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Episode 12: What’s Functional Medicine’s Role In Gut Healing?

Functional medicine doc, Dr. Vincent Pedre

You may have heard the term functional medicine being thrown around by holistic practitioners and nutritionists. But do you really understand what it means?

On today’s episode, functional medicine doc, Dr. Vincent Pedre, joins Andrea on the show to explain how functional medicine is different from visiting your everyday doctor and why it’s especially well-suited to heal the gut lining.

As an OG of the functional medicine movement, Dr. Pedre has a booming practice in New York City and is the author of “Happy Gut: The Cleansing Program To Help You Lose Weight, Gain Energy, and Eliminate Pain.” He’s regularly featured talking about gut health and functional medicine on national media outlets, such as Dr. Oz, Good Morning America, and The Martha Stewart Show.

On this show, Andrea and Dr. Pedre dig into the differences between functional medicine and conventional medicine, chat about why Dr. Pedre believes all disease begins in the gut, and explain how a well-designed cleanse can help put you on the path to healing.

To learn more about Dr. Pedre, visit and connect with him on Instagram, Facebook, and Twitter.


On this show, you’ll learn:

  • What is functional medicine? (1:25)
  • Conventional medicine and functional medicine working together (6:00)
  • Why do we focus first on the gut? (13:34)
  • Happy Gut and The Gut Care Program (17:06)
  • Dr. Pedre on cleanses (21:38)
  • Why legumes are taken out on a cleanse (28:06)
  • Innocent looking ingredient labels (30:11)

biohm gut quiz


Andrea Wien: I'm Andrea Wien and you are listening to The Microbiome Report powered by BIOHM Health. My guest today is Dr. Vincent Pedre, an OGE of the functional medicine movement and the author of Happy Gut: The Cleansing Program to Help You Lose Weight, Gain Energy, and Eliminate Pain. Which helps people resolve their digestive and gut health issues. In addition to his role as a private practitioner, he's also certified in yoga and medical acupuncture. Dr. Pedre believes the gut is the gateway to a better brain and excellent health, which is why we're thrilled to have him on the show today.

On this episode, Dr. Pedre explains the difference between functional medicine and Western medicine, plus how the two can work in harmony instead of an opposition. He also dives into the controversial world of cleanses and talks about why he's a believer in giving the body a helping hand in detoxifying from the world around us. If you're not familiar with functional medicine as a way to truly heal the body from the inside out, you're in for a real treat with this episode. Dr. Pedre, thank you so much for coming on the show. How are you?

Dr. Vincent Pedre: I'm great. Thanks for having me.

Andrea Wien: So I think to start, we haven't talked a whole lot on the show yet about functional medicine. Can you give us a bit of a background on what functional medicine is and how it's different from what we might know about going to the doctor?

Dr. Vincent Pedre: Well, functional medicine is interestingly based on a systems biology approach, which dates back to Chinese medicine. In some ways functional medicine has its roots in Chinese medicine, even though it is not Chinese medicine per se, but just the concept that the body is this whole system that is functioning together. And what causes disease is an internal imbalance or something going awry in one of these systems or maybe multiple systems because everything is interrelated. Basically the goal of functional medicine is to find the root cause. The underlying reason for why a patient is presenting with the symptoms or disease that they have. It's a very different approach.

It's almost like saying if you're looking at a tree and you're looking at the entire tree and you can see the whole root system, functional medicine is looking at the roots to understand why the leaves look the way they look. Whereas Western medicine does not look at the roots. It's looking at the tree from the outside and saying, "Oh, the leaves don't look right. We have a medicine to make them look better." So in other words, Western medicine, a lot of times is treating the symptoms of disease, not always going underneath and treating the root cause of disease. Sometimes it's somewhere in the middle where it may be treating a pathway that's involved in a disease, but it's not really digging deep.

And it's really interesting to use that analogy because if you asked any hortacologists or any farmer, if their plant is sick, so if the leaves are looking unhealthy, the first thing that they do is they look at the roots and the soil and see what is the health of the soil? What is the health of the roots? And our bodies, if you think of our body as equivalent to that and the gut and the microbiome is almost like the soil. And we live just like trees live in symbiosis with the soil, we live in symbiosis with our gut.

