EP 33: Autoimmune Disease And The Gut Microbiome With Kiran Krishnan

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23.5 million people in the United States suffer from at least one autoimmune condition, and that number is rising fast. Worldwide, autoimmune diseases are increasing by 7% each year, with the biggest increases in celiac disease, type 1 diabetes, and myasthenia gravis. The most significant jumps are happening in the northern and western hemispheres. There are now over 100 different types of autoimmune diseases, and I see them in over half of the people I serve in my clinic here in the United States.

Autoimmune disorders impact every body system, including the brain, thyroid, blood, GI tract, nerves, lungs, skin, muscles, and bones. And let’s not forget the female reproductive system in conditions like PCOS and endometriosis, which I classify as autoimmune diseases. Where is this exponential rise coming from? And why do most people develop more than one autoimmune condition?

To help explain why this is happening, I’ve brought back microbiologist Kiran Krishnan to talk about triggers, why diet and detox alone don’t work, and why taking a deeper look at your GI tract and environment is key to healing.

Kiran Krishnan is a Research Microbiologist and has been involved in the dietary supplement and nutrition market for the past 18 years. He spent several years with hands-on R&D in the fields of molecular medicine and microbiology at the University of Iowa. He is a co-founder and Chief Scientific Officer at Microbiome Labs.

In this episode, we discuss:

  • How the immune system relies on the microbiome to learn and adapt to your environment.
  • A breakdown of two major immune system processes and how they can trigger autoimmunity in a dysfunctional microbiome.
  • The three components of how autoimmune disease is triggered.
  • Why trendy diets like keto might alleviate some symptoms now, but have big repercussions for your microbiome and immune system later.
  • Five warning signs of systemic inflammation that merit talking to your doctor.
  • A gut microbe you’ve probably never heard of that is associated with lots of autoimmune issues.

Listen to the podcast here:

Within the below transcript the bolded text is Samantha Gilbert and the regular text is Kiran Krishnan.

Autoimmune Disease And The Gut Microbiome With Kiran Krishnan

There are now over 100 different types of autoimmune disorders. I see them in over half of the people I serve in my clinic. Here in the United States, 23.5 million Americans suffer from at least one autoimmune condition. This number is rising fast. Autoimmune disease is increasing by 7% each year with the greatest increases in celiac disease, Type 1 diabetes, and myasthenia gravis, with the greatest increases occurring in countries in the Northern and Western hemispheres. Autoimmunity attacks every body system including the brain, thyroid, blood, GI tract, nerves, lungs, skin, muscles, and bones.

What is going on to trigger such an exponential rise? Why do most people develop more than one? Is this phenomenon genetic or epigenetic? As with autism and infertility, inflammation, along with environmental triggers, are the biggest drivers of autoimmunity. To help explain this, I’ve brought back Kiran Krishnan, Microbiologist and Chief Scientific Officer at Microbiome Labs, to talk about triggers, why diet and detox alone don’t work to correct these conditions, and why taking a deeper look at your GI tract and environment is key to healing.

Kiran Krishnan is a research microbiologist and has been involved in the dietary supplement and nutrition market for the past several years. He comes from a university research background, having spent several years with hands-on R&D in the fields of Molecular Medicine and Microbiology at the University of Iowa.

Kiran established a clinical research organization where he designed and conducted dozens of human clinical trials and human nutrition. Kiran is also a Co-founder and Partner in Nu Science Trading, LLC, a nutritional technology development and research company. He is also a Co-founder and Chief Scientific Officer at Microbiome Labs.

Kiran is a frequent lecturer on the human microbiome at medical and nutrition conferences and an expert guest on national and satellite radio. Kiran has appeared in several international documentaries and has been a guest speaker on several international health summits as a microbiome expert. He is involved in sixteen novel human clinical trials on probiotics and the human microbiome. Kiran sits on the scientific advisory board as a science advisor for seven other companies in the industry.

Thank you for joining me again, Kiran. I am so excited for this episode.

It’s my pleasure to be here. Thank you for having me.

Are Autoimmune Diseases Related to Gut Health?

My clients are often shocked when I tell them that their autoimmune disorder is mostly caused by environmental triggers and that they often take decades to develop. They’re also surprised to know that the health of their GI tract plays a major role in the development of their condition. Can you walk us through what disruption of immune balance looks like and the development of autoimmune disease?

