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Terrain Theory Versus Germ Theory | Understanding Your Immune System

What if everything we know about germs is wrong?

What if handwashing, sanitizing surfaces, and social distancing isn’t the only way (or even THE way) to avoid getting sick?

Medicine has made many advancements since doctors weren’t even washing hands between sick people and delivering babies, and it’s clear that we’ve figured out how to help people live longer lives. But do we know everything yet?

Terrain theory is the new kid on the block (in a way), and I can’t wait to help you understand it more.

hand sanitizing

I’ve had this post on my list for over 18 months, maybe two years — I really wanted to dive into terrain theory at the very beginning of the COVID-19 pandemic.

I was starting to see articles about spraying disinfectants on beaches, basically disinfecting the world. I thought, “This can’t be good, this absolutely can’t be good.”

I was reading a little bit about terrain theory and getting super interested when it hit me, “Wait a second, I’ve subscribed to germ theory forever.”

I’d never put a speck of cognizant thought to the fact that the word theory is in “germ theory,” meaning that it’s not even necessarily proven yet. But boy, do we certainly act as though the only way to prevent the spread of disease is to wash your hands, don’t touch your face, wash your surfaces, use sanitizer, etc.

But what if, just like 150 years ago when doctors washing their hands between patients was revolutionary — What if there’s still more revolution to come in what we know and understand?

Rather than do a bunch of research on my own, I decided to go to the expert on terrain theory, Dr. Catherine Clinton.

Can’t see the video? Watch my interview with Dr. Clinton on YouTube!

I highly recommend watching the video, but if you don’t have time, here is a synopsis/edited transcript:

What Is Terrain Theory?

A few hundred years ago, when microbes were first discovered under our microscopes, there were two camps looking at and debating what was happening in the microscopic world.

Louis Pasteur led the germ theory side which says that it is the germ that causes disease.

There are different takes on what the terrain theory people were saying in the beginning. Some of them were saying that the disease is actually inside of ourselves, and we are detoxing that out. Other people were saying that the microbes don’t cause the disease, it’s the interaction between the microbe and the terrain.

That’s really the bottom line when we’re looking at germ theory versus terrain theory on a surface level.

Does the germ cause disease? Is this an agent acting on its own coming to infect us all and cause disease? Or is it an interaction between this microscopic world and the world around us and how that interacts with our terrain?

The fundamental difference in practice is that germ theory is looking at how to fight the germ and terrain theory is more about how to support your internal terrain.


Germ Theory Played Out in Practice

I think it’s clear that modern medicine and healthcare are grounded in germ theory. Even when the medical community recognizes the value of terrain, it is so disregarded and pushed aside, that is almost nonexistent.

I just saw a joke on social media this week that said,

“A conversation that never actually happens:

Me: ‘Doctor, I’m feeling kind of poorly.’

Doctor: ‘How’s your diet?'”

Sound familiar? Unfortunately, not enough people are looking at the human, we’re looking at the germ.

What those guys looking at microscopes long ago missed was that health and disease aren’t just isolated, microscopic interactions.

We have so much research out there showing how interconnected our health is: to the world around us, the air we breathe, the water we drink, the food we eat, the thoughts we think, the safety we have in our families, and communities.

Our modern life has marched us steadily away from our natural environment that we’ve adapted to live in concert with.

gut health

Why Terrain Theory?

So much of our medicine and our health care is this war-like confrontation of germs, and that’s so counterproductive.

First of all, we can’t get rid of microbes. They’re vital to our health, and they’re vital to the world around us.

Secondly, framing it in such a way really disregards the fundamental pieces of what it means to be human: having a safe community and a belief in something greater. These things directly impact our health yet are disregarded by the bigger picture of healthcare and medicine.

There’s a much better way to do this, a much simpler way, and it’s really exciting.

When you look at the research, it’s not a competitive, war-like defense, it’s cooperation.

Our world is really cooperative. It’s not so much survival of the fittest. It’s the survival of the ones that are cooperating in resilience.

We’ve seen that for so long in the natural world, with trees, plants, mycelium, and fungus. It’s time that we understand that we too are part of this ecosystem, and it applies to us as well.

Supporting Our Terrain

With terrain theory, it’s less about “building up defenses” against the “bad guys” and more about balancing signals of safety and danger.

When we talk about the immune system, we’re so ingrained to think of it that way: boost our defense system and protect ourselves against the outside.

Microbes, air pollution, water, the food you eat, safety, community, spirituality, all of these things, are messages that your body responds to.


For example, our bodies react to processed food as a danger signal. We have to balance it out.

When I’m explaining it to my kids I (Dr. Clinton) say, “Your body takes that stuff as a dangerous signal, and it’s looking for signals of safety to balance it so it doesn’t go into overdrive.”

So if you’re going to expose yourself to danger signals like processed food, perfume, or alcohol, it’s necessary to balance it with some safety signals, getting to sleep on time, getting enough water, and eating your vegetables.

Want to be able to easily refer back to this list of gut-healing steps so you don’t forget any of the actionable tips?

