Why Healthy Eaters Can Still Have Broken Guts, and What You Can Do About It.
29 Jan 2026 · 42 min
Podcast interview (Ben Greenfield with Dr. Alejandro Junger) exploring gut health and Junger's Clean Gut approach. Topics include gut–brain and gut–immune links (serotonin, allergies, autoimmune disease), modern contributors to gut dysfunction (processed foods, water contaminants, lifestyle/stress), the Clean Gut 'Rs' (remove, reinoculate, repair, restore; plus relaxation), fasting/liquid meals for gut rest, practical diet and supplement suggestions (kale, garlic, ginger, lemon, glutamine, probiotics, magnesium), and resources at CleanGut.com.
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Hey folks, it's Ben Greenfield. And as you know on the podcast, we like to talk about your gut, about your stomach, even about your poop. And today I have a physician on the call with me who is the expert when it comes to getting a clean gut. I'm actually holding right now a book that he wrote by the very same name, Clean Gut. His name is Alejandro Junger. He is a physician. He's the New York Times best selling author of the book Clean the author of this book, the Clean Gut. He also has a website over@cleangut.com which is jam packed with information too. And today we're going to be talking all about your gut issues and what you can do about them. So, Dr. Junger, thanks for coming on the call today.
Yes, thank you for having me.
Well, you know, I gotta tell you, when I got your book and read through it, you know, I was a little bit surprised because a lot of what you talk about, there are things that kind of fly under the radar in I guess what you would call kind of modern medicine. So what I wanted to ask you was like, as a physician yourself, you know, as an md, you hear a lot of this stuff from like natural doctors and alternative medical practitioners and people like that about the gut. But how'd you end up kind of stepping outside the mold in your medical education or after and going on to kind of become an expert in this whole gut issue thing?
Well, thank you for the expert title. That's kind of debatable. But yeah, I've been giving the gut a lot of attention and the reason why is from sheer need. I got really sick as I was finishing my training in internal medicine and cardiology in New York. And of course I visited my colleagues. I have access when you're a medical doctor and you're training in hospitals and you know a lot of people. So I had access to the best doctors in every area. And by the end of my day of consultations, I ended up with three diagnoses and seven prescription medications. And when I got home with all these medications, I was looking at prescriptions and it just didn't make sense to me. So I set off to look for a different solution for my health issues and through my, you know, my travels, because I quit the hospital life and I moved to a monastery in India and I studied. And the reason why I did that is because one of my worst symptoms was depression and I found meditation. And that's why I went to India. But there I was exposed to many different modalities of healing and different schools of medicine, like, like the Indian school of medicine, Ayurvedic medicine and Chinese medicine, chiropractors. And that opened my mind to start looking for different solutions. And I found first the concepts and practices of cleansing and detoxification, which are the subject of my first book. And then zoned in the gut, and that's the subject of my second book. And as I said, this was just for my personal health that I did this. But then I started using these concepts and practices in my medical practice with incredible results and became aware and became convinced that the gut is where health and disease begins.
Now, with the gut being the place where health and disease begins, what kind of things do you end up seeing that are kind of like gut issues that are disguised or that are showing up as other issues?
Well, in my case, for example, all my problems were gut related and my diagnoses were depression, severe allergies, and irritable bowel syndrome. You can right away figure out that irritable bowel syndrome is a gut problem. But how is depression a gut problem? Through my study and through my research, I found out that 90% of the serotonin, which is a neurotransmitter that we think of as being responsible for the feelings of well being and happiness is produced in the gut. In the neurons around the gut, you know, around our intestines, we have more neurons than in our skull, which is the subject of Dr. Gerson's book called you'd second brain. And that is how depression, which may for a lot of people seem completely unrelated to the gut, is mostly originated in the gut. And so were my allergies, because also within the walls of the intestines and around them, we have 80% of our immune system. And when the gut is disrupted, then the immune system gets altered and starts functioning in different ways that lead to many, many problems. You know, the simplest forms of these problems are the allergies, but the more complex forms are the autoimmune diseases.
So if you've got like, let's say like hay fever or, I don't know, exercise induced asthma or something like that, you should be thinking about looking into Your gut.
