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Episode 5: The Ketogenic Diet's Impact On The Gut Microbiome

Episode 5: The Ketogenic Diet's Impact On The Gut Microbiome

Dr. Will Cole is a functional medicine practitioner and author of the book, “Ketotarian: The (Mostly) Plant-Based Plan To Burn Fat, Boost Your Energy, Crush Your Cravings, And Calm Inflammation.”

On this show, we discuss how the conventional ketogenic diet of high-fat, low fiber could have detrimental impacts on the health of the microbiome. While many people certainly see short-term gains from going keto (more energy, increased weight loss, and better sleep, to name a few), Dr. Cole is concerned about what’s happening long-term.

In this episode, Dr. Cole talks about the importance of short chain fatty acids like butyrate, why someone with an imbalanced microbiome may not be able to jump straight to a high-fiber, plant-based diet, and how the types of fats we’re eating impact our microbial communities.

If you’ve ever considered keto but just felt like all that bacon and whipped cream couldn’t be good for your gut, this is an episode that you don’t want to miss.

To follow Dr. Cole, find him on Instagram, Twitter, Facebook, and Pinterest, or visit

BIOHM gut quiz


Andrea Wien: Welcome to the Microbiome Report powered by BIOHM Health. I'm your host, Andrea Wien and today we have a very special guest, functional medicine practitioner, Dr. Will Cole. Dr. Cole runs a virtual clinic that can assist patients with various functional lab tests and then advise them on the best steps to take to better their health. Dr. Cole is also the author of the book Ketotarian: The Mostly Plant-Based Plan to Burn Fat, Boost Your Energy, Crush Your Cravings, and Calm Inflammation. On this episode, we're discussing why the conventional keto diet that's often portrayed on social media and in the blogosphere might be detrimental to our microbiome. We also talk about how we can shift our thinking around what it means to be ketogenic in order to improve our gut health.

The show is packed with insights on things like short chain fatty acids, plant foods that increase microbial diversity and actionable tips on how to start incorporating more fiber rich foods into your diet while still staying keto. Toward the end of the episode, we also talk about the shift from sugar burning to fat burning metabolization, which does more than simply help you drop pounds. Make sure you listen all the way to the end for all the details. As a thank you to listeners, BIOHM is also happy to offer 10% off any purchase at Just enter BIOHM10 B-I-O-H-M one zero at checkout. Now onto the show. Dr. Cole, thank you so much for joining us today.

Dr. Will Cole: Yes. Thanks so much for having me.

Andrea Wien: There seems to really be two schools of thought when we're thinking about keto and gut health. There's one side that thinks the keto diet is detrimental to gut health, and then there's those that sing its praises for the microbiome. So the ones that say it's detrimental really point to the research that shows that fat changes the gut microbiota in negative ways. Who's right?

Dr. Will Cole: Well, I think it's both sides can be right. And it's about the context of what you're talking about. There's a lot of different ways to do the ketogenic diet, just like there's a lot of ways to do the plant based diet and we're all different too. So you have to look at the person that you're talking about as well. So one thing that I try to avoid and I think is really at the heart of functional medicine, is that you can't make very many broad sweeping statements about things and over-generalize stuff. But I think that a conventional ketogenic diet, the way it's done today on social media could definitely long-term have some negative impacts on the microbiome. And the reason why I say that is because I find that many people in the conventional keto world where they're just eating anything as long as it's high fat, low carb, and they limit or avoid plant foods.

I feel like long-term that could definitely impact microbiome diversity and just healthy, robust microbiome. In the short term, I think that people have this honeymoon period with the ketogenic diet done conventionally, where they lose weight, they're off of the junk food of the standard western diet and this is great. And then long-term, and that's what I'm concerned with from a functional medicine standpoint, what does this mean for the microbiome? And I think it could impact the microbiome's health and in turn the health of the person.

