Foundations of Integrative Health

Foundations of Integrative Healing Manual
Foundations of Integrative Healing Manual

Inflammation & Immunity



Functional medicine gives us an elegant model for drilling down to the core of what causes diseases and treating those fundamental, underlying causes.  

Perhaps the most important of those root causes is inflammation. Inflammation has been linked as a primary cause of essentially every chronic disease. This section will discuss the underlying mechanism of inflammation, how it’s formed, and the relationship between inflammation and the immune system. This is essential to understanding the mechanism of chronic diseases, particularly autoimmunity. As you’ll learn, even if you don’t have an autoimmune condition, many confusing, seemingly disjointed symptoms like skin issues and body aches have their roots in the relationship between inflammation and the immune system. Hopefully, this will also clarify confusing issues like food sensitivities, allergies, and chronic pain.

If you’re suffering from a chronic disease, it’s essential to reduce your inflammation. Our goal is to get your body in a state of no inflammation. When you have no inflammation in your body, that means your immune system is at rest. It’s calm, responsive, and prepared to do its job. However, everyone has some degree of chronic inflammation.


What causes inflammation?

There are two primary types of inflammation:

Acute Inflammation:

Your body will regularly generate acute inflammatory responses when you have a healthy immune system. Let’s imagine someone at your office is sick, and you are sitting next to them at lunch. Their flu virus enters through your nose and burrows its way inside you without realizing it.

Your immune system will quickly create a variety of inflammatory chemicals designed to kill off the virus. Later, you might get symptoms like fever, achy pain, swelling nose, and mouth, or mucus. Remember that the flu virus does not cause your flu symptoms; your immune system causes them. In fact, your flu symptoms are actually helping you fight off the invader, so it doesn’t wreak havoc on your other, more sensitive organs and brain. So symptoms of acute inflammation are part of the body’s brilliant way of staying alive!

The same thing happens when you cut your finger. Suppose you cut your finger on a nail. In that case, your immune system will mobilize inflammatory chemicals, including similar symptoms like swelling, heat, and pain, to the area of the cut to neutralize the potential bacterial invaders. 

In both the instances of the flu and the nail, your inflammatory response will subside once the threat is over. Soon after all the flu virus is killed, and the bacteria on your finger is gone, the inflammatory responses will stop, and you can go back to feeling normal.

Acute inflammation is always turned on by a particular cause and subsides when that problem is solved. Yes, it’s painful and uncomfortable, but when it’s done, it’s done.

We often misunderstand the basic nature of the immune system and our illnesses. Let’s imagine that you accidentally ingested a highly toxic, poisonous mushroom. Your body would do several elaborate things to expel this toxin from your system, starting with:

  1. Making you immediately throw up.
  2. Have diarrhea. 

But let’s imagine your digestion was backed up (probably from processed food) and your body couldn’t expel it through throwing up or through your bowels. If your body can’t remove the toxin through your digestive tract – which is always the fastest, most efficient method – it would push the toxin into your blood. So you might develop a rash or acne. Your body also might encapsulate the toxin in mucus to be expelled through your lungs and sinus in a phlegmy cough or runny nose. Soon after, you might also develop a headache or muscle soreness. This is the immune system trying to expel the toxin through your blood.

It’s important to recognize that these uncomfortable symptoms are actually evidence of the body healing itself. Your immune system will devise strategies to expel the toxin in the quickest, most efficient way it has. Diarrhea, skin conditions, mucus, and muscular pain are the exact same symptoms of autoimmunity. This means that our symptoms are actually the body trying to remove a toxic agent that it desperately needs to expel. And though the immune system is overactivated, it’s still trying to do its job, helping protect us by removing a toxin. And what do we often do when this happens? We take medications that suppress these symptoms, only masking the real, underlying problem and pushing the toxic agents deeper into our cells. 


Chronic Inflammation: Our True Enemy

Chronic inflammation is a slightly different process. Chronic inflammation is perhaps the greatest health risk in the world today. It’s the underlying cause of nearly every chronic disease, including heart disease, cancer, mental health issues, and autoimmune. 

Chronic inflammation is distinct from acute inflammation in that it’s a lower level, barely detectible form of inflammation that lasts much longer (often forever). Your body’s reaction subsides once the threat is over with acute inflammation. However, when your body is constantly fighting off threats, the inflammation stays around with no time to rest fully. As a result, your immune system remains on high alert. Imagine that your body was constantly exposed to a small dose of the flu virus daily. It wouldn’t have time to gather itself and prepare for the next battle because it’s always turned on.