If you have any health issue practically, you should be thinking about your gut. Listen. In the book, I explain how the gut functions very much like the roots of a plant. And the soil around the roots is very much like the food that we eat. The plant extracts the nutrients from the soil through the roots and sends them to the leaves and the flowers and the fruit. And we do the same thing. We extract the nutrients that we need through our gut from the food that we eat, and we send those nutrients up to our hair and our bones and our organs, which are kind of like the leaves and the fruit and the flowers of a plant. Now, when a gardener comes to your garden and sees the leaves discoloring and falling off, he doesn't really focus on the leaves themselves. He goes to the root, and by correcting the conditions in the roots and around the roots, he fixes most of the plant's problems. And it's the same thing with the gut. When you fix the gut, most of the chronic diseases of the modern world either improve or completely disappear, you know, in a second.
I want to ask you a little bit about, like, how the gut kind of breaks in the first place. But you talk about all these different issues, and we just hit on a couple of them, like depression that are linked to gut dysfunction. But one of the things you talk about is back pain. And that one kind of surprised me because usually we think about back pain as being like, whatever, a slipped disc or a torn muscle or something like that. How can a gut issue be related to back pain?
Well, you know, the body adapts itself to. To different circumstances and situations. For example, if you injure your foot, then you would try to put less pressure on that foot as you walk. And so your whole body would start adapting, and your back will take a different shape in order to adapt to the different pressure points and so on and so forth. In the same way, when the gut is inflamed, it applies pressure on the organs. And your body will automatically try to correct and adapt itself by taking different shapes. And the back is one of the things that suffers during the process.
Interesting. So people who, like, whatever, maybe an athlete who gets back pain while they're out running, or somebody gets back pain while they're sitting all day at the office, they can look into more than just, like, their shoes or their chair and actually dig into the gut a little bit.
There are problems that are related to position and trauma and injury that may have nothing to do with the gut. I'm not saying that every single case of Back pain is directly related to the gut. So in the case of athletes and people are sitting down all day long in different positions, that may be just the problem. But back pain is one of the number one reasons for people to seek medical attention. And not all of them are injury related or not all people are athletes. So the rest of the people that don't have a simple explanation for the back pain, like injury should look into their guide.
Got it. So, you know, we actually have, speaking of athletes, we have a lot of active people that listen into this show. Like they already kind of, kind of eat sort of healthy. You know, they're not spending a lot of time at McDonald's shoving Big Macs down the hatch. And, you know, a lot of people are even like, you know, looking into the whole gluten free thing and they're trying to take pretty good care of their bodies. Now, if. If you look at people who are quote, unquote healthy or who do a decent job taking care of themselves, what are some of the big issues that you see among them with gut dysfunction? What kind of things do people forget to do when it comes to taking care of their gut? Or how do people who are even healthy and athletic and active break their gut? What are the mistakes that you see people making?
How many people do you know that are healthy and eat right and they exercise and they look good, get cancer or they get an autoimmune disease? There's a lot of them. So what is the problem with these people? The thing is this. The world, the modern world that we have created and are living in is not gut friendly. Take the example of city supplied water. In most cities in America, the water supplied has chlorine and all kinds of medications and even antibiotics. Just Google it. And you see, so when you're showering, you're absorbing many of these toxic chemicals through your skin that end up going into your blood and end up in your gut as well. And they end up killing the good bacteria in your gut and disrupting the growth of the cells that line the intestines. And this is how things start breaking up. In the same way, when you eat processed foods, a lot of people that eat healthy, they have processed foods in their diet. And processed foods, anything that comes in a jar, in a box, in a can, in a bag, in a tube has to have preservatives. Now preservatives, if you think about it, are chemicals that you put in the food in order for them not to grow bacteria and fungus. So they are really antibiotics. And when you Eat these processed foods, you're killing good bacteria. So wherever you look, you will see that living in the modern world today is a health risk for your gut. And slowly the gut gets eroded. And that's how health issues are born. So things that people normally don't even think about and that are being now proven and written about all over the literature and the news and the medical journals is giving us a better awareness of how the gut bacteria affect our health. So taking probiotics, making sure that your intestinal flora has the right conditions to thrive, that's one of the things that is very important now and it's coming into people's awareness.