So that's why I don't really advocate the conventional ketogenic diet. I advocate ketotarian, which is this plant centric ketogenic way of eating, where it's tons of plant foods. And we know that the more diverse your plant food intake is, the more diverse your microbiome is and it's associated with better health in general. So there is some exciting studies done on the ketogenic diet, namely the research done for seizure disorders and the impact that the microbiome can be positively influenced with the ketogenic diet and its impact on the gut brain access. But for the average person, long-term wellness, I think that if you're avoiding plant foods and eating tons of fat, namely animal fats like dairy, cheeses and creams and bacon, I think that this could be not the best thing for a microbiome.

Andrea Wien: Yeah. I actually did strict keto for about a year where I was measuring my ketones. And I think you're right that the traditional community of ketogenic people, it's all packed with heavy cream and bacon and it almost feels like vegetables are vilified in a way. So I was so happy to see your book come out because that was something that I missed so much in being able to partake in because everyone was saying, "Vegetables are bad. Don't go that way." And I think I started to notice changes in my own digestion. And so I think what's really happening when we're only eating those types of fats? What's happening in the gut and in the body? Is it just that there's no fiber material for the bacteria and fungi to be eating?

Dr. Will Cole: I think that's the main thing. Our microbiome eats what we eat and they predominantly like to eat fiber from plant foods. And this is food for our microbiota and it allows them to populate and to produce short chain fatty acids, which you need for healthy brain function and hormonal function and mitochondrial function. And it's interesting enough, we're talking about the ketogenic diet and the microbiome and plant foods. And one of the short chain fatty acids that is a product of bacterial fermentation from plant fiber from plant foods is butyrate and butyrate is related to beta-hydroxybutyrate, BHB, the main ketone that people are measuring when they test their blood ketones. And our gut microbiota produce this naturally relative to beta-hydroxybutyrate in the microbiome because it's fermented plant foods and butyrate the short chain, fatty acid has similar health benefits as beta-hydroxybutyrate, meaning it's good for metabolism. It's good for lowering inflammation levels. It's good for mitochondrial function, all of the same things that the ketone has, your gut can produce this as well, but it needs plant foods to properly produce it.

Andrea Wien: For someone who might be new to all of this and all of the terminology and might not know, what are short chain fatty acids?

Dr. Will Cole: Short chain fatty acids are end products of bacterial fermentation. So basically when you eat plant foods, when we eat salads or really any plant food out there, the fiber, the bacteria eat this fiber and produce short chain fatty acids, which are used for metabolic purposes and immune purposes. That's what they're used for. So in functional medicine, when we run microbiome testing and stool testing, one of the things we're looking at is the proper ratios of short chain fatty acids. And we also want a healthy levels of them specifically butyrate, which is one that's pretty well-researched to be a beneficial part of a healthy human microbiome.

Andrea Wien: So let's say someone gets one of those tests back, and I know you guys run them through your virtual clinics. So if someone's listening and they wanted to be able to test and see if they had some of these things in their gut, that's something you are able to do, right?

Dr. Will Cole: Yeah, absolutely. We would just drop ship the labs to them and they can have these labs done wherever they're at.

Andrea Wien: Great. So say someone gets this result back and their butyrate is low, is it as simple as just taking a supplement? Or is there something we can do dietarily?

Dr. Will Cole: I think it's definitely food should be first here. And I think probiotics and things that promote a healthy microbiome, but food is important here. And any plant food, just increasing plant foods in general, resistant starches can be good as well. And resistant starches are in plant foods. I think that these are definitely things that I'd like to slowly increase for people that have lower butyrate levels. It definitely has to be done to the individual, meaning that some people, when you give them tons of plant foods and you do too much too soon, you can see negative responses because their microbiome is not used to this new food and there has to be this adjustment period. So sometimes you take it sensitive, be sensitive on a microbiome that maybe isn't as healthy. Maybe it isn't balanced. So starting off with more cooked vegetables, soft things, soups and stews, but still having the plant foods in it, even if it's pureed and soft like that.

And then from there, you can slowly graduate to more maybe steamed vegetables or plant foods and then raw vegetables. But it's definitely important to talk about the nuance here that we're talking about plant foods. I'm not saying okay, people with looking to improve their health, go have tons of raw vegetables. I don't think that's going to work for a lot of people that are listening out there, especially people with gut problems. You have to lean into some of these things and start off with what your body can even digest. Because a lot of people's systems are having problems with even digesting real plant foods today. The amount of gut problems are ubiquitous sadly, and we need to start off with gentle food sometimes. And that sort of that soup, stews, pureed foods, but still focusing on plant centric meals.