The important thing to note about the immune system is that we often think of it as a system on its own that already has capabilities and knowledge base and understanding of the world around it, and what to attack and what not to attack and so on. That’s not how the immune system functions. The immune system has certain capabilities in the beginning. When your immune cells are made, whether in your bone marrow or thymus, but the immune system has to be trained. That’s the way the immune system is designed to function.

The reason for that is we need adaptability. Imagine if we had an immune system that had a set of rules from day one that said, “These things are all bad. These things are all okay.” If you change your environment, your immune system would not be able to function to protect you because the rule sets changed.

The immune system is specifically designed by nature to be adaptable. It has to adapt to the environment that the host is in. If you live in Mexico City, all of a sudden, the things you’re exposed to is going to be different than if you lived in New Mexico. It’s a different world in each ecosystem. Your immune system has to be able to adapt.

With that in mind, the immune system is heavily influenced by the environment around it because of that adaptability. The immune system is constantly learning and trying to learn the environment that you’re in, and trying to figure out what is friend and what is foe. The vast majority of the things that you encounter on a day-to-day basis, your immune system doesn’t need to deal with.

Most of the things you encounter aren’t going to harm you as a host. They’re not going to kill you. Most of the microbes you encounter are not pathogenic. Most of the microbes you encounter are not designed to kill you. The vast majority of microbes that you encounter are beneficial or they’re benign to the system. That learning is important because if there’s an absence of learning, the immune system will attack too much or attack too little.

Due to the need for learning, the immune system is designed to interact with the environment around you and learn from the environment around you. The biggest teacher or trainer of the immune system is the microbiome. The microbiome adapts faster to the environment than your immune system can. When it does, it instructs the immune system on what is happening within the environment.

Autoimmunity can come about in several different ways, driven by a dysfunctional microbiome.CLICK TO TWEET

It’s your microbiome that teaches the immune system what to attack, what not to attack, when to scale back, when to recover, when to rebuild, and how to build tolerance to the things that the host needs to be exposed to that aren’t going to harm the host. Being able to understand and have that concept in mind. The immune system is not a binary thing. It’s not an on or off thing. It’s not a, “This is good. This is bad,” thing. It’s constantly adapting and trying to learn. It’s counting on the microbiome in order to learn. If the microbiome starts getting disrupted by environmental effects, then the microbiome, the trainer of the immune system, is no longer functioning. The immune system is going to go haywire.

You’ve talked a lot about it in the past, and I’ve done some trainings with you in the past where you talk a lot about the trigger, the breakdown in oral tolerance. You spoke beautifully into the microbiota and that permeability aspect, and then how that then creates the immune reactivity, and then we have autoimmunity. Would you mind speaking into that a little bit more?

Autoimmunity can come about in a couple of different ways. Both of them are driven by a dysfunctional microbiome, to begin with. Let’s talk about the first way. The first way is something we call the bystander effect. Let’s say you get an infection. It’s a simple, normal infection like a rotavirus infection in your gut. Kids get it all the time. Adults can get it too. It’s an infection that might cause GI upset, maybe some vomiting, some diarrhea and so on. It’s infecting the lining of your gut. This virus has come in and now it starts infecting the lining of the gut.

The way it all is supposed to go is the resident microbes around that area where the virus is attacking will start to signal to the immune system that, “Something is going on here that we’re not comfortable with, that’s not normal as part of this environment. We need you to come to this space and deal with it.”

The microbiome recruits the immune cells to that space. The immune cells come in and it’s the innate immune cells. Those are the guys that are nonspecific that are the blowtorch type of immune cells. That’s like if you get a bunch of bugs that come in through your window in your room, you’re trying to kill the bugs with the blowtorch. You’re going to kill the bugs, but you’re going to burn the wall a little bit as well. Think about the innate immune system as the people that are running in with blow torches to try to deal with that infection, but they’re the fastest to get there. They are first.

The adaptive are the immune cells that are highly specified for that particular pathogen. They have all these tools that they can use to go after that specific pathogen, but they take longer to show up. That’s why the blowtorch people show up first to try to control things, not let it go haywire, then the adaptive shows up. The only way that the blowtorch people know to get there and start the process of protecting the host is from signals from the microbiome.

The microbes signal to the blowtorch people, they show up to the spot, and they start blowtorching things and trying to control the infection. In that process, they’re creating damage. Your own cells are getting damaged. They’re killing anything in that area. Your own proteins, your own cell structures, your own cell membranes, all of this stuff is getting damaged in the process, which is fine.

