When Good Bugs Go Bad: How Toxins and Terrain Are at the Root of Disease

What Happens When Your Body Is Full of Toxins

Here at Microbe Formulas, we follow what’s called foundational medicine. We look at the very foundation of your health and wellness — which, in this case, is your body. As with anything, you need a good, solid foundation on which to build. You wouldn’t construct a house on a rocky slope without doing some prep work first. You can’t run before you can walk. And you wouldn’t bake a cake in a dirty pan.

The same applies to your health. You have to start at the bottom and work your way up. Before you can seek treatment for your Hashimoto’s, headache, or heart condition, you need to get to the root of the problem and fix that first.

Laying the Foundation

You should begin by working on the foundation. It’s just like priming the walls before you paint them. To start, try to discover the underlying issues that might be making you sick in the first place.

You want to be fully well and feel good for the long term, not just use a temporary patch that doesn’t really solve the baseline causes of your health problems.

The first step is to prepare your body for treatment, including getting rid of any of those underlying causes. These could be infections or toxins.

The goal in the early stages is to achieve optimal organ function through detox and drainage. It’s also helpful to concentrate on getting good immune support so that your body is better able to recover on its own.

Try focusing on energy and healing at the mitochondrial level. Just to remind you, the mitochondria are those tiny energy factories inside nearly all of your cells. They produce energy molecules, known as ATP, for your cells, organs, and tissues, and, therefore, for your body as a whole. When your mitochondria are functioning properly, they give you energy, help you to stay healthy, and help you heal when you’re sick. (1, 2)

These first steps should allow your system to find an equilibrium. After all, a body in balance is easier to heal.

Germ Theory vs. Terrain Theory

In the medical world, the battle of germ theory versus terrain theory seems to be as hotly debated as cat versus dog or chicken versus egg. Many people in functional medicine lean toward terrain theory. Let’s consider both these concepts and how they differ.

germ vs. terrain (square)

Germ theory

Germ theory suggests that all disease is a result of “germs” — or, usually, bacteria and viruses. We get exposed to them, and they make us unwell. And because these things are contagious, we can pass them to other people we contact, and they become ill, too. It’s all about “catching a bug” and getting sick. (2, 3)

Then, to treat the illness, germ theorists turn to medications and vaccines in hopes of killing the bacteria or virus. (2, 3)

Terrain theory

Terrain doesn’t only count in wine and real estate. It’s also an important consideration for someone’s health. The terrain theory of medicine focuses less on germs as the cause of disease and more on our body’s reaction to them. The terrain, or environment, of our bodies plays a huge role in how healthy we are and how susceptible we are to illness. (3)

Have you ever seen this happen and wondered why: If two people both order the same lunch special from Joe’s Diner on the same day, why is it that sometimes only one of the two comes down with food poisoning?

Terrain theory explains why sometimes, several people who are “exposed” to the same disease or conditions don’t have the same reaction and don’t get sick. Everyone’s body behaves differently. It’s also why foundational medicine starts with getting the environment of our body ready to heal before beginning any treatment. (3)

Bacteria are not the enemy

The concept of terrain suggests that it’s not a question of being exposed to bacteria. Instead, the bacteria are already inside us. In fact, bacteria actually outnumber us — we have around 37 trillion human cells in our bodies, and far more than that in bacterial cells — perhaps as many as 100 trillion. That’s equal to approximately 12,500 times the population of the entire world, and that’s inside of every single one of us. (3, 4, 5, 6)

In general, we have a symbiotic relationship with these bacteria and other parasites. Yes, they freeload off of us, using us for food and a free place to stay. But they somewhat earn their keep and give back by helping us with things like brain function, cell creation, digestion, protection against disease, and more. (1, 4, 5)

For instance, around half the entire world’s population has H. pylori in their bodies. While this bacterium is often given a bad rap for causing peptic ulcers, the truth is that it may also protect us against: (7, 8)

And as for that notorious E. coli that most people fear, it actually produces vitamins B12 and K and protects us by fending off unfriendly pathogens inside us. Bacteria can be beneficial. (9, 10)

The gut microbiota

Most of the bacteria in our bodies reside in our gut. In fact, it’s estimated that there are 10 times more bacteria in the gut than there are cells in the entire human body! (1, 11)

The term “microbiota” refers to the army of microorganisms that call our gastrointestinal system home, including 500-1,000 different species of bacteria, along with archaea, fungi, and viruses. These microbes have a range of helpful roles, including: (1, 5, 12, 11)

  • Aiding with development of new blood vessels
  • Assisting with digestion
  • Helping with bile biotransformation
  • Making nutrients such as vitamin K and folic acid
  • Producing fatty acids that are necessary for a healthy gut
  • Supporting nerve function

You may have heard about the “gut-brain axis.” The microorganisms within our gut also produce neurotransmitters and help control the development and function of our central nervous system, including our brains. (1, 5, 13)

They support immune function and ward off aggressive pathogens that would otherwise harm us. As a result, our gut microbes help fight conditions and diseases such as colon dysfunction, irritable bowel syndrome (IBS), and obesity. (1, 14)

The microbiota is so important to our health and so much an integral part of the human body that some even call it the “forgotten organ.” Research has shown that infants who don’t cultivate sufficient gut microorganisms develop more diseases later in life. (1)

It’s no wonder that gut health is regularly associated with overall health, and that a healthy gut means a healthy body.