You know, I think that's really interesting because so many people like eat healthy and a lot of them take probiotics or, you know, many of them even go above and beyond and take gut healing compounds like gluten, glutamine and stuff like that. But they don't think about their, you know, freaking shower head filter or you know, the preservatives in that organic jar of nut butter that they bought at the grocery store. And yeah, it's, it's kind of one of those deals where you really have to go out of the way toto protect your body and protect your gut, huh?
And listen, I don't want to be an alarmist, but even people that eat completely healthy and eat only fruits and vegetables and no processed foods whatsoever, the quantities, the frequency and the kind of combinations that we are consuming also affects your gut. So you could be eating perfectly chemical free food. And if you're eating it in the wrong combinations and in the wrong quantity, you are going to be promoting the unhealthiness of your gut flora. So we don't fully understand yet how the gut flora is maintained. Because the thing is, when you look at animals in the wild, they're eating what nature designed them to eat, and they're living in the conditions that nature designed them to live. But we have lost that knowledge. We don't even know what nature designed us to do. This is a big debate now. So because we're living in such unnatural conditions, then we're suffering the consequences. One way to think about it is this. If you know anything about fish tanks, especially saltwater fish tanks, you know that you have to maintain the ph and you have to maintain the right temperature and the right acidity and the right conditions for these fish to thrive. And when those conditions change, less oxygen or more acidity or temperature changes, the fish die in the same way. Your gut is like a fish tank, and it should be maintained meticulously in certain conditions for the gut flora to thrive. And this is a big problem that we're only now beginning to really understand.
So, you know, you talked a little bit about quantity. Like, you used the word wrong quantity when you were talking. Are you a fan of giving the gut a break every now and again? Because I've seen this written in some books and kind of spread around the Internet a little bit in the form of fasting and things of that nature. Do you find that when it comes to repairing the gut, just whether or not you're eating healthy food, giving it a little bit of a break now and again with some kind of a fasting protocol helps, or do you find that that's more stressful to people?
The thing is this. We talk about two things. One is the maintenance of a healthy gut, and the other thing is the repair of an unhealthy gut. So think about the maintenance of a healthy gut, right? We have evolved through thousands and thousands of years. And for thousands and thousands of years, men, humans did not have food available all the time. They were like the rest of the animals. They found food, they consumed it, and then they went on to find the next food. And they didn't have fridges and things like that. So there were periods of feasting and periods of impulse fasting. So people didn't used to eat as much. Their guts were resting by default, by design. They were not eating breakfast, lunch, and dinner and snacks and things like that. So it's been only recently in our evolution that we have food available 24, 7, and we are eating it 24 7. So just for maintenance of a healthy gut, I believe in. In resting the gut, but for repair. There's no question in my mind that resting the gut is important. Just like resting any organ that needs to be repaired is important. If you break a bone, you got to rest it. That's why you cast it and you don't move it as much, because you have to give biology the chance to repair. And the repair needs resting of whatever it is that is being repaired. So definitely, resting the gut is an important issue both for maintenance of a healthy gut and definitely more even so, for repair of an unhealthy one.
Yeah, yeah. I gotta tell you, I talk to so many triathletes and marathoners and crossfitters and people who are eating 3, 4, 5,000 calories a day, and it's all healthy food. They have gut issues. And I think a big part of it is there's just A lot of strain on the gut digesting all that food. Now you talk about the four Rs of the clean gut program in your book. What are the four Rs?
Well, those are the pillars of the repair, right? So the first R is removed to remove all the negative influences, the negative conditions for repair to happen. One of the main aspects of the remove pillar is removing the bad bacteria and yeast and parasites or whatever organisms may be in the gut. But there's also the removal of other conditions like acidity and things like that, and removing the exposure to toxic chemicals. The second R is re inoculation. That is about reintroducing, replanting, re inoculating the good bacteria. The third R is repair. So in the repair process, the body will need an extra amount of raw materials. You mentioned L glutamine, for example. And that is the best example of what the repair aspect will need. So you will have to take extra glutamine and other things that promote the repair. So remove, reinoculate, repair, and then restore. And then restore is about restoring the right conditions and restoring the rest of the right nutrients that the body needs in order to do its work.