And in order to understand the pathophysiology of disease, you have to go to the root of it. And almost literally with trees, you don't treat a disease leaf. What you do is you look at what's happening in the roots and what is it that you need to improve? Maybe there are nutrients, maybe the tree is not getting enough water, maybe the microbiome in the soil is off. And you can tell by how healthy the soil is. If there are earthworms and all sorts of bugs in there. So it's basically a bottom up approach versus a top down approach. Which is Western medicine. A lot of times, Western medicine, we described as band-aiding things. It's really good at treating symptoms, but if you want to go to the root of it, then you have to start looking at diet and internal inflammatory processes.

Sometimes there's been like, well, is it functional medicine versus conventional medicine? And I really don't think of it that way. I think that it's complimentary. There's a place for Western medicine and there is a place for functional medicine and they should be living in symbiosis as well. Just to bring that word back. We need Western medicine. Western medicine has saved lives. You can say. It's evolved to save people and antibiotics, for example, it's very important to have that balance between the two. Because it's really is in the summation of the two systems that we can achieve optimal health. And I think what has to happen is, functional medicine is just so much better at dealing with chronic disease and chronic metabolic issues. Because the foundation of functional medicine is really understanding the biochemical pathways in the body and understanding the biochemistry of inflammation and of the immune system and all that, and how we can change it through diet, through lifestyle, through exercise.

Andrea Wien: That's great. Yeah. I love that analogy of the tree. And I think you're so right to say that they're symbiotic in each other with conventional medicine and functional medicine. If I got hit by a car, I certainly wouldn't want to go get my stool sample done. And all of these tests, maybe that functional medicine. Work on my microbiome, eat more fermented foods. I'd want be taken to the hospital. And I would want that care.

Dr. Vincent Pedre: If you have an acute cholera or an acute severe diarrhea where you're losing so much fluid, then going to the hospital and getting intravenous fluids is going to be lifesaving for you. And perhaps you got an E. coli 157 and you need antibiotics and that's going to save your life in that situation.

Andrea Wien: So tell me a little bit about how you came to this field of work and how you became interested in the microbiome.

Dr. Vincent Pedre: I've always been interested in looking for more natural ways to heal the body. And it dates back to my own anxiety around needles when I was going to go to medical school and I almost decided not to become a doctor because I was really afraid of needles. And I hated getting my blood drawn, I hated getting vaccines. And I thought, "Well, this is ridiculous." How can I become a doctor if I can't even see my own blood taken and not pass out, have a sinkable episode.

Andrea Wien: You sound like my husband.

Dr. Vincent Pedre: Instead of running away, I decided, well, my family was like, "Okay, you have no option. You're becoming a doctor." I'm like, "Okay, I can't run from this." Why does this happening? And that took me to studying the autonomic nervous system. And this is before I went to medical school, I was in college. And I decided, "Well, I need to figure out what's happening in my body. Why does my heart start racing and I break out into a cold sweat?" And I started learning about the parasympathetic and sympathetic nervous system and how you can use breathing exercises to control what seemingly is not under your conscious control. And then I started meditating, then I started doing yoga and I started doing all these breathing exercises. And I did that for eight months before I went to medical school. And by the end of it, I had conquered my internal reaction to the point where even if it started, I could get it under control and I stopped passing out.

And I think that really shaped the type of doctor that I wanted to become. Because I just saw the power of my own mind in non-medication method. Like it wasn't in my family philosophy that if you feel anxious you take a medication for it. It was more like, well, anxiety is in the mind and if it's in your mind, then there must be a way to rewire the mind in order to not feel so anxious about things. And that led me on a lifelong journey of figuring out these things and learning how to relax and meditation yoga. And so that was already the way my mind was open before I went to medical school.

And during medical school, I just knew I had read so many books. My big influencers were Deepak Chopra and [inaudible 00:08:52] back then and Dr. Mark Hyman, and I knew that that was the type of doctor that I wanted to become. I just didn't know what the path was going to be to get there because when I was in training, there was no integrative medical residency program. It didn't exist. So, all of these doctors that had done this, they were trailblazers. They had done it when there was no system to support that path. So after I finished my residency training I decided to... I had actually, before that I had done a yoga teacher training. And that really brought me back to looking at the body in a holistic fashion and really talking to my patients about breathing and relaxation.