That’s normal, but what is supposed to happen next is your immune system is supposed to migrate from this blowtorch light response to the highly specific adaptive response. The adaptive response doesn’t damage the host because it’s specific to the pathogen. That transition between that innate blowtorch response, the highly specific adaptive, is also facilitated by the microbiome and signals from the microbiome. In fact, the microbiome, when healthy, will start producing signals in that area to bring down the inflammatory blowtorch aspect of the response.

EFL 33 | Autoimmune Disease
Autoimmune Disease: The immune system is specifically designed by nature to be adaptable. It has to adapt to the environment that the host is in.

The microbiome knows that that initial blowtorch response is important, but we can’t have that going for too long or the host will get too damaged. What starts to happen is a healthy microbiome will signal the blowtorch guys, they’ll start doing their work. The microbiome starts to say, “Simmer down. Turn down those torches. Things are under control. We need to move to the highly specific adaptive response.” They start recruiting the highly specific adaptive response to that site as well. That’s how it’s supposed to go.

Let’s say your microbiome in that area is already dysfunctional. The virus comes in and starts attacking. Number one, because you don’t have good commensal microbes in that area, they’re not signaling to the immune system to get to that spot right away. The virus has a longer period of time to keep infecting the gut cells and start causing more damage. The infection is growing more than it should be able to grow because you don’t have the signals from the microbiome to get the blowtorch people there.

By the time the immune system notices this infection, the infection is five times bigger than it would have been had you had the right microbes signaling for the blowtorch people to show up. Now you’ve got a bigger infection. When the blowtorch people finally show up, then they’re alarmed by the size of the infection. They turn up their torches even more and they’re blowing up that area. The response is even bigger. What happens when you turn up the flame? You’re going to kill more of those viruses, but you’re also going to damage the host even more. Now there’s even more host damage going on.

There are dendritic cells and macrophages that play both roles. They’re part of the blowtorch response, but they’re also trying to facilitate and bring about the adaptive response. One of the ways in which they do that is they eat up parts of the virus or the bacteria that’s causing the infection, and then they present parts of that, they’re called antigen-presenting cells, to the adaptive immune system, to the T-cells and B-cells, so that the adaptive immune system can go, “This is the target that’s causing us problems.” The highly specific antibody-producing cells against that target are the ones that get recruited to the site. All of this is being facilitated by the healthy microbiomes.

You’ve got this in a dysbiotic situation. You’ve got a much bigger initial phase of the infection. You’ve got a much bigger blowtorch response so you’ve got a lot more host damage as well. You’ve got the host’s cell debris flying around, cell parts, protein parts and so on. When those dendritic cells make it to that area and start gobbling up stuff to try to present to the T cells and B cells what is causing the infection, in some cases, they will accidentally gobble up your own cell parts because there’s so much your own debris there.

They might present to B cells that, “This is part of what’s causing the problem,” but it’s your own tissue that’s accidentally presenting. Now you’ve got a B cell that becomes activated to form antibodies against that part, but that happens to be your own part. This whole process can be prevented. This accidental presentation can be prevented if you have an upregulation of part of your immune system called the T regulatory cells. They’re the T-cells that go, “No, guys, you’re presenting the wrong thing. Stop it. You present this instead.” They regulate that.

The T regulatory cells require signals from a healthy microbiome to function. If you don’t have a healthy microbiome, that virus comes in and attacks, not only is that initial part of the infection bigger, not only is the damage occurring bigger, you don’t have the T regulatory cells there to stop the wrongful presentation of your own tissue.

It’s a triple whammy when your microbiome is dysfunctional. That’s called the bystander effect. Without the microbiome, you’re going to have a bigger initial infection more, your own cell debris because of the damage, and there’s more chance of accidental presentation of your own tissue to your immune system that that’s a target. That’s one and probably a big major way in which a normal infection that most people would clear in a couple of days could end up triggering an autoimmune response against your own tissue.

The other way that’s quite prominent is something called molecular mimicry, where you’ve got these latent viruses and bacteria. When I say latent, I mean that they can remain in your system for years upon years, and hide and act and exist at low levels without causing any trigger to the immune system. Every once in a while, when they feel the opportunity is right, they try to proliferate. When they do to try to trick the immune system, they produce proteins that look like parts of your body.

Your immune system is constantly trying to learn and adapt to your environment. It’s the role of your microbiome to train and teach your immune system. CLICK TO TWEET

When the immune system comes to figure out, “What is happening here? What’s causing damage to the host?” those antigen-presenting cells may accidentally present your own protein. It’s like a flare to distract from the actual virus or bacteria. The virus or bacteria is producing these molecular mimics of your own tissue.

The way that’s stopped is if you have a healthy microbiome that upregulates the T reg cells that can stop it and go, “That’s the wrong protein. Don’t make antibodies against that. That’s the virus trying to trick you. This is what you need to present against.” In both of those major cases of how an autoimmune disease develops, you’ve got the microbiome being the key to making sure the immune process goes the way it’s supposed to and you don’t end up having these accidental presentations, too much damage, and so on.

Autoimmune Disease and Coronavirus

I appreciate you going deeper into that. What I was thinking the whole time you were sharing that is what we’re seeing with Coronavirus.

Coronavirus is a perfect example of something that causes lots of inflammatory damage because of the initial response to the virus, especially because this virus attacks the ACE2 receptors. It’s already attacking tissue under inflammation and damage because those are the tissues expressing the ACE2 receptor. Now, it’s already going into a bit of a mess and it’s making the mess worse. When the innate immune response finally shows up, it’s amplifying the flame on the blowtorch.

When you look at who has the worst outcomes against the Coronavirus, it’s people with chronic low-grade inflammatory conditions, diabetes, heart disease, age-related dysfunctions, you’ve got people with autoimmune conditions. People who are already in this inflammatory state are the ones that have a poor reaction. That’s because their inflammatory state is drowning out the signals from the microbiome that are trying to recruit the immune cells to where the virus is infecting.

On top of that, because they are in that inflammatory state, it means that they’re already under dysbiosis. It’s their gut dysfunction that’s leading to their diabetes, heart disease, and obesity. They’re already in a gut dysbiotic state, so they don’t have a healthy microbiome to protect them against this virus. Along the hall of the syndrome is a trigger of systemic autoimmune response. It can be neurological and muscular. It can end up triggering an unfavorable response against almost any tissue in your body.

Autoimmune Disease Triggers: Diet, Toxic Chemicals, Infections

Thank you for walking us through that as well. I’m sure you are too. It’s truly astounding to me that 70% of the autoimmune risk is environmental. That’s great because I feel that that provides people with a lot of hope, knowing that our genes aren’t “fixed.” Can you walk us through autoimmune induction and those three main categories of triggers: diet, toxic chemicals, infection? You just walked us through infection. Diet and toxic chemicals specifically would be helpful for people to understand better.

For them to appreciate that, it’s important to understand the triangle, three components that have to occur in order for an autoimmune disease to even be induced. In some cases, the first one, which is some genetic predisposition. Some people do have genetic predisposition, but just having genetic predisposition does not mean in any way that you’ll ever develop an autoimmune disease. That’s a risk factor.

The second thing is dysbiosis in the microbiome. The third thing is an environmental trigger. All three things have to come together in order for you to develop an autoimmune disease. As it turns out, in our society, in many people, we’re having all three come together quite a bit because many years ago, we had maybe 30, 35 autoimmune diseases. Now, we’ve got over 110.

EFL 33 | Autoimmune Disease
Autoimmune Disease: The microbiome adapts faster to the environment than your immune system can. And when it does, it instructs the immune system on what is happening within the environment.

In the last few decades, we’ve created new diseases that we have to deal with. All of that is because all these three components of this triangle coming together more often than they should. The only two parts of the triangle that we can control are our microbiome and environmental triggers. Those are the things we need to focus on.

Talking about the environmental triggers, I talked about infection. In my view, infection is probably one of the biggest drivers of autoimmune conditions in people, but there are lots of toxins in the environment that can do it as well. Anything that initiates an inflammatory response can create the condition in which you can develop your autoimmune disease.

Diet is a powerful way of creating systemic inflammation, right? If you’re eating processed foods, if you have a leaky gut and if you’re eating a high-fat diet, you could trigger systemic inflammation. If you are sensitive to things like gluten, and then you eat lots of gluten, that’s going to trigger all kinds of inflammatory responses in your gut lining. If you are super sensitive to dairy and you’re eating dairy all the time, that’s triggering inflammation. Anything that triggers systemic inflammation or even localized inflammation can start the ball rolling towards an autoimmune response.

Remember, inflammation is the start of that immune response, the blowtorch response. If you don’t have a healthy microbiome to curb that blowtorch response to upregulate the T helper cells that help prevent the accidental presentation, if you don’t have those two factors, then anything that triggers inflammation and immune activation can lead to an autoimmune response. That includes environmental chemicals like Roundup, glyphosate that can get into the system, create dysbiosis and trigger inflammation. It can be mold toxins from your environment that triggers inflammation.

