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RHR: How We Can Strengthen Our Gut-Immune System To Avoid or Recover From Viral Illness, with Dr. Robynne Chutkan


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Gastroenterologist Dr. Robynne Chutkan joins Chris on Revolution Health Radio to discuss how we can strengthen our gut-immune system to protect us and/or recover from viral illness. They review what the research indicates about the link between the health of our microbiome and our likelihood of catching viral illnesses, and talk about the ways we can repair and strengthen our microbiome by optimizing diet, exercise, sleep, and time outdoors to boost our host defenses and overall health.

In this episode, we discuss:

  • The connection between the gut microbiome and our immune defense against viral pathogens
  • How we can repair and strengthen our microbiome
  • Why it’s important to focus on both the internal and external environment when it comes to the microbiome
  • Ways we can use nutrition to improve our gut bacteria
  • Why spending time outdoors is key for gut health
  • How practicing mindfulness, meditation, and other stress management techniques helps the microbiome

Show notes:

Hey, everybody, Chris Kresser here. Welcome to another episode of Revolution Health Radio. Back in 2021, which was still pretty early in the pandemic, I started seeing some really interesting studies come out on the role of the microbiome in COVID-19 infection. The early research suggested that a disrupted gut microbiome may be a predisposing factor to acquiring the SARS-CoV-2 pathogen, and it might also affect the course of the illness. There were also some interesting studies suggesting that one of the impacts of the virus itself was to disrupt the microbiome, and that impact could persist for weeks or, in some cases, possibly even months after the infection was cleared. This wasn’t really talked about in the mainstream media, but I discussed it a little bit on my podcast and in some emails and articles. Since then, [there’s] been really robust literature on this topic, looking at how the microbiome protects us against [not only] viral infections like SARS-CoV-2, but many other infections, as well, and how we can support our gut microbiome as a means to upgrade our immune defense. I’m really excited to welcome Dr. Robynne Chutkan as a guest to discuss this topic.

She’s recently written a book about it called The Anti-Viral Gut, and Dr. Chutkan is one of the most recognizable gastroenterologists working in the [United States] today. She has a bachelor’s [degree] in science from Yale and an MD from Columbia, is a faculty member at Georgetown University Hospital, and the founder of the Digestive Center for Wellness. She has a great pedigree in conventional medicine and is a conventionally trained gastroenterologist, but she also very early in her career recognized the limitations of a conventional approach to gastroenterology and started to branch out and learn more about the function of the gut and the many different ways that the gut impacts our health and wellness. [She] became interested in the antiviral capacity of the gut most recently during the pandemic. She is a wealth of knowledge on this topic [and] has a lot of experience as a gastroenterologist, as a researcher, and [as an] expert in the gut-immune defense capacity.

I really enjoyed this conversation. I learned a lot, and I think you will, [too], particularly if you’re looking for ways to enhance your immunity and protect yourself against COVID-19 and other viral pathogens. Okay, so without further delay, let’s dive in.

Chris Kresser:  Robynne, it’s a pleasure to have you on the show. Welcome.

Robynne Chutkan:  Thank you so much for having me. It’s great to be here.

Chris Kresser:  So, you’re a gastroenterologist, [and] you’ve been looking at gut health for many, many years. I’m just curious—you’re a gastroenterologist, but you’re outside of the realm of purely conventional gastroenterology at this point. What led you down the Functional or integrative medicine path and led you to seek answers outside of what your traditional training might have taught you?

Robynne Chutkan:  Chris, that’s such a polite way of saying, “How come you’re a gastroenterologist and you’re interested in more than doing colonoscopy on people?”

Chris Kresser:  I didn’t say that. You said it.

Robynne Chutkan:  Thank you for approaching it in such polite terms. Exactly. No, I’m taking the words right out of your mouth. As you said, I’m conventionally trained. I went to [medical] school at Columbia, did my residency there, and was Chief Resident for a year there. Then I did my [gastroenterology] (GI) training down the street in New York at Mount Sinai Hospital, which has a really strong tradition of treating patients with inflammatory bowel disease, Crohn’s [disease], and ulcerative colitis. Dr. Crohn and [his] colleagues first described Crohn’s disease there in 1932. But for me, it was really a personal shift. I came to Washington, DC in 1997, joined the faculty at Georgetown [University] Hospital, and was practicing pretty conventional gastroenterology, doing a lot of colonoscopy, upper endoscopy, [and] prescribing a lot of medications, by virtue of the odd fact that in 1997, when I joined the faculty at Georgetown, they’d never had a woman on the faculty. Gastroenterology is still, in terms of the patient population, very female-predominant, and, in terms of the doctors, very male-predominant. [I] was the only one on the faculty. We had a lot of patients in the GI clinic, and many of them wanted to see a woman. There’s a strong desire for gender-concordant physicians in some of the subspecialties. In urology, a lot of men want to see a male urologist; in gynecology, a lot of people want to see a female gynecologist. It turned out [that] in gastroenterology, there was also a strong desire.