Andrea Wien: So this isn't a case of just powering through, if you are starting to have some of those digestive symptoms, because you've added more fiber and plant foods into your diet, it's not like I'll just keep going for a few weeks and hopefully my system will catch up. It's really let's scale it back, start it slowly and as gradually as possible and then work up from there.

Dr. Will Cole: Absolutely. Yeah. You don't normally want to push through things too much because really what it's saying is the microbiome said, "I'm not ready for this." The bacteria that may be just some dysbiosis or imbalance in the microbiome that, your microbiome, all of our microbiomes changed pretty quickly with the foods that we eat. And there has to sometimes be this adjustment period of the microbiome getting used to a different foods or fiber rich foods as it were today that we're talking about. Yeah. So lean into it, work with your body and don't be too aggressive just because we're talking about plant foods and you get over eager and you want to load up more vegetables. That's all fine in theory, but you have to work with your body.

Andrea Wien: Now you mentioned resistant starches and some of the plant foods, but are there certain specific foods or even strains of microbiota that are better friends for us to have in our gut when we're eating keto?

Dr. Will Cole: Yeah, I mean, I think in general, when you're talking about... I'm a big fan of having bacterial diversity through supplementation and fermented foods to get a variety of bacteria in the gut. Specifically, some of the ones that are the most well researched is a Lactobacillus bifidobacterium. These are linked to not only healthy digestion, but a healthy brain. For example, people with anxiety and depression, they're link to lower levels of Lactobacillus, helveticus, and bifidobacterium longum. So these are some things that I like my patients, especially when we run labs and we see these levels are lower or they're having these brain issues or digestive problems to start getting these levels up. So that's two examples, but I like to look at a more comprehensive microbiome panel to see which levels are lower and then work on diversity where things are lacking.

Andrea Wien: I think it's so interesting now with the science that's coming out that we can actually say, "Okay, maybe your Lactobacillus is a little on the lower side. Here are the foods to avoid and here are the foods to consume that might be able to better balance that microbiome." And we're starting to learn that about so many different strains, which is so exciting.

Dr. Will Cole: Yeah, absolutely. It's so exciting. We're really at the forefront here of learning about this vast universe within us and what an exciting place to live in. If you think of a parent's generation or a grandparent's, they didn't know about all of this, and we can start applying things and taking action on our health, whereas before it was really not even thought of. I'm really excited to be a part of this conversation and talk about things that no one in human history has really talked about to the level that we're talking about today.

Andrea Wien: When you think about all the things that are coming out around the microbiome and all this information that's at our fingertips, what makes you most excited for what comes next?

Dr. Will Cole: I think it's unlocking the potential to human health and the reversal of health problems. Previous generations in our culture said, well, there's really nothing you could do if your mom had it, your dad had it, it was genetics, it was immutable and nothing you could do. And now really that when you think of what Hippocrates said thousands of years ago, "All disease begins in the gut." That the majority of health problems that we see today, at least to some degree begin in the gut, if not entirely, it can be a major facet or a piece of the puzzle to someone's health journey.

So this is really, and when you talk about genetics and epigenetics, studies that show the majority of how long we live or the majority of the power that we wield over our health is due to epigenetics. These are the lifestyle things that people can control, that constantly and dynamically instruct our genetics on how they are expressed. And you look at the power, the gravity of the microbiome and its ability to govern biochemistry and govern genetics. It's exciting. And we're just beginning to understand exactly how to apply that clinically or practically in real life. But the things that we do know so far, it can make major differences in someone's health in a positive way. So that's what I'm most excited about.

Andrea Wien: Yeah. I think there's so much on the horizon and we're just at the tip of the iceberg, which I think can be both a little dangerous when some people try to implement things too quickly without the research there to back it up, but also so exciting to know what's coming down the pike. In terms of, obviously keto is all about the fat, we hear about the fat all the time. Does the type of fat matter for the microbiome? For example, if someone's eating something that's very high in hydrogenated oils versus a grass fed beef tallow, how is that impacting the gut and maybe beyond even our microbiota?

