Decoding Autoimmunity: The Gut-Environment Connection in Disease Evolution

by | Sep 6, 2023

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In this episode of The Modern Vital Podcast, host Dr. Ben Reebs delves deep into the nature of autoimmune diseases, discussing their progression through three distinct stages. Starting with a focus on oral tolerance, he elaborates on how our gut’s microbiome, which houses approximately 40 trillion cells, plays a pivotal role in the onset of autoimmune conditions. A disruption in this ecosystem, possibly from environmental factors or pathogens, can lead to what’s termed as “intestinal permeability” or “leaky gut.” This condition allows undigested food contents to seep into the bloodstream, potentially triggering an immune response, which may set off an autoimmune process. 

Dr. Reebs then transitions to discuss central tolerance, spotlighting the crucial role of the thymus gland in our lymphatic system. This gland is responsible for training white blood cells to combat diseases and infections. A malfunction in the thymus might cause the body to misdirect its defenses against its organs, leading to autoimmune reactions. Finally, he touches upon peripheral tolerance, emphasizing its significance in curbing rogue B and T cells that could bypass central checks. An intriguing point Dr. Reebs raises is the role of environmental factors, such as heavy metals. These can attach to cell nuclei, deceiving the body into identifying its cells as foreign threats. For example, increased mercury levels in the bloodstream, possibly from consuming specific seafood types, might initiate an autoimmune response. 

If you’re looking to dive deeper into understanding the intricacies of chronic disease and its impact on your overall well-being, consider checking out Dr. Reebs’ book, “The Serpent & The Butterfly: The Seven Laws of Healing.” In this book, he discusses the laws of healing essential to resolving chronic disease and much more to help you on your journey to optimal wellness. Click here to purchase your copy: 

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Complete Transcript of Episode 13544406

Dr. Ben Reebs: On today’s episode of the Modern Vital Podcast, we’re going to discuss how autoimmune disease can be triggered or caused by environmental factors. Our Modern Vital factor of the day is that autoimmune disease occurs in three stages. In stage one, we have antibodies, but no symptoms. This could last for a few years. 

For example, we might have a positive rheumatoid factor which we see in things like rheumatoid arthritis, but no symptoms of arthritis, no joint pain. In the second stage, we have antibodies in the blood and we begin to see symptoms and our function is beginning to be a little bit affected, but it’s not significantly impacted. For example, we might have a positive RF factor or rheumatoid factor and have a little bit of joint pain. 

But we can still get around and go through our day without significant impact. And then in the third stage, we have antibodies and symptoms and our function is significantly impacted, right. It’s beginning to falter. Our function becomes compromised. This is full blown autoimmune disease and our body is now under attack. According to research, it can take anywhere from 1 to 19 years for this stage to be reached. 

And then we are in full blown autoimmune disease. So let’s start our talk by defining autoimmune disease. In autoimmune disease, the body’s immune system attacks its own cells, its own tissues and organs perceiving them as foreign threats. And this then leads subsequently to inflammation and tissue destruction and damage as well as a wide variety of symptoms and complications depending on the disease we’re talking about and depending on what body organs are targeted in that specific autoimmune process. It’s now known that autoimmune disease takes place as a result of two factors or two things, genetic susceptibility and environmental stimuli. In other words, our genes meet a factor from the environment which triggers them and then our immune system becomes dysregulated as a result. And we start an autoimmune process in our bodies. 

For example, there could be an infection in our microbiome in our gut which then could create or generate what’s called an autoreactive T cell, autoreactive just means self reactive. And this is a

type of lymphocyte, a white blood cell, which could potentially damage our tissues. And it could go and then bind to another cell called an antigen presenting cell, which is presenting some foreign particle to the immune system. 

For example, it could be a peptide from gluten in this case. So this autoreactive T cell could then go and bind to this antigen presenting cell presenting a peptide of gluten. And then that could set off a cascade and generate more autoreactive T cells which then could eventually go and destroy tissue. Now, examples of genetic susceptibility include our Aire gene. 

This gene also called air could have mutations that affect the expression of auto antigens. Now, auto antigen just means self antigen, these are antibodies that are made to our own tissue. For example, we see this in things like Hashimotos where there’s an antibody made to an aspect of our thyroid. Now, these mutations in our Aire gene would basically affect the expression of these 

auto antigens. 

And they could be, let’s say in the epithelial cells of our gut. And then our body, our body’s tolerance, it’s called tolerance, is thrown off. We no longer are tolerating our own tissue. We also have what’s called the HLA system. And HLA stands for human leukocyte antigen, leucocyte is just another word for white blood cell. And it’s critical in helping with an antigen presentation in proteins that are inside and outside of our cells aiding in the regulation of our innate and our specific immune response. Now, certain mutations are highly correlative with different autoimmune diseases. For example, a mutation that our HLadQ genes are involved in celiac and type one diabetes. And so, those of us who have these genes are more likely to be susceptible to reacting to gluten peptides presented to T cells. And our T regulatory cells can then become defective. 

