Foundations of Integrative Health

Foundations of Integrative Healing Manual
Foundations of Integrative Healing Manual

Optimizing Digestion


The unique innovation of functional medicine is its unique framework for drilling down the root cause of complex chronic diseases. Most of the primary fundamental causes of disease are related to digestion. By studying digestion, we can put the pieces of the story together of how conditions form in the first place. 

Digestive pain, bloating, and discomfort are common (80 million people in the US are diagnosed), but that doesn’t make them normal. We’re not supposed to feel any of these symptoms; good digestion is smooth, easy, and regular. You know you’re on the right track when your digestion begins to improve. Have you ever smelled something delicious and noticed your stomach begin to churn? When you smell food, a healthy digestive tract creates a unique alchemy of stomach acid, bile, and digestive enzymes in just the perfect balance for the food it smells. Getting the right balance of digestive chemicals is one of the most critical aspects of your overall health. 

 It’s impossible to reverse a chronic disease without first fixing your gut. That’s because:

  1. Our digestive tract is where we absorb almost all of our vital nutrients.
  2. 70% of our immune system lives in our gut.
  3. We eliminate most of our waste and toxins through digestion.
  4. Our guts have over 500 million neurons, which is why many scientists refer to it as a “second brain.”
  5. 90% of serotonin and 50% of dopamine are produced by your gut cells and the trillions of microbes living there. 

Digestion is complex; small changes in the digestive process in the first portion of digestion can cause significant issues as the food moves through our intestinal tract. For example, a shortage of stomach acid can cause larger, undigested food particles to move into the small intestine, causing many issues, including malabsorption, gas, leaky gut, and inflammation. If you’ve been eating healthy but not getting the results you want, it’s likely because there are aspects of your digestion that you’ve yet to optimize. Fine-tuning our digestion to digest, absorb, and assimilate what we eat is a process and will be the largest and most significant portion of what we study in this program.


Small Intestine & Leaky Gut- The First Stage in Inflammation & Most Chronic Diseases

Gas & bloating. Allergies. Brain fog. Acne and rashes. Hormone imbalances. Mood swings. Anxiety. Cancer. All of these mysterious symptoms begin with something called leaky gut. This is crucial to understand how chronic inflammation begins to develop throughout the body and sets off the set of confusing health symptoms. 

The small intestine is likely the most underrated part of human biology. It’s responsible for two major roles:

  1. Food breakdown 
  2. Absorption. 

Food passes from the stomach into the small intestine, which breaks down the food into tiny particles that get absorbed through the small intestinal wall directly into the blood. 80% of nutrient absorption happens in the small intestine. It’s so vitally important that it’s one of the quickest regenerating parts of the body. Before your body fixes its bones, organs, and heart, the body knows to repair your gut lining. Actually, our gut lining regenerates entirely in as little as 5-7 days, which is good news if you’re trying to repair your gut. 



It surprises many people to learn the inner lining of the small intestinal gut wall is not smooth but fuzzy! This is because there are millions of little hairs (villi) that gently brush food down the small intestine while also providing an incredible amount of surface area through which nutrients are absorbed to break down foods into smaller particles that can be absorbed directly into the blood. One of the first chains of events in the chronic-disease creation process is these villi begin to get damaged or atrophied. Tiny little hairs on your gut wall getting impaired might not sound like a big deal, but it can potentially initiate a disastrous chain of events in the body. 

You’ve likely heard of celiacs disease. Celiac disease is when the small intestinal villi atrophy or break down. When you have celiacs and eat foods containing the protein gluten (contained in the grains wheat, barley, and rye), the gluten triggers an attack by your immune system on your intestinal villi. Only 1% of the population is estimated to have celiac. The Marsh Score system was developed as a quick and easy way to rate the damage to your small intestine caused by celiac disease. A Marsh Score of 1 would be healthy villi, fully functioning, and fuzzy. In the worst-case scenario with celiac disease, your villi can be completely destroyed — total villous atrophy. That’s considered Marsh Score 4, and people with that score are likely to be severely malnourished and may be at risk for lymphoma. It’s safe to assume that everyone, to some extent, has damage to their intestinal villi. So, everyone has a spectrum of damage to their small intestinal villi. This is a crucial distinction functional medicine makes, which is not often addressed by conventional medicine. Conventional medicine only addresses Celiac (Marsh score 4) as a diagnosable condition, but where you are on this spectrum is crucial and directly related to the amount of inflammation in your body. Why is that the case?

