the next level. Bacteria and fungus that are mixed with the food are killed by the acid, and mineral absorption is enhanced at the same time. The food bolus is converted into a yellowish liquid, called chyme, that then enters the small intestine.

Figure 1
Figure 2


3.1 Small Intestine

The job of the small intestine is quite complex. The one-cell thick lining forms both a barrier to undigested food and nutrients and a portal for these to enter the body. Figure 1 shows how specialized each section of the digestive system is for nutrient absorption. The bulk of the absorption occurs in the small bowels and the processes that happen in each section along the way improves the absorbing capacity of that section.

The pancreas is the first organ to add digestive liquids - called enzymes - to the small bowel to continue the digestive process. It secretes: Proteases (enzymes to break down protein), Lipases (enzymes to break down fat), and Amylases (enzymes to break down carbohydrates). All these enzymes are in an alkaline rich fluid that neutralizes the acid from the stomach. Otherwise, the acid would ulcerate the lining of the small intestines. At the same time, bile from the liver is mixed with the fluid from the pancreas. Bile has several important functions. It emulsifies fat for digestion and removes cholesterol and toxic chemicals from the body. The toxic chemicals excreted in the bile include medications, chemicals, and toxins that the liver detoxifies and then excretes into the bowels for elimination in the feces. This adds complexity to the digestive process: now your gut lining has to keep these toxins in the bowels and at the same time absorb the life-giving nutrients you just ate. This complex process occurs at the level of the cell walls that line your GI tract.

Figure 2 illustrate how all of this occurs. The villi, which are finger like projection into the space in the small intestine, increase the surface area to the extent that if laid out, the surface area of the small intestine would be the same as that of a double’s tennis court. This allows space for all the nutrients we consume to be absorbed. At the same time, the immune system is scanning all the material absorbed to prevent any bacteria or viruses from entering your body; it is training your immune system to ignore the food you just ate. If this system becomes confused, you can start to react immunologically against the food you have eaten. This is where food allergies begin. This task is so important that 80% of your immune system resides around your intestines to moderate the whole process.


3.2 Large Intestine

Once most of the nutrition has been removed by the small intestines, the undigestible residue enters the large intestine. It used to be thought that the only thing that happened here was absorption of the remainder of the electrolytes (like sodium and potassium) and water but now we know that this is where 99% of your microbiome resides.

So, what is the microbiome? You likely have heard of it as it has become the focus of intense research worldwide over the last ten years. It is the sum of all the microbes (i.e. bacteria and fungi) that live in and on our bodies. Here are a few interesting facts about the microbiome:


  • There are over 100 trillion cells in the human microbiome, compared to 10 trillion cells in the rest of your body. Only 10% of the cells in your body are you!
  • The human genome contains 23,000 gene while the microbiome contains over 1 million genes. This microbiome based genetic diversity allows us to adapt to live in any environment in the world.
  • The microbiome makes compounds like butyrate that are crucial for brain and gut function.
  • Changes in the microbiome contribute to the development of diabetes and obesity.
  • There are 10× more viruses in the human virome than the human microbiome.
  • The microbiome plays an important role in preventing infectious diseases.
  • The microbiome changes as we age:


Assimilation is the next step in the process. This is where the digested nutrients, proteins and fats are transported by your vascular system to your various body parts and then to the individual cells for use. This process requires the right balance of nutrition so that the mechanisms required for processing will work. Organic acid testing is a form of advanced testing we use in clinic to see if assimilation is working correctly. For example, someone could have enough Vitamin B12 in their diet and a blood test would show adequate B12 in the blood. However, if it wasn’t getting into the cells and then then cells power house (called the mitochondria) wasn’t working optimally, metabolic byproducts would build up like homocysteine. We can test for this and then either boost that nutrient in the diet or use a high dose pharmaceutical supplement to get B12 into the cells.

Related Reading: Mito Food Plan Diet



The final function of the digestive tract is excretion. Once all the work of digestive tract is done the waste products must be excreted out of the body. This is an obvious fact of life, but what is not-so-obvious is that the lumen or opening in our digestive tract is a continuation of our outside environment. If you swallow a special camera it will go through the entirety of your GI tract and come out the end. The same thing goes for anything you consume that is indigestible.

All the functions related to our digestive tract work together in a complex symphony. Almost on a weekly basis we are discovering new properties related to the gut. A few of these are the following:

  • Immune regulation
  • Hormone secretion
  • HPA axis modulation
  • Conversion of thyroid hormone T4 into T3
  • Neurotransmitter production (50% of dopamine and 90% of serotonin are made here)

What’s Next?

In part two, we will discuss what happens when things go wrong. How do malfunctions in this complex system relate to our health and affect our health?


Since 2010, Richmond Integrative and Functional Medicine has been helping people to restore their health and hope with an integrative approach to conventional and alternative medicine that’s entirely science-backed. We at RIFM believe everyone is made for health. We offer a comprehensive, in-person patient membership program to ensure you get access to the care you need to thrive.