And from there I decided, "Well, I don't want to become a yoga teacher, but I do want to bring this into practice in some way." And the closest thing for me felt to train in acupuncture. So I did a medical acupuncture training. Studying Chinese medicine opened my mind to looking at the body as a system. This interrelated system. Almost like an orchestra. And it was through Chinese medicine studying acupuncture that I started researching, "Well, what was my next thing? What was I going to do next?" And functional medicine just made so much sense now that I understood the language better. I had heard of functional medicine. I had met Dr. Frank Littman and read his book. He told me about functional medicine but it didn't make sense to me until I had done my Chinese medicine training. And then functional medicine made a whole lot of sense and I decided to embark on that training back in 2006 was my first functional medicine conference. And then the certification program, which started in 2008. And I went through their entire certification.

But coincidentally, just kind of long story short, I had a nervous stomach as a child. I had been on multiple, multiple antibiotics as a teenager, and I really didn't understand the impact of that on my gut microbiome and my health until I started studying functional medicine and learning about the microbiome and learning about the effects of antibiotics and realizing that what I thought was normal was not normal. And that perhaps I didn't have to live with irritable bowel syndrome or sensitive stomach. And it was through functional medicine that I was able to heal my gut and reboot my microbiome. And I found that this was, wow, this is something you can really impact people's lives with. Because I always found it to be a mystery to me and now that mystery, that veil of that mystery was lifted studying the microbiome, and how the digestive system works, and understanding tight junctions and leaky gut syndrome that I started working with patients on their gut health.

And that really fascinated me. And I just kept building that part of my practice. So it was almost accidental in a way, and of course, motivated by my own desire to fix my gut health and undo the scorge of all the antibiotics that I had been on and the food sensitivities I had developed as a result. And so I changed my diet. I worked on my gut microbiome and that's what really got me into this field of functional medicine, but really through the prism of the gut. And I think it's so apropos because in functional medicine, the gut is the foundation for everything. So for any issue that a person comes in with, you have to think about their gut health as something that you want to address, because almost anyone has been on antibiotic courses in their life, which we know alter the microbiome and it doesn't completely recover on its own.

Andrea Wien: The Microbiome Report is brought to you by BIOHM Super Greens. A super greens formula that combines 31 super greens with prebiotic digestive enzymes and BIOHM probiotics, giving you a supercharge in a single scoop. To check out BIOHM Super Greens, go to That's B-I-O-H-M and make sure to use the code BIOHM 10, to get 10% off of your order.

We hear this all the time, right? The gut is the place of all health and disease. It's where everything starts. You mentioned it's the foundation. Why is that the case? Why is the gut where we focus first, when we're really focused on healing the body?

Dr. Vincent Pedre: I want to go back to the analogy I used at the beginning of the tree and the root system. If you look at the gut microscopically, the small intestine has all of these tiny villi that stick inwards. Hundreds of them. Like little finger like projections. They are our root system. The gut is the biggest interface that we have with the outside world. The surface area of the small intestine is almost the size of a tennis court. It's about 20, 21 feet long. The large intestine is six feet long. And all along that lining is 70% of our immune system patrolling and checking everything that comes through. So it's almost like our border patrol.

So it is a huge surface area of interaction with the outside world that is potentially the biggest source of inflammation for the body. If there is an increase in intestinal permeability, then our immune system is getting activated by exposure to bacterial peptides or lipopolysaccharide, which is a lipid sugar molecule that is one of the most potent stimulators in the immune system. And that creates system wide alert. So the belief is that a lot of disease starts there because if you turn on the immune system in the gut, then it creates a renegade immune system that is overly active throughout the body. It is believed that is the instigator and beginning for auto immune disease. But any inflammatory disease in the body can be connected to the gut.

And then we have the gut brain connection, the connection to the blood brain barrier, connection with the thyroid, that doesn't even begin... That's talking about just the gut and the immune system, but then the microbiome, our biggest reservoir for microbes is within the intestine, especially the large intestine. And there is a crosstalk that is happening between that microbiome in our body that either can create health imbalance, or it can create inflammation and wreak havoc and cause insulin resistance and cause weight gain and obesity, depending on the types of microbes that are in there, you can develop mental fog, brain disorders.