Our intestinal lining was designed to be somewhat “leaky” or penetrable to allow the easy transportation of nutrients from the intestines into the bloodstream through what are called “tight junctions.” These tight junctions are the literal space between the cells that make up the intestinal wall. Because the intestinal wall is just one cell thick, a disruption in the integrity of the intestinal lining can cause significant issues. The more atrophied the villi become, the more the tight junctions begin to “leak.” Leaky gut syndrome happens when this intestinal damage creates larger-than-normal gaps in the intestinal lining. This is crucial because villi atrophy is an essential first step in causing inflammation, leading to all chronic diseases. 

When our villi are atrophied and our gut wall beings to “leak,” foreign substances like bacteria, viruses, and undigested food particles begin to enter the bloodstream directly from the small intestine. This is a crucial moment in the functional medicine paradigm of disease. 

Your blood is waiting to accept tiny, fully digested, broken down food particles (fatty acids, amino acids, and glucose) that it recognizes and can easily absorb. When your villi are healthy and your gut wall is intact, foods get broken down into these small particles, which the blood is accustomed to receiving. However, the leakier our gut becomes, the more complex food particles and bacteria/viruses enter the blood. 

Why is this problematic? Well, the immune system is constantly monitoring your blood like a highly efficient security system. It identifies foreign invaders and plans a perfectly efficient attack to neutralize the invader when it’s working correctly. However, when an abundance of foreign particles enters the blood from the leaky gut, the immune system can get confused. “Why are there all these new particles in the blood that aren’t supposed to be here,” it says.

So your immune system begins to create an inflammatory immune response (more on this in the Inflammation & Immunity section). This moment here is what many functional medicine doctors believe is the root cause of inflammation, the underlying cause of almost all chronic diseases. Alessio Fasano, a professor at Harvard University, believes that all autoimmune patients, and potentially even all cancer patients have leaky gut. That means if you have a leaky gut or damaged intestinal villi, you are putting yourself at risk for future chronic diseases of all types. So if you want to heal an autoimmune condition (and most conditions), you have to heal your leaky gut. 

So what causes the breakdown of the villi and leaky gut in the first place? 

  1. Too many processed foods
  2. Toxin exposure (herbicides, pesticides, heavy metals).
  3. Chronic Stress. 
  4. Excess use of Medications, particularly antibiotics, Proton Pump Inhibitors (Prilosec, Prevacid, Nexium), NSAIDs (Advil, Aleve, Motrin).
  5. Drinking coffee (particularly on an empty stomach, coffee is ideal after a meal.)
  6. Digestive infections or parasites (talk to your doctor about these, as they require testing).
  7. Perhaps the most common and direct cause of intestinal hyperpermeability is dysbiosis, an imbalance in the microbiome. We’ll discuss this in the next section.


The good news is that leaky gut is entirely reversible. The intestinal lining is one of the fastest regenerating tissues in the body. Every 5-7 days, we have an entirely new intestinal lining. However, to heal the gut lining for good, we have to remove the main source of villi atrophy and leaky gut. That’s why when we start with a new client, we recommend you to go on at least a 5-7 day “reset period,” where you follow a protocol strictly to rebuild your intestinal gut walls. 

So, quick review, before we move on:

  1. Digestion is vitally important and is the primary root cause of chronic disease.
  2. The process begins when our intestinal villi begin to get damaged, and the gut walls begin to “leak.”
  3. This allows bacteria, viruses, and undigested food particles into the bloodstream, which generates a chronic inflammatory response.
  4. We can fix this in a short time if we avoid the leading causes of intestinal damage.

