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....