How Obesity Affects the Microbiome - with Dr. Gerard Mullin | The Empowering Neurologist EP. 2

In this interview, Dr. David Perlmutter talks with Dr. Gerard Mullin, an associate professor of medicine at Johns Hopkins, about the central role of the gut microbiome in obesity, metabolic health, and systemic disease. Dr. Mullin explains how the gut acts as a hub connecting the brain, liver, kidneys, and cardiovascular system, and how modern lifestyle factors—Western diet, excessive antibiotics (including those used in livestock), proton‑pump inhibitors, NSAIDs, artificial sweeteners, and genetically modified foods—disrupt microbial diversity, increase gut permeability, and trigger chronic inflammation. The conversation details the cascade from dysbiosis to leaky gut, systemic inflammation, and conditions such as obesity, type‑2 diabetes, autoimmune disease, and cardiovascular disease. Practical strategies are offered: eliminating pro‑inflammatory foods (gluten, dairy, refined sugars), adopting a high‑protein, vegetable‑rich, mildly ketogenic diet, and re‑introducing prebiotic (asparagus, Jerusalem artichoke, bananas) and probiotic foods (goat kefir, yogurt, sauerkraut, miso). Dr. Mullin also discusses the limited reliability of over‑the‑counter probiotic supplements, the importance of gut‑derived metabolites in immune regulation, and future directions including outcome studies, fecal‑transplant technologies, and deeper investigation of GMOs and herbicide residues. The interview concludes with a call to view the microbiome as an actionable target for weight loss and overall health.
Chapters
Hello, I'm Dr. David Perlmutter. Today I'm really looking forward to our discussion with Dr. Gerard Mullen. Dr. Mullen is Associate Professor of Medicine at the Johns Hopkins Hospital. He is board certified in internal medicine, also gastroenterology, integrative medicine, and functional medicine. Dr. Mullen will bring to our discussion over 20 years of clinical experience. And just keep in mind, he is the author of 9 books. His most recent book is The Gut Balance Revolution that really begins to explore this incredible topic of the role of the microbiome in terms of health. And as Dr. Mullen will be telling us, how critical it is to pay attention to our gut bacteria as it relates to maintaining proper body weight and even losing weight. So let's get right to our discussion. Hello, Dr. Mullen. Thank you for joining us today. We've got a lot of questions for you, a lot of information that I'm really anxious to have you impart. And first, I'd like for our viewers to just get a sense as to what it's like for you as a gastroenterologist at Johns Hopkins, though a gastroenterologist who is embracing this really fundamental role of the microbiome. How is it for you in terms of your relationship with your colleagues?
Thank you for asking. The— 2 years ago, Dean Rothman, who recently took over for Ed Miller at the School of Medicine as dean, put together a microbiome workgroup. He identified a number of people working with, in collaboration, with a psychiatrist, Glenn Treisman, and also Cindy Sears, who's a C. diff infectious disease expert, put together a collaborative working group that's turned into a weekly journal club, and put together all the basic and clinical research interests, and tried to, you know, pool resources. And so there's a very strong interest at Hopkins about the microbiome and its relationship to health and well-being. This may be the first trade book that's come out about this from, you know, my work group. We're talking about perhaps a textbook at this point in time, was contacted by a publisher to do so. But otherwise, I think this is a good group of people who really respect the science. As I had really well referenced, you know, Gut Balance Revolution, as your book is strongly referenced, And I think here it's a matter of they're not so used to a doc talking, speaking to the trade.
But it does seem as if you're in a very lucky situation that you're getting a lot of support from your— the people that you're working with. And, you know, certainly we see that at least in the community approach to gastroenterology, there seems to be obviously less interest in the role of the gut bacteria in terms of health. And this goes beyond gut health, doesn't it?
Yes. And, you know, I think to echo what you're saying about Hopkins is that because I'm coming from a very evidence-based scientific rubric with, you know, I think that delivery from an academic is respected. And I think that at this point, you know, it's been a very good relationship in terms of how, you know, my work and being in the process of being promoted to full professor That, you know, that doesn't happen, you know, every day here. And you have to have really an international reputation and, you know, good work to do that. So thank you for, you know, bringing that up. And, you know, I'm really excited to address that.