When your immune system is overworked, like an overworked factory worker, it starts making mistakes. It starts attacking cells it’s not supposed to attack. It starts generating strange, seemingly disconnected responses all over the body. Everything starts to hurt a little bit. This underlying process is how chronic inflammation can cause chronic health conditions, even if you are not genetically predisposed. 


The primary sources of chronic inflammation are:

1. Stress

We know when we’re stressed, we metabolize food differently. Our body is encouraged to be in its quick burning glucose metabolism, where it’s looking for a quick fuel source. The metabolites of glucose are more likely to be inflammatory.

2. Gut Dysbiosis.

We carry 39 trillion microorganisms in the microbiome. When the balance of the gut is in dysbiosis, regardless of what we eat, our microbiome will create metabolites that generate an inflammatory response in the body.

3. Food sensitivities

Food sensitivities are a tricky issue. Food allergies are obvious in most cases. If you’re allergic to cashews and you’re exposed to a cashew, you’ll have an immediate, extreme reaction. Food sensitivities or intolerances often go unnoticed while silently wreaking havoc on your health.

On the other hand, food sensitivities can be much trickier to discover because the immune response can happen up to 72 hours later. If you’re eating a combination of 5 foods for breakfast, by the time you have a response, it’s almost impossible to identify which one of them you’re sensitive to the next day.

One way to get to the bottom of your food sensitivities is to use IgG food sensitivity testing, and you can speak to your doctor about this test. At-home food sensitivity tests are often wildly inaccurate. Like most things, with labs, you pay for what you get. We recommend working with your doctor to find a more comprehensive food sensitivity test. We often use Vibrant Wellness’s food sensitivity test.

4. Toxic Exposure

Heavy metals in pollution, many home products, low-cost cookware, and vaccines can all trigger inflammatory responses. If you suspect heavy metal exposure, please talk to your doctor. 

5. Infections

Many unresolved infections are a risk factor for inflammation, including the Epstein Barr virus, creating ongoing, low-grade inflammation. This would also be something to speak to your doctor about. 



When you see the body through the functional medicine lens, its clear that “autoimmune disease” is not a single, binary disease, rather, we learn to see autoimmunity on a spectrum. That spectrum is largely determined by the total level of inflammation in someone’s body. On the low end of the spectrum, inflammatory antibodies might attack our skin, thyroid, or pancreas (type 2 diabetes), and develop to where it begins attacking the brain and spinal chord, in the case of Multiple Sclerosis. We can measure the total inflammation in someone’s body with a blood test known as CRP (C-reactive protein). 

In the conventional medicine view, autoimmunity is a genetic condition, and there’s not much you can do about it. However, if this were true, the incidence of autoimmunity would generally be consistent throughout time, as human genetics evolve very slowly. However, the number of diagnosed autoimmune conditions has tripled in the past fifty years, suggesting that it’s another symptom of our industrialized lifestyles.

On one end of the autoimmune spectrum, you have those who have low to moderate inflammation. This is usually a result of a bad diet, and symptoms usually appear as minor digestive or skin issues. Usually, people on the low autoimmunity spectrum know their triggers and experience symptoms when they indulge. Perhaps they have short stints with anxiety, weight gain, heartburn, rashes, or acne, but these symptoms quickly go away. 

People with significant autoimmune symptoms have not yet turned into long-term disorders like asthma, allergies, joint pain, muscle pain, fatigue, or digestive issues in the middle of that spectrum. Even If you don’t have a full autoimmune condition, these symptoms indicate you are at risk of developing one.

On the other end of the spectrum, you have people will full-blown autoimmunity, with high chronic inflammation, who have conditions such as Lupus or Multiple Sclerosis, where your immune system attacks your spinal cord and brain. 

Warning signs of autoimmune conditions:

  • Arthritis
  • Acne
  • Severe Allergies
  • Anxiety or Depression
  • Eczema
  • Chronic Fatigue
  • Hair Loss
  • Infertility (PCOS)
  • Chronic, unexplained muscle pain

The critical thing to understand is that these are on a spectrum, and that spectrum is actually a measurement of the underlying inflammation in your body. If you continue to accumulate chronic inflammation, your symptoms will likely worsen, and you’ll move closer to full-blown autoimmunity. If you learn to manage your inflammation by reversing the underlying cause, you’ll move back down the spectrum with reduced symptoms and gradually return to health. The autoimmune spectrum explains why having one autoimmune condition makes you three times more likely to develop another. 