Anything that triggers inflammation in your environment, in your diet, that you put on your skin, that you consume can start that process. You’re at risk of that process ending up in an autoimmune condition if your microbiome is not healthy. If you have a healthy, diverse microbiome, it’s there to protect you from this miseducation of the immune system. Your immune system is constantly trying to learn and adapt to your environment. It’s the role of your microbiome to train and teach your immune system.

Can Bacteria in the Gut Cause Autoimmune Disease?

When you say dysbiosis, we understand what that means, but for our readers that aren’t familiar with that term, would you mind explaining what dysbiosis means?

The best way to describe dysbiosis, which generally applies to everybody, one of the confusing things about the microbiome is everybody at the species level of bacteria and viruses have completely different populations. If everyone’s population at the species level is different, then how do we know who has a healthy and correct microbiome? There are a couple of key features of a healthy microbiome that is universal. If you don’t have these features or you’re low in these features, then you’re dysbiotic.

Feature number one is diversity. If you have low diversity in your microbiome, you are dysbiotic. You don’t have enough of the right microbes to conduct all of these important functions, especially all of the immune training and immune facilitating. Diversity is number one. Number two is the presence of protective keystone species. Keystone species are named keystone because they play such an important role, not only in the structure and the function of the microbial ecosystem in and on your body, but also they play an important role in protecting the host against a host of chronic illnesses. They are specific as critically important protective organisms.

In the US population, we tend to have low levels of these keystone species. Without the keystone species, your microbiome is already tenuous because it doesn’t have leaders that are maintaining the system. Any little thing, like a single course of antibiotics or traveling overseas and eating something different for a little while, or stress, all of those things can trigger dysfunction in your microbiome and it starts to fall apart. Your immune system ceases to function the way it should. You’re much more susceptible to the effects of infection, toxins, and so on.

We are designed to eat a very diversified heavy plant-based diet. That is what was accessible to humans for the vast majority of human evolution.CLICK TO TWEET

Thank you for walking us through that. I also appreciate how you brought gluten and dairy into the picture along with things like Roundup and all those chemicals that are utilized. I didn’t even realize it because people love their oatmeal in the morning or their steel-cut oats. I learned from you that glyphosate is used as a desiccant with oats. I always try to push people more toward vegetables. I also love how you spoke about the high fats. Keto is still popular, but it’s dysregulating people’s guts. That’s my concern about the long-term use of a high-fat diet.

We’re not designed as a species to sustain on high levels of fat. Fat is a luxury in our diet. The largest population of microbes in our bowel can’t do anything with that. They require plant-based materials. That’s not an advocacy for going vegan or vegetarian. We, as species, need to be pretty well-diversified in our diet.

When you start making 70%, 80% of your caloric source from fat, and when the vast majority of the microbes in your large bowel produce all of these helpful compounds for you, when they can’t utilize fat, then you’re missing out on some stuff. The problem is temporarily, you might see some changes and feel some relief. In the long-term, and I’m not talking about 15 years, I’m talking about 3, 4 years in the long-term, it will cause more disruption, risk and problems.

Whatever condition you think you’re helping at the moment, you may be helping to some small degree, at least symptomatically, but you will be causing bigger problems down the road. We are designed to eat a diversified heavy plant-based diet because that is what was accessible to humans for the vast majority of human evolution. People will always point out and go, “What about the Inuit Indians? They sustained predominantly on a diet of fat.” They do, but what you have to recognize is number one, they’ve had to adapt to do that because of their environment.

Number two, a study came out that shows that the Inuit Indians that made it through the systems of a high fat diet were ones that have a genetic mutation that allows them to utilize fat a little bit differently and better. That was through a course of specific natural selection. If you’re of European descent or you’re like me, my ancestors come from the equator, we didn’t sustain on a diet predominantly in fat.

These labeled diets and all that become sensationalized. You might hear a few people that feel different. One person eats a carnivore diet for five years, and then it was good for them for some reason. They write a book on it and now, all of a sudden, the carnivore diet is good for everybody. Those kinds of things, to me, become problematic and hurt people more often than they help.

Autoimmune Disease and Glyphosate

I’m glad you said that. I see that clinically when I start working with a patient that has been doing keto for a certain number of years, and suddenly they’re having all these challenges, whereas in the beginning, they felt a lot better, “I’m feeling great. I have more energy. I’m going to continue this for an extended period of time.” I’ve seen that time and time again. If we can circle back to things like gluten and dairy, and I do want to talk about glyphosate a little bit more if you don’t mind because there’s a cascade there. There’s the chemical that’s used in growing and harvesting, and then there’s that whole process. I was wondering if you could speak into that a little bit more.

The use of it as a desiccant?

Yes, and also in general. We can’t get away from it now. It’s everywhere.

EFL 33 | Autoimmune Disease
Autoimmune Disease: For an autoimmune disease to be induced, three components must occur: genetic predisposition, dysbiosis of the microbiome, and an environmental trigger. The only two parts of the triangle that we can control are our microbiome and the environmental triggers, so those are the things we need to focus on.

Unfortunately, it is. There’s a lot of cross-contamination. They don’t use it in the agricultural process, but unfortunately, the water that’s being sprayed on the food and all that has it. It’s something we have to deal with. Your neighbor might be using it all over his or her garden and lawn and so on. It’s a factor of our modern existence. It’s one of the most egregious things for our gut microbiome because not only does it act as an antibacterial so it’s killing microbes in your gut, it is one of the few chemicals that I’m familiar with that selectively kill your good bacteria.

Take a typical antibiotic. If you’ve had to go through courses of antibiotics, it’s not a great thing for your microbiome. It’s going to damage your microbiome. We know that. We know the damage can be long lasting. What happens when you take an antibiotic is all of the microbes in your system get knocked out, good and bad.

What comes back faster is what decides how dysfunctional your gut becomes after an antibiotic. In the case of glyphosate, you’re taking small amounts daily. It is specifically going after the most beneficial microbes in your system. A lot of the opportunistic pathogens like Klebsiella and pseudomonas and all are resistant to it. It is a selective change to your microbiome over time that specifically enhances the growth of opportunistic pathogens. It’s disruptive. The disruption doesn’t have to occur over years. It occurs pretty quickly.

We did a study that we hope to publish sometime soon on a pediatric microbiome. A pretty pristine three-year-old microbiome exposed to normal, what the EPA would even decide to safe levels of glyphosate. What we saw is within a three-week period, the microbiome shifted from being a healthy child microbiome, all the right features, good diversity, good keystone species, producing short chain fatty acids, and all that towards the microbiome that looked like somebody who’s dealing with inflammatory bowel movements.

It’s a huge impact. What can we do about it? We can’t leave this planet obviously, at least not yet, although Richard Branson and some of these guys are trying to make it so that maybe we could leave this planet at some point. What we have to do is figure out what we need to do to undo the continuous damage that something like this is doing to us. The right probiotic, the right prebiotic, the right fasting and dieting and all that can help dramatically. The reason we did that study with that pediatric microbiome is we wanted to see if the spore-based probiotics could start to reverse or undo some of that damage. The exciting thing about that is, sure enough, we did see that it’s not like we fed that microbiome glyphosate for three weeks and stopped.

We fed it for three weeks. At the end of the three-week period, we measured all the damage and then continued to feed it the glyphosate at the same level and then add in the spores, even though it was still exposed to glyphosate. Even with the continued exposure to glyphosate, we started seeing the spores dialing back some of that damage that’s occurring already. We have microbes within our fold that can undo the continuous damage that we, as a human race, are doing to our microbiome.

I can’t wait for that to come out. I love MegaSporeBiotic so much. We talked about that last time you were on the show. I appreciate you again walking us through how damaging these things are because it’s crazy how I am still asked to this day, and it’s not to anyone’s fault of course, “I’m not reactive to gluten. Dairy is not a problem. Why can’t I continue to have them in my diet?” There’s always that educational piece. When that happens, people start to understand more. To hear you speak into that is helpful.

The Warning Signs of Autoimmune Syndrome

Cosmetics, BPA, sodium chloride, smoking, we know that a lot of our readers are thinking, “What are the warning signs? How can I know if I’m developing an autoimmune condition?” Could you walk us through maybe some of those warning signs and what autoimmune syndrome might look like for most people?

The gut impacts virtually everything because your gut controls your immune system and your brain, and your brain controls all the parts of your body.CLICK TO TWEET

To get the most accurate assessment of this, you should go and get a blood test done. There are some types of blood tests that you can ask your doctor to do, like a set rate or you can look at your CRP levels. You can look at inflammatory markers. If your system is constantly high in interleukin-17, then you’re more leaning towards a potential autoimmune issue.