But to be sure, your focus on the microbiome has wide-ranging implications. And I think, yes, for our viewers, that might be an area I'd like to explore a little bit. I mean, here you are, a gastroenterologist, but the implications of what you're saying in your new book with regards to the rest of the body, I think, are really profound.
They're incredibly profound in that really the gut is one of the controlling influencers of the body and that there are axes between the gut and the brain, the gut and the liver, gut and the kidney, and other body systems. Circulation, cardiovascular. The gut really is one of the really key players and drivers of the body's health. And that research has really exploded in the last 5 years and its linkage with diabetes and autoimmune disease and even prediabetes and all these conditions, brain disorders, behavioral disorders. It seems like you name it, all start in the gut. So the gut itself has to be integral to our knowledge and in our, you know, our way of dealing with health.
You mean to say that different parts of the body are connected? In this case, the gut is playing a role in the health of the rest of the body. Who knew?
Right, right, right, right, right.
One of the central themes of your book really is, you know, the microbiome and the role of the microbiome. So what are we doing these days that is threatening the health of our gut bacteria?
Well, unfortunately, what we're doing is polluting this otherwise biodiverse ecosystem with junk. And that junk means food, or what I'd rather call ingestibles, which really is the standard American Western diet of pro-inflammatory fats and, you know, sugary foods, refined, quote unquote, grains. All these things shift the biome in a very adverse way. And on top of that, we're really overdosing ourselves with antibiotics. We're giving it to our children indiscriminately. Studies show in predictive behavior, the more antibiotics you have as a child, the more likely you'll be obese later on. Antibiotics in our meats at enough levels to cause obesity in experimental animals. So we're really doing immeasurable harm to our gut biodiversity, and we're reaping the consequences.
You were just alluding to antibiotics in— actually in our food. And what can you tell us about that? I know that Dr. Blaser has talked about that in Missing Microbes, but you get into that a little bit more deeply. What is the implication of the fact that 70% of the antibiotics used in America are actually going into raising cattle that we will then consume?
It's interesting to use the word raising. It's kind of really fattening them up for commercial, you know, for commercial reasons and
for profit.
For profit, purely for profit. You know, since the '40s and '50s, they really, really delved into antibiotics, and they're creating superbugs, meaning that we have C. difficile epidemics that we don't know how to handle. And there's enough in our meats that in so You would think minuscule amounts that— what Marty Blaser did was he— and Dr. Cho— is that he actually took that amount of antibiotic levels in meats that we consume and was able in animal models to give obesity to otherwise rats that were lean. You think it's so little, it's enough to make someone fat. So that's profound.
So in other words, antibiotics are given to cattle to make them fat. So it's not that far of a reach to think that the same mechanism may be happening in humans, and particularly in children.
Oh yes, in fact, I mean, if you look at the cattle's microbiome, it's disrupted, but it's disrupted by design, and it disrupts our microbiome, and it can have lasting consequences. There's been studies where a 7-day course of Clinda can last up to 2 years. And disrupting the microbiome. So it can have a lasting effect.
And again, for our viewers, Clinda, you're talking about clindamycin.
Yes, clindamycin.
Now, what then can we do if we've jeopardized our microbiome? Well, let's stay with that topic for just one more moment. Aside from antibiotics, what other medications are out there that people may be using that might be threatening the health of their microbiome?
Well, one of my favorites to discuss is called the proton pump inhibitors. Now, that's a class of medications that are very strong suppressors of stomach acid, and we need stomach acid to really kill the bacteria in our upper GI tract to keep it sterile. But when you do not have stomach acid in the setting of taking those kind of medications, Then what happens is that you start to colonize your upper gut with bacteria that do not belong there, and particularly in large quantities. And that condition is called small intestinal bacterial overgrowth. And that can wreak havoc throughout your body, systemic inflammation, endotoxemia. And the bottom line is that taking those medications, it can disrupt the microbiome. And that, in fact, could be one of the reasons why we're seeing so much obesity is because The PPIs are always amongst the top 3 classes of medications that are sold in the US since the year 2000.
So just to be clear, what you're saying is this overusage of these acid-blocking drugs that everybody is buying over the counter because they have acid indigestion or reflux or whatever you want to call it are changing the microbiome, and you're saying that this may have a strong role to play in terms of making people fat.
Yes, and furthermore, they found that these PPIs actually induce the symptoms that they are trying to treat.
In other words, we need stomach acid.