So the reach of what the gut affects in the body is vast. And even including the hormone system and processing, and either reactivating or activating hormones or releasing hormones that have been deactivated and causing them to recirculate in the body. So a lot of stuff is connected to the gut, along with it being one of our primary detox organs, because you need to poop in order to get rid of body toxins that are excreted in the stool.

Andrea Wien: So, I mean, when we talk about all of this and there's so much information there, and I think for some people it can get overwhelming to think, "Oh my gosh, this one aspect of my health, my gut, my digestion is really impacting everything. And so you wrote your book happy gut, and you also developed the Gut C.A.R.E Program, which I think makes it easier to follow, I would say, for people who are maybe new to this, it breaks it down into steps into how to really start to care for your gut. Can you talk a little bit about that program and how it was developed.

Dr. Vincent Pedre: Yeah. So the Gut C.A.R.E Program is my gut healing protocol, and it was basically based on functional medicine and root cause medicine. And I wanted to make it simple for people to understand. So C.A.R.E Is an acronym representing, Cleanse, Activate, Restore, and Enhance. And I think it's just like anything, like things need to be broken down into bite size pieces that are easier to digest for people. And that's what I did with the Gut C.A.R.E Program is I just broke down what it takes to rebalance the gut into this much easier to understand program that people can do.

And also it's broken down in a way that they can understand, "Well, why am I doing these things?" So the C for cleanse means cleansing out, not just the bad bugs in the gut, which a lot of times we need to get rid of. Things, bugs, parasites, yeast that we don't want to be there because they're wreaking havoc and causing inflammation, but also cleansing out the diet of the inflammatory foods, the high sensitivity foods like gluten and dairy, but also foods that tend to be genetically modified and speckled with pesticide, with the glyphosate. And that's like soy and corn, for example, and really cleaning out the diet and making a gut friendly diet that allows for healing to happen, not just in the gut, for the entire body.

And along with cleansing the diet and cleansing the gut I talk about cleansing the mind of negativity. It's so important to have an attitude of wellness, an attitude of gratitude to be able to change your behaviors and be able to transform your health. You can't just do that on the surface and not work on your mind. Then activate is all about activating the digestive process. A lot of people have had problems with their digestive system or not making enough enzyme. So activate is about reintroducing necessary enzymes that aid in the digestive process. And they kind of also give the gut a break to allow the gut lining to heal itself.

Restore is about restoring the microbiome, which I know has a lot of what you talk about. And that can be through probiotics, through fermented foods and especially through prebiotic foods and nutrients which feed the microbiome. And the best way to create diversity in the microbiome, which is the key to health is through a varied diverse plant based diet. So a big range of colorful plant foods. And then enhance is all about healing the gut lining, healing the leaky gut that most people it's kind of based on the assumption that most people have been on antibiotics. People have used over the counter medications like ibuprofen, aspirin, even birth control pill increases gut permeability and causes leaky gut, but even stress can increase the permeability of the gut and cause leaky gut syndrome.

So enhance is all about using nutrients like L-glutamine, DGL which is derived from Licorice, DGL, Deglycyrrhizinated Licorice, and aloe as another example. Quercetin, which is a bioflavonoid, which is found in a lot of foods. Especially in capers are the highest in quercetin. And thus healing the gut lining. So putting this program together, which is a whole... It's a food supplement mind body program to healing the gut, but also to help to create total wellness.

Andrea Wien: Yeah that's amazing. And it's very easy to digest, as you said, pun intended for people to read that and be able to do those step-by-step. I do want to talk about cleanses for a minute because they're very controversial, right? There's a lot of naysayers, even some doctors out there who say that the body doesn't need help detoxifying. It's meant to do that. It cleanses on its own. And yet we know from the functional medicine side of things that maybe it takes some help to optimize the body's natural systems to really get through that cleansing process. And obviously you feel it's very important with the C in the acronym. So does everyone need to do a cleanse?