Troubled Terrain

When something goes wrong in the body, it alters the body’s terrain. And when their home is perturbed, the otherwise helpful bacteria and parasites get disturbed and aggravated, and that turns them into something harmful. Essentially, they turn on us. It’s a little bit like poking a sleeping bear with a sharp stick until it growls.

For example, if a body part dies, the bacteria are sent to the scene of the disaster to begin breaking down that body part — basically, what occurs during decomposition. As a result, illness and disease occur inside our bodies. (15, 16)

The same occurs in the gut. When the gut microbiota are living harmoniously with their human hosts, they are extremely advantageous to our health. However, when something interferes with their serenity, and their environment gets to be a little off-kilter, they are suddenly capable of causing health problems throughout the body. (1, 5, 14, 16)

For instance, if someone has leaky gut or insufficient stomach acid, excess bacteria may grow in the small intestine, potentially leading to health disorders or sepsis. Sometimes, people can develop autoimmune reactions to the bacteria that are really there to help them. And taking antibiotics can also kill off useful bacteria and allow dangerous pathogens to step in and harm us. (1, 14)

Changes in the microbiome can affect the immune, endocrine, and nervous systems, causing disorders such as autism, depression, and inflammatory bowel disease (IBD). (5, 15, 16)

What is pleomorphism?

When their living environment is disturbed, microorganisms have the ability to change completely — essentially, to “shape-shift” like something out of a sci-fi film — through a process called pleomorphism. Pleomorphism is defined as “the ability of microorganisms to alter their biological functions, morphology, or reproductive modes in response to environmental conditions.” (17, 18, 19)

Pleomorphism could be the reason for ongoing problems with parasites, even if you’ve gone through a parasite cleanse. It’s not always that you suddenly have more parasites in your body, but rather, the number of harmful parasites could be on the rise. Plus, your terrain becomes a breeding ground where it's not only easier to catch parasites, but it's easier for them to stay around and multiply. That might be why it sometimes feels like an uphill battle to eliminate them.

But what causes these changes in the body’s environmental conditions that, in turn, lead to changes in bacteria?

The Root of All Disease

The major cause is toxins. Toxins change the terrain of the body by damaging tissues. In response, the microorganisms pleomorph into disease-causing organisms at the site of the damaged tissues.

What happens when your body is full of toxins?

According to the terrain theory, we don’t get sick from microorganisms invading our bodies. Those microorganisms are already inside us, peacefully coexisting within us until something comes along to stir things up. We’re exposed to toxins, not to germs — toxins are the true invaders, not the bacteria themselves. (3, 14)

That means that disease and illness are really caused by an imbalance in the body. When someone is sick, it is typically due to an immune dysfunction. But underneath that immune dysfunction lies the true culprit: exposure to a poison or toxicant that has altered the body’s environment, leading to a domino effect of negative health outcomes. (14)

That’s why it’s so important to get the foundation of the body balanced and in good shape first. Because toxins are the root of so many of our health issues, if we don’t address that toxicity at the foundational level, the body will continue to be a regular refuge for pathogens and bacteria — and not the helpful variety.

How do I cleanse my body of toxins?

First, work on changing the environmental terrain of your body so that you can feel better. Cleansing the terrain by eliminating toxins means that you won’t be as prone to infections nor to an excess of harmful, rather than benevolent, bacteria. It means starting with a clean slate.

This can help not only with healing, but also with resistance against future toxins and disease.

Toxic Environment

what disrupts the body's terrain (square)

Which toxins should we be worried about, and how do they affect us?

So, what are the toxins that we’re being exposed to regularly that are messing up our body’s environment and leaving us vulnerable to disease?


Chemicals are everywhere. The problem is that we can’t escape them; they’re so ingrained into our daily lives. Certain chemicals we can steer clear of — we can limit pesticides by going organic, or we can use natural bug sprays and herbicides and eat fresh foods to weed out hardcore chemicals like glyphosate and BPAs.

Yet that won’t protect us entirely. Chemicals are hiding in our beauty products, our household goods, and our water. They’re in foods where we least suspect them. They’re in plastics that make up so much of what we use every day. In fact, it’s estimated that nearly everyone (specifically, 98% of the population) in the U.S. has measurable levels of plastic in their systems. (20)

And when drinking water across the country was tested at random locations, 118 of the 120 sites tested showed levels of polyfluoroalkyl chemicals (PFAS) higher than the recommended maximum, along with lead. (21)

Nowadays, there are some 84,000 chemicals in regular use in the United States alone, at least 1,500 of which are endocrine-disrupting chemicals (EDCs). (6, 8)

EDCs interfere with our hormones and lead to issues such as developmental problems, infertility, obesity, and reproductive disorders. And obviously, they interfere with the body’s terrain and lead to immune dysfunction and illness. (6, 7, 8, 9)

According to some statistics, 10 million new chemicals are produced every year, which translates to 1,000 every hour. Although not all of these will make it into common use and cause exposure risks, the prevalence of chemicals and related toxicity is obviously a major concern for our health. Chemicals can cause endless health problems. (22, 6, 7, 8, 9)

No matter how clean you live, it’s impossible to avoid all these chemicals. They’re out there. The best defense against them is detoxing and keeping the body’s terrain in balance to be better equipped to deal with them wherever they turn up.

