Getting to the Root Cause of Inflammation: Infections, Toxins & Nutrient Deficiencies

Getting to the Root Cause of Inflammation: Infections, Toxins & Nutrient Deficiencies

Getting to the Root Cause of Inflammation: Infections, Toxins & Nutrient Deficiencies

Inflammation is a hot topic right now, particularly when it comes to the human body and health issues.

In fact, Time Magazine recently published an article that discussed the role of inflammation as an underlying root cause in the majority of major illnesses that lead to premature death.

In our modern era, we’re increasing inflammation on the daily, as we’re constantly bombarded by triggers. From the air we breathe to what we eat to the stress we’re under to the nutrient-sucking foreign invaders inside us, it’s incredibly difficult to reduce inflammation effectively.

The top 3 factors in inflammation are: infections, toxins, and nutrient deficiencies. These are all critical components that influence our overall health and well-being. 

Understanding how these factors interconnect and become the root causes of diseases, including heart diseases, autoimmune disease, neurological disease, and myriad other health problems can empower us to make the changes we need to reduce inflammation and speed up our natural healing abilities. 

Let’s dive into what inflammation is, how it works (the good side and the bad) and how you can address the top 3 factors causing chronic inflammation so you can restore your natural energy levels while slashing your risk of getting a serious or chronic medical condition.

The Root Cause of Disease: Inflammation

Inflammation is your body’s natural defense mechanism against harmful invaders like pathogens, and as a healing mechanism for injuries. 

Acute inflammation plays an important role in healing wounds and fighting infections, but chronic inflammation can be detrimental. 

Let’s break down the difference.

Acute Inflammation (Good)

Acute inflammation is one type of inflammation. It’s a short-term, rapid response by the immune system to an injury, infection, or tissue damage. It’s a natural and necessary process that helps the body heal and protect itself.

Acute inflammation serves as the ultimate protector.  It’s typically localized to the site of injury or infection. When you experience an injury or infection, immune cells, white blood cells, and cytokines rush to the affected area to remove pathogens, clear damaged tissue, and initiate the healing process. Acute inflammation is a targeted response aimed at resolving the issue quickly. 

For example, you know how when you get a cold or the flu, you may get a fever? That’s acute inflammation. One of your body’s ways of attacking viral and bacterial pathogens is by burning them up. That’s why you get a fever—your body is literally throwing an inferno to eliminate those foreign invaders.

You can also think about inflammation as targeted energy that’s going to work on a specific problem. All that energy generates heat, right? That’s why other symptoms of acute inflammation include redness, swelling, warmth, and pain—like when you get an injury. These are signs your immune system is actively working to restore health.

Acute inflammation is also self-limiting. Meaning once the threat is neutralized or the healing process is underway, the inflammation subsides. It stays in its lane and then goes away. It’s a sign your body is responding appropriately to a challenge.

Chronic Inflammation (Bad)

Chronic inflammation, on the other hand, is a long-term, persistent state of inflammation that lasts for weeks, months, or even years. It’s not a normal response and can actually harm your body.

Unlike acute inflammation, chronic inflammation does not effectively resolve an underlying issue. Instead, it can cause ongoing tissue damage and disrupt normal cellular function.

You might be wondering, Why do we experience chronic inflammation? 

Well, it’s because in our modern lives, we are actively taking in more toxicity than we can push out. Our body is on high alert all the time which means our immune response is trying to tackle multiple problems all at the same time, and not really getting anywhere.

Chronic inflammation can affect the entire body, leading to a range of health problems. It has been linked to chronic illness, including heart disease, diabetes, autoimmune diseases (like rheumatoid arthritis and inflammatory bowel disease), cancer (including colon cancer), and neurodegenerative disorders (such as Alzheimer’s disease).

Chronic inflammation can be triggered by many different factors, including persistent infections, exposure to negative environmental factors (like pollution or heavy metals), an unhealthy diet, obesity, nutritional deficiencies, and even chronic stress.