How do we fix this? We need to understand the delicate details of what happens to our food before it enters our small and large intestines.


Fix Leaky Gut By Optimizing The Digestive Process

Many people think digestion starts in the mouth and stomach, but it actually begins with the sight and smell of food. You may have noticed that the texture of your saliva changes depending on what you are eating. When we smell and see a delicious meal, our salivary glands start to secrete enzyme-rich saliva. 

With every coming batch of food, the upper digestive tract creates just the right concoction of chemicals to digest what smells perfect and tastes. The stomach begins creating hydrochloric acid; the pancreas starts secreting digestive enzymes into the intestines, and the liver and gallbladder release bile into the small intestines (more on this later). The proportion of chemicals is not the same every time; it’s a unique alchemy based on what you smell and taste.

This is all initiated by the sight and the aromas of food. When we allow ourselves an extra moment to be present with the meal we are about to eat, we allow the digestive system the time it needs to prepare for the food it’s about to receive. 

Have you ever noticed your stomach hurts after eating while stressed or rushed? Many people suffer poor digestion as they’ve become accustomed to eating in a rushed, stressed, or distracted state. The nervous system regulates the activation of the digestive system. This means that the digestive system, particularly the creation of digestive chemicals, functions most optimally when we are in a relaxed and present state. When you eat while working, on the go, or watching TV, the sympathetic branch of the nervous system (the “Fight or Flight” branch) is activated. This impairs the secretion of stomach acid, bile, and enzymes. These small changes in the first portion of your digestive tract can cause food to wreak havoc as it moves its way down the digestive tract, where leaky gut and other chronic digestive diseases begin to form. We’ll talk more in detail about this later on.

The simple habit of slowing down and taking 15 seconds to smell and look at our food is one of the most crucial habits to adopt in this entire program. It’s deceptively simple and deceptively powerful, as it’s tough to have good digestion without the right stomach chemicals. Without them, it’s almost impossible for your body to digest, absorb, and assimilate food properly.


Mealtime Ritual For Optimal Digestion:

You can’t begin healing your gut until your upper digestive tract works properly. This eating ritual will help you make sure your stomach, pancreas, and liver start creating the right proportion of chemicals to optimize your digestion. 

Follow this mealtime ritual to help optimize digestion. This is the first and most crucial step in healing your gut.

1. Create a peaceful eating setting: Before you start eating, find a quiet place where you can sit down to enjoy your meal. Try to avoid eating while standing or walking. Turn off the TV and put away your phone. The more present you are with your food, the better you will digest it.

2. Pause for gratitude: Take a brief moment to pause and appreciate the meal in front of you. You can either inhale the delicious aromas from the food, take a few deep breathes of gratitude, or say a few words of appreciation, either internal or aloud. 

**Tip – Taking five deep breaths while extending the exhalation is a highly effective method for turning on the parasympathetic nervous system. 

3. Chew your food thoroughly: Thoroughly chewing allows your teeth to break apart the food mechanically. This takes a significant burden off the downstream digestive organs, including the stomach and intestines. Make sure you chew each bite of food at least 20 times before swallowing, especially if you are eating meat or other heavy food items. 

4. Enjoy your meal slowly: Rushing through a meal gives your body the feedback that you are under stress, activating the sympathetic (fight or flight) branch of the nervous system and impairing digestion. Leisurely enjoying each bite and being present with the flavors, on the other hand, enhances digestion.

**Tip – putting your fork down between bites is a helpful strategy for slowing down the pace of eating. 

5. Do not overeat: Overeating taxes the digestive system with more food than it is designed to handle. As you become more present with your food at mealtime, you will also become more present with your body’s satiety cues, knowing when you have received enough fuel. Because your digestive process will be more efficient, you’ll also absorb more nutrients in your small and large intestines, which will help you resist intense food cravings.


