It this episode of Functional Medicine Research, I interview Dr. Lucy Mailing in a discussion about the best diet for your gut microbiome. We had a fascinating discussion focused on all of the different diets out there and how they affect the gut microbiome including the ketogenic diet, plant-based diets, high-fat, low FODMAP, and the autoimmune paleo diet.
We also talked about fiber, protein, hydrogen sulfide, resistant starch, butyrate, gluten, lectins, stool testing, and whether or not you should take probiotics after taking antibiotics. I think you'll find this conversation quite eye-opening about a number of exciting topics related to the gut micobiome.
Below is a transcript on the best diet for your gut micobiome:
Dr. Hedberg: Well, welcome, everyone to "Functional Medicine Research". I'm Dr. Hedberg and I'm really looking forward to my conversation today with Dr. Lucy Mailing, PhD. She is a microbiome researcher, educator and passionate scholar of integrative, evidence-based gut health. Lucy received her bachelors in biology from Kalamazoo College and her PhD in nutritional sciences from the University of Illinois where her graduate research focused on the impact of diet and exercise on the gut microbiota. She has authored numerous peer reviewed journal articles, regularly presents at national, international conferences and was named an emerging leader in nutritional sciences by the American Society for Nutrition in 2017. Lucy is the founder and sole author of lucymailing.com, a website dedicated to integrative, evidence-based articles about the gut microbiome, health and nutrition science.
Dr. Mailing, welcome to the show.
Dr. Mailing: Thanks so much for having me.
Dr. Hedberg: Great. So you've done some great writing and research on some topics that a lot of people are interested in. That's why I wanted to have you on. So why don't we begin by really focusing on diet and the gut microbiota and what the research is really showing at this point? So why don't we start with one of the very popular diets out there which is the ketogenic diet and we can kind of lump in just the high-fat diet in general with that. So what can you tell us about high-fat diets, ketogenic diets and how it affects the gut microbiota?
Dr. Mailing: Sure, yeah. That's a great place to start. I think one of the key things to keep in mind here is that we're still in the infancy of microbiome research and especially in our understanding of what constitutes a healthy microbiome. And we have certainly done a number of studies looking at how diet can impact the microbiome. A lot of this has been done in animal models where we can essentially really control the diet of the animals and determine what effects that has on their microbiome. So a lot of the studies with the high-fat diet in the literature are kind of misleading because they're labeled as a high-fat diet but they're really more accurately a diet that is very high in refined fats and also high in refined sugar and low in fiber. So we can't really take that and compare it to the equivalent of a very healthy, like a health-conscious ketogenic diet that's got lots of non-starchy vegetables, healthy fats. There's just really not much comparison we can make there.
And the other thing is that the gut microbiome has really evolved with us, often in the context of periodic ketosis. So if we think about human evolution, we've been coevolving with our gut microbiome for thousands of generations. And the environment we evolved in required regular adaptation to changing conditions. When there was nutrient scarcity or even just carbohydrate scarcity, our metabolism would shift to reflect what was available in our environment to consume.
And so we have that metabolic flexibility in our host genome, right. As humans, we have the ability to metabolize carbs or metabolize fats in periods of carbohydrate scarcity. So the real question is why would our bodies not have this...why would our bodies have this metabolic flexibility to deal with the shifting availability of foods and our gut microbiome not also have that same metabolic flexibility and ability to be healthy even when carbohydrates are scarce?
Dr. Hedberg: Interesting. You brought up a really great point about some of these research papers that, you know...the media's guilty of this and different websites and things like that where they'll post a kind of really catchy tagline about this diet does this and this diet does that and it's just focusing on one variable like fat, but they fail to discuss all the other factors in the diet of those individuals. Like you said, what is the quality of the carbohydrates, the fat, the protein, the sugar intake and then everything else in someone's life? You know, how much are they exercising? Do they smoke? Do they drink alcohol? And things like that. Do you see any good science out there where they take those considerations into account?