So I started seeing a lot of these women, and many of them wanted to know what else they could do besides [take] the medications that were prescribed, etc. Now, I’m not trying to say that this is something unique to women. Men are also curious and inquisitive about what they can do about their health. But in my clinic, my area of expertise, if you will, was autoimmune diseases in the gut—Crohn’s disease and ulcerative colitis, which together make up inflammatory bowel disease (IBD). And the medications we have for IBD are pretty rough. We have steroids, we have biologics, and those drugs can be really effective, but they have some really undesirable side effects. They either suppress or change your immune system, and in so doing, they can cause cancer [and] they can cause serious infection. So people, not just women, are really interested in alternatives. They had questions, and I didn’t really have answers, Chris. I was conventionally trained, and I didn’t know much outside of a pharmaceutical cure, if you will. But I went in search of answers. This is the late ‘90s, [and] I remember trying every diet out there. Going on Atkins, and South Beach, and the specific carbohydrate diet, and all these different [sorts] of regimens, and researching stuff that I hadn’t been taught in my medical training. I’ve been taught how to identify what something is. This is Crohn’s [disease] versus ulcerative colitis versus diverticulosis. But there hadn’t been much attention to the why. Why does this person have Crohn’s [disease] or ulcerative colitis? Or diverticulosis? And what can they do to reverse engineer this disease into remission?

So I embarked on a journey that I think is still continuing. Then that journey became really personal about 18 years ago when my daughter was born. I was a healthy person having my first child, and I had the flu when I went into labor. And because I had the flu, they decided to give me prophylactic antibiotics, just in case. And that “just in case” piece never turns out to be a good idea. At the time, I had no idea, right? I really hadn’t made the connection between antibiotics, disruption to the gut microbiome, and problems down the road, as many of us in the medical community had not, and many still haven’t, unfortunately. So I got these antibiotics during labor, [and] I ended up with a C-section. Another thing I had no awareness of [was] the incredible differences for the baby in whether they’re born vaginally and have the opportunity to travel through that birth canal, swallowing a mouthful of microbes and colonizing their microbiome with those founding species, versus babies who are born via C-section, pulled out of the uterus, [and] don’t have that colonization. Instead of having those important founding species [like] the mother’s bifidobacteria, etc., they’re colonized with hospital-acquired Staphylococcus. I don’t think you have to be a gastroenterologist or a microbiologist to know that hospital-acquired staph doesn’t sound like what you want for your founding species.

So my daughter was born via C-section [and] missed out on that important first step, colonization. She received potent intravenous antibiotics at birth, just in case, and that embarked her and our whole family on a journey that would last quite a few years of real sickliness. She constantly had pharyngitis, throat infection, strep, [and] ear infections. She ended up being prescribed more than 20 rounds of antibiotics before she was two. And it seemed, Chris, [that] she was always either about to get sick, actually sick, or recovering from being sick. I was a first-time mom, so even though I was a doctor and I’d received great medical training, I just wasn’t connecting the dots. I remember asking friends who had babies saying, “Well, how many rounds of antibiotics has your kid been on?” And they’re like, “None.” It just was so abnormal, but I really didn’t know any better. It wasn’t until she was almost three, [when] she had yet another illness. She had a chronic cough, sort of a post-infectious bronchitis that was more inflammatory, but my husband insisted on taking her back to the doctor. At this point, I had boycotted. I said, “Yeah, I’m not going,” and they walked in. I will never forget, she’s carrying this nebulizer machine for asthma with stickers, of course, on it. And my husband had four prescriptions. He handed me four prescriptions. He handed me a prescription for an antibiotic, an antihistamine, a bronchodilator, and a steroid. And that really was such a pivotal moment for me, personally as a mom, as well as professionally, to say, “We are going down the wrong path. We need to veer off this path and move in a new direction.” And that new direction, for my daughter and our family, involved being aware that many, if not most, of the illnesses she was suffering from were actually viral. Antibiotics weren’t of any efficacy and were only disrupting her microbiome. And also, just waiting it out a lot of the time.

I’m always quick to point out here that I am a physician, so I had some additional knowledge and expertise that made it safe for me to decide, “Okay, we’re not going to the doctor. We’re going to watch this illness, [but] we’re not going to treat [it].” I always recommend that people do this in conjunction with their healthcare provider. So we just stopped giving her antibiotics every month and, lo and behold, she got better. We changed her diet, we took her off dairy, we took her off wheat, and she really started to perk up. It took a while. It took a year or two, and she’d still get sick, but instead of getting strep and being out for the count for three weeks, now she’s sick for five or six days and just gradually got out of that cycle of perpetual illness. For me, it was an important change in direction because, on the other end, on the professional end, I was treating patients with Crohn’s [disease] and ulcerative colitis who had [the] same history Sydney had. C-section babies, lots of antibiotics in childhood, [and] minimal breastfeeding because, of course, my breast milk dried up quickly. We know that there are important ingredients in breast milk called human milk oligosaccharides that aren’t there to feed the baby; they’re there to feed the baby’s burgeoning microbial army. Without that breast milk coming in, the human milk oligosaccharides, the baby’s microbiome is even further disrupted.