Dr. Vincent Pedre: I think it's very important because I mean, if you think about, who has 100% clean diet processed carbs, or too much sugar, or being exposed to environmental toxins? We're living in a swamp, but the environmental toxicity from car fumes, to industry exhaust, to jet fuel, to even just what is found inside the household, all the different products that you can put on your skin or makeup that have endocrine disruptors. So our systems are overwhelmed. So perhaps if we were living hundreds of years ago and living from eating from the earth, and there was no processed foods, yeah, the body could take care and detox itself, but we're living in an overburdened system. I have yet to see, and now I've seen so many hundreds of patients go through cleanses. I've yet to see a patient go through a cleanse that did not feel better in the end.

Now, sometimes you go through a healing crisis when you go on a cleanse, and this is something for people to know because some people that want to do a quick cleanse and they're like, "Oh, I'm just going to do a two week cleanse." And that might be fine if you're generally healthy and your diet is pretty clean to begin with. But if your diet is pretty heavily loaded with sugar, and starches, and you're out drinking. So I forgot to say in my cleanse, we take out alcohol because that's a burden on the liver. And we also take out coffee for many reasons, because it's so acidic for the stomach, but also it tends to tax the liver detox systems. And we want that to be... We want the liver to be completely free to detox the body from internal toxicants as well as external ones that are coming in.

So we take out coffee and alcohol. We allow things like green tea because green tea actually turns on phase one and phase two liver detox and helps the body flush out toxins. So it's actually very helpful for detoxification. And it also has some caffeines for those people who are afraid like, "Oh, I can't live without my caffeine." Well, you can have it in a much better way that is also anticancer, which is green tea.

But to answer your question. So if you do a short cleanse two weeks, your body may take two weeks to clear out a lot of toxicity and you may not feel so good. And that's why after just looking at cleanses and working with patients, when I came up with my Gut C.A.R.E program, I decided, well, this needs to be four weeks long. It's 28 days. And the reason for that is that it may, for some people, depending on how toxic they are, how bad they've been with their diet and pretty much people know who they are. If I ask them, have you been bad with their diet? People will self-report, you have like raise their hand. It may take them two weeks to clear out the inflammation that has been caused by those choices.

And then it really takes the second two weeks to settle in and create what I like to call the blank slate. Like we're trying to get the body back to this dis-inflamed state of being. So I haven't seen people not do well on the cleanse unless they're doing a poorly guided cleanse. So if you're doing a cleanse that has no protein support, there are cleanses out there that might be just complete juice cleanse, or you're just drinking water with maple syrup, that type of cleanse is going to shut down liver detox because the liver needs amino acids in order to detoxify. And that's why it's so important when I have people do my cleanse to have some sort of hypoallergenic vegan protein powder that provides the amino acids that the liver needs in order to do phase two liver detoxification, which is what we call the rate limiting step. Because there's two phases. So let me explain that.

Phase one is a really inducible step. That means it can go from one to 500 times as powerful and very little time. And it creates an intermediate that is very reactive. And sometimes it's more toxic than the initial chemical that's being detoxified. And that has to go through phase two. Well, phase two is like a sloth. It's kind of lazy. And if phase two doesn't have the right nutrients, it needs B vitamins, you need magnesium, but very importantly, you need amino acid substrates for phase two. And if you're starving yourself of amino acids by going on some vegetable juice cleanse where you're not getting a lot of protein, then you can stall that and you start feeling... You might feel good the first couple of days, and then you start feeling really bad. So you always need to balance out a cleanse with some sort of protein source.

Andrea Wien: Yeah. And I've always liked the analogy. I have clients who ask me, "Why would the body do that? Why would it take something in phase one and then make it more harmful before it's excreted from the body?" And I always use the example or the analogy of a recycling plant. We have a glass bottle that needs to be broken down into pieces, which arguably is much more dangerous, the shards of glass than the bottle was. And then those are melted down and recycled. And the body works in a very similar way.

Dr. Vincent Pedre: I love that. Yeah, that's really great. And it's almost like the way I think of it is that the reactive intermediate tags, the substance, it's also what allows that substance to then be conjugated with the anchor, which is what happens in phase two, the intermediate is anchored and that anchor pulls it out of the body in different ways. Whether it's through the bile or through the urine, through the kidneys. So you can anchor the substance. As it is you have to almost create this rough surface, which is this reactive, oxidative, intermediate, which then allows it to be anchored and then pulled out of the body.