Digestion in the Mouth

Chewing is an essential step for indigestion that is often overlooked. We chew so we can mechanically break apart food into smaller particles to prepare it for easy digestion in the stomach and intestines. Ayurveda advises practitioners to chew each bite of food at least 20 times for optimal digestion. 

The longer we chew a bite of food, the easier it is to break down food in the rest of the digestive process. Our teeth and jaw are designed to mechanically break down the food of many textures: soft, rough, chewy, crunchy. But it’s our saliva that significantly eases the process by adding salivary enzymes into the mix. Saliva contains :

  • Amylase to help break down carbohydrates,
  • Lipase to break down fats, and
  • Proteases to help break down proteins. 

When we swallow a mouthful of food, and it works its way down the esophagus and into the stomach, the digestive process is already well underway. 


The Importance of Stomach Acid:

When the chewed food has made its way down the esophagus, through the lower esophageal sphincter, and into the stomach, it is greeted by a highly acidic environment of hydrochloric acid. 

An empty stomach that is ready for food has a pH between 1.5 and 3.5. That is so acidic that it would burn your skin if you were to touch your stomach acid. Fortunately, your stomach has a thin layer of enzymes and mucus that protects it from being burned by the acid. This mucus layer can degenerate, and if it does can cause significant health issues like peptic ulcers. There are many causes of the mucus lining breaking down. If you experience ulcers, please notify your doctor.

Acid reflux and heartburn are extremely common. Antacids are the #1 prescribed medication in the US. For this reason, stomach acid gets a bad reputation. However, it’s a crucial chemical, and we want it to work correctly. The acidic nature of the stomach kills off foodborne pathogens. Stomach acid also triggers the release of an enzyme called pepsin that digests protein in the stomach. While the stomach secretes the necessary acid and pepsin, it also mechanically churns the food, further breaking it down. Food is then emptied out of the stomach and into the small intestine in small amounts.

It’s counterintuitive, but it’s more common that heartburn, acid reflux, and GERD are caused by low stomach acid, not high acid. 

This happens because stomach acid also regulates the activity of the esophageal sphincter (LES), the little faucet-like sphincter that opens and closes to separate the stomach from the esophagus. 



When we swallow, the LES relaxes and opens to allow food into the stomach. When the stomach begins to churn and digest food, the LES is designed to stay closed to ensure that the acid in the stomach does not move up into the esophagus. When the stomach produces enough acid and a specific pH is reached, the LES is signaled to stay tightly closed while the stomach starts to churn the food. If the stomach does not produce enough acid, the LES will remain loose, allowing food to reflux into the esophagus. Low stomach acid has many causes, including:

  • Fried foods
  • Excess spicy foods
  • Excess citrus foods
  • Processed foods
  • Eating with an already full stomach. This can cause the food to come back up.
  • Eating right before bed.
  • Being overweight with a large belly—which can displace your stomach up, causing reflux.
  • Hiatal Hernia , which cause the stomach to get trapped into a higher position than where it normally sits. This makes it easier for stomach acid to flow back up into the esophagus and cause acid reflux.
  • Drinking Alcohol
  • Excess Caffeine
  • Smoking
  • Chronic stress affects the nerves in your stomach, making it difficult to properly digest food. This can cause food to go up instead of down. 
  • Loss of magnesium caused by stress. Magnesium is required to relax the sphincter at the bottom of your stomach that allows food go down. When you lack magnesium, the food can start to go back up.
  • Food sensitivities that may not be undiagnosed including gluten and dairy.
  • Bad bacteria or stomach yeast overgrowth. If you’ve taken antibiotics or have been on hormones, you could grow bad bugs in your gut which ferment and cause reflux.
  • H. Pylori, a common bacteria overgrowth can sometimes be linked to reflux.

Acid reflux is a severe condition that not only affects your stomach and upper digestive tract but throws off your entire digestive process, running the risk for other digestive diseases. When the function of the stomach is impaired, it is more likely to have digestive issues downstream. 

