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Your Gut Microbiome and Optimal Health and Fitness | Amy Shah MD

Episode 55, duration 1 hr 09 mins
Episode 55

Your Gut Microbiome and Optimal Health and Fitness | Amy Shah MD

Amy Shah, MD, is a double-board-certified medical doctor and nutrition expert with training from Cornell, Columbia, and Harvard Universities. Drawing from her background in internal medicine and allergy/immunology, as well as her own wellness journey, she has dedicated her practice to helping her patients feel better and live healthier through her integrative and holistic approach to wellness. She was named one of mindbodygreen’s Top 100 Women in Wellness to Watch in 2015 and appears regularly on national television shows and podcasts and in national magazines. She lives in Arizona with her family. To learn more, visit her on Instagram at @fastingmd or online at


In this episode we discuss:
• The connection between what you eat, your gut, and your mood
• What you should eat for longevity
• Natural ways to control your appetite
• Does your gut microbiome affect your body composition?

00:00:00 Intro

00:03:39 New Perspectives

00:04:59 Hunger vs Cravings

00:10:27 How to Lower Hunger

00:14:06 Intermittent Fasting

00:24:11 Food & Mood

00:27:21 Probiotics

00:36:46 Psychobiotics

00:47:45 Gut Microbiome and Menopause

00:51:02 GLP-1 Agonists

00:57:56 Gut Health in Clinical Practice

01:06:17 Why Write A Book?

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Dr. Amy Shah, Dr Gabrielle Lyon

Dr. Gabrielle Lyon [0:00:01]

Welcome to the Dr. Gabrielle Lyon Show where I believe a healthy world is based on transparent conversations. In today’s episode of The Dr. Gabrielle Lyon Show, I sit down with Dr. Amy Shah. I love having other providers on the show because it allows us to discuss what is challenging for patients in real time. She got her nutrition degree from Cornell. She went on to medical school, did a residency in Internal Medicine at Harvard, then did a fellowship in allergy and immunology at Columbia University. We had a great conversation, and in this episode, we talked about the connection between the gut, the microbiome, and mood, how what you eat, how the bugs in your belly dictate how you feel.

We also discuss the difference between cravings and hunger. Finally, we cover when you should be eating, what you should be eating to really leverage food for mood and longevity. If you like this episode, please like it, subscribe it. We put out this content for free. Your support means the world to us. Let’s dive in.

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This episode is sponsored by BetterHelp. That’s Better H-E-L-P. Why is BetterHelp so amazing? In this episode, we talk all about mood, and mood is not something you should really deal with by yourself. If you’re like me, if you let your mood go, it’ll for two weeks before you’re even addressing whatever that underlying issue is. This is why I love BetterHelp. BetterHelp is online therapy, offers video, phone, and even live chat-only therapy sessions, so you don’t have to see anyone on camera. It is much more affordable than in-person therapy. Let’s face it, because of COVID, we’ve all gone more to computers, and it is a bit of a hassle to go to do things in person. It is true. You will be matched with a therapist in under 48 hours, all remote, whether it’s video, phone, or live chat. It’s amazing, and it’s so important to take control of your mental health.

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Dr. Amy Shah, I’m so grateful you are in a clinic right now, which is so gracious of you to take time out of your busy day to come and join us on the show. I’m really excited to talk to you. It’s not often that I have people talk about books just because. Because I want to hear about clinical experience. We want to hear about some of the latest research, and you and I both know that in writing a book, it takes, I don’t know how fast of a writer you are, but it took me two years. By the time the information comes out, who knows where it stands? But your book is what I believe to be on the forefront because it talks all about the gut microbiome. And number one, Dr. Amy Shah, welcome.

Dr. Amy Shah [0:05:09]

Thank you. And thank you for saying that because I feel the same way about books. Often, by the time you get the book, it’s two-year old info. But the cool thing about the gut microbiome is that there’s just mounting evidence on so many of the things I was talking about. We have new evidence to support a lot of the things we were talking about, so I feel really excited about the future of this. We’re right at the edge of it.