I would say that some of the general things that if you feel would be worth for you to go talk to your doctor and get checked out. Things like continuous fatigue, that whole fatigue and malaise syndrome where you’ve gotten 7, 8 hours of sleep, but when you wake up, you’re pretty tired and groggy, and it’s hard to get going. If you start to see rashes or redness appearing on your skin. When you look at kids and they get infected with something, whether it’s a cold, flu, whatever it may be, one of the danger signals that this is a bigger problem than a normal infection is if you’d find a rash or some redness patches all over their body. That’s indicative of systemic inflammation, something deeper going on. You’re constantly getting red patches, itchy parts of your skin and dried up parts of your skin, that could indicate as well.

If you start seeing slowness in your cognition, recalling things becomes harder. You’re stumbling on your speech a little bit. Your alertness and your cognition is slow. If you start to notice any of that, that could be systemic inflammation that can be setting up some autoimmune type of response. For the GI tract, if you have continuous diarrhea or continuous constipation, if your food intolerance is getting worse, there are more foods that you can’t tolerate, then you’re going down a path of significant inflammation in your gut lining and dysbiosis as well. You don’t have the right bacteria to deal with those foods. You’re not producing enough enzymes. Your gut is inflamed. Any food triggers more inflammation. If you’re going down the wrong path, then you should start getting things checked out.

The most obvious ones are things like you would carry any hives and things that pop up for people, continuous red eyes, itchiness in the scalp, and that uncomfortable feeling overall. For some people, it can be an autoimmune condition that targets the heart. You might feel cardiac symptoms or it could target certain muscle groups or nerves. You feel like misfiring in your arms or your arms go dead and sleepy easily. You’ve got neuropathy where you’ve got numbness and tingling in the tips of your fingers.

All of these things could be early signs and symptoms of a lot of inflammation in your body and that some tissues or organ systems may be attacked and dysfunctional. I don’t want people to freak out and go, “My arm was numb the other day. I have an autoimmune disease.” This is not diagnostic at all. It’s a way for you to be a little bit more aware. Talk to your doctor and go through proper testing.

Thank you for walking us through that. There’s the GI tract that we’ve been talking about throughout this conversation, and a lot of people have symptoms that aren’t gut-related. I want to make sure that I speak into that a little bit because you can have a lot of autoimmunity and have great bowel movements every day. I’ve seen that too. I know that you have as well.

Gut dysbiosis, as you rightly pointed out, it doesn’t necessarily mean gut symptoms. The inability to sleep is a gut symptom. Too much stress and mood swings and mood changes is a gut symptom. Skin issues are all gut symptoms. The gut impacts virtually everything because your gut controls your immune system and your brain. Your immune system and your brain is controlling all the rest of the parts of your body.

Also, people have a misinterpretation of a healthy gut. I’ll have people that say, “My gut is totally fine,” but they have learned to live with certain dysfunctional symptoms. “I’m totally fine as long as I don’t eat this, this, and this. As long as I stick to this, I’m fine. I get loose stool three times a week only. It’s gotten better from four.” People learn to live with this dysfunction. We think it’s normal, but it’s not. If you’re not somewhat regularly forming good-looking stools, everyone should go look at the stool charts and get familiar with what healthy stool looks like. If you’re forming pasty stool every day, but you’re having bowel movements, 1 to 2 bowel movements, you might think, “I’m perfectly fine,” but you look at your stool and it’s all pasty and lumpy.

Autoimmune Disease and Pathogenic Activity

That’s a challenge. Each person’s microbiome is unique. I’m curious, what kind of pathogenic activity or other imbalances do you see in stool samples of people with autoimmune disorders?

EFL 33 | Autoimmune Disease
Autoimmune Disease: A healthy microbiome’s key features include diversity and protective keystone species.

More often than not, you see certain opportunistic pathogens show up in people with autoimmune conditions. You’ll see certain classes of clostridia that tend to be higher. You’ll see organisms like streptococcus and staphylococcus that can be elevated. One that we’ve been seeing a lot in the BiomeFX stool test that we do, which is a whole genome sequencing, it’s the most accurate way of doing a genetic stool analysis, is an organism called Bilophila Wadsworthia.

Most people have never heard of it. No other stool test tests for it. We’ve been picking it up because we do something called whole genome sequencing, which means we pick up anything that’s there. We’ve been seeing that associated with more and more GI and systemic inflammatory conditions. Bilophila is predominantly in the small bowel as well.