Low stomach acid has been proven to increase the likelihood of small intestinal bacterial overgrowth (SIBO), generalized imbalance of microbes in the large intestine (dysbiosis), malabsorption of nutrients, gas, bloating, and bowel irregularities. If you experience any of these symptoms, please be sure to notify your doctor and nutritionist for specific protocols to address these. 

Stomach acid is also essential for the proper absorption of specific vitamins and minerals, including Vitamin B12, calcium, magnesium, zinc, copper, iron, and selenium. Iron deficiency is a common clinical diagnosis that is often attributed to low iron intake in the diet. However, it’s also possible for people eating an iron-rich diet full of meat to develop iron deficiencies due to low stomach acid production. 

Low stomach acid is more common than you may think. It’s estimated that 90% of the population experiences low stomach acid production at some point in their life. Many factors can cause this, including the use of acid-blockers, excessive use of painkillers, thyroid diseases, chronic overeating, and H. pylori overgrowth. However, the most common causes include eating a diet that is high in processed foods and chronic stress. 


4 Simple Ways to Optimize Stomach Acid

There are easy ways we can increase natural stomach acid production to optimize digestion downstream. 

  1. Eat a whole-food diet free from processed foods. Eating aligned with the principles that are outlined in the food chapter will support the proper production of stomach acid. This is because there are several vitamins and minerals that are required in the production of stomach acid. Deficiencies in these minerals from processed foods are one of the major causes of low acid production.
  2. Utilize the mealtime rituals (above). Since chronic stress is one of the leading causes of low stomach acid, we want to do everything we can to upregulate the parasympathetic branch of the autonomic nervous system (rest & digest) around mealtime. Being in a relaxed state when you eat will immediately enhance stomach acid secretion for optimal digestion. 
  3. Reduce Snacking. Every time we eat, our stomach needs to turn its acid back on. The body can get confused when we’re constantly eating. Just like all our body functions, our upper digestive tract needs rest. Avoiding snacking and intermittent fasting can be a miracle for many people to help heal and regulate acid production. 
  4. Include more bitter foods into your flavor profile. The bitter flavor is especially beneficial for digestive function. 80% of the foods that grow in nature edible to humans are bitter. However, it’s very common for many people to include no bitter foods whatsoever in their diet as we prefer sweet and salty tastes. The bitter flavor plays a crucial role in many biological processes, particularly in the upper digestive tract. In spring, in particular, the more bitter plants grow. This is part of nature’s design, as historically, we would be coming out of hibernation. The bitter taste sends a signal to our cells to release hydrochloric acid. A recent study demonstrated participants lost weight after 12 weeks simply by drinking a tablespoon of apple cider vinegar mixed with a glass of water before meals. 


Exercise: Creating a Relationship with Bitters. It’s important to start cultivating a relationship with the bitter taste profile, particularly if it’s a taste you rarely get. The next time you have something extremely bitter like cranberry juice, notice the sensations in your stomach as it hits your tongue. Thirty seconds – to one minute after the taste hits your tongue, you may feel some gurgling or movement in your stomach region, even before swallowing it. This is the digestive process turning on! Learning to work with bitters is like magic for digestion as it stimulates cells to release.

When the bitter receptors on the tongue are stimulated, the mouth starts to salivate, and a signal is transmitted to the brain to turn on digestive processes. The digestive juice starts flowing, including stomach acid, bile from the liver, and enzyme-rich juices from the pancreas.

Some delicious bitter foods include cranberries, raspberries, arugula, artichoke, broccoli rabe, brussels sprouts, chicory, dandelion greens, endives, kale, and other raw leafy greens. For those who want to take a more direct approach to optimize stomach acid production with bitters, digestive bitter tincture formulations are designed to apply to the tongue before meals to stimulate the digestive process. Digestive bitters should be taken 5-10 minutes before every meal. For those with upper digestive issues (and even those who just want to optimize digestion), the regular intake of bitters should be considered an essential habit.