Dr. Gabrielle Lyon [0:5:35]

Yes, I couldn’t agree more. I wanted to touch a little bit about you and your background; that’s really important for the listener to understand who you are. You have an undergraduate degree in Human Nutrition. You went to medical school. You then did training in internal medicine, and then went on to go into allergy immunology.

Dr. Amy Shah [0:05:58]

Yes, and I had a few research years in between there somewhere. But definitely, when I see studies, I look at it from both my personal view, from when I was in the lab, from when I was in fellowship, when I’m seeing patients in the clinic, so it’s kind of a conglomeration. That’s why I love still seeing patients because even though a lot of what we do is intellectual and dietary and lifestyle-based, I love to see what the real world looks like. What are people struggling with? What are the things that we can help them with? It gives it a different perspective.

Dr. Gabrielle Lyon [0:06:37]

Yeah, and that’s really a beautiful thing. I just want to mention that there’s Harvard in that lineup for where you train, there’s Columbia and Cornell, all of which are individual places that are the best in their field. That becomes really critical when we have this conversation as to who we are bringing to the audience. Now, let’s talk about what is the difference between hunger and cravings, because ultimately, everybody wants to have an optimal body composition?

Dr. Amy Shah [0:07:09]

Yes, and everyone wants to be happy. I think what we don’t realize is that food creates mood. Our gut-brain connection is responsible for our mood, our metabolism, how we feel how we look. That’s why it’s so important to understand the difference. Hunger, in its true sense, is a biological need for nutrients. We are wired in multiple different ways to make sure that we search for food, that we eat food that is nutritious to our body, and of course, we know now that there’s lots of problems when you don’t do that. Hunger is a true biological need. Cravings is a whole different pathway. Cravings is your desire for anything. It could be food, but also desire for alcohol, desire for drugs. It can be desire for gambling. It can be good. It can be desire for getting to the next level in your career. It’s based on the dopamine pathway, and this dopamine pathway is the strongest driver, stronger than any other mechanism in our body to make us do something. Dopamine will make you get up out of your chair, drive across town, and get that food, drug, item, thing. There’s no other pathway like it.

Dr. Gabrielle Lyon [0:08:36]

The mechanism between that drives craving is actually different than the physiological mechanism that drive hunger.

Dr. Amy Shah [0:08:46]

Absolutely. That’s why it’s so confusing to people because sometimes, we are actually craving food, and we’re not needing those biological nutrients. I give people the exact example of processed food. You could have eaten a full day of nutrient-rich food, you could be completely full, but you could still sit down for a movie late at night and then want to eat snacks or want to eat ice cream, want to eat dessert. That’s your dopamine pathway seeking that comfort rather than the hunger pathway.

Dr. Gabrielle Lyon [0:09:26]

Can you just touch very briefly a broad overview of the hunger pathway of some of the physiological drivers of hunger? What happens in the body?

 Dr. Amy Shah [0:09:37]

There are a few multiple different ways because for our body, this is an essential need. Food, feeding is an essential need for survival. We have lots of different reminders in our body to eat food. One of the pathways is your hunger hormones. Your hunger hormones, like ghrelin, a lot of people know ghrelin, which is a hormone that gets released and it makes you hungry. Ghrelin is released in a cyclical pattern. It’s a reminder, because your body does not want you to forget to eat for days. Even though we can physiologically go for days, weeks, actually months without food. It doesn’t want you to do that. It’s a lot of stress on the body, and so we have hormonal pathways. We have neuronal pathways, so brain and vagus nerve pathways. We have gut pathway. Our gut bacteria releases signals to our brain to signal that we’re hungry. We have different signals that our stretch receptors even in our GI tract can send to our brain to say, hey, we haven’t felt food coming in for a long time. These pathways all go to your brain and make you seek food. If you think about it, it also hits on the cravings pathway. So when you are starving yourself, and a lot of women can relate to this case, and you’re on crash diet, you will start to notice your craving pathway being activated as well. Not only do you seek food, but you’re also seeking comfort from food. You’ll want a snack more. You’ll want more sweet, fatties processed foods, because that cravings pathways gets recruited because they’re like, okay, this lady is not eating enough. We’ve already sent her the hormonal signals. We’ve already sent her the neuronal signals. Now, we’re going to hijack the dopamine pathway, so now she gets cravings, and we can protect ourselves from starvation.

Dr. Gabrielle Lyon [0:11:52]

Essentially, what you’re saying is that hunger is incredibly complex. Hunger is not just, oh, I’m feeling hunger, I’m just feeling hungry, but there is a biological drive to feed. There is a gut hormone component, whether it’s CCK or a handful of other hormones. There’s a vagal component and a stretch component, which I love. In your book, you said the raw veggie test. It’s funny; maybe we’ll mention that. What do you think is the easiest lever to pull for an individual to lower their hunger? Again, when we think about optimal body composition, it does require caloric restriction. What are the ways that we can pull these multiple levers to help mitigate hunger?

 Dr. Amy Shah [0:12:43] 

What I talked about in the book is that it’s not our fault that we’re so hungry and craving all the time, really just craving all the time. Some of the things that we can do to reduce our cravings for unhealthy foods is to change our gut. If you’re trying to change your gut microbiome, so the trillions of bacteria that live inside your intestines that pull the strings on your hunger and cravings, you’re going to have to change what you eat, what you input into your body. What I talk about is replacing foods with other foods, instead of just talking about restriction, which is really hard. The dopamine pathway does not like you to restrict something that it’s craving, because it will just make the craving stronger and stronger and stronger. Unless you retrain it, or replace the foods with something else that’s similar, you’re always going to have those cravings.

One of the simplest things I talk about is matching your eating with circadian rhythms. That’s a very easy way to start to retrain your hunger and craving pathways to be in tune with what your cell needs and what your brain needs. So 80% of our genes work on circadian rhythms. Our light is the strongest source, but food and temperature is second and third. So when you time your food appropriately, you can start to rewire those signals, so for example, stop eating two to three hours before bed so that the body can start to know, oh, food’s, not coming in, light’s not coming in, time to shut down, renew, rewire, like putting your brain to sleep. We know how important that is. There’s also a good body of literature that your microbiome, your gut bacteria, and your cells need that break from food as well. That’s one thing, and then changing your dietary habits, including decreasing simple sugars and carbohydrates. If you can stop that insulin roller coaster, that whole crash, first you get the big high and then you have the roller coaster crash, you can really start to improve the things that you crave. Then I’ll say your favorite, increasing your protein intake. Protein is a really great way of inducing your satiation hormones, the hormones that tell you that you’re full. The neuropeptide Y, the CCK, the things that tell you, I’m full, the leptin, these are things that are actively activated when you eat protein. That’s why a lot of people when they’re working on retraining their cravings, lower their simple processed sugar, increase their protein intake, start to add in foods that communicate in a positive way to the brain, including glucosinolates, which is one class of foods that I put in the book that they communicate with the brain in a positive way. You want to be eating things that support positive thinking, so dopamine-rich foods, serotonin-rich foods, and that’s how you start to train.

Dr. Gabrielle Lyon [0:16:04]

I love that. You mentioned this idea of circadian biology, and a circadian rhythm is typically that 24-hour cycle in which we are all accustomed to. There’s a huge push for intermittent fasting and fasting. The question becomes, which I believe I know your answer, do you think that there is benefit for fasting in the morning? Or how do you recommend individuals implement a fasting or intermittent feeding schedule? What would be specifics?

 Dr. Amy Shah [0:16:38]

Intermittent fasting is very personal. It’s like exercise; you can say some people run ultra marathons, and other people do yoga, and it has different benefits. It’s the same with fasting. There are people who do three-day fasts. There are people who do overnight fast, and they’re totally different things, and they have different effects on our metabolism, and they can have different benefits. What I say is that if you’re looking for something to just start, and you want to improve your metabolic markers, so say your fasting insulin. You want to improve your cholesterol levels. You want to improve your physique. The first thing I would do is start to fast according to circadian rhythms. What I mean by that is that you don’t just roll out of bed and eat a pop tart and orange juice like thousands of years ago. Your body’s programmed to seek food, exercise, or at least get a little break. Even when you look at coffee, coffee is best consumed 60 to 90 minutes after waking. Food is best consumed 60 to 90 minutes after waking. You can stretch it a little longer than that if you’d like, but you really don’t want to just get out of bed and have a big cup of coffee and a bagel, which is what a lot of people in the modern world do.

Then the harder part, and people hate this part because our culture is so anti is to cut out that evening alcohol, to cut out the evening snacks, to cut out the food that’s two to three hours before bed as much as possible. It doesn’t have to be a complete fast, but if you can do that, the more you can fast before bedtime, the better your metabolic markers will be. So doing a fast based on what maybe you would have done if you were alive 1,000 years ago, or when you go camping. Like for example, I just went to Peru, Machu Picchu, and we camped. We did the five-day hike. And I kept thinking about circadian rhythms through the whole day because when it was sundown, that was when you had your last meal because it’s not like you’re watching Netflix and eating popcorn. You pretty much end your meals at the end of the day, shortly after sundown was how we did it and pretty much ate nothing except for tea or water until the next morning. In the morning, we didn’t just roll out the bed and have a big breakfast ready for us. We packed up our things. We got ready for the day. We went to a place to sit down to have a quick breakfast, but it was at least 60 to 90 minutes. I thought wow, this is exactly how circadian rhythm biology works. It makes sense because except for the last 100 years, we were on that kind of schedule. Our bodies functioned optimally. When we release melatonin before bed, it’s not just our brain that has melatonin receptors. They’re in our pancreas, in our gut. There are receptors that say oh, it’s time to turn down. It’s time to focus on repair or renewal because it’s bedtime now.

Dr. Gabrielle Lyon [0:19:56]

In an ideal world, basically individuals aren’t not pushing a fasting to 11 or noon, assuming you wake up really late. What you’re saying is this is really shifting the window to when the sun is up, this is the time that you should be eating. I’m guessing that when the sun goes down, this is the time that you would stop, therefore, shifting the fasting and feeding window earlier may be of some benefit. But what you said was, it wasn’t just necessarily about the circadian biology, which again, is that 24-hour pattern, but it’s the impact on the microbes, the gut microbiome. That’s what I think is so fascinating. When we think about the gut microbiome and the interface with mood, you mentioned something called psychobiotics. Tell us what is a psychobiotic? What do we know from the literature?

Dr. Amy Shah [0:20:52]

This is the area that’s so shocking, that you can actually change someone’s mood simply by changing their gut bacteria. I think this kind of world has opened up the science. For example, now we know that if you transplant gut bacteria from a depressed human into a mouse, and a non-depressed human into another mouse, the mice will display depression when they get the microbiome from the depressed individual. The same thing has been shown with schizophrenia; you can actually create a situation where just the gut microbiome is transplanted into an animal, and the animal starts to display characteristics of schizophrenia. That, to me is just so crazy, because now we have it with Alzheimer’s. We’re looking at autism. We’re looking at cognitive decline. Not only just mood disorders, but we have anxiety, depression. What we’re seeing is there is a key aspect of mental health that’s located in that gut microbiome, and if you transplant it from one person to another, we could potentially change their entire mental state. Now in humans, it’s been shown in case studies. Mostly, there’s case reports. You need, obviously, larger studies, but it’s tough because transplanting a gut microbiome from one person to another, it has a host of issues, including the fact that the FDA has banned it, except for in cases of severe gastrointestinal infections. Repeated C. difficile is the only indication right now for a microbiome fecal transplant from one person to the other.

Dr. Gabrielle Lyon [0:22:56]

What does the evidence show as to why? Why do we see significant mood changes? Is it a neurotransmitter issue? Are these things crossing the blood-brain barrier? What do we believe that the interface is?

Dr. Amy Shah [0:23:14]

This is what’s so interesting. There’s a few different theories. Obviously, we know that the vagus nerve connects our gut to our brain; that is the strongest neurological connection. The neurological pathway from the gut to the brain, the direct link is the vagus nerve. But now, we know that there’s multiple other pathways, and one of the strongest pathways that we know is through our immune system. When our gut bacteria produce a very magical compound called the short chain fatty acids, so it’s a very short-chain of fatty acids in a certain sequence, the body takes that information, and it creates all kinds of changes. It’s anti-inflammatory. It goes to the brain. It changes the immune system. It’s basically like a calming veil of all of your inflammation, and it boosts your mood. We now know that increasing the short-chain fatty acid production through gut bacteria is one of the strongest ways to achieve mood change, achieve anti-inflammatory benefits, immune benefits. The big question is, how do we do that? We know that you can transplant bacteria, the good bacteria, from one person to another. That’s the fastest way to do it. But are there other ways that we can get more short-chain fatty acids, that we can get more bacteria that create short-chain fatty acids to boost our mood, to make us fitter, to make us feel less inflamed, and basically change our entire metabolism from that pathway? That’s the most promising.

Dr. Gabrielle Lyon [0:25:08]

How can an individual increase their short-chain fatty acids? What are the foods or the actions they can take?

Dr. Amy Shah [0:25:16]

One of the best actions is free; it’s exercise. Exercise is one of the most potent drivers of short-chain fatty acid production from gut bacteria. I always say the best probiotic is exercise. You’re making the gut bacteria that produce short-chain fatty acids super happy. They produce a lot of short-chain fatty acids. They produce more of themselves, so you’re increasing the amount of bacteria and the amount of short-chain fatty acids. We think one of the key anti-inflammatory effects of exercise actually is mediated through that gut bacterial pathway. Exercise is number one, probably, I would say, out of anything. Then of course, diet is equal or at least similar to exercise in creating short-chain fatty acids. There are many foods, including prebiotic fiber, probiotic fiber, that feed that quote, unquote, good gut bacteria that’s creating short-chain fatty acids. We know that some of the short-chain fatty acids are directly set to the brain to change our mood. We know a lot about short-chain fatty acids.

There’s also of course, an increase in dopamine or serotonin, that can change the mood in the brain. There’s interplay between the neurotransmitters and the short-chain fatty acids to create a change in your mood. When you say food creates mood, you’re seeing a huge milieu of changes in the gut that’s being translated into the brain. We know there’s at least four different ways that they communicate with each other, and there’s new ways discovered all the time. I got interested in it because when I was in medical school, we had an immunology small group session where we talked about why there was such an increase in autoimmune inflammation, allergic diseases in the modern world. The leading theory was because of the changes of our gut microbiome leading to immune and body changes. I thought, oh, my God, that’s crazy. We’re doing something very wrong to our gut microbiome because it’s creating all kinds of diseases, obesity, diabetes, but also autoimmune diseases and allergies.

Dr. Gabrielle Lyon [0:27:47]

That’s fascinating. Where do you recommend individuals get prebiotics as it relates to food, the prebiotic, probiotic? I’m curious as to what the listener could do, and also how much?

Dr. Amy Shah [0:28:05]

Probiotic foods are better studied. Probiotic foods are fermented foods, things like yogurt and cottage cheese. Then there are things that are non-dairy like apple cider vinegar that’s non-pasteurized with the mother, and then kombucha, kimchi, and natto; there’s a host of fermented foods. What we found is in new studies that the higher your intake of fermented foods, the more bacteria and the more diverse the bacteria become in your gut. In the beginning, when I would talk to people I worked with, I would say, oh start to get some yogurt into your diet. But now, the new studies show that you can really push this, like four to seven servings, and you’re really getting the highest level of microbiome changes. The problem with probiotics is there’s really no consensus on which probiotic or what dose; we’re still working on that. I still think that getting it through foods, because of the complex structure of probiotics and the way the foods carry it in a net, just you think about like a matrix, and the probiotics are in that food, it gets to where it needs to go faster and more effectively than just taking a pill version. I love increasing the amount of fermented foods in your diet. It can be as easy as yogurt. It can be as fun and complex making your own kefir, trying all kinds of new fermented foods.

The prebiotics is really a matter of eating more vegetables because prebiotic fiber is really the fertilizer for your gut. It’s a food that your gut bacteria eat, and then when they eat prebiotics, