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  • Writer's pictureDr. Kari Young

Germ Theory vs. Terrain Theory and our Innate Immunity

Updated: Oct 19, 2022

Before any autoimmune disease (Hashimoto’s, Graves, RA, Fibromyalgia, etc.) can be healed, the root of the problem must be identified and removed. Many people are still suffering, and told that they will always have autoimmunity, and as a result may need surgery or medication for the rest of their lives. This is actually true, if one is only treating symptoms and not removing the source of the autoimmunity itself.

For those who desire to live with optimal health, the practice of foundational medicine is essential. This is the practice of addressing the foundation of the body, starting at the bottom and working up. Many people jump in too quickly to build their health with advanced detox or other health strategies without taking care to first build a strong foundation.

The concept is similar to building a home on a foundation that is faulty or not completely set. Over time, the home’s structure will be compromised, resulting in repair or destruction. Taking the time and having the patience to ensure that your health is built on a strong foundation ensures that you can achieve health over the long term.

Preparing the drainage pathways and optimizing organ function is an essential part of creating a strong foundation. This includes detoxing at the cellular level properly and opening and supporting all drainage pathways. Removing the root cause which are the toxins and interferences at the cellular level while also repairing any damaged mitochondrial health.

All of this will allow your body to reach biological homeostasis so it can repair, restore, and heal.

Germ Theory vs. Terrain Theory

It is no surprise that conventional medicine focuses on the germ theory, while doctors of functional medicine focus on the terrain theory.

Germ Theory

Simply stated, the germ theory tells us that all disease is caused by “germs”, which is a generic term for bacteria and viruses.

When we are exposed to “germs”, we get sick and pass the germs on to other people, who also get sick. This theory leads us to the creation of medicine and vaccines that claim to kill the germs and prevent contagion.

Terrain Theory

The terrain theory of medicine takes the focus away from the germs themselves and to the body’s reaction to those germs. As you have likely experienced in life, not everyone who is exposed to germs actually gets sick. And, not everyone gets sick at the same level. So why would that be?

The reason that some people can be exposed to others carrying germs, and not get sick is because of the strength of their foundation. It is extremely important to work on strengthening the foundation of health as the first step to any healing treatment.

Don’t be Afraid of Bacteria!

The terrain theory informs us that bacteria already live inside of our bodies, and the notion of bacterial exposure is incorrect. This makes sense since over 100 trillion bacterial cells currently live in our body, far outnumbering human cells.

The human body has generally a symbiotic relationship with bacteria and parasites, even though they live off of us. When we are healthy, they provide benefits to us, such as helping us with brain function, digestion and a strengthened ability to fight disease.

Here’s a great example - would you be surprised to learn that 50% of the global population carries H. pylori? However, it is only a problem for individuals with disease or a weak foundation.

H. pylori can be beneficial to the body, and protect us from asthma, esophageal cancer, and gastrointestinal disease.

The Gut Microbiota “The Forgotten Organ”

The term “microbiota” refers to the many microorganisms that exist in the gastrointestinal system. This “forgotten organ” includes 500-1,000 different species of bacteria, archaea, fungi, and viruses. These microbes have a range of helpful roles, including:

  • Produces fatty acids that are necessary for a healthy gut

  • The creation of new blood vessels

  • Produces vitamin K and folic acid

  • Digestion

  • Bile biotransformation

  • Supports the nerve function

  • Strengthens the immune system

  • Helps to fight diseases such as IBS, colon cancer and obesity.

The link between gut health and autoimmune disease is vast, and it is essential that the foundation be optimized for total healing.

When Bacteria Turns Against Us

Anytime the body is in less than optimal health, it causes a disruption to the body’s terrain. This disruption can cause bacteria and parasites to become harmful and to turn on the body.

This concept is similar to what happens when a part of the body is diseased, or dies. The body sends the bacteria to the scene so that it can break down the body part, similar to the process of decomposition. This causes disease within the body.

For example, someone with a leaky gut will suffer from excessive bacterial growth in the small intestine. This can lead to an autoimmune reaction to the bacteria that are really there to help. Sometimes people are prescribed antibiotics; however, they do not discriminate and kill off the good bacteria as well, which allows the dangerous pathogens to harm us.

An imbalanced microbiome can damage the immune, endocrine, and nervous systems, causing disorders such as autism, cancer, and inflammatory bowel disease (IBD).