PRINT ME - Heal Your Gut Checklist

I made a printable checklist of what to seek out and what to avoid to promote gut healing, and I’d love to send it to you!

Terrain Theory and Autoimmunity

Dr. Clinton was diagnosed with several autoimmune conditions and Lyme disease in medical school. The definition of autoimmunity is your body attacking itself. What a disempowering definition that is!

From a terrain theory viewpoint, autoimmunity is your body reacting to those dangerous signals in overdrive.

Our biology was designed to interact with the world around us, and we need that interaction to stay healthy.

Once we start to remove those danger signals and replace them with signals of safety, then the body calms down, the inflammation comes down, the autoimmune symptoms disappear and the conditions reverse.

It’s really remarkable, but there’s no room for that IF the definition of autoimmunity is your body attacking itself. Our bodies are not betraying us, but they are working with us in the way they always have.

Let’s get into some free things that you can do to improve your terrain starting today.

Tending Your Terrain Through Diet

One of my favorite things for tending our terrain is tending to the diet. Things like eating more resistant starches, and getting omega-3 fatty acids in your diet can build your resilience to infections, disease, trauma, chronic stress, so many different things.

When we eat resistant starches, they go undigested through the gastrointestinal tract, they reach the colon, and our gut microbiome ferments those resistant starches and turns them into short-chain fatty acids.

Those short-chain fatty acids go directly to fuel the mitochondria of the GI tract, creating less intestinal permeability or leaky gut.

Most American's are deficient in Omega-3's. Here's why we need them and some great place to get them- salmon and flax!

At the same time, we see a boost in T regulatory cells. Our T regulatory cells go through the body and put out inflammatory fires. They stop autoimmune reactions, cytokine storms, and deal with the inflammation of the chronic stress of living a modern life.

If we have high T regulatory cells, we’re more resilient to pollution, infection, trauma, and stress: just from eating resistant starches that we find in whole grains, garlic, onion, leeks, and asparagus. Think of them as safety signals.

RELATED: All About Prebiotics (another name for resistant starch)

One of my (Dr. Clinton’s) favorite studies out there on omega-3s is with infants in the NICU. Because these infants needed medical care, they were separated from their mothers, and that was a seed of trauma. There was a predictable shift from beneficial microbes in the biome to more harmful species.

Then researchers supplemented the breast milk bottles with omega-3 fatty acids and saw a complete reversal in that composition of the gut microbiome!

Look at your diet, are you getting enough resistant starches? Are you getting omega-3 fatty acids? Those can have a tremendous impact on our overall resilience.

I always thought of the gut microbiome as something that would shift slowly over time, except in the case of antibiotics. However, you can see microbiome shifts within a day or two based on singular impacts of safety or danger signals.

Mindfulness Practice to Impact Your Terrain

My next favorite thing to attend to our terrain is some kind of mindfulness practice so that we are creating a safe harbor for ourselves and our children.

Danger and safety signals impact our biology instantaneously. We have neurons that go directly from our brain to our gut lining. That’s a direct link between what we’re thinking and the state of our gut health and our immune system.


On the flip side, that’s where fear and anxiety can cause people to get sicker.

In summer 2021, the CDC released a study looking at comorbidities that cause negative impacts with the recent virus. Obesity was number one, while fear and anxiety disorders were number two.1

I like to think of it almost like an orchestra. We’re working in concert with the environment around us and our inner biology. There are all these different instruments coming together to play a tune. When we create a chaotic message, our body goes into panic mode after a while.

Fear and anxiety cause a shift to a more harmful composition in the gut microbiome, which increases our intestinal permeability, which increases our systemic inflammation, which increases our risk of autoimmunity and chronic diseases. 70% of those dealing with autoimmunity have had some early childhood trauma, and that damage can last a lifetime.

As soon as we can recognize that, especially as parents, and start tending to that in our children, there is an amazing ripple effect that impacts our families and our communities.

I think a lot of people understand that stress impacts mental health. That’s easy, I’m stressed and anxious, maybe I’ll feel more depressed or have brain fog.

Not enough people understand that it’s all one package, that stress and anxiety are literally at the cellular level making you more vulnerable.

It’s life-changing when we start to view the world around us as it really is, as this supportive, nurturing, cooperative ecosystem that we live in. The power of our thoughts is so under-recognized in our healthcare system.

What’s wonderful is the flip side is also true. Getting a positive or calming thought in there holds as much impact as the negative thoughts that cause the damage.

It doesn’t always have to be a shift in our thinking to bring our gut back into balance. When we have trouble calming our thoughts, we can use physical strategies like consuming more resistant starches, and omega-3s, really aligning ourselves with the cycle of the sun and tending to our circadian rhythm. These things can help equip us to better deal with that anxiety.

Aligning Yourself with the Cycle of the Sun

Getting in the sun in the morning, a little bit of sun in the afternoon, and watching the sunset at the same time as lowering our indoor lights can really make a huge difference in balancing your terrain.

More red, more warm tones impact our circadian rhythm differently. You can start wearing blue-blocker glasses after dark to get the same effect.