Yeah, I thought that entire section was interesting. And again, I'm going to recommend that folks read your book to dig into that a little bit more. Go ahead.
And then there is another R, which is a fifth R, which I didn't include specifically in the gut repair aspect of the book, but it's an important R for. For most aspects of our life, which is relaxation. We are a nation or a world, if you will, of stressed people. And relaxation is now undisputable in terms of the effect it has in all aspects of our functioning. Not only a physical, but mental and emotional and spiritual.
You know, thatthat kinda makes me think. You Talked about how 90% of your serotonin neurotransmitter, which is, you know, essential to mood regulation, is made in your gut. I would imagine that because of that gut brain link that it goes the other way too. Like if you're stressed out mentally by something going on in your life, that it would directly affect gut function. Are all those nerve pathways kind of going both ways?
Absolutely. Listen, everything is connected and one thing affects the other, and you don't really know which one is first. But if you focus, because a lot of people that are not relaxed find it very difficult, you tell them, yeah, relax. And then how do I do that? And that may be because of the lack of serotonin, in part. So if you just Begin by focusing on your gut and repairing your gut. You will eventually be able to relax more and learn to relax more. But it can work the other way too. Somebody that eats completely healthy and rests their gut and whatnot, if they have a very stressful existence, it eventually will end up affecting your gut as well.
You know, it's interesting. Have you ever heard of the heart brain connection? Yes, it seems.
I not only heard of the heart brain connection, I experience myself.
Yeah, because it's interesting because like if you're stressed out, it affects your heartbeat. But then if you, you know, I do heart rate variability training and I find that if I use certain techniques that I've learned to adjust my heart rate variability, that that automatically adjusts the way that I feel in my brain as far as stress goes. And it's so interesting how we have these, these two way paths in our body that are so interdependent on each other. It's really fascinating.
Listen, you, you, you call it, you call it heart rate variability and, and it sounds intelligent and important, but we can really boil it down to a much simpler way of explaining, which is you get nervous, your heart rate goes up, right? You can feel it when you get angry, you can feel your heart racing. And a simple explanation is when you are stressed, which is basically your fight or flight systems activating, even if there is no danger, even if the danger is in your head, your body will react as if there is danger and it will pump adrenaline and noradrenaline and that will make your heart go up and your blood pressure go up and everything else? Yep.
Running from the lion, running from the bear. It's something we all do too much of. Now you've got kind of a cleanse, kind of like a detox kind of protocol in your book. How is what you recommend any different than like all these other detoxes and cleanses that you're gonna find all over the place, you know, like on the Internet or in other books and magazines and stuff like that.
Listen, the thing is you gotta see where, you gotta see where the cleanse is coming from, who put it together, what's their experience, what is it that they understand? I'm a doctor. I've been studying medicine for the last 20 years. I've been seeing patients for 20 years. And I understand biological process, disease processes. And with that understanding, I came into the world of cleansing and detoxification. And then through functional medicine also, I really got into the nitty gritty of how these things affect your health biochemically, physiologically, so my program was created from that experience, but even more from trying it myself because of the need to heal. You know, if you talk about there's cleanses out there that are designed or started by actors or movie stars, and I ask myself what is their experience? And many of them are based on thousand year old techniques like fasting and things like that. But the times are different now. So you can't come up with a cleansing and detox technique that was created 5,000 years ago and apply it to modern day life and expect that it works fine. So my cleanse is designed through research, through trial and error, through study, to really be used by people that are living in the modern world today with the problems that are affecting us today. That is how my cleanse is different from most of them out there.
Now, do you have on your website kind of like a sample of some of the things that go into your cleanse if people wanted to check that out?
We have tons of information. You can go to our website. The whole protocol is explained, recipes are given. We have a web community which is kind of like the Facebook of cleansing and detoxification. At the Moment we have 57,000 plus people, people from all over the world that are doing the program right now. I mean, not the 57,000, but there's thousands that are doing it right now. And they're blogging daily about their experience and asking questions. And not only my team and myself answer these questions, but other people answer. And this is the power that is created in numbers because I learn a lot from the people that I do. Everybody searching, everybody is researching and people find things that I never even heard about. And that's how things evolve. We're constantly changing and improving our program in order to keep up with everything that we are finding out and improving around there.