Toxic heavy metals

Heavy metals are another danger. They exist in abundance and, like chemicals, have body-changing powers.

There’s mercury in our dental fillings and the fish we eat. There’s aluminum in everything from our cosmetics to our cooking utensils, aspirin to antacids. Children’s toys, consumer products, and some paints are simply swarming with lead — as is our air, dust, soil, and water. And our poultry, mushrooms, rice, and seafood are all chock-full of arsenic. (23, 24, 25, 26, 27, 28)

When the toxic load of these metals get inside our bodies, they change the environment there in a way that weakens our immune system and allows bacteria to harm us.

Lead envelops our mitochondria, preventing them from producing that energy-carrying ATP. This results in fatigue and other issues. Arsenic causes cardiovascular disease, diabetes, and neuropathy, and aluminum is known to kill brain cells. And mercury, which also loves the brain, causes several mental health issues. (29, 30, 31)

These are just a few of the many toxic heavy metals that we are exposed to every day. Only with proper detox can we keep our bodies stabilized enough to have a fighting chance against their damaging effects.

Mold toxins

Mold is nearly as prevalent as chemicals and harmful heavy metals, and just about as dangerous. Mold spores produce toxic compounds known as mycotoxins. These poisonous substances usually enter the body either through inhalation or via contaminated food. (10)

Whatever organs and tissues they come in contact with, they destabilize the terrain there and make the body more sensitive to illness. Specifically, they are known to cause allergic reactions, cellular damage, and inflammation. This most frequently affects the immune, nervous, and respiratory systems. (10)

When mycotoxins are absorbed via the mouth or nose, they can cause:

  • Airflow obstruction
  • Bloody noses
  • Conjunctivitis
  • Cough
  • Fever
  • Lip inflammation
  • Mouth sores
  • Nasal irritation
  • Sore throat

As the poisons continue to disrupt the body’s environment and immune function, symptoms worsen and may result in: (10, 32, 33)

  • Asthma
  • Blindness
  • Blood problems
  • Cognitive deficits
  • Lung congestion and swelling
  • Pneumonia
  • Pulmonary hemorrhaging

Nearly 22 million people have asthma in the United States, and around 4.6 million of them are suspected to have contracted asthma due to exposure to dampness and mold. (10)

To test the dangers of breathing in mold toxins, researchers injected particles of the toxic black mold Stachybotris into the nasal passages of mice. The result was inflammation, irritation, and atrophy of the nose and up into the brain. (10)

Similar results were discovered with tests on rat and mouse lungs. When injected with black mold spores, the animals suffered from lung inflammation and hemorrhage, and many didn’t survive the study. (10)

Radioactive elements

Another terrain-changer in the body is radioactive elements. This is a major health concern and one that takes on many different forms.

For example, research has shown that there are radioactive elements in the drinking water of more than 170 million Americans. On top of that, 158 public water systems in 27 different states were found to have radium levels exceeding federal legal limits. For that reason, experts recommend drinking distilled water, which is safe and contaminant-free. So, consider getting a water distiller for this purpose. (34, 35)

Radioactive elements can also come in the form of electromagnetic fields or frequencies (EMFs). These are emitted from our Bluetooth devices, cellphones, laptops, microwaves, televisions, Wi-Fi, and other electric and electronic devices and systems. These gadgets produce EMFs that interfere with our body’s own electric and energy fields, including our meridians, metabolism, and nerve impulses. (11, 12, 13)

Because EMFs disrupt the way our bodies are “wired,” they effectively alter the body’s environment and open it up for disease. EMFs change our chemical balance, damage our enzymes, and interfere with cell division. This can lead to health problems such as: (11, 12, 13)

  • Cardiovascular disease
  • Depression and anxiety
  • Premature aging
  • Reproductive problems
  • Tumors

Additional toxins

Other types of toxins that can cause changes in bacteria include: (14, 15, 16)

  • Emotional toxins triggered by divorce, financial issues, loss of a loved one, stress, etc.
  • Nutritional deficiencies
  • Physical injury or accident
  • Tissue death

Prepare Your Body for Wellness

Whether you believe in the germ theory or the terrain theory (or some combination of the two), it’s still important to get at the root cause of your illness. This involves opening yourself up to the healing process by ridding your body of any toxins that could be hurting your internal environment and your ability to get better.

Through cleansing, detox, and drainage, you can ensure that you have a biological terrain that’s ready for wellness. Deal with toxicity before treatment, and prevent an environment where good bugs go bad.