Dr. Will Cole: I think that when you're looking at the healthiest types of fats for the microbiome, I would say you're going to want to get healthy polyunsaturated fats from fish like wild caught fish, omega fats, which really has a positive effect on the microbiome and lowering inflammation just systemically and the monounsaturated fats like extra virgin olive oil, avocado oil, and obviously the plant fat full food versions of them like the olives and the avocado. But the polyphenols specifically found an extra virgin olive oil can play a significant role in improving the microbiome environment and other healthy fats like this. And I feel like most people, when I've seen clinically thousands of patients over the years, and when I look at the literature as well, you can really see that most people tolerate these fats very well. What I feel like for some people, depending on what they have going on in their microbiome, they don't do well with lots and lots of saturated fats.

For example, having the butter coffees, they can work great for some people, but for some people you can see that if they're depending on that, that can increase inflammation in the bodies and other saturated fats like red meat and things like that. It can definitely drive inflammation in some people. People that have higher levels of ground negative bacteria, this can increase lipopolysaccharides or the LPS, these bacterial endotoxins in certain people to pass through the gut lining because of these liquid fats and the saturated fats. And it's increasing inflammation in the body and endotoxemia and things like that. That's not good. So you're eating this whole food fat, or it looks very keto, but definitely I would say not having it as the majority of the source of fats, especially if you're running labs and you see that your lipids are not looking so great, your cholesterol levels are out of whack or your inflammation levels like the C reactive protein levels are increasing too, or you're having any other inflammatory symptoms.

I prefer people focusing on more of these plant fats and wild caught fish as well. And then there's obviously genetic reasons for that too like the APOE e4 mutation where it has nothing to do with the microbiome, but basically people that are focusing too much on saturated fats all in the name of being keto, they're just focusing on fats that don't work the best for their body either because of the microbiome or because of genetics or because of both.

Andrea Wien: What are some examples of plant fats that you like most?

Dr. Will Cole: So my favorite plant fats are going to definitely be extra virgin olive oil and avocado oil and olives and avocados. And I like nuts and seeds. I think those would be my favorite ones. I think coconut oil can be great. That is a plant fat that is saturated fat, but some people don't do great with tons of coconut oil, but it definitely could be a great thing to have as far as being a plant based keto eater. And I think that if you look at some non plant-based fats that most people do well with, it would be ghee, clarified butter if it's grass fed and eggs, I think are a super food if someone doesn't have an albumen or egg white sensitivity, the yolk specifically. The egg yolk can be a great source of omega fats. And obviously B vitamins like choline as well, which are really healthy for our brain.

Andrea Wien: I want to switch gears a little bit, talk more on incorporating this into a lifestyle. So I see a lot in my work as a functional nutritionist, working with clients that have gone, maybe other places to other clinics, they've done it on their own where they'll do a crash keto diet, maybe for six weeks, they'll lose some weight and then they'll go back to eating their regular diets. Can you talk a little bit more about how to incorporate these keto principles and keto plant-based principles into a lifestyle versus approaching it like just another crash diet?

Dr. Will Cole: Yeah, that was definitely a part of when I wrote Ketotarian, there's all this exciting science and practical application and just things that people can get really revved up about in a positive way. But we have to make this sustainable and we don't want this to be another fad diet to add to your pile of fad diets that you've tried for a little bit and then you left to no avail long-term. I want this to be a sustainable act of wellness. And I think that has to happen when you get your head and your heart right first. And it may seem a little bit not so sciencey, but I think that people have to really check in with their relationship with their body and check in their relationship with food. Because a lot of times people get excited about something and we're all good as humans at three weeks of this or four weeks of that and it sounds great, but really we all know instinctively that that can be a launching pad for something positive, but this has to be a lifestyle change.

And I feel like most people fail at these sort of in a positive food choice plans because they don't have a healthy relationship with their body and food. And we cannot heal a body we hate. We cannot just grit our teeth, eating a certain way for long. And we have to kind of shift our relationship with ourselves and food and say, "Look, how can I nourish my body with good foods?" Not focusing on all the things you can't have and punishing your body by restricting it from certain foods, but really saying what foods make me feel great? What foods are going to move me towards my goal? And really focusing on that. And I think that that to me has to be the foundation of any acts of wellness.