Now I want to throw a few kind of rapid fire questions at you real quick to give people some good places to start. Let's say you're going to the average grocery store and you want to pick one thing that you know, like one real food that's going to be really soothing and really restorative and really help to heal the gut. And you're walking through the grocery store with your shopping cart. What's one thing that you could grab and throw into your shopping cart that right away is going to be good for your gut?
Kale. Green leafy vegetables. Those are the royal family of healthy foods. And kale is king in this royal family.
So the fiber and stuff in kale doesn't hurt your gut. In terms of being disruptive to your small intestine lining or anything like that.
Yeah. And it contains a lot of nutrients that are soothing to the body and, and calm down the immune system and help repair the gut. But listen, your question is a little bit crazy, if you will. It's like me asking you, if you're walking around Home Depot and you're trying to build a house, what's one thing that you can pick up that's going to be important? And listen, light bulbs are important. Water pipes are important. Everything is important. Because if one thing is not working, then nothing else is working. So your question is kind of like a little bit misleading. There's not one thing that you can. That you can use. There's tons of things that have to be used in combination. To answer your question in a more practical way, this is what I would say. If you look at a supermarket with a bird's eye view today, you will see that 90% of the products that are being sold that people are consuming daily come in a box, in a jar, in a can, in a tube, in a bag. Avoid those. It's more important today to know what not to eat than to know what to eat. So you go to the supermarket, stay on the sides where the vegetables and fruits are and where the fish and the chicken is, and make sure that you go to a supermarket that uses products. I mean, that buys produce that is not chemically affected, like pesticides and insecticides and fish that are from farms that eat all kinds of garbage and meat that are from cows that never saw the light of the day and that are fed unnaturally and given hormones and antibiotics and things like that. The best practical advice I can give anybody when they go to the supermarket is staying on the back and the sides of the supermarket where the fresh things are.
Yeah, well, I can tell you by thumbing through the recipes in your book. I don't know if this gives people a little bit of a roadmap, but I can certainly tell you three things appear quite a bit, and that's garlic, ginger and lemon. I'm seeing those pop up a lot in your recipes. So I'm assuming you approve of all three of those as being gut healthy compounds.
Well, listen, we can go one by one. Lemon, for example, it's a great natural antimicrobial that targets mostly the bad bacteria. It also alkalinizes your blood, even though it's citric acid. And we know that oranges and other citrus plants acidify your blood. Lemon has the opposite effect. And it Alkalinizes your blood. So those are two things that, right off the bat, are going to help with gut repair. You mentioned also garlic and ginger. The same thing with garlic, kills parasites, kills bad bacteria, and promotes all kinds of healthy processes in the body.
Now, how about, and we've obviously kind of name dropped a few supplements like glutamine and probiotics and stuff like that, but how about a supplement that perhaps flies under the radar when it comes to being something that's healthy for the gut that a lot of people aren't aware of? Because, frankly, I think a lot of people hear about probiotics and digestive enzymes and things of that nature. But is there something that you've found that a lot of people aren't aware of when it comes to, like a supplement that seems to be helpful for gut issues?
Magnesium? Magnesium, Yeah. I find that, first of all, we are a nation of people that are depleted on magnesium because our soils are depleted, our foods are depleted of magnesium, and magnesium is already hard to absorb. When everything is healthy and you're eating the right amounts, you only absorb 10% of the magnesium that you ingest anyway. So when the gut is unhealthy and you're eating less of it, imagine the depletion of magnesium that occurs. And magnesium is very important in many, many aspects. And one of the aspects in which it's important is because it's used in the stabilization of membranes, of electrically conducting membranes in the body, and everything is electrically happening in the body. A cell is alive because it maintains an electrical charge between the inside and the outside of the cell. When that electrical charge goes off, then the cell dies. Brain activities. When doctors tell you you are brain dead, it's because your brain is not producing electrical activity, so everything is electricity. And magnesium is one of the things that stabilizes the electrical membranes. And we have so many electrical membranes around the gut itself in the rest of the body, of course. But magnesium is a really important nutrient that a lot of people are not aware that they're lacking, and that could be really beneficial to them.