I was seeing patients who were in their teens and 20s and 30s and had pretty severe autoimmune diseases with that very similar history, so I had that inside knowledge to know that this was potentially not going to lead to a good outcome. For me, Chris, that journey of experimenting with myself, learning from patients who were doing things differently, who were doing things in addition to conventional things with diet, mindfulness, meditation, etc., as well as that experience with Sydney, really caused me to change the way I practiced medicine and to look for some of these integrative solutions. To look beyond the scope, if you will, for a little bit of a GI analogy.

The Connection Between the Gut Microbiome and Our Immune Defense

Chris Kresser:  That’s a great segue, I think, into the main topic of this show, which relates to your book, The Anti-Viral Gut, and the connection between the gut microbiome and our immune defense against viral pathogens. You just described how much of a difference [looking at the gut holistically] made for your daughter’s health and for the patients [who] you were treating. Understanding that the gut doesn’t exist in isolation from the rest of the body, and [that] problems in the gut are not just limited to [GI] symptoms and manifestations like IBD, or [irritable bowel syndrome] (IBS), or diverticulosis, or diverticulitis, but that the consequences of a disrupted gut microbiome are almost shockingly diverse and can affect every system and tissue in the body. Research has shown us this over and over.

So let’s rewind a little bit. Back in 2022, I remember seeing some initial studies published. These weren’t surprising to me, but it was good to see that researchers were already doing this work. One paper was “Alterations in microbiota of patients with COVID-19: potential mechanisms and therapeutic interventions.” There were some very similar papers that were looking at this from two angles—How does a disrupted gut microbiome predispose us to getting a viral infection in the first place, or any other kind of infection? And then, what is the effect that infections can have on the gut microbiome? And what can we do about both of those things? So I’m really curious to hear how you got interested in the connection between the microbiome and viral defense.

Robynne Chutkan:  Chris, I just want to say, before we even get into this, that you and I were chatting before we started recording about when we first met, almost 10 years ago at the first mindbodygreen revitalize live conference at Miraval, and how exciting it was to meet people in person who I’m still in touch with. You, and Joe Cross, and Whitney and Danielle from Sakara. And I have to say that, even before that, when I started well over a decade ago down this journey and investigating this stuff, your name would pop up a lot in the literature. I remember reading an article you’d written, [and] it was something to do with the gut–brain connection. I remember thinking, “Who is this guy? He’s not a physician, but he knows so much. He knows more than my physician colleagues,” [and] being so intrigued. As a physician, [and] this might sound almost obnoxious, I’m thinking, “How come he knows so much and he’s not a doctor?” And it really opened my mind to the idea that, yeah, the medical community doesn’t necessarily have all the answers. I mean, we contribute a lot, and there’s important information, but there’s information to be found outside those walls, outside your doctor’s office, etc. And you were one of the early people bringing that information forward. So I just want to acknowledge that and thank you for that.

Chris Kresser:  You’re welcome and thank you.

Robynne Chutkan:  Now, let me answer your question. In terms of predisposition, you’re absolutely right about those articles. There have been quite a few studies, but there was one in 2021 from UMass Medical School that showed that the composition of the microbiome was the most important predictor of outcome from [COVID-19]. It was more important than age, gender, comorbidities like heart disease and hypertension and even lung disease, things that we were paying a lot of attention to. To drill down a little bit into what they found, they found that people who had high levels of a [bacterium] called Faecalibacterium prausnitzii, or F. prausnitzii for those of us who are on a first-name basis with this bacterium, high levels of F. prausnitzii were associated with good outcomes. Those patients were much less likely to end up on a ventilator, to have acute respiratory distress syndrome (ARDS), and to die. Conversely, high levels of a [bacterium] called Enterococcus faecalis, E. faecalis, [which is] different from F. prausnitzii, were associated with worse outcomes. And we know Enterococcus faecalis is associated with not just bad outcomes in [COVID-19], post-op infections, etc. Enterococcus faecalis seems to be able to penetrate the gut lining and get access to the bloodstream and internal parts of the body and wreak havoc. But more importantly than what the individual bacteria can do, it’s the association and the company they keep. We know that F. prausnitzii is the most prevalent [bacterium] in people who eat a lot of plants. Not necessarily vegans; you and I both know plenty of vegans who don’t eat that many plants and plenty are omnivores who eat lots of plants. It is much more related to the amount of plants you’re eating than to what name you apply to yourself. But people who eat lots of plants have high levels of F. prausnitzii,and F. prausnitzii isn’t just protective against [COVID-19]. It is protective against colon cancer, metabolic syndrome, diabetes, etc. So, really, what the study was telling us was that the microbiome of people who eat a certain way has more of these certain organisms and can be more protective.