Andrea Wien: I think most people realize also that the main offenders to the diet like gluten and sugar, these things that we hear about, aren't great for them. They understand that. But what about lagoons? Why lagoons? Aren't chickpeas and lentils supposed to be healthy for us? Why are those taken out on a cleanse?

Dr. Vincent Pedre: Mainly because a lot of people... Well, one, a lot of people have lectin issues. So lagoons have lectins and they also have phytic acid. Phytic acid acts as an anti nutrient and blocks the absorption of other minerals. Most people are not going to be going through traditional food preparation techniques that help reduce these substances, and for a lot of people they create a lot of gas in the guts. So if we're doing a gut cleanse, we want to create a happy calm gut. We need to first repopulate the microbiome, diversify the microbiome so that it can handle these types of foods. So surprisingly for people, even peanuts are taken out and a lot of people think it's a nut, but it's actually a lagoon.

Andrea Wien: And when you talk about traditional food preparation techniques, you're talking about things like sprouting and soaking of grains and things that would really help to break down some of these anti-nutrients so that they're easier to digest.

Dr. Vincent Pedre: Exactly. And that's what I always recommend when possible, like eating nuts to sprout almonds, cashews, pumpkin seeds, not only does it make it easier for the gut to digest, it also makes the nutrients more available and accessible to the body.

Andrea Wien: I know we're coming up on time here, but I just wanted to ask you one more thing. I was laughing because I was looking through your Twitter feed in preparation for our conversation. And I saw that Fran Drescher who's everyone's favorite TV nanny is talking about gut health. So it seems like everyone is getting on board with it. Even celebrities who we think maybe might be a little removed from this whole world. But she did bring up an interesting point that even food additives, these things that many people might gloss over when they're looking at ingredient labels can have really profound impacts on our gut microbes. So can you talk a little bit about those types of substances that might be seemingly innocent looking when we're going through food labels that are actually really causing damage?

Dr. Vincent Pedre: Absolutely. I mean, we can start with the artificial sweeteners and we know that they cause shifts in the microbiome that increase insulin resistance leading to a weight gain by increasing blood sugar. But we also know there are food additives, for example, in nut milks, a lot of them add guar gum, gallium gum, and other thickeners that are using the food industry to kind of create that milk like texture on the tongue. But for some people they can be problematic because they're are fibers that then get fermented and they can produce a lot of gas. And in kids, some of these substances can cause behavior issues. They can produce substances that affect the way the brain functions and can increase anxiety and increase behaviors or acting out. And we think it's our child, but it really is you have to look at well, what are they eating? Even food coloring and things like that are just not good.

Andrea Wien: Yeah. That makes a lot of sense. And I know that there's obviously a huge field of study now about the gut brain connection. And when we start to look at the auto immune diseases and autism and the rise of those types of things, I can only imagine that the microbiome plays a huge role in protecting us from maybe some of the heavy metals that are in vaccines, for example, or some of the foods that our kids might get when they're away from home or at a birthday party that the microbiome and the gut integrity really likely plays such a huge role in those.

Dr. Vincent Pedre: It does. And we're living at a time in society when the integrity of the gut lining is under attack continuously because of our food supply antibiotics and toxins, pesticides in the food. And the microbiome itself is really under attack from the over... Really the over prescribing of antibiotics to begin with that. But also the antibiotic like substances that we are exposed to like glyphosate, which is a pesticide that's sprayed on wheat, corn and soy.

Andrea Wien: Yeah, absolutely. All right. Great. Well, thank you so much for coming on the show. If people want to learn more about the gut care program, check out your book, where can they go to find you?

Dr. Vincent Pedre: People can go to And if they go to, I have a free gift for them, which is basically kind of a giveaway. It's my quickstart. Basically everything you need to get started on the Gut C.A.R.E Program and healing the gut.

Andrea Wien: Dr. Pedre, thank you so much for coming on the show. We will hopefully talk to you soon. I know that there's so many topics that we could dive into and go so much deeper on this, but really appreciate the overview today. So thanks so much.

Dr. Vincent Pedre: It's been my pleasure. Thanks for having me

Andrea Wien: As always, thanks for being here and for tuning in. To connect with Dr. Pedre head to's blog for his information and all the show notes from this episode. I'm Andrea Wien and I'll catch you next week with a new episode of The Microbiome Report.


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