There is a counterargument to this theory; that we’ve simply become aware of autoimmunity in the last 50 years. However, there are many documented cases of people who have autoimmune conditions with no family history. There are also many cases of patients who have autoimmune diseases who reverse them. This all points to one thing: autoimmune conditions are environmentally driven and have their root causes in our lifestyle habits.


Leaky Gut – The Missing Link

So how does inflammation turn into autoimmune symptoms? Why are they so random and different for everyone? 

Remember back to our conversation in the optimizing digestion section, where we discussed leaky gut being the first link in the chain of chronic disease? If not, here’s a quick refresher.

Our intestinal lining is supposed to be somewhat permeable or “leaky” to allow nutrients to move into the bloodstream. These tight junctions are literally the 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 lining of the small intestinal wall isn’t smooth; it’s actually fuzzy, due to the millions of hair-like villi and microvilli. These villi are crucial as they brush the food particles down the small intestine, helping break food down into smaller food particles (i.e., proteins into amino acids and fats into lipids) to be easily absorbed. Processed foods, toxins, too many medications (particularly antibiotics), and stress cause these villi to atrophy. The more atrophied the villi become, the more the tight junctions begin “leak.” Leaky gut syndrome happens when this intestinal damage creates larger-than-normal gaps in the intestinal lining. This is crucial to understand because this is often the first step in creating chronic inflammation.

But you might be asking, how does leaky gut lead to chronic inflammation, and how does chronic inflammation lead to autoimmunity?

This is where the plot thickens… When we have an excessively leaky gut due to dysbiosis and damaged intestinal villi, nasty things like bacteria and undigested food particles begin to leak through the small intestine. They are supposed to live in the guy, but they enter the bloodstream because of the leaky gut. This generates a lower-grade, perpetual immune response or chronic inflammation. 

When this happens, all sorts of toxic items slip out of your gut and enter your bloodstream, including toxins, unfriendly microbes, and partially digested food. Why is this so important? When toxins, unfriendly bacteria, and other things that should only be in your intestines begin leaking into your bloodstream, suddenly, your immune system has a host of new problems to deal with. It starts initiating inflammatory responses to the new, sudden flood of toxins in the blood that should never have been there in the first place. Then, the “random” side effects begin with acne, muscle pain, and joint swelling. The blood running through your entire body is carrying foreign, toxic agents, and your immune system doesn’t know how to respond. It continues to get overworked, eventually getting to the point where the antibodies start confusing our own human cells as foreign invaders. 


The Adaptive Immune System:

When your immune system is working properly, it’s one of the most remarkable aspects of the human body. It wreaks havoc when it goes off, attacking things it’s not supposed to attack. The conventional medicine’s approach is to suppress it with prednisone, methotrexate, or other immunosuppressants. These drugs of course, may reduce your symptoms, but suppressing your immune system too much can come with significant dangers. This, of course, is not a long-term strategy. Instead of suppressing your immune system, we will learn to optimize it by removing the underlying issue and root cause; the toxic chemicals pushed into the blood through a leaky gut.

We already talked about your innate immune system. Your innate system generates acute inflammation. The innate immune system is your body’s first line of defense and generally initiates the same response each time. You might say your innate immune system never really learns anything. 

The part of your immune system that is more relevant to our discussion, as it is correlated with chronic inflammation, is known as the “adaptive” immune system

The adaptive immune system evolved because we experience a wide variety of threats (new strains of bacteria and viruses) in a diverse organic ecosystem, not just cuts from nails. It recognizes these new threats and develops permanent protection from them. The adaptive immune system is constantly learning, generating new attack strategies each meeting with a new invader. It literally keeps an “enemies list”; When your body experiences a new virus or threat, it remembers it and what antibodies it produced that neutralized the attack. It stores that information to quickly mobilize a new attack the next time it’s met with this invader.

When you cut your finger, you are vulnerable to infection and bacteria and your body needs a quick, rapid fix. That’s why open wounds are the job of the innate immune system. But when you encounter unique diseases like chickenpox, you never have to worry about getting that particular disease again. It’s the adaptive immune system’s job to retain the information so that when it encounters the chickenpox virus, it knows exactly what to do. This is the basic function of a vaccine. When you’re vaccinated from a disease, you are injected with small amounts of the virus, which begins to train your adaptive immune system to recognize it.

The adaptive immune system is smarter and works much slower than the innate immune system. It can take months or years for the adaptive immune system to learn to neutralize a threat (particularly when you are dealing with chronic inflammation). This is why many vaccines need to be administered multiple times.