Here’s why part of what we talked about earlier very much pertains to this. Bilophila, as the name suggests, is an organism that loves bile. Bile is an antimicrobial. It is part of what tries to control microbial growth in the small bowel. Bilophila happens to be a microbe that likes bile. If you’re producing a lot of bile, it helps select for Bilophila. Bilophila will also take sulfates that are coming in from your diet, for example, from lots of healthy foods. A lot of marine foods are fish, shrimp and all that, also different types of vegetables like mushrooms have high sulfates. It will convert that sulfate to hydrogen sulfide, which is super inflammatory for a large bowel, and causes massive dysbiosis, and is a major risk for inflammatory bowel disease.

Bilophila is also associated with an increased risk of cardiovascular disease and other systemic dysfunctions. Bilophila is going to be increased in its population the more fat that you eat. If you’ve had symptoms associated with Bilophila, and I encourage everyone to go look it up so you understand what Bilophila is associated with, it’s a lot of different stuff such as upper GI issues, cardiovascular issues, systemic inflammation, large bowel issues.

Bilophila is at the linchpin of many of these things. You might be experiencing these things. You might be going towards an autoimmune type inflammatory process, and you say, “I’m going to go keto because this guy’s book said that keto is the best with that.” Now you’re eating keto high-fat all the time. You might get some temporary relief, but you’re increasing the growth of Bilophila, which expands your risk of all kinds of other things.

We have to be smart and scientific about it. We have to follow the data. Sensational things that worked for one person aren’t the course of action that makes a sense. In my view, people need to test and get their microbiome tested, do a good history, work with the practitioner, and go after your specific issue. Just because this person ate two steaks a day and is healthy enough, or this person went full vegan and was healthy enough to write a book about it, or this person ate nothing but cabbage soup and was great and it feels good and lost weight, it doesn’t mean it’s the right approach for you clinically. That, to me, is the most damaging and scary about our world, where science doesn’t necessarily take the front row.

Sensationalism can outdo science in many ways. One of our whole focuses as a company is, “Let’s bring the science back to the front,” because we have to let the science drive these decisions and not sensationalism. That’s indicative with what we’re seeing with this Bilophila. Everyone I’ve talked to in our industry, doctors, nutritionists, they have no idea what this is. We’re seeing it in such a high number of their patients that are doing the BiomeFX test.

The reason why they never picked it up in any of the other tests is because those other tests are based on sensationalism as well. It’s not based on science. Using sequencing techniques, sampling techniques that don’t pick up stuff. One of the reasons why I love having opportunities and programs like yours is let’s start shedding more and more light on what the realities are, what the signs say, what the truth is, and then how you follow a reasonable scientific process and understanding what is good for somebody.

What I love about Microbiome Labs is the fact that you put so much, not only money, but time and effort into the R&D aspect of what you do. I use your BiomeFX stool test with the people I work with. I see the results. I can see more clearly, as you’ve shared with us, why that is important and how it is different. Thank you for what you do, your knowledge and your wisdom, and your ability to explain things in a way that is powerful for people to understand.

It’s my pleasure. I want you to know that every time you use the BiomeFX and every time your client gets a BiomeFX test, you’re adding quite significantly to the science and understanding of the microbiome. We developed BiomeFX as a way of studying the microbiome on a much larger scale. We now have a massive data science team. We’ve got 18-20 people who are focused on microbiome data science.

In fact, we acquired a company that specializes in analyzing data from the microbiome to figure out how different aspects of the microbiome relate to disease and so on. That not only gives us a better understanding of the microbiome and its role in disease, but it also provides us targets for therapeutics. Like Bilophila, we now have an R&D team working on what we can do about Bilophila, how we control this pathogen. We’re seeing it associated with all of these massive conditions. Everyone that uses a BiomeFX test is contributing to the science significantly because that’s the big purpose of the test. It’s not only to give you a helpful tool and give your clients and people’s patients insight into what’s going on, but it also contributes to the science.

Now, we’ve done several thousand of those tests and we’ve got an amazing dataset. We’ve got this amazing, highly-qualified data science team that’s working through the data. Every time you do a test, you’re adding to that pool. We’re going to let the therapeutics, the science, all that evolve out of that data, and all of you that are out there using BiomeFX and all that is contributing to it massively.

What an amazing way you’re contributing to humankind. Bless you. Thank you for coming on the show. As always, it’s a pleasure to have you.

It’s my pleasure to be on. Thank you for having me. We’ll do it again, I’m sure.

I truly hope our conversation has brought clarity and understanding into the underlying causes of autoimmune diseases, and how your gut impacts virtually everything because your gut controls your immune system. Autoimmunity takes decades to unfold, which in my opinion, should be encouraging because that means that you have the power to heal and to take action. If you or a loved one are currently struggling, please know that healing is always possible.

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