We also know that F. prausnitzii and other similar organisms take plant fiber and ferment it and create something called short-chain fatty acids. I know many of your listeners know all about short-chain fatty acids [like] butyric acid, propionic acid, etc. Short-chain fatty acids help maintain the gut lining, the health of the gut lining, keeping it intact, and preventing stuff from penetrating through. But short-chain fatty acids also modulate the immune system. They guide the immune system. And this is a really important point because for most people who succumb to [COVID-19], who end up with ARDS, the cytokine storm we’ve heard so much about over the last few years, it’s not a direct result of the virus itself; it’s the immune response to it. It’s an overblown immune response, where your immune system responds too aggressively and, in the process of trying to clear the virus, it destroys normal tissue. In the case of ARDS, it’s destroying healthy lung tissue along with the virus. That’s an overblown immune response. On the other hand, you don’t want to have an underactive immune response, where it’s not strong enough to clear the virus. So, as I’m fond of saying, you want to have that Goldilocks immune response—just right. And in order to have that Goldilocks immune response, you need to have lots of short-chain fatty acids. In order to have lots of short-chain fatty acids, you need to have lots of F. prausnitzii. In order to have lots of F. prausnitzii, you need to eat a lot of plants [and] you need to have a high-fiber diet.

So this is how it’s all connected. What that UMass Medical School study was telling us, and several others like it that came out of China and other parts of the world, is that, at the end of the day, how we live, what we eat, etc., and of course, it’s a lot more than just diet, which hopefully, we’ll have a chance to talk about. But diet is a pretty significant factor. That informs what’s going on in our gut microbiome, and what’s going on in our gut microbiome informs our overall health and, particularly, our immune health. Remember that those microbes are separated from all those immune processes by a single layer of cells, just one cell thick, and they’re constantly interacting. So if your gut microbiome is disrupted, you are going to end up with a disrupted immune response, and possibly an overblown immune response, because it’s not modulated, it’s not guided properly, and [you’ll] potentially [have] a poor outcome. So, that’s one of the direct effects. We know that there are other things the gut does. Stomach acid that unravels and denatures viral proteins can protect us from infection. We have a study from 2020, [a] 53,000 [person] population-based study that showed that people taking those potent acid-blocking drugs, proton pump inhibitors, are two to four times more likely to end up with [COVID-19]. And this isn’t new. We know that. That’s true of rotavirus and other viral illnesses for people taking these drugs.

So, Chris, one of the main goals in writing this book was to open people’s eyes a little bit to the idea of the gut as a defensive organ. Everybody knows the gut as a digestive organ, but I don’t think people really think of the gut as a defensive organ, as an organ system that can keep you safe from viruses and other pathogens. That was really the challenge with this book, to explain to people all the different things the gut does. Stomach acid, the gut lining, the microbiome, all the different ways that it is keeping you safe, and to really promote this idea that you can be a healthier host, and healthier hosts have better outcomes. You have less susceptibility, and you have better outcomes if you do get infected.

Multiple studies have confirmed a dramatic link between the health of our gut microbiome and the strength of our immune system. The good news is that our microbiome is constantly evolving, offering a pathway back to health for those who are suffering, and proven protection for those who want to stay well. #chriskresser #guthealth #immunity

Chris Kresser:  One of the things I like to remind people of is that the contents of the gut, what’s inside the gut, are actually outside of the body. The gut being a hollow tube [that] intersects the mouth and the anus. We mostly think of what’s inside the gut as being inside of our body, but it’s not inside of our body until it gets absorbed across the lumen of the intestine into the bloodstream. That’s one of the many ways that the gut protects us, is [by] discerning what gets in and what gets out when it’s functioning optimally. What are some of the other ways that the gut protects us? You just listed a couple, but maybe you could talk a little bit about the [gut-associated lymphoid tissues] (GALT) and the percentage of the immune system that we think resides in that tissue, and the role that the gut plays in the immune system, in general.

Robynne Chutkan:  Sure. And Chris, I’m so glad you mentioned the inside-out thing. I wager that most of my GI colleagues have never thought about that and are not aware of what you just said. So I’m going to say it again for people to absorb this. What is in your gut is not inside your body. It’s in a hollow, digestive superhighway, a tunnel that goes from your mouth to your anus. And the purpose of the gut lining is to keep a lot of what is in your gut lumen, namely outside your body, to keep it outside. That could be things like pollen, things that you swallow from the environment, it could be viruses [or] bacteria that you’re exposed to, it could be poorly digested food particles, [or] it could be toxins. An intact gut lining is a selective barrier. It’s selectively permeable, and it’s only going to let things of a certain size and things that it’s vetted [through]. It’s like the bouncer at the club. It’s like, “No, you’re not coming in. You’re a troublemaker; you’re staying out here. Yeah, you can come in.” And it’s not just the pore size of the membrane. There are other things, too, that determine what can get in. So it’s a very selective barrier. And when we damage that barrier, kind of like a fishing net, if we make big, huge holes in the net, now all sorts of stuff that shouldn’t be able to penetrate through that gut lining and gain access to the inside of your body through that membrane can get in.