If the process of leaky gut continues, and your blood gets flooded with toxins and undigested food particles, the adaptive immune system continues to broaden its spectrum of what it attacks. It thinks it’s getting smarter, finding and removing new foreign agents like it was designed to do. The blood is used to receiving finely broken down amino acids, lipids, and glucose from the small intestine. However, when larger, stranger, more complex food particles begin seeping into the blood, your adaptive immune system starts to go bonkers. It starts making new antibodies for all sorts of invaders like dairy, gluten, eggs, and other foods that otherwise might be healthy for you. Every time you eat one of these foods, your adaptive immune system begins to send signals to your body to produce antibodies, putting your body on high alert and increasing its sensitivity. All sorts of foods and chemicals now trigger your chronic inflammation it never had antibodies for. The adaptive immune system is why it feels like you’re becoming sensitive to almost everything you eat when you’re inflamed. 

Eventually, your immune system gets so overloaded and confused it begins to attack your body tissues. We still don’t completely understand how this happens, but we do know the process often begins through a leaky gut. In Chinese Medicine, it’s suggested that diseases will start to attack our weakest organs first, which might be an anecdotal explanation for how autoimmune symptoms progress. However, science currently has no idea why autoimmune diseases attach to certain body tissues and not others. 

For these reasons, understanding how to heal your gut, rebuild your intestinal villi, and reduce your inflammation is an essential part of healing any disease.


Removing Toxins

Our immune system also prevents toxicity from overwhelming our vital body systems. Truth be told, if you live on earth today, you are exposed to a high level of toxicity. It’s as simple as that. It’s in the air, water, food, self-care products, fragrances, and in many places in the home. 

Toxins literally mean poisons, and they affect everyone. Toxins include heavy metals (lead, mercury, arsenic), mold & mycotoxins (often found in old homes, office buildings, and schools), and the millions of industrial chemicals used in just about every product created in a factory. 

In 2003, the Environmental Working Group ran an interesting study with Mount Sinai in New York City. The study intended to quantify the “toxic body burden” carried by the average Americans. They tested people living in different parts of the country for 210 other substances, and the results were scary. Keep in mind, that they aimed to test average Americans, not those living in highly polluted areas near waste dumps or industrial parks. The results? each participant had an average of 91 toxins! Of the 91 of those chemicals, 53 are known to damage the immune system

If you aren’t taking dramatic steps in your life to limit your toxic exposure through the products you buy and the environments you live in, it’s likely damaging your immune system, and potentially leading to symptoms that otherwise might seem “random.”

The Center for Disease Control (CDC) was alarmed by these findings, so they ran their own study the following year in 2004, testing a much larger sample of the population. Their study showed an average of 116 toxic chemicals in their participant’s bodies. 

Here’s the thing about these studies: yes, they are scary. However, the process of testing for chemicals is not random. It’s not like you can run a blood test looking for all known toxins. To find a toxin, these researchers had to be looking specifically for this set of 91 and 116 chemicals. These studies only tested for a couple of hundred possible toxins. However, more than 80,000 chemicals are registered for use in the United States, with many thousands more added to this list every year. There are potentially thousands of other chemicals in our bodies that we don’t even know about. 

The EPA and the FDA receive as many as 2,500 applications a year for permission to use new industrial chemicals. That’s an overwhelming amount of chemicals to test appropriately. They might have only a few days or less to review each application, and 80% of those applications are approved. And how could they possibly test for the effects of these chemicals over the course of a lifetime? The truth is, most of the decisions made by these agencies are not made to protect us; lobbyists make them. Additionally, when these agencies study a chemical, they typically only study whether or not it causes cancer. There could be thousands of other ways these chemicals could harm us, including suppressing the immune system, that fall out of their view. 

These chemicals’ actual effects on our bodies are hard to measure because the effects don’t come from a single exposure but a cumulative effect. To understand this, we’d need to have studies on how this overall chemical burden affects humans over decades or longer. And while we don’t have these studies done yet, we do know that the rates of autoimmunity and all chronic diseases are skyrocketing.

Instead of diving into the research of specific toxins (this would take you a lifetime), a better approach is to look at your overall toxic burden. Think of it like this; Your body is like a glass of water. Every time you’re exposed to a toxin, it’s like adding another drop of water to the glass. Each time you wash your body with soap with industrial chemicals… another drop. Each time you drink water from a plastic water bottle with Polyethylene… another drop. Each time you spray on commercial perfume or use deodorant with heavy metals… another drop. There’s nothing wrong with this, necessarily, as your body is designed to handle toxicity. You may not even notice any symptoms from all this… until your toxic burden reaches its threshold and your glass of water overflows. When this happens, your body can break out in confusing autoimmune spectrum symptoms, including skin flare-ups, chronic pain or joint pain, digestive issues, headaches, fatigue, or flu symptoms. 