Dr. Mailing: Yeah, definitely. There have been quite a few studies actually now on ketogenic diet and how it impacts the human gut microbiome where they're using a relatively healthy ketogenic diet and generally controlling for all those other variables or at least including them in their analyses. And so for example, in 2014, there was a study by Dr. Peter Turnbaugh's group at UCSF where they essentially put healthy human volunteers on a short-term plant-based diet or an animal-based ketogenic diet. You know, just for five days but they found that there were distinct gut microbial communities that emerged within as little as three days.
So there was a distinct shift with the animal-based ketogenic diet. And not necessarily one that was, you know, any more pathogenic. There was some increase in hydrogen sulfide producers, which we can talk about a little more later if you want. So in some cases, there might be certain gut microbial patterns that might be...you know, certain overgrowths that might be exacerbated on a ketogenic diet for the average person going on a ketogenic diet, I don't think we have any real evidence to suggest that that's gonna be bad for the gut microbiome.
Dr. Hedberg: Excellent. Yeah, that makes sense just because it was...like you said, we evolved with various types of diets and there were certainly sometimes long periods where very low fiber, not much plant food was available and people were only eating meat. We can see certain populations around the world that eat diets like that.
So based on your research and what's showing now, there...correct me if I'm wrong. So there's not much evidence that a ketogenic diet is necessarily bad or pathogenic for someone's gut microbiota other than you mentioned if there's some level of bacterial overgrowth. Is that correct?
Dr. Mailing: Yeah, specifically hydrogen sulfide overgrowth because there's certain hydrogen-sulfide-producing organisms like Desulfovibrio and Bilophila wadsworthia being the two most common. Those, if they're overgrown, they tend to really thrive on animal protein and fat and so if you have an overgrowth of those particular bacteria at baseline and then you go on a ketogenic diet, you're probably going to exacerbate those overgrowths just because they thrive on those particular types of foods.
Dr. Hedberg: Yeah, that makes sense. So a lot of people...you know, there's talk about diversity and the importance of that but there's also, at least from my research, that's not necessarily all that conclusive either and it seems from my understanding that the real key is reducing inflammation in the gut and if you can reduce inflammation in the gut, then the type of diet isn't going to have much of a negative effect on the microbiome. What can you say about diversity and where we are as how we look at that and is it really important to have a lot of diversity or are we okay...certain individuals for some periods of time eating a diet that is going to decrease diversity of the gut microbiota?
Dr. Mailing: Yeah, great question. So diversity is definitely tricky to think about. It's clear that Western populations have significantly reduced diversity compared to much more traditional cultures like the Hadza hunter gatherers, some Nepalese populations that have been studied that are more agrarian. They definitely tend to have higher microbial diversity and that's also associated with a lack of chronic disease. So we think that this loss of diversity in our essentially industrialized microbiota is potentially contributing to our predisposition to chronic disease.
Now within a western population we tend to see that higher microbial diversity is more associated with health but that's not always a perfect correlation. I think I've seen a few studies. For example, there was one with individuals with major depressive disorder and they found that those individuals actually had higher diversity than healthy controls but it wasn't necessarily a healthy type of increased diversity.
So diversity does tend to correlate with health but it's certainly, you know, not the only thing we should be considering when we're determining, you know, whether we've got a healthy microbiome. And honestly, like I mentioned earlier, we're still really in the early stages of defining a healthy microbiome but I think what you said about inflammation is really key because if we have...you know, there's many unique states of a healthy microbiome. You know, you and I only share about a third of our gut microbiota and the rest is unique to us. But if we're both healthy, we should both have, you know, very low inflammation. And so that seems to be a key that is shared across healthy individuals is lower inflammation and a healthy colonic metabolism that actually promotes a healthy microbiota that's unique to us.
Dr. Hedberg: And just wanna ask you about protein because usually the conversations tend to revolve around fat and carbohydrate and fiber intake.