For example, if we look at something like food sensitivities and food allergies, we see improperly digested food particles getting through and triggering some sort of reaction in the body. [That’s] a common one, and we know that a lot of that is associated with the damaged gut lining. We [can] look at multisystem inflammatory syndrome (MIS) and [MIS in children] (MIS-C). So, again, this sort of [MIS] that we’ve seen with [COVID-19]. We have really good data from Heenam Kim’s lab in South Korea [showing] that a lot of people who suffer from MIS-C have a damaged gut lining. They have increased intestinal permeability, and that’s how the virus is able to penetrate in. We see high levels of a protein called zonulin, which is associated with an increased intestinal permeability, [and] we see the virus getting into the bloodstream. That is one of the mechanisms. It’s probably not the only mechanism, but [it’s] one of the mechanisms. When we scratch our head and we say, “Okay, why does this person have MIS?” A lot of it has to do with this damage to the intestinal lining. Again, the gut lining, it’s only one cell thick, people. That’s not very thick. That’s razor, razor thin.

How We Can Repair and Strengthen Our Microbiome

Robynne Chutkan:  So you think about the things that you do, maybe even on a daily basis, that damage that gut lining. Top of the list is non-steroidal anti-inflammatory drugs (NSAIDs). As we’re reaching for that ibuprofen, you really have to think, “Okay, what am I doing to the gut lining?” Alcohol, stress can do it, things that sometimes we have less control over [like] radiation, etc. If you’ve had malignancy and you’ve had some sort of radiation to the body, that can damage the gut lining. Infections, fungal infections, etc., can do it. Food can do it. Lots of artificial sweeteners, highly processed foods, a lot of emulsifiers and things they use in ultra-processed foods are damaging to the gut lining. That’s how we’re seeing an association with Crohn’s disease and other gut-based disorders as a result of eating lots of ultra-processed foods. And of course, the medicine cabinet. In addition to ibuprofen, antibiotics [are] also problematic. In terms of how the gut protects you, having an intact lining literally keeps bad players like SARS-CoV-2 out of your body, keeps them in the gut lining where they can pass through and be excreted. And we know we do excrete SARS-CoV-2. We can see the viral shedding in the stool long after a nasal swab is negative, so some of that elimination continues even after we can detect it in the nasal swab. We talked about stomach acid, and that’s another potent way our gut defends us. It literally acidifies. That acid literally denatures a viral protein and makes it so that the virus is inactive. We know that the gut is a common portal of entry for SARS-CoV-2 and other viruses. Poliovirus, too, lots of other RNA viruses. We have about 100 times more [angiotensin converting enzyme 2] (ACE2) inhibitor receptors, [the] receptor for SARS-CoV-2, in the gut compared to the lungs. We know that when the virus gets in through the gut, it can bind to intestinal cells and enter the body that way. But if you have intact stomach acid, that’s less likely to happen.

When we look at a population of people, and we say, “Okay, all of these people were exposed, but how come only these people got sick, and these people didn’t get sick?” There are things like extremes of age—the young, where the microbiome is just forming, and the elderly, where the microbiome is sort of waning. There’s whether somebody’s on an immunosuppressive drug or not, there’s comorbidities, etc. But we know that some of these gut-based defenses are really critical. Is your gut lining intact? Do you have adequate levels of stomach acid? Do you have a healthy, diverse microbiome? Or has your microbiome been disrupted by antibiotics, acid-blocking drugs, poor diet, etc.? These are some of the things. Mucus, we didn’t even talk about mucus. And I’ll tell you, when I was in medical school, I did not like mucus. I thought mucus was kind of gross. I liked critical care medicine. I loved being in the [intensive care unit] (ICU). But the pathway to being a critical care doctor, what they call an intensivist, where you work in the [ICU], is primarily through doing a fellowship in pulmonary medicine. I was like, “Oh man, no way am I dealing with snot.” And when you consider that I ended up a gastroenterologist, it’s like, “Okay, but you deal with stool.” But I gotta tell you, Chris, stool is a lot less gross than snot. I’ll take stool over snot any day.

It turns out, though, that snot and mucus [are] really important, too. [When] people think [of] mucus, [they] think [of] the lungs. But the truth is most of the mucus is made in your gut, about a liter and a half a day. And mucus is this weird mix of, like, Jell-O and glue. It’s a sticky matrix, and it traps things. It traps things like pollen and other irritants, [and] it traps viruses. But it doesn’t just trap them; it also neutralizes them through releasing enzymes. So it’s like, “I’m going to trap SARS-CoV-2, and then I’m going to secrete these enzymes to destroy, like the stomach acid to denature the viral protein.” And then the cilia in the lungs, those little hair-like projections, are going to move the mucus up, and then you’re going to spit it out, or you’re going to swallow it where it will be excreted in the gut. Mucus is really a key part of this gut defensive system. And it’s also a lubricant, right? It lines all these hollow organs, like our vagina, our GI tract, our nose, our mouth, etc. But mucus also has a really important defensive role. We know people who don’t have healthy mucus, who are smokers, who are dehydrated, etc., where the mucus isn’t as healthy, are not able to degrade the virus as well. So when we look at super spreading, we know that for many viral illnesses, for measles, for Ebola, and for SARS-CoV-2, it’s [a] small percentage of people, less than 10 percent, who are responsible for more than 90 percent of the infections. We’ve seen super spreader events from the Rose Garden at the White House to that early one, the choral group in Seattle, Washington, where I think there were like 57 out of 65 people infected or something, which is much higher than you would expect. And it turns out that the person, the sort of incident case, was a super spreader. Part of how we think super spreaders work is that there’s something different about their mucus, where their mucus is not destroying the virus as it should. So if you get sneezed on or coughed on by a super spreader, you’re much more likely to become infected than by somebody whose healthy mucus has killed the virus.