Like a ninja, chronic inflammation often operates silently in the body, with subtle or no symptoms. This makes it particularly dangerous because it can quietly contribute to the development of chronic diseases over time. And, it can actually impact how your body responds to medical intervention.

For example, research is now showing the connection between inflammation and medication response. In a recent study, when scientists addressed inflammation in patients with severe asthma, some displayed an improved sensitivity to corticosteroids, opening up a new treatment option for patients who previously struggled for relief.

The same is true the other way—conventional medicine often will add more prescriptions and external interventions when their treatment plans aren’t working effectively. In many cases, pumping people full of antibiotics and other medications actually increases inflammation, making the body work harder, which reduces efficacy and actually increases toxic load.

Interestingly, many of our clients are experiencing great benefits by adding lifestyle changes to their medical protocols and are able to get off of medications faster with fewer side effects. That’s because they’re working to clean up the toxicity inside them, and reduce widespread inflammation that’s the real culprit behind the health problems.

Now, let’s dive into the main factors that cause inflammation.

Top 3 Inflammation Factors: Infections, Toxins & Nutrient Deficiencies

Infections – Battling the Intruders

Infections occur when harmful microorganisms invade our bodies. 

When you think about infections, you probably instantly think about viruses and bacteria, but there’s actually a lot more nuance to it than that.

Where Can Infections Happen?

Infections can happen anywhere in your body, but the most common areas are:

  • In your mouth and gums
  • Sinuses
  • Bladder
  • Bloodstream
  • Gut / Microbiome
  • Liver
  • Skin

What Causes Infections?

Infections can be caused by more than just viruses. You can also get infected by bacteria, fungus, and parasites—and you don’t even need to travel abroad to pick them up!

Here’s a list of some of the top viruses, bacteria, fungi, and parasites known to cause health problems in humans. Of course, this isn’t an exhaustive list, but these are some of the most well-known and significant ones in the United States and other developed countries.


  • Influenza Virus: Responsible for seasonal flu outbreaks, which can range from mild to severe.
  • SARS-CoV-2: Responsible for the COVID-19 pandemic, with a range of symptoms from mild to severe respiratory illness.
  • Human Papillomavirus (HPV): Linked to various cancers, including cervical cancer.
  • Hepatitis Viruses (Hepatitis B and C): These viruses can damage the liver and lead to chronic liver diseases.
  • Herpes Simplex Virus: Causes oral herpes (HSV-1) and genital herpes (HSV-2), leading to painful sores.
  • Epstein-Barr Virus (EBV): EBV is a member of the herpesvirus family and is associated with immune system dysfunction and serious, chronic conditions, such as certain cancers and autoimmune diseases.
  • Human Immunodeficiency Virus (HIV): The virus that causes AIDS (Acquired Immunodeficiency Syndrome) and weakens the immune system.


  • Escherichia coli (E. coli): Certain strains can cause food poisoning and urinary tract infections.
  • Staphylococcus aureus: Can lead to skin infections, abscesses, and even severe conditions like MRSA (Methicillin-resistant Staphylococcus aureus).
  • Streptococcus pyogenes (Group A Streptococcus): Responsible for strep throat and can lead to more serious conditions like scarlet fever and rheumatic fever.
  • Clostridium difficile (C. difficile): Can cause severe diarrhea and colitis, often associated with antibiotic use (you’ll also find it prevalent in nursing homes and other long term care facilities).
  • Salmonella: A common cause of food poisoning, leading to gastrointestinal symptoms.
  • Helicobacter pylori: Associated with stomach ulcers and gastritis.
  • Borrelia burgdorferi: Responsible for Lyme disease, which is primarily transmitted to humans through the bite of infected black-legged ticks (Ixodes scapularis or Ixodes pacificus).


  • Candida: Can cause yeast infections, including oral thrush and genital yeast infections.
  • Aspergillus: Can lead to lung infections, especially in individuals with weakened immune systems.
  • Tinea species: Responsible for various fungal skin infections, like athlete’s foot and ringworm.
  • Stachybotrys chartarum (Black Mold): Yes it’s a mold and also technically in the fungus family. Many people get exposed to black mold in their homes and offices, without even knowing it as black mold is sneaky and often hides in your walls, grout, or bathrooms. Exposure can create respiratory problems such as coughing, wheezing, nasal congestion, skin rashes, and persistent fatigue.