The Root of All Disease

The root cause of all disease is the bioaccumulation of toxins which causes chronic inflammation at the cellular level. Toxins alter the body’s terrain and cause the microorganisms already living in our bodies to be disrupted and imbalanced.

The terrain theory informs us that our bodies are exposed to toxins, not to germs. Toxins are the true invaders, not the bacteria themselves.

It is important to address the foundation of the body first. Since toxins are the root of health problems, we must remove that toxicity at the foundational level in order to prevent the body from becoming a breeding ground for parasites.


Chemicals are all around us, and we must be aware of where they lurk and understand exactly how they can be avoided.

There are over 84,000 chemicals in regular circulation in the United States alone, at least 1,500 of which are endocrine-disrupting chemicals (EDCs).

EDCs are extremely dangerous and lead to hormone disruption, cancers, developmental problems, infertility, obesity, cognitive deficits, and reproductive disorders. These chemicals severely disrupt and damage the body’s terrain and lead to immune dysfunction and illness.

Some chemicals are right under our noses, such as the foods we eat and water that we drink and use. Consuming organic foods is necessary in order to avoid exposure to pesticides, glyphosate and BPAs. And, drinking distilled water is the gold standard in order to completely rule out exposure to the polyfluoroalkyl chemicals and lead, commonly found in tap water.

No matter how clean you live, it’s impossible to avoid exposure to every chemical. The best defense is to become knowledgeable about how to create a toxic-free environment and to achieve a balanced terrain in order to overcome these toxins.

Heavy Metals

Heavy metals can be a huge problem, especially for folks with weak terrain. Like chemicals, heavy metals are also difficult to completely avoid. However, having the knowledge of where they lurk and how to mitigate exposure is helpful. Common sources of heavy metals are:

  • Mercury is found in dental fillings and fish causes brain and mental health issues.

  • Aluminum is found in cosmetics, cooking utensils, aspirin, and antacids and kills brain cells.

  • Lead is found in children’s toys, consumer products, paints, air, dust, soil, and water. Lead envelops our mitochondria, preventing them from producing energy-carrying ATP. This results in fatigue and other issues.

  • Arsenic is found in conventionally farmed poultry, mushrooms, rice, and seafood. Arsenic causes cancer, cardiovascular disease, diabetes, and neuropathy.

Toxic heavy metal exposure changes the environment in the body and causes a weakened immune system. This is a perfect formula for those bacteria to harm us.

Of course, there are many more examples of heavy metal toxicity, and the key is to become informed in order to know which heavy metals are present in your own body. Proper detox at the cellular level ensures that we completely remove the targeted toxins so that our body’s foundation can be rebalanced and healed.


Mold is extremely common and very dangerous to the body. Mold spores produce mycotoxins that enter the body through inhalation and contaminated food. Mycotoxins can damage the organs and tissues and make us more susceptible to illness and disease.

Common symptoms of mycotoxin exposure are:

  • Nose bleeds

  • Red eye

  • Mouth sores

  • Swelling of the lips

  • Difficulty breathing or cough

  • Nasal irritation

  • Fever

  • Sore throat

When mycotoxins are allowed to exist in the body chronically, more long-lasting and significant health problems can occur:

  • Blindness

  • Asthma

  • Inflammation of the lungs

  • Blood disorders

  • Cognitive decline

  • Pulmonary hemorrhaging

Radioactive Elements

Radioactive elements are all around us, and cannot be seen or smelled. They also cause disruption to the body’s terrain and can trigger illness and disease.

EMFs disrupt the body’s wiring, or electromagnetic fields, and can change our chemical balance, damage our enzymes, and interfere with cell division. This can trigger health problems such as depression, reproductive problems, heart disease, and tumors and growths.

Most people are aware that the greatest source of EMFs are from our electronic devices such as bluetooth devices, cellphones, computers and WiFi devices and appliances. They are also emitted from microwaves and televisions.

It surprises people to learn that EMFs are also in our drinking water! In fact, in the US alone, , 158 public water systems in 27 different states were found to have radium levels exceeding federal limits.

Additional toxins

Other types of toxins that can cause changes in bacteria include:

  • Emotional or stress toxins

  • Nutritional deficiencies

  • Physical injury

  • Tissue death

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