We need stomach acid, yeah, but also when you give a normal person who's healthy a PPI, you can induce symptoms that many docs try to treat those symptoms by giving a PPI, meaning that we're really overprescribing them like the antibiotics, and they are both You know, one-two punch to really hurting our microbiome.
Another class of drugs that is certainly so popular now are the nonsteroidal anti-inflammatories. What is their effect in this scheme that we're talking about?
Well, here's another class. Thank you for bringing it up, is that they are injurious to our gut lining. And unfortunately, in the setting of dysbiosis, or this disruption in the microbiome, is that that allows their toxins to disseminate through the body in the model that many call leaky gut.
So in other words, where we— where you've taken us now is to the actual lining of the gut. And when that breaks down and the gut wall becomes leaky or more permeable, that does what? I mean, we know it increases inflammation. How does that work?
So what's happening is that as the gut integrity breaks down, The toxins from the bacteria become broadcasted in the circulation, and then an inflammatory cascade ensues, which generally becomes chronic and also causes disruption in many, many metabolic functions.
And are there changes that happen to gut bacteria that can also enhance leakiness of the gut?
That's a very good question, because let's say in that setting of that small bowel overgrowth, that we were discussing is that what happens is that their bacterial byproducts break down the gut barrier directly, and also indirectly through inflammation. And once those junctions become loosened, then their byproducts become broadcasted. So yes, those bacteria can actually break down the barrier too.
And when that barrier is broken down, then you induce inflammation in the body, What sorts of things, what kinds of disease processes may be implicated by this inflammation?
The spectrum is quite large. For example, cardiovascular disease, arthritis, autoimmune disease, diabetes, prediabetes. All these bad actors are really tied into chronic inflammation and gut dysbiosis. And a disruption in the barrier may be very, you know, permissive in allowing this all to happen.
And clearly, the type of diet that we're focused on in Western cultures is a diet that does tend to lead to this change in the diversity of the bacteria and ultimately the gut permeability. So what's the good news here? What do we do?
Well, first, we recognize the bad actors. And understand that unfortunately in our culture in today's day and age with the pharmaceuticals being so widespread and the food or ingestibles being so poor that I think we got to just kind of reset ourselves by restricting if not eliminating these toxic injurious agents and allowing our bodies to kind of rebuild and renew and kind of shepherd along the gut to really rebuild and the lining to regenerate, and also the microbiome to be rebalanced.
So, I mean, you've been known to lecture on making food the first choice. So what do we do in terms of our food choices? What do we avoid? And then what do we favor to allow us to push the reset button on our gut bacteria?
Terrific. So first, we try to cut off the supply of those bad bugs, right? So, and those that are pro-inflammatory, and those that certainly can spike our blood sugar. So, I tend to restrict the foods that are more gluten-rich, the ones that some dairy is not well tolerated. They're rich in lactose, and it's a fermentable food that many cannot tolerate. So, I restrict that and cut back on the dairy. Certainly, the gluten and the sugary foods are on the high end of the list. And what I try to do is transition people into a more higher protein, a vegetable-rich diet so they can actually start burning fat and have mild ketosis. And then once we kind of weed out those bad bugs and get the biodiversity amplified, then we start to do a rescue regimen where we start to give prebiotic foods as fertilizer and probiotic cultured foods to start putting in back the good healthy gut microbiome.
So let me go back for a moment. I think you mentioned gluten as being threatening to the gut bacteria and the integrity of the gut lining. I seem to have heard that said before. What brings you to that conclusion?
Aside from hearing it from you for many years, but our mutual friend Alessio Fasano, his research has been quite revolutionary. And I've been personally, you know, a friend of his for many years, seeing him lecture We were just out together in Salerno last month at this gut-brain conference. And really, the driving force is that gluten may be the initiator of a lot of what we see in autoimmunity by disrupting this integrity of the tight junctions that we see and loosening these barriers by working on this protein called zonulin-1. And by dysregulating zonulin-1, Then you're allowing these barriers to become loosened, and the endotoxemia and inflammation ensue. And once you have the right genetics, that could become a disaster, and you have the beginnings of autoimmunity, which, you know, I mean, it's at like 50 million, and years ago when I wrote my first book, The Inside Tracker, it was at 20 million, the prevalence. So we're seeing a lot of autoimmune disease.
And more and more every year. 17% of Americans now are diagnosed with an autoimmune condition.
Oh.