  • Giardia lamblia: Often associated with contaminated water, this microscopic protozoa causes giardiasis, leading to gastrointestinal symptoms.
  • Toxoplasma gondii: Can be harmful to individuals with weakened immune systems and is associated with toxoplasmosis.
  • Hookworms: Usually picked up when walking across contaminated soil barefoot, hookworms can lead to an itchy rash known as “ground itch”, anemia, and abdominal pain.
  • Tapeworms: symptoms vary depending on the type of tapeworm but may include abdominal discomfort and weight loss and is caused by consuming undercooked or raw meat.
  • Entamoeba histolytica: Common in travelers, this amoeba causes dysentery and can lead to severe gastrointestinal issues.

When exposed to any kind of infection, our immune system kicks into action, causing inflammation to fight off the invaders. While the immune response is crucial for defense, persistent infections can lead to chronic inflammation, impacting our overall health.

Think of infections as tiny armies of germs attacking our bodies. Inflammation is our body’s defense system, trying to fight off these armies. Sometimes, if the fight goes on for a long time, it can affect our energy and well-being.

Practicing good hygiene, such as washing hands frequently and avoiding close contact with sick individuals, as well as adding a functional medicine approach to a healthy lifestyle with sufficient sleep and proper nutrition, are vital in preventing infections.

Environmental Toxins – Enemies Hiding in Your Cells

Where Do Environmental Toxins Come From?

The most common toxins that cause inflammation are found in the environment: air pollution, water pollution, pesticides/herbicides, or a myriad of other chemicals. 

Similar to what happens when faced with viruses, bacteria, fungus, and parasites, when we encounter environmental toxins, our bodies initiate that natural inflammation response to protect us. While this is useful in the short term, prolonged exposure can lead to chronic inflammation and health problems.

Toxins are like sneaky troublemakers that can enter our bodies from many different sources in the environment. Because we’re constantly bombarded with them, most of us have a hard time flushing them out. And when toxins stick around in our cells for too long, they produce widespread, chronic inflammation, which can make us feel tired, mentally/emotionally drained, as well as unmotivated.

How to Remove Environmental Toxins

The first thing to do in order to decrease inflammation caused by environmental toxins, is draw those toxins out and get them out of your body. 

One of the most effective ways to do that is by opening up your internal drainage pathways, so your body is able to pull out the toxins clogging up your cells, bind them, and flush them out regularly. Not only will this help you regenerate energy more quickly, but you’ll actually begin to look and feel better! Way too many people try to detox without opening up their internal drainage pathways—and all that does is recirculate the toxins and make you feel worse. 

Once you’ve opened up those pathways and are getting the toxins out, it’s time to minimize your exposure to environmental toxins as much as possible. 

That means avoiding smoking (including being around those who smoke); ensuring you have access to clean, purified water; changing air filters in your home regularly; getting rid of your highly toxic nonstick cookware, and reducing dependence on chemicals in your cleaning products, skincare, and personal products. Using natural cleaning products can drastically decrease the effects of toxins on your health. 

It’s also critical to limit toxicity caused from what you consume. For example, eating organic foods can help reduce exposure to harmful chemicals and limit the propagation of free radicals.

Nutrient Deficiencies – Enemies to Your Immune System

Essential nutrients, such as vitamins and minerals, are like fuel for the immune system.

They help keep chronic inflammation in check and support overall health. When we lack these nutrients, the immune system may weaken, leading to a higher risk of infections. Poor nutrient absorption also zaps your energy not only because your cells are starved of the fuel they need, but also because all the organ systems and natural processes in your body have to work way harder to do their jobs.

Think of nutrients like superhero power-ups that help your immune system stay strong—and keep energy high. 