These are some of the things I think we don’t really think about. We don’t think about these differences in hosts’ susceptibility, and how they can affect not just us, but the people around us in terms of how these things are transmitted. We have a real opportunity, I think, with this pandemic, and with all the others that are coming down the pike, to really think about these things and to both collectively as a society and individually think about how we can become healthier hosts so that we can be more resilient.

Chris Kresser:  Absolutely. And I think that’s such a shift in the dominant paradigm. The conventional paradigm that we grew up in was really mostly about disease management. Most people go to the doctor when there’s a problem, and they ask the doctor to help them fix the problem. Fair enough, there’s a need for that. There will always be a need for that. But there’s very little focus in our conventional medical system on prevention and on all the things that we can do to prevent a problem from happening in the first place. And I don’t care what context you’re talking about, whether it’s running a business, health, [or] environmental concerns, Ben Franklin was right when he said, “An ounce of prevention is worth a pound of cure.” I think that’s especially true with gut health, as you’ve mentioned in several different contexts now. How we treat our gut, from what we eat to the personal care products we use, to our exposure to toxins in the external environment, to how we manage stress, to how much sleep we get, what medications we take or don’t take and their impact on the gut flora, like ibuprofen, NSAIDs. Even hormonal contraception has been shown to affect the gut in various ways. It’s the mindset shift for getting from just waiting until something bad happens to more of a gardening analogy, like nurturing the soil, so that good things can happen in that garden of the gut, rather than just being reactive.

Robynne Chutkan:  Absolutely, I love the soil analogy. When you think about the whole concept of terrain theory, Louis Pasteur popularized this idea of germ theory that says [a] bad bug gets into your system and it makes you sick. And that’s certainly true. Ebola, SARS-CoV-2, these are organisms that shouldn’t be in our body, and when they get in, they can create illness. But another Frenchman, Antoine Beauchamp, championed terrain theory at around the same time. And he said [that] if your terrain, your soil, is healthy, [then] the pathogen can pass pretty harmlessly through your system with minimal disruption. And we see that all the time. I don’t know, Chris, how much of this was because of the media on both sides, liberal and conservative. There was so much, maybe not intentional, but just fear that they were instilling in people. I don’t know if it’s partly because of the media, or maybe because this was a novel virus, but if you think rationally for a moment about illness, in general, if you think about heart disease, if a 35-year-old healthy person has a heart attack, they are much more likely to survive than if a 70-year-old smoker who’s hypertensive, has obesity, eats a terrible diet, and is sedentary has a heart attack, right? And the same is true for cancer, a broken leg, whatever it is. If we are healthier hosts, we are much more likely to survive whatever illness comes our way. We’re much less likely to get the illness in the first place. That’s the first thing. And we’re much more likely to have a better outcome. Some of the things we can’t control. We can’t control age. There is some genetic predisposition, but by far, most of this is a result of how we live. It’s a result of things we have control over. And one of my biggest complaints about the medical industrial complex is that it wants to make you feel helpless. It wants to make you feel like the only thing you can do is take an antiviral or get a vaccine. And those are all reasonable things to do, but there’s a whole bunch of other things that you can do that are going to have a significant impact on whether you get infected, and if you do get infected, because there is a little bit of inevitability to this exposure, whether you end up asymptomatic, mildly symptomatic, or very ill, and maybe even leaving the hospital horizontally, God forbid.

So that is really the message. And I know, because so much of what happens in medicine, there is commerce at the root of it, right? Particularly with the pharmaceutical companies. It’s not a message that is propagated within the medical community, for the most part. What’s propagated within the medical community for the most part is pharmaceuticals and more pharmaceuticals, and there’s not much you can do. And that’s true whether we’re talking about viral illnesses, diabetes, heart disease, cancer, [or] anything else. It is, “This is what’s going on, and here’s a drug to treat it.” And again, those drugs can be lifesaving; they can be critically important. But there’s a lot of additional stuff that you can do that’s going to improve your outcome when you bump up against things like SARS-CoV-2, or heart disease, or cancer, or anything else. And again, part of why I love the work that you do is very much about empowering the individual. You’re a lot stronger than you think, and here are 16 things that you can do to improve your health.

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Chris Kresser:  So let’s talk a little bit about that. I mentioned before that some of the research I had seen suggested that [with] SARS-CoV-2 (and other viruses, as well; we don’t need to make this just about that. It’s the one that most people are thinking about now, but this is true for other viruses), not only does having a disrupted microbiome and poor gut health increase the likelihood of us getting the infection, [but] we’ve seen studies that show that the infection can disrupt the microbiome and that disruption can persist for some period of time after being infected. There’s some speculation, although I think this is reasonable based on what we understand about the connection between [the] gut and well-being, but there’s speculation that a disrupted gut microbiome caused by the SARS-CoV-2 virus could actually be, at least in part, driving some of the phenomenon known as long COVID for some people in some situations.