And I think that true sustainable wellness is born out of self respect for yourself. Specific to the ketogenic diet, I would say I put in Ketotarian a lot of practical, just keeping it simple options because most people that are listening and most people that I talk to just want to keep it simple. They don't want to overthink things. They don't want to be overly dogmatic about macros nor do I think that that's necessarily healthy long-term to be overly focused on macronutrients. I like keeping it simple myself. So the way that I structure it in Ketotarian is if you eat like a non starchy vegetable, add a healthy fat. Eat when you're hungry eat until you are satiated. Focus on real food. I think if you do that, that's going to be a really good foundation for this sort of plant based ketogenic approach I advocate for.

But it has to be coming from a healthy place. And I think a lot of times people get really anxious and there's a lot of really stress and anxiety about getting it all right when it comes to diet. And stress isn't good for your health. It's not good for our gut. It's not good for our brain. It's not good for our hormones. So I feel like if you're coming with these things with a positive mental state towards it, then that's great. But otherwise I would just keep it simple.

Andrea Wien: I also like how you've written and talked about the difference in how we metabolize and how people could be sugar burning metabolizers or fat burning metabolizers. And I think this concept is not something that many people have thought about, but really our bodies are meant to do both. And so many people nowadays are walking around only in glucose and sugar burning mode. Can you talk a little bit about that shift and what that looks like?

Dr. Will Cole: Sure. So most people in the west are in various forms of sugar burning for energy. And this is akin to sort of kindling on a fire. You put kindling on a fire, you'll get a burst of light, you'll get energy, you'll get fuel, but it's short lived. You have to keep putting more kindling on the fire to maintain that light, to maintain that fuel for the day. You can have the more dirty kindling and that is the standard western diet with refined carbohydrates and sugar. And then you have the cleaner kindling of real foods and starches and whole grains and things like that, that ultimately break down into sugar, which is better. I would say the cleaner kindling is better than the dirty kindling, but it's still kindling nonetheless. And that's going to leave many people depending on their biochemistry, the microbiome, the genetics.

That's going to leave them hangry if they miss a meal, irritable, fatigued with digestive problems or inflammation level. It is not sustainable for a lot of people. And that's why 50% of the United States is estimated to be insulin resistant to some degree, whether it's full blown type two diabetes or prediabetes or metabolic syndrome or weight loss resistance. We know these issues are sadly commonplace. So that is the sugar burning fuel mode that most people find themselves in. The alternative is being a fat burner. So instead of kindling on a fire like burning sugar, this is more like a log on the fire. It's more sustainable. It'll burn longer, it'll last longer, and this is burning fat for fuel or ketosis. And the ketogenic diet is burning fat for fuel. And this allows people to get off of this sort of volatile blood sugar rollercoaster, and allow this sort of even keel throughout the day. It sustains metabolic energy and maintains brain energy. And that's what the ketogenic diet is really centered around.

But that's why I wanted to have it be sustainable for the average person. And I think that having more of a clean keto approach, a more plant centric ketogenic approach allows you to really leverage the benefits of ketosis becoming a fat burner without falling prey to the potential pitfalls of the way that keto is done today that we see on social media and in the blogosphere. So that's what being a fat burner is. But the cool thing is, is this ketone, this beta-hydroxybutyrate ketone, is beyond just losing weight and being a log on the fire for your metabolism. It's also an epigenetic modulator. So it really does really great things at lowering inflammation levels and providing clean fuel for your brain, increasing mitochondrial biogenesis, basically making new mitochondria, which you need for cellular energy. So much cool stuff. I think most people are motivated by the weight loss, which is certainly cool, but once they kind of get in on that metabolically speaking, I hope that they get to see all the other great benefits that are out there as well.

Andrea Wien: Absolutely. And I think now too, when we see the baby boomers who took care of their parents and watched them rapidly decline, and now they're saying, "Hey, wait, I'm on these same four or five medications that my parents were on. It didn't work out so well for them." And so eating this way really as maybe an antidote to some of the things that they're looking at that are very real right now.