When we lack these power-ups, it makes it harder to fight off infections and keep the engines running.

What Causes Nutritional Deficiencies?

It might sound crazy that in today’s world—where we seemingly have access to all the food we could ever possibly need at any given time—that we have nutrient gaps, but the fact is nutrient deficiency is on the rise. 

Wild, right? But here are actually many reasons for this, including:

Poor Diet

Most Americans don’t eat a balanced and varied diet. In our go-go-go culture, we’ve become reliant on quick access to heavily processed foods (both in the drive-through and in the grocery aisles). Even “healthy” foods are loaded with hidden sugars and refined grains that have been stripped of all bran, fiber, and nutrients. Common “empty foods” that hide in pretty much every kitchen in America include pizza dough, pasta, pastries, white flour, white rice, and breakfast cereals. 

Soil Depletion

In order to meet the food demands of our overpopulated planet, growers have resorted to unsustainable farming practices. They’re trying to feed a growing world population, so to do that, they often grow the same type of crop in the same field year after year because it’s more efficient. When farmers grow a lot of crops in the same soil over and over again, it can lead to “soil depletion.” This happens because the plants use the nutrients in the soil to grow big and healthy. Over time, if the same nutrients keep getting used up without being replenished, the soil becomes less fertile and the nutrients that would normally show up in the crops become depleted—which means they’re depleted when we consume them, as well.

Malabsorption Issues

When we don’t have specific nutrients and enzymes in our microbiome, it can make it difficult for all the food nutrients to be absorbed by the digestive system. This means even if we do eat high quality, nutrient dense foods, the digestive system simply can’t extract the nutrients—and they pass right on out “the back door” (if you know what I mean).

Digestive Disorders

When we experience digestive disorders caused by dysbiosis, leaky gut, or other inflammation-related problems, the body simply can’t absorb or recognize the nutrients. In some cases, the disorder actually “attacks” the food source and causes unpleasant symptoms. For example, conditions like gastritis, gastric bypass surgery, or chronic diarrhea are known to disrupt the digestive process, affecting nutrient absorption.

Food Sensitivities or Allergies

Individuals with food sensitivities or allergies may avoid specific foods that are rich in essential nutrients, potentially leading to deficiencies. For example, let’s say you experience a reaction when you eat bananas, so you eliminate them from your diet. Bananas are high in potassium and if you aren’t getting that nutrient elsewhere, you will likely experience a deficiency. This can show up as fatigue, muscle cramps, and physical weakness. Since we’re on the topic, the concept of food “allergies” is an interesting one to me. Many of us assume that because we experience sensitivity to a food, we have become allergic. But, for many of us, this food sensitivity isn’t a true allergy at all, rather due to an imbalanced microbiome and leaky gut. Fun fact: Much of the time, creating a more hospitable environment in the digestive system actually resolves food sensitivities and reactions. 

Vegetarian or Vegan Diets

While plant-based diets can be very healthy, individuals who follow strict vegetarian or vegan diets need to pay extra attention to ensure they get all essential nutrients, particularly vitamin B12, iron, and calcium, which non-vegetarians usually get from animal-based products including meat, seafood, eggs, and dairy.

Age-Related Factors

As we age, our nutritional needs may change, potentially putting us at a higher risk of certain deficiencies. For example, older adults may need more vitamin D and calcium for bone health. Not making appropriate shifts as you move through the stages of life opens up higher risk factors for falls, osteoporosis, and other health problems.


Some medications can interfere with nutrient absorption. For instance, certain antacids can affect the absorption of minerals like calcium, magnesium, and zinc. Pay attention to the labels on your medications and supplements so you can proactively adjust your plan to not accidentally create nutrient gaps.

Chronic Diseases

Chronic health conditions, such as diabetes, kidney disease, or cancer, can increase the risk of nutritional deficiencies. This can be due to the body’s impaired absorption ability or not proactively increasing nutrients needed to counterbalance the disease. For example, those with diabetes often benefit from adding more fiber to their diet. That’s because a high-fiber diet can help stabilize blood sugar levels by slowing the absorption of carbohydrates. If you don’t increase your fiber intake, you may experience more severe diabetic symptoms.