Whereas in the rest of the world, that statistic is really 7% up to 10%. So it isn't something genetic. It is certainly something that's environmental. The upside of that means, being environmental, we can change it. And you're all about that. And there's a nice chunk of your book that really is very wonderful to read because those are real people, real patients of yours who've had such dramatic improvements in their lives. And you do focus a lot on weight loss. So I'd like if you just could take us through what is a mechanism here that relates changes, the maladaptive changes in the gut bacteria, to people not being able to lose weight.
See, what happens is that on this type of program, people who have gut dysbiosis have a number of pathophysiological issues that are going on. One is inflammation that we've been talking about through membrane integrity. Gut hormones are dysregulated, appetite is dysregulated, right? Insulin sensitivity is dysregulated. So you have all these fundamental physiologies, physiologic issues that relate to weight and metabolism. And what happens is that as we reset the microbiome in the gut and rebalance it, and it becomes more healthy and biodiverse, The appetite shifts. People are less hungry. People feel great. The energy goes up because there's less inflammation. That's one of the first things we see on this program before weight loss is people feel revived. Inflammation starts to go down. So this is the— this is the approach to really healthily lose weight and not go into a crash diet, which ultimately fails.
Yeah, you know, I have to say that we all see patients who are failing on their diets. They're on this diet, that diet. They bring in their food, the list of the foods they've been eating, and they weigh their foods, etc., and they can't seem to lose weight. And I think what you've uncovered here in your new book, what you've uncovered in your clinical work and described in the new book, is this is the missing link. And then really, as we've experienced as well, Until you pay attention to revamping your gut bacteria, you may have a tough time in finally gaining control over your weight. What about artificial sweeteners?
Well, yes, the artificial sweeteners are disruptors. They disrupt the microbiome tremendously. And a study came out in the spring, early spring, showing that the aspartame itself can lead to diabetes. Here we are, giving NutraSweet to avoid diabetes, right, instead of sugar. And yet we are actually giving people diabetes because we're disrupting the microbiome. And we're misleading people, unfortunately, down the road to perdition with these artificial sweeteners, as we are with these PPIs.
And so here people say, I'm stopping the sugar-sweetened beverages because I've heard that they're bad. And they opt for the diet this or that, and they've actually doubled their risk for type 2 diabetes. And according to the study you quoted, it's thought now to represent a change in the microbiome that makes that happen. So, so what do we eat? What's, for example, you know, one of the toughest questions I always get is, well, one is, what do I do when I travel? And it's always compelling, but what do we do for breakfast is always a real difficult question. How do we start the day?
So let me tell you how I, when I travel, I drive people nuts to make sure I get the right food. To eat. And, you know, it's quite challenging. But the breakfast thing, what I try to do is have a very good breakfast regimen that'll just reboot my microbiome on a morning basis that's loaded with protein. So, I'll have a mixture of, let's say, goat kefir, some goat yogurt, obviously both organic, blueberries, raspberries, and then a mixture of chia and flax and a little cocoa, because dark chocolate is one of those superfoods that are just having profound health benefits. So it kind of spices that up a little bit, maybe a little cinnamon. And that's really a breakfast of champions.
And you have also talked in your book a lot about prebiotic foods. What does that mean?
These are the foods that actually selectively help the good and friendly bacteria grow. And one benchmark for that scientifically is the species Bifidobacterium. So if you have asparagus, and you have Jerusalem artichoke and banana, these foods have been shown to selectively stimulate the growth of the bifidobacteria, and not the pathogenic bacteria that we want to keep under wraps.
And is all fiber that you might get wherever— is that the same as what you're talking about?
Well, soluble fiber is good to build up your microbiome. There's a lot of prebiotic soluble fibers on the market. But the foods that I try to concentrate on people is those that are more of the prebiotic kind. As I mentioned, asparagus is another really great example of a food that'll do that. But for me, any of the fruits and vegetables will help establish a healthy biome. And I think that's the important thing to have people focus on.
I know there's a question that has many of our viewers on the edge of their seats and trying to figure out what they should be doing. What are your thoughts on the use of the oral probiotics that you'll find at the health food store or even at the grocery store these days?