Are you a fan of a particular form of magnesium, like glycinate or citrate or something like that?
Well, I'm a fan of what works. And for different people, different things work because some people take magnesium citrate and they get diarrhea, so they can't really do that. So they would need to take a different form of magnesium. Right. So you got to try a couple of forms and see what works for you.
Interesting, interesting. I tried one form called oxygenated magnesium. I forget what brand it was, but definitely cleaned me out the next day. I'll say that.
Yeah. And there's all kinds of new developments, like many nutrients that are now given in colloidal form, which is more highly absorbable. So as the time goes by, we go finding out what works better, and different options are available.
Got it. So let's finish with this. Let's say that someone wanted to know what a sample day of nice, clean eating for their gut was going to look like. Like, what are they going to eat for breakfast, for lunch, for dinner, and maybe what's kind of a safe snack? If maybe they're having some gut issues right now and they want to see if things change, Maybe if they throw in a few days of clean eating. Can you give people kind of an idea of what a decent breakfast, lunch, and dinner might be?
Yeah. Again, I want to stress the first point that I made that today it's more important to know what not to eat than to know what to eat. So if you only avoid certain things, you are already going to be promoting gut repair and the repair of many other things, and that is the gut diet. And so avoiding certain things like coffee, alcohol, sugar, grains, dairy products and things like that, avoiding those already puts you in a better position than you were in. So let's say you don't listen to what I'm going to say next about the example of a healthy day in a gut repair program. Just avoiding those things is a great start. But the way that I do it is, first of all, we talked about giving the body a rest and giving the gut a rest more specifically. So one of the things, one of the principles that we promote is substituting a meal or two a day for a liquid meal. So substitute a solid meal for a liquid meal. Best one to do, and the easiest one to do is breakfast. So I have breakfast with a shake, and I put people that are on the gut repair program on a liquid meal for breakfast. And a shake can contain lots of things. For example, with the base of plant protein powder, you can do all kinds of things. You can add certain fruits. You can add coconut milk, you can add coconut water. Sometimes I add bee pollen. There are so many ingredients that you can put in that are healthy that the list is long. But breakfast with a shake is great. For lunch, I usually put people on a salad and some kind of protein like fish or chicken. And for dinner, if you are in intense repair mode, then another shake would be great. Or a liquid meal like a soup and if not a big salad for dinner. That is what is going to be the best option for people that are doing a gut repair program.
It's good to know.
And then you can. And then you can snack a little bit during the day. You can have some berries. You can have many of the things that are on the allowed list of foods you can snack. Because the reality is that people are busy and they're going around and they feel hungry and they need to have a snack in order to be able to comply with the rest of the program.
Yeah, well, I'm a big smoothie fan, so you got me there. That's my go to every morning. It's my second stomach. My blender.
That's a good way to put it. Do you have a Vitamix?
The one I have is called an Omni Blender, but it's pretty much the same engine as a Vitamix.
Cool.
Yeah, it's good stuff. Your book is Clean Gut, and it was actually, I got to tell you, pretty easy to read. Like, it wasn't difficult to get through. I think a lot of these books like this, for the average person, they just. They're almost like, intimidating because there's just so much information. It's pretty simple. You just lay out how the gut breaks, what you can do about it, and then a bunch of meals and recipes and supplements and kind of like your sample kind of cleanse detox.
Yeah. And I also wrote it in the first form of a story, which is really the story of how I found these things and how they affected my patients, because people relate to stories and are easy to get through.
Yeah. Cool. Well, I like it. I'm going to put a link to it in the show notes for this episode over@BenGreenfieldFitness.com and folks can check it out. It's called Clean Gut. And you could also check out the website, too, which has a bunch of resources on it over@cleangut.com so, Dr. Junger, thanks for coming on the call today and sharing this stuff with us.
My pleasure. Thank you for having me.
All right, folks, it's Ben Greenfield and Dr. Alejandro Junger from Clean Gut signing out.
Visit BenGreenfieldFitness.com for even more cutting edge fitness, nutrition, and performance advice. It.
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