Here are some of our favorite pre-digestive bitters:


Tastes And Their Medicinal Qualities: Chinese Medicine & Ayurveda

Bitter isn’t the only taste profile that can help optimize digestion. Actually, in both Chinese Medicine and Ayurveda, all the different taste profiles have different healing effects on our digestion. 

  • Bitter – Stimulates cells to release (particularly in upper digestive organs), increases energy and vitality. 
  • Astringent- Pulls water into the cells, also stimulates release (particularly in the colon)
  • Sour- Heats the body and stimulates release. Tends to dehydrate. 
  • Pungent- Heats the body, tells it to “wake up!.” Also helpful in killing bacteria and parasites.
  • Sweet- Nourishing, cooling, and hydrating. Too much can cause stagnation. 
  • Salty- Nourishing, energizing, grounding. Provides energy through electrolytes. Also dehydrates. 

Have you ever noticed how you often need to go number 2 after drinking coffee? That’s because coffee has a highly astringent quality, which stimulates the release of the colon. Astringent is earthy and brings a slight puckering. It pulls water into your mouth and affects the digestive tract as it moves down your intestines. Pulling water helps hydrate digestion, making it move and flow. Other astringent foods have the same effect, like green tea, aloe vera, walnuts, and unripe bananas. 

An Ayurvedic doctor might tell you the root cause of many digestive issues is too much exposure to only one flavor profile. For example, if you’re only getting the sweet and salty tastes in your diet, both these tastes have the propensity to slow down digestion and make it more sluggish. 

Understanding the taste profiles and their effects on your digestion is a vast area of study. It’s also one of the most practical ways to get digestive optimized. You can use this simple guide as a roadmap. If you’re feeling stagnated, stay away from sweets and salty foods. Go for a lighter meal that favors bitter and astringent foods – perhaps a fresh summer salad with arugula, cranberries, and radishes. If you’re feeling too light in your body, go for a nourishing sweet and salty meal, like a nourishing soup with baked sweet potatoes and black forbidden rice

In Chinese medicine and Ayurveda, they believe the healing properties of a food or herb are actually derived from its taste. That means it’s crucial that we taste the food or herb and not take it as a pill or supplement. In both these traditions, medicines are given in powders or teas so you can taste it. Yes, they don’t often taste good, but the medicine is in the taste. Our taste profiles ideally would mirror how we would eat in nature. 80% of what grows in nature is either bitter, astringent, or pungent, yet most Americans will make up 80% of their taste profile with sweet and salty tastes. Unfortunately, there is a movement to genetically modify the bitter and astringent tastes out of foods like celery, cranberries, cherries, and more. 

One great way to quickly get a daily dose of our most missing flavor profiles is with an ayurvedic herb called Triphala. Triphala, literally (three flavors) includes a dose of the three flavors we most commonly ignore in our diets: bitter, astringent, and pungent. Legendary Ayurvedic doctor Vasant Lad is famous for saying, “If you’re not sure what’s wrong with your digestion, close your eyes and take Triphala.” You can consume your Triphala daily by putting a teaspoon in a glass of warm water. Admittedly, it doesn’t taste great, but the more you drink it, the more you get in touch with its amazing ability to help optimize your digestion. After a few days of taking Triphala regularly, you should feel your stagnated digestion begin to move slowly.

Again, it’s essential to consume Triphala in a powder, not a pill, because the healing properties are derived from its taste. The moment you taste it, it triggers a set of physiological reactions, which prepare your body to use the medicine. You don’t truly get the medicine if you don’t taste it. 


Digestion and Absorption in the Small Intestines

Even with the strongly acidic environment of the stomach, the food is still not ready to be absorbed into the bloodstream when it leaves. The food molecules that are emptied from the stomach into the small intestines are still too big to move across the intestinal lining and be absorbed into the blood. 