I know you’ve helped a lot of patients recover from [COVID-19], [and] you talk about this in your book. What do you think about this, the impact of the virus on the gut and how people can tend to their gut health as a means of recovering if they’re dealing with persistent symptoms?

Robynne Chutkan:  You’re absolutely right about the microbiome disruption. So the general term, dysbiosis, that we use for disrupted microbiome, is both a risk factor for [a] worse outcome and a potential result of infection. So when SARS-CoV-2 binds to those ACE2 receptors, ACE2 receptors control, not completely but have some impact on, gut diversity. That binding process can induce changes in the microbiome that create a more imbalanced, disrupted microbiome, what we generally refer to as dysbiosis. At the same time, people who have a dysbiotic gut, a disrupted microbiome, are more likely to get sick in the first place. So it’s both cause and effect. And you’re also correct in pointing out that dysbiosis, whether you had it before you got infected or you had it as a result of the infection, is associated with post-viral syndromes like long COVID. And not just long COVID. If we look at [myalgic encephalomyelitis/]chronic fatigue syndrome (ME/CFS), we also see a disrupted gut microbiome. We see a microbial signature with [CFS], where researchers at Cornell are able to identify people with ME/CFS just by looking at their gut microbiome. They can tell with a pretty high degree of accuracy. We have similar studies in the gastroenterology literature where people with acute [COVID-19] were followed, and the ones who developed long COVID, a high percentage in this study, had some typical microbial changes. So we know that there is something about the gut microbiome in people who are having these post-viral syndromes that is different.

So, even if there are other things involved, there’s dysautonomia, where the autonomic nervous system is involved, there’s autoimmunity often going on, there are other things, we know that really doubling down on trying to improve the gut ecosystem can be a really successful way to help combat a lot of these symptoms. And what’s the worst thing that can happen? Well, your gut health improves, right? Even if your long COVID doesn’t completely go away. If we look at something like postinfectious [IBS], it’s really a constellation of different signs and symptoms that can develop after infection in the gut. So, after infection with Campylobacter, with amebiasis, with a lot of different things, and even after infection with [COVID-19], and [there are] lots of similarities to what millions of people are now experiencing with long COVID. In addition to the disruption of the microbiome, we also see disruption of the intestinal barrier function, changes in intestinal permeability, what I was talking about with the MIS, the multisystem inflammatory syndrome, etc. So, we have to think about all of those gut defenses we talked about earlier. We have to think about what you can do to strengthen the gut lining, what you can do to repair your gut microbiome, what you can do to maintain stomach acid levels, [and] all of these different things. Avoidance is a big part of this, Chris. The medicine cabinet. You’ve got to make sure that everything you’re taking, you’re taking for a good reason, and that the benefits outweigh the risks.

There was a study published in the journal Nature in 2018, where they looked at 41 different classes of medications, and they found that half of them were disruptive to the gut microbiome. Not the obvious ones. I mean, of course, antibiotics, acid blockers, etc. There were certain laxatives, there were antidepressants, there were all kinds of medications, there were beta blockers for the heart that were found to be disruptive to the gut microbiome. So, high up on my list is judicious use of medication. This idea that you can just take a probiotic and all is well is a little bit of magical thinking. When I think about my approach to somebody who’s struggling with post-COVID symptoms, I think about removing medications, practices, and foods that are damaging to their microbiome. We talked about some of the medications. Other practices, they might be under a lot of stress, [and] they don’t have a good strategy for handling the stress. They may not be sleeping well, [and] they may not be getting enough exposure to the outdoors. In terms of food, they may be eating an ultra-processed diet high in sugar. So, some of those things that we know are damaging to the microbiome. I think about replacing missing or depleted gut bacteria, and that’s much more about exposure to soil microbes and ferments, fermented foods, and prebiotic foods than it is [about] taking a probiotic pill. Maybe eating some sauerkraut, [and] making sure you’re getting a lot of these prebiotic foods, whether it’s oats, legumes, greens, however you’re getting them. I tend to get them through beans and greens, but there are lots of other ways. And then some of these scientifically backed mind-body practices that we know are really helpful, like stress and sleep deprivation. We have a study from the British Medical Journal that showed there’s an 88 percent increased risk of [COVID-19] in people who are chronically sleep deprived. We know that vaccine efficacy is profoundly affected by sleep deprivation. If you are sleep deprived in the two days prior to receiving a vaccine, the efficacy can be decreased by as much as 50 percent. Sleep reboots that immune computer in your body, and if you’re sleep deprived, you literally cannot recruit enough T-cells to have a proper immune response, to get to that Goldilocks immune response. You’re going to have an underactive immune response.