Katie Wearing Blue Blocker Glasses

There are a lot of places that don’t have pretty sunshine. So just to be clear, I am not talking about pretty sunshine. I’m talking about sunshine that comes through the clouds. The most important thing is to get sunlight in your eyes before 10 am.

What does that do? It boosts our serotonin which is our creative, feel-happy hormone. Then at night, the morning sunlight that we got that increased our serotonin is our available store for melatonin. Our melatonin has a huge impact on our immune system and our sleep.

Something as easy as making sure we’re getting sunlight in the morning, a little bit of sunlight in the day, and lowering those lights at night can have such a profound effect.

Try this for a week and see how you feel. It’s free, it’s easy, it doesn’t need to take much time!

I like to combine getting my sunshine with earthing, which is coming into contact with the earth with your bare feet (or hands or any other skin really) to absorb negative ions from the earth. Syncing with the sun and allowing ourselves to receive and absorb those negative ions completely changes our biology. It’s an easy thing to incorporate once it becomes a routine.

Terrain Theory Explains Viruses and Colds

We’ve talked about some chronic health issues like anxiety and autoimmune disease, but what about those acute illnesses like colds, viruses, and infections?

Germ theory doesn’t have much to say about why one person may have a worse outcome than another when encountering the same virus or bacteria. What does terrain theory have to say about this?


Think back to those danger signals, how is our body interacting with that microbe? The health of our terrain dictates that conversation.

What does our terrain look like? What do our inflammatory pathways look like? What do our detox pathways look like? All of those things impact that conversation between microbes and the body.

If we pulled any doctor up here, they would say, “Absolutely, diet is important, exercise is important, and having love is important,” but that’s never translated into treatment, care, policy, and education.

People are desperately wanting a change. The time is now.

Terrain Theory Vs. Sanitizers

A huge piece of the worldwide response to the Coronavirus pandemic was “sanitize, sanitize, sanitize, sanitize.” Sanitize the beaches, sanitize the desks, wear masks (for protection from germs).

RELATED: Check out some natural hand sanitizers here

If we over-sanitize everything, we may disrupt both our internal personal terrain and the ecosystem in which we live.

I (Katie) predicted back at the beginning that kids who wore masks for a year would have trouble when the mask came off because their immune systems would be weak. I know in our schools, we’re seeing a ton of communicable disease that has nothing to do with COVID-19 going rampant.

The CDC has a whole program of practitioner awareness about antibiotic resistance. There has been education and outreach about how the pressure we put on the global microbiome with antibiotic use creates superbugs that are resistant to anything that we have in the pharmaceutical toolkit.

We can’t just look at this “under the microscope” context, because that’s not where we live. That has taken out the most important piece: the human being interaction. There’s so much we don’t know about microbes and how we interact with them.

fight germs with hand sanitizer

The war on germs is so ingrained that spraying your surfaces, spraying outside playgrounds and beaches, is the next logical step. The paradigm is defense, defense, defense, fight, fight fight, and there’s no connecting the dots — it’s past time we connect the dots.

When we see humans taking new grandiose, far-reaching actions, consider the possible downstream consequences to the human microbiome and to the terrain of the environment.

It’s past time we connect the dots, lift our sights out of the microscopic investigations, and plug that back into the greater world because we have so much research, so much data, so much knowledge, so much intuitive knowing that we need to build that momentum.

What are your thoughts on terrain theory versus germ theory?
Dr. Catherine Clinton ND is a licensed naturopathic physician with a focus on gut health, autoimmunity and psychoneuroimmunology.

Respected author, speaker, pediatric health advocate, Dr. Catherine practices in Eugene, Oregon.

When in medical school Dr. Catherine was diagnosed with and healed from an autoimmune disease that affects the gastrointestinal tract, leaving her with a passion to prevent autoimmunity in children everywhere. Dr. Catherine addresses the psychoneuroimmune system and gut health of children and families through a deeper connection with the world around us.

Dr. Catherine is passionate about the connections we have with the world around us and how these connections can regenerate our health and the health of the planet. She sees an urgent need for healing our internal terrain as well as healing the terrain of the world we live in. Dr. Catherine has multiple peer-reviewed medical journal articles as well as guest writing for several publications.

You can follow Dr. Catherine Clinton on Instagram here.


  1. Kompaniyets, L., Pennington, A.F., Goodman, A.B., Rosenblum, H.G., Belay, B., Ko, J.Y., et al. (2021, July 1). Underlying Medical Conditions and Severe Illness Among 540,667 Adults Hospitalized With COVID-19, March 2020–March 2021. Prev Chronic Dis 18:210123.
Unless otherwise credited, photos are owned by the author or used with a license from Canva or Deposit Photos.

2 thoughts on “Terrain Theory Versus Germ Theory | Understanding Your Immune System”

  1. Thank you for this! It’s a complicated topic and not one I’ve been very successful in getting across to others (without their eye glazing over). However, you’ve compiled all that I want to convey into a neat little package. I’m looking forward to sharing this with my children.

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