The digestive process at its essence is complex food molecules (carbohydrates, fats, and proteins) being gradually broken down into smaller and smaller particulates (glucose, lipids, amino acids, so they can be absorbed into the blood and then by the cells. In order to be adequately absorbed, food particles need to be broken down into their smallest and most simple forms. This is extremely important to understand. The smaller the nutrient, the easier it is for it to be absorbed and assimilated. The body loves these small, short-chain fatty acids, amino acids, and glucose. This is where the pancreas, liver, and gallbladder come in to help.

The pancreas is an amazing organ. In addition to creating insulin to support blood sugar regulation, it also secretes essential digestive enzymes to prepare food molecules for absorption. But the first job it has is to neutralize the acids coming from the stomach. The pancreas secretes carbonic acid (H2CO3) into the first portion of the small intestines to create an alkaline environment. It then secretes many digestive enzymes, including lipases to break down fats, amylase to break down carbohydrates, proteases to break down proteins, and more. Don’t worry, you don’t need to memorize all these 😉

These enzymes help digest the bigger food molecules into their most simple form. Because the pancreas is only stimulated to secrete these digestive juices when the parasympathetic (rest & digest) nervous system is activated, it’s crucial to practice the mealtime ritual.

The liver, another amazing organ, is responsible for over 500 functions in the body. One of its primary functions in the digestive process is bile production. When we eat fat, our gut signals to the liver and gallbladder (the bile storage organ) to secrete bile into the small intestine. Bile is an essential step in absorbing fat because it breaks it down into smaller lipids. Same principles here; smaller particles are better. The body loves tiny little lipids (broken-down fats) because it can better absorb and assimilate them.

Poor bile secretion can occur when the liver is overburdened and becomes “sluggish.” This can happen when a person’s lifestyle includes too much alcohol, processed foods, toxin exposure, and insufficient hydration and nutrition. One of the best ways to support and maintain liver health is, you’ve guessed it, bitter foods!

While the bitter flavor is incredibly effective at turning on the parasympathetic (rest & digest) branch of the nervous system to stimulate all digestive processes, it also directly stimulates bile secretion. This is why many of the classic liver-supportive foods like dandelion greens, artichoke, and kale, are bitter. 

The cell wall of our gut is only a single cell thick. One cell! That’s why nutrients have to be tiny for nutrients to move and permeate this wall. If anything impedes the breakdown of our food in the upper digestive tract, things go haywire as it moves into the intestines. Once all the complex nutrients are broken down, they are prepared for absorption; they move across our single-cell-thick intestinal wall and into our circulation. 

Carbohydrates and proteins are absorbed directly in the blood, while fats are absorbed into the lymph fluid and later transported to the blood. At the same time, all of the micronutrients (vitamins, minerals, and phytonutrients) we’ve consumed in our meals are also absorbed at various points along the small intestinal tract. The best way to support optimal absorption of nutrients is to optimize all the upstream digestive processes that we’ve already discussed and maintain a solid and intact intestinal lining. 


Poop Analysis

Finally, after the food has been digested, absorbed, and prepared for elimination, it ends up in the rectum, the storage organ for stool waiting to be eliminated. The gold standard for stool is when the stool is formed, light brown, smooth, soft, resembling a sausage or snake, and eliminated without pain or straining. 

You could say the goal of this entire module on optimizing digestion is to get you to this point. Ideally, we want to eliminate 1-3x daily. If your stool meets these standards, you know you are setting yourself up for great health and healing.

There are many factors that contribute to creating a well-formed stool. Stools come in all shapes and sizes, and the appearance of the stool can tell us a lot about one’s digestive health. You can think of the stool as a window into your digestive health.


Small, Dry Stool (Pellets)

If you have small, dry, or cracked stool, it’s a sign the body or digestive tract is dehydrated. The average meal takes between 1 and 2 liters of water to digest. With the epidemic of chronic dehydration, dehydrated stool is extremely common. 