I always remind people, what they think is in their head is also in their body. In the book, I have, I think, 24 sections of solutions for how to get a good night’s sleep. I really went down a rabbit hole with sleep because it has such a profound effect on our viral susceptibility. The same for stress. There’s a remarkable study from [the] University of North Carolina [at] Chapel Hill looking at men with [human immunodeficiency virus] (HIV). They found that men who did not have strategies for mitigating stress—not men without stress, men who didn’t have a strategy—whether it was exercise, or mindfulness, or whatever it is, men with HIV who did not have any sort of stress management strategies, their HIV progressed to [acquired immunodeficiency syndrome] (AIDS) four times faster. It’s crazy, right? But then, it’s not crazy when we think about it. If we look at other viral illnesses like shingles, varicella, the virus that causes chickenpox, is latent in the body and then becomes active again as shingles in an older age. Who gets shingles? People who are stressed. You don’t get shingles on vacation; you get shingles while you’re stressed out. Something stressful is happening. The death of a loved one, stress at work, marital problems, etc. That’s when you get shingles. So we see that stress is a potent, potent facilitator of viral illness. Not just acute illness, but also chronic and latent viral illness.

We know that the environment makes a huge difference. The Japanese practice of shinrin-yoku, or forest bathing, we know [is] good for stress. There have been studies in Japan that show a decrease in stress hormone production, improvements in the immune system, [and] better recovery from illness. We know there’s something called an open air factor, the OAF. I think people are pretty aware at this point that viral transmission is less outdoors. If there’s a big bump in numbers of viral infections, you might move to start having functions outside because there’s going to be less transmission outside compared to inside. But there’s also better recovery. We know from studies more than 100 years ago with the Spanish flu epidemic [in] 1918, that soldiers who recovered outside in the fresh air had much lower mortality than people who were inside the hospital. In some cases, 13 percent mortality versus 40 percent mortality. That’s because of this thing called open air factor, which is described as a germicidal constituent in open air that is somehow harmful to these viruses [and] that can kill viruses.

So these are the kinds of things when we think about how to approach this. It’s not, “Okay, here’s a probiotic.” It is all of these things. You’ve got to master your mind; you’ve got to focus on your sleep hygiene and your stress mitigation strategies. You’ve got to think about your environment and how you [can] get outside. You’ve got to be more thoughtful about therapeutics and think of ways to tackle health challenges that don’t destroy your precious gut microbes in the process. Which involves, for example, knowing those critical questions to ask your doctor when you’re sick and they’re handing [you] your prescription for antibiotics, starting with, “Is this antibiotic absolutely necessary? What would happen if I didn’t take it? Could this illness I’m suffering from get better on its own?” It’s shocking how much of the time the doctor is just handing you something because [they think] you want something and they think this is a viral illness, and they know that antibiotics aren’t going to work. So all of these things are really important.

And of course, knowing how to feed your microbes, right? Making sure you’re getting adequate amounts of plant fiber, in addition to whatever else you’re eating, that can feed those F. prausnitzii so they can start churning out the short-chain fatty acids. It’s really a very broad approach. It focuses on these innate host defenses in our gut. But I think the plan, which is [the] whole second half of the book, pulls from a lot more of these areas, too. It does show what the relationship [is] of sleep to the gut, etc. It is really challenging people to think more broadly about what gut health is and [that] gut health isn’t just what you eat, or a probiotic you might take.

Chris Kresser:  Amazing. I love this conversation, Robynne. I love your book. And I would love for you to let people know where they can find out more about it and pick up a copy.

Robynne Chutkan:  Oh, thank you so much, Chris. The book is called The Anti-Viral Gut: Tackling Pathogens from the Inside Out. It’s available on Amazon, Barnes & Noble, wherever books are sold, and you can follow me on Instagram at Gutbliss. I have a couple of websites that are full of lots of great free information. One is RobynneChutkan.com, my difficult to spell first name and last name, or Gutbliss.com. We have, I think, 37 different topics in the free gut guide section, everything from small intestinal bacterial overgrowth to hemorrhoids. We have a great blog that you can search with lots of this stuff. I also do a free office hours series on Instagram live every Tuesday at noon. You can go back and look at some of those archived ones. We have a YouTube channel. Everything’s a little bit disorganized. I’m trying to get things [organized]. We’re overflowing with content, so I’m trying to bring a little order to the chaos. But if you poke around, you’ll find it all, and I’m hoping to reorganize our YouTube channel and have all the video stuff there in another couple [of] weeks.

Chris Kresser:  There’s a lot of great resources there. Thank you for sharing, and thank you, everyone, for listening. [I] hope you enjoyed the episode. Keep sending your questions to ChrisKresser.com/podcastquestion. Robynne, thank you for coming on. Congrats on the book. I’m really glad that I’ll be able to recommend this to people because I think it’s such a foundational issue that a lot of people don’t even consider when it comes to immune defense, in general, and defense against SARS-CoV-2 and other viral pathogens, specifically. So thank you so much. I can’t wait for our next conversation.

Robynne Chutkan:  Thanks, Chris. I really appreciate it. And congrats to you on all the great work and the information you put out there.

Chris Kresser:  Okay, we’ll see you next time, everybody. Thanks for listening.

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