Chronic stress can affect digestion and nutrient absorption, potentially leading to deficiencies over time. The reason why depends on how you metabolize stress. For example, stress can affect appetite, leading to either increased or decreased food intake. Some people turn to comfort foods high in sugar and unhealthy fats, while others may lose their appetite altogether. These changes in eating patterns can impact the intake of essential nutrients. Another example of why you may experience nutritional deficiencies due to stress is because chronic stress can lead to changes in the excretion of certain nutrients, such as magnesium and zinc, through the urine. These minerals play important roles in stress management and overall health, so do yourself a favor and get ahead of your stress with a regular routine of self-care practices.

How to Fix Nutritional Deficiencies

Obviously, an easy way to begin to fight off nutrient deficiencies is to eat a balanced diet with a variety of colorful fruits and vegetables. 

We call that “eating the rainbow” and it’s important to do because different colors often correspond to specific phytonutrients, vitamins, and minerals. For example, orange and yellow fruits and vegetables are rich in beta-carotene (a form of vitamin A), while leafy greens are abundant in folate and vitamin K.

The natural pigments responsible for the colors in fruits and vegetables often indicate the presence of specific phytonutrients, such as anthocyanins in purple and blue produce or lutein in yellow and green vegetables. These phytonutrients have various health benefits, including antioxidant and anti-inflammatory properties.

Too many of us eat the same foods over and over again—and it’s why we don’t get all the nutrients we need from our food. 

It’s recommended to eat the rainbow each day, so get creative with your meals. If you have a family, make “eating the rainbow” a game with the kids. If you have picky eaters, find ways to “hide” different colors in favorite foods. For example, grate or finely chop vegetables like carrots, zucchini, or mushrooms and mix them into meatballs for spaghetti night. The colorful foods add moisture and nutrition.

How to Reduce System-wide Inflammation

Conventional medicine often focuses on reacting to a disease: solving symptoms after a disease has already taken hold. However, integrative medicine takes a different approach. It comes at health from the other end—working to eliminate the key risk factors before disease can form. This means solving the root cause of disease before it becomes a big problem. 

For example, a sedentary lifestyle is often a key reason why we experience chronic inflammation. So the best ways to address inflammation from a functional medicine perspective include regular physical activity, reducing stress levels, getting to a healthy weight you can maintain, and shifting to anti-inflammatory diets. These lifestyle behaviors go a long way to reducing the inflammatory response that creates unhealthy weight gain, chronic pain, skin disorders, and a multitude of avoidable health problems.

Most people try to tackle inflammation a little at a time, which isn’t necessarily bad but not the most effective way to fix it. After all, it’s better to do something than nothing. But this is usually ineffective because you’re taking a shot in the dark and hoping for the best.

Of course, if you know you’re low in a specific nutrient—say B12 or iron—supplementing your diet is a no-brainer. But the fact is, reaching for a supplement bottle first thing is like slapping a bandaid on a bullet wound. You’re not really addressing the underlying cause of what’s creating that deficiency.

The best way to address inflammation is to pinpoint the source(s) creating that inflammatory response.

When we work together, one of the first things we usually do is use microbiome testing to identify exactly what’s causing your imbalances

A microbiome test is kind of like taking a screenshot of your internal health. A functional medicine practitioner (like me) can see what infections are present (including parasites, candida, and other invaders inside you) and help you interpret the results of the test. We can also identify if you are at risk for nutritional deficiencies and toxins.

Once we know what’s happening, we can create a customized protocol and treatment to target those root causes of inflammation: infections, toxins, and/or nutrient deficiencies—one you can actually follow.

Of course, we also work with you on the basics, such as making meaningful lifestyle changes, reducing your toxic load, and making informed choices about what to eat. The majority of people we work with begin to feel better right away, with more energy, better mental clarity, and a stronger healing response. 

Want to see if we’re a good fit? 

Take your first step here.

Take Good Care,

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