Well, you know, probiotics do work for some people. I mean, as Forrest Gump once said, it's like a box of chocolates. You just never know what you're going to get in these bottles. So, you know, some will have good bacteria to a large degree and others not. There's been studies showing there's variability in the strength Yeah. Of the probiotics can vary widely. There's very little regulation. But I'm like you, David. I'm a food-for-medicine guy. I try to rebuild the biome by really good foods, like kefir is loaded with good cultures, and also homemade yogurt. Those 2 are, like, amongst the best ways to get in your good bacteria. But the days of sauerkraut are kind of forgotten, and pickles, and The fermented foods are kind of like— people don't eat them like they used to, but they're out there. Miso soup. Yeah.
Now, we do know that the good gut bacteria are manufacturing various things that have a role to play in keeping us healthy. Can you comment on that a little bit?
Here's the thing. You know, our health really depends on a number of factors. And the gut itself, I think one of the key things that it does is prevent inflammation, control inflammation. So, the good gut bacteria, these probiotic bugs, they regulate our immune system and they control inflammation. And a lot of the degenerative diseases that we've been speaking about, the autoimmune diseases, the chronic arthritis— I mean, the people in America, over half the people in this country have a Chronic disease, and inflammation is the root cause. And these good bacteria, one of their main roles is to balance immunity and prevent inflammation. So those are the ways that I try to actually counsel patients, and they really connect with that type of thinking.
And when you talk about inflammation and immunity, you're throwing, as I mentioned, a wide net for coronary artery disease, type 2 diabetes, And even cancer to some degree. Absolutely. So, you know, when we look at the implications of keeping the gut bacteria healthy, or the implications of what happens when we have what's called dysbiosis, or changes in the balance of the gut bacteria, the exciting news that you really bring to our attention in your new book is that we can be active players in this. So where do you think this science is going to go, let's say, the next 5 years?
I think we're going to look at more outcome studies of balancing the biome and preventing and mitigating and treating disease. I think we're going to see much more of that. You're going to see studies of people try to do engineering experiments. You'll see fecal transplant technologies being pursued. I think people will start doing that kind of science, which is still more magic bullet medicine. I think we've got to take a look in terms of naturally rebalancing the biome. Let
me, if I can, touch on a subject of GMO. I think I'd love to hear your opinion. I know our viewers would like to hear your opinion about genetically modified foods. What are your thoughts?
Yes, genetically modified foods, 90% of them, the gluten-rich products that we see are genetically modified, and soy and corn. The problem with them are twofold. One, certainly the GMOs, the problem there with Roundup being the herbicide was not designed really to be an herbicide. It was meant to be a cleaner, a can cleaner. So, it's really toxic and there's residual Roundup in your foods even though it's supposed to be very light. It's still measurable and enough to disrupt the gut microbiome. at least in animals. And finally, it was labeled by the WHO as being a pro-carcinogen. So, I am like— I counsel my patients to stay away from them as much as possible because it's like one of those things that, like tobacco was for so many years, is that people would deny there was a health problem, and then they would take this aggressive stand against people who, you know, like our friend Mehmet Oz, who would say something against GMOs, they would get attacked. It's the same mantra. I mean, they are harmful, and I'd like to see more research along those lines too with GMOs.
All Dr. Oz said was that we as Americans have the right to know whether our food is GMO or not, and then we have the right to be able to choose. That's all he said. I would completely agree with that. Well, let me— Dr. Mullen, thank you for sharing this really valuable information with us. For our viewers, You stick, stay with me a few more moments. I'm going to give you all the information you need to learn about Dr. Mullen's new book. But again, thank you, and I'm hoping that we get a chance to speak soon.
Thank you. Same here.
Okay, we'll talk soon. Bye-bye. That was a wonderful discussion. Dr. Mullen has so much actionable information, and what I mean by that is really so we get the understanding of the microbiome in terms of its role in keeping us healthy, helping us maintain a normal body weight. But Dr. Mullen gives us the tools in terms of what we can do to make that happen, how we preserve our gut bacteria in the first place, and then what we can do to rehabilitate it if in fact it's been altered or traumatized. His book, The Gut Balance Revolution, I strongly recommend that you consider reading this book. Again, what's so great about this book is it is actionable, meaning it's going to give you tools to make changes in your lifestyle, specifically in your diet, that can bring about rejuvenation of your gut bacteria and pave the way for health. Thanks for watching. I'm Dr. David Perlmutter.
More from David

Newsflash: Alzheimer’s Is Not Caused by What We Thought | Dr. David Perlmutter