For example, our Fox P three and our CTL four T cells are essential for tolerance. For example, our Fox P three and CTL four T cells are essential for what is called tolerance and they can be thrown off by this whole process. There are basically three forms of tolerance or three ways that the immune system keeps autoimmunity in check. 

The first is oral tolerance. The second is central tolerance and the third is peripheral tolerance. Now, in oral tolerance, we’re talking about the mouth, right. Basically, we have this tube running from the mouth to the anus, also known as our gut and we have a microbiome in it that contains about 39 trillion cells. According to research, let’s just round it up and call it 40 trillion cells. 

Literally, we’ve talked about this before 70% of our immune system lives in this tube. And when this microbiome in this tube or in our tube becomes overgrown with pathogens and gets thrown off, then we end up or can end up with what is called intestinal permeability. Basically, I like to think of this as like, like a hose that’s been sitting in the sun for quite some time. 

Think of our tube, of our gut as a hose sitting in the sun. When a hose is sitting in the sun and let’s say it’s got some water in it, it begins to swell a little bit. It becomes sort of inflamed and, an old hose, or a hose that is not in the best shape, might become a little bit porous. We might see some leaks. It might become a little bit like a sieve or kind of like a cheese cloth.

This is exactly what happens in the gut. Our gut becomes a little porous and we have intestinal permeability or leaky gut. And then, when undigested or not fully digested food contents are kind of moving down our tube. Let’s say we had some bread again. We broke it up into peptides. It hasn’t actually become amino acids yet. Anyway, it could be moving down this tube and then where there’s areas or holes or permeability, it can breach that barrier and what runs alongside the other end of that tube, but blood vessels. So basically, these peptides and undigested food contents can breach the barrier and then they can end up making their way into our blood. And then our immune system can kind of go a little haywire. It’s going to see that and depending on the person and their genes and their environment, and also their constitution, their body, they’re going to respond accordingly and it could be with an inflammatory or, or an autoimmune response. 

So, in other words, our oral tolerance then fails and we can end up with the beginnings of autoimmune disease. For example, peptides from gluten or dairy could end up in our blood and then cause this response. Now, the second type of tolerance is central tolerance and this mainly has to do with what’s called our thymus gland and it’s a critical part of our lymphatic system. 

It’s a small gland located behind our lungs and behind our sternum. And it sits just in front of and above the heart. Now, just a reminder, the lymphatic system is a lot like our sewage system in our body or I like to think of it as like the sewage system of our body. It helps to identify, to sequester and to carry away the garbage and toxins and breakdown products that might otherwise make us sick. 

Now, the thymus gland again, an organ in our lymphatic system helps to make our white blood cells. The ones known as T lymphocytes also known as T cells. You can think of, you know, the T and thymus standing for T cell. And these cells can also be or there’s forms of T cells that can be made and activated in our intestines and so on. But for purposes of simplicity, we’re just gonna focus here on the thymus gland. 

Basically, it’s where training takes place. Our white blood cells are trained to fight disease and infection. And if our thymus gland begins to defectively express certain molecules such as ICA 69 then it could induce an autoimmune response in different organs of our body. Now, the third type of tolerance is called peripheral, which kind of makes sense because the thymus gland is more centrally located. 

So you think of peripheral areas of the body and basically this peripheral intolerance ensures that defective B and T cells which escape the thymus gland do not run rampant and cause autoimmune disease. So let’s talk a little bit about ANA, also known as anti-nuclear antibodies. These are sometimes positive in patients and they can be a precursor to certain autoimmune diseases, not in every case, but they can be diseases such as lupus,Sjögren’s disease, even rheumatoid arthritis. 

Now, this is actually an antibiotic to the cell nucleus in our bodies or to the nuclei of our cells. Now, how in the world could this possibly happen? How is it that our body could make an antibody to our own nuclei? Well, one answer is in environmental factors such as heavy metals

or chemical toxicants, they can actually enter the cell and they can bind to our nucleus and then our body can begin to attack its own nuclei because it sees that there is something foreign attached to or bound to our own cell nuclei. Now, here’s an example and this, this is some recent research, some recent studies that have come out have shown that mercury, for example, can enter the cell and it combines to the nucleus. So let’s say that a person consumes a lot of canned tuna and they are consuming a variety that’s particularly high in mercury. 

And they end up with high levels of mercury in their blood. Well, these mercury molecules can penetrate through the cell membrane and they can cause our ANA to rise and they can initiate an autoimmune reaction by binding to the nuclei of our cells. And that could lead to stage one of autoimmune disease. So this is an example of how an environmental factor such as mercury could trigger an autoimmune process in our body and lead to stage one and perhaps progress to stage three of autoimmune disease. 

So that concludes today’s episode of the Modern Vital Podcast. We would love to hear from you. We value your feedback. If you have any questions or suggestions, please reach out to me at Also, please leave us a review if you enjoyed this episode and we look forward to having you join us next week for another exciting episode of The Modern Vital Podcast.


About Me

Dr. Ben Reebs, ND, is an award-winning, naturopathic physician with a focus in environmental medicine, which looks at how environmental factors can cause chronic disease. He specializes in chronic infections, autoimmune disease, and digestive health.

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