When the body is dehydrated, it will extract more water from the colon, leaving a hard and dehydrated stool that is often more difficult to pass, aka constipation. When the stool is on the loose side, it is unformed and may come out as soft blobs, fluffy pieces, or in the most severe cases, watery with no solid pieces. 

Loose stool & diarrhea

Many things can cause diarrhea (infections, dysbiosis, laxatives, etc.), but the liquidy nature of the stool can be explained by either a failure of the colon to absorb the fluid before elimination or an increase of fluids drawn into the gut from the body. 

Diarrhea can be classified as either osmotic or secretory. Osmotic refers to increased osmotically active particles in the intestine, causing more water to be pulled into the lumen. Osmotic diarrhea is often caused by maldigestion of nutrients(ex. lactose) or excessive fructose intake. Secretory diarrhea also occurs because of excessive fluid in the intestine and an underlying disease such as a bacterial infection. 


Color matters as well!

Brown: A brown stool indicates that your system has digested the food matter properly. 

Green stool: A green stool can indicate that you ate more green vegetables than your microbiome is used to. This will normalize in time after continuing to eat more greens consistently. 

Orange or Yellow: An orange or pale yellow stool can indicate fat malabsorption, pointing to liver or gallbladder issues. Talk to your Wisdom doctor if you notice an orange/yellow stool. 

Red Stool: Any sign of red in the stool would also be a reason to consult with your doctor, as this could be blood in the stool. One normal cause of a reddish-tinted stool is eating beets! So before you call your doctor, you can think back to what you at the day before and make sure beets weren’t in any of your meals.

Black Stool: Also concerning is a black stool, which can be oxidized blood from an upper GI bleed. 

Mucous or Oily Stool

Finally, we also want to be aware of any mucus or undigested food that might be in the stool. While mucous may be hard to see in the toilet, it is often felt on the toilet paper when wiping. Mucous can be a sign of intestinal inflammation, so it would be good to bring this up with your doctor. If you see an oily appearance on the stool or in the toilet water, this is a sign of fat malabsorption and can indicate liver or gallbladder issues, in which case, you should contact your doctor.

Undigested food (corn kernels)

Some amount of undigested food can be normal. For example, humans don’t have the enzyme needed to break down the outer husk of a cooked corn kernel. This is why many people see corn in the stool. Occasional appearances of specific undigested foods may be a sign that your microbiome is not used to that particular food. 

Over time, if you continue to eat that food in reasonable amounts, your microbiome will adapt and be able to break down its fibers fully. However, if the stool is composed of several undigested foods, it could be a sign of weak digestion and malabsorption. If this happens only now and then, it could signify that you ate while stressed, transiently impairing your digestion. 

Timing: The timing of our bowel movement can also give us good information. Many people are surprised to hear that it is ideal to have a bowel movement 1-3x/day, ideally after each meal. While they don’t always have to come after meals, having a bowel movement frequently ensures that your body is detoxifying its wastes efficiently. Stool is not made up of bacteria and useless food matter; it also contains compounds that the body is ready to expel, including toxins and cholesterol that the liver has excreted in the bile, old dead colon cells, and much more. If elimination is slower than this, it may signify dehydration, dysbiosis, or an infection. 

Remember, the body needs to be relaxed for the bowls’ peristaltic action (the action that pushes stool along). This is why some people may experience constipation when stressed or traveling. If elimination is more frequent, it could be a sign of inadequate digestion and absorption, dysbiosis, or infection. 

Some people rely on either laxatives or anti-diarrheal agents to help normalize the frequency of their bowels. Still, this is because it ignores the underlying cause of diarrhea or constipation. To normalize bowel movements for good, one needs to consider the health and function of each aspect of digestion, starting at the mouth and moving down through the stomach, small intestines, and colon. When digestion is optimized, the result is healthy, brown, well-formed, timely stools. 


Optimizing Digestion Action Steps:

  • Practice Mealtime Rituals.
  • Include more bitter & astringent foods in the diet.
  • Address the many causes of leaky gut – this may require you to speak to your doctor.