Dr. Will Cole: It's true. I mean, we see a rise of health problems and people shouldn't settle for it. And just because something's common, doesn't make it normal. And we see health problems that are ubiquitous, but they are anything but normal. And most of the health problems that we see today are reversible, improvable, manageable, overcomeable with lifestyle changes, the things that you talk about on this show. So I hope that this really sheds light on this fact and empowers people to start making positive changes.

Andrea Wien: That's a great segue into my last question, which is, is there anyone that shouldn't eat this way? Is this diet better for some people than for others?

Dr. Will Cole: I think that from a foundational standpoint, being a fat burner is in alignment with our DNA and the human race would have been in times of ketosis for a long time. I think it's a foundational metabolic place that people should reset their body, their metabolism, to being in a state of being a fat burner. The variable is, is the person suited or is it going to be beneficial for them to be in ketosis forever and ever, or long-term? And I think the answer is no for everybody. Not everybody needs to be in ketosis forever. In Ketotarian, I recommend to go eight weeks plant-based keto and by plant-based keto, I mean there's vegan keto, vegetarian keto, and pescatarian keto options like with wild caught fish. So it's not entirely plant-based if you don't want it to be, even though it can be for people who enjoy that way of eating. But then from there, I think you can personalize it.

And I recommend doing a few ways to find out where you feel the best and take inventory with where do you find your energy? How's your energy? How's your digestion? How's your brain function? How's your mood? All of this stuff. And because we're all different, and this is really the heart of functional medicine is finding out what does your body love? What does your body hate? So when talking about all these different types of people, they've created this metabolic foundation of being a fat burner, they've lowered inflammation levels, they got the benefits of ketosis, but then from there they can find out their sweet spots. So some people, for example, they do well, or I should say their body tolerates more carbohydrates from real foods. So they may choose to moderate their carbs and go out of ketosis, but still be more in the lower carb or a moderate carb diet from real foods.

Again, real foods, nothing processed or junk food. And then they can go back into ketosis when they want to. And they want more of a metabolic reset. A lot of people do great with more of a cyclical, ketogenic or ketotarian approach where they'll do about four to five days in ketosis throughout the week. And then the remaining days of the week, they'll moderate their carbs, and go out of ketosis. And they liked the variability of that and maybe they center their carb moderation around a workout or a more high intensity activity just to get that extra kindling on the fire when they need it. And then some people like to do more of a seasonal ketotarian approach where they will in the summertime have more fresh fruits. They'll have watermelon, they'll have blueberries and the raspberries and all this extra fruit that they maybe don't have in the winter time.

And this is more in alignment with, I think a lot of ancestral populations, depending on where they were at in the world is that during the summer months they would eat more seasonal fruits. And in the winter they would be in times of ketosis. And then some people do great with long-term ketosis. People with persistent insulin resistance, people with inflammatory issues, people with brain issues. And obviously we know seizure disorders, but beyond that, there's other brain problems that do great with long term ketosis. And they know when they go out of ketosis, they don't feel as well. The brain doesn't function as well as it did before. Their energy levels get lower whenever they go out of ketosis or their weight or their blood sugar, triglycerides, their insulin levels go up when they are out of ketosis. So this allows them, everybody to find their foundation. And then from there they can ebb and flow depending on what their body feels the best at.

Andrea Wien: Dr. Cole, this has been so helpful. Thank you so much for coming on. If people want to pick up the book it's full of recipes, so there's so many ideas in there. Where can they find that and find more of your information and your writing and the information that you're sharing?

Dr. Will Cole: Everything is at That's We have links to Ketotarian on there to Amazon and Barnes and Noble. We have video classes for people to learn more about functional medicine. We offer a free web camera phone health evaluation that people want to get a functional medicine perspective on their case. There's so much stuff there, but everything's on

Andrea Wien: Great. And we will link to that in the show notes. Thank you so much for coming on. Have a great one. We'll talk soon.

Dr. Will Cole: Thank you.

Andrea Wien: As always, thanks so much for listening. To check out the show notes, head to See you next week.


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