The good news is that it’s pretty easy to dramatically reduce your overall toxic burden in a rather short time period. The best way to do this is:

  1. Clean Your Water & Air. In the hydration and oxygenation section, we give our recommendations for the best HEPA air and water filters. This is the best place to start because if there’s toxicity in our air and water, it will almost guarantee we will reach our overall toxic burden.
  2. Buy Organic, Local Foods. Big industrial food brands almost always use toxic chemicals in their food. Go for small, local brands with minimal ingredients. Study the ingredient list on whatever you buy. If there’s anything you can’t pronounce, you shouldn’t be eating it. Buy organic produce and grass-fed, pasture-raised meats and dairy always.
  3. Eliminate Plastic Use. Plastics are leaching toxins into almost everything we eat. Two of the best things you can do to eliminate toxic exposure from plastic is buying glass tupperware, and a glass waterbottle. Carry your glass water bottle around with you everywhere, and fill it up every time you find a high-quality, filtered water source. Make sure you ask restaurants if their water is filtered so you’re not drinking tap water.
  4. Change Your self-care products. Deodorant, toothpaste, make-up, shampoo, moisturizer, and anything else you put on your body. 


Our List For Self-Care Products:

*Tip, under all circumstances, avoid any of the major brands like Dove, Proctor & Gamble, Loreal, Colgate, Olay, Gilette, Dove, Crest, etc. Always go for smaller, organic, and minimal ingredient brands. 


Body Soap:

  • Dr. Bronners All One Soap – An absolute staple in our homes. Comes in great scents and can be used for the entire body. You can also use it as a detergent and home cleaner if needed!


Anything without sulfates, sulfites, parabens, heavy metals. 

  • Acure Great reasonably priced hair care products with no harsh chemicals, can be found at most whole foods. 
  • Native Good overall value. 

Skin Moisturizers:

Generally, you shouldn’t use moisterizer on your skin. It’s much better (and more cost effective) to use oil.


  • Hello Toothpaste – Good reasonably priced option at $6 a bottle
  • Dr. Bronners – A great brand for all self-care products
  • Davids – Pricey option, but delicious tasting. 

Face Wash:



Supplements and herbs to regulate the immune system:

Vitamin C – Vitamin C is an important antioxidant that supports immune function by increasing one’s defenses against infection at the level of the mucous membrane. It is found in high concentrations in white blood cells and aids in the proliferation of white blood cells, our immune cells. It also protects against environmental toxicity by scavenging free radicals, and reducing oxidative damage. We recommend finding Vitamin C in its “ascorbate” form rather than the more common “ascorbic acid” form. It is also helpful to take Vitamin C in conjunction with bioflavonoids to increase absorbability. Ester-C Bio by Klaire Labs is a good example of a high-quality Vitamin C supplement.  

Vitamin D – Vitamin D plays a crucial role in the immune system. Vitamin D deficiency increases susceptibility to infection and autoimmunity. Vitamin D interacts with white blood cells to increase the body’s innate antimicrobial response, protecting us from infection. It is ideal to have your blood Vitamin D levels tested annually to determine the appropriate dosing for you and to ensure you have not fallen into a Vitamin D deficiency. We recommend taking Vitamin D3 (cholecalciferol), which is the most bioactive form of Vitamin D. An example of a high-quality Vitamin D product is Pure Encapsulations Vitamin D3 Liquid.

Zinc – The relationship between zinc and the immune system is complex. Zinc directly affects the production and function of white blood cells. It also acts as a cofactor (activator) for over 300 enzymes that influence various organ functions and have secondary effects on the immune system. It is an important mineral in shortening acute infection and speeding up the healing of wounds. Zinc is found in many forms. We generally recommend zinc in the forms of zinc sulfate and zinc picolinate. One word of caution with taking zinc is that you always make sure you take it on a full stomach. Otherwise, it can cause nausea. Here are some examples of a good quality zinc sulfate and a good quality zinc picolinate.

Quercetin: Quercetin is a phytonutrient mainly known for its anti-allergenic response to the immune system, as it stabilizes mast cells and reduces histamine release. However, it also supports immune defenses because it is a zinc ionophore, which helps drive zinc into cells where it can then fight against infection. Vital Nutrients makes a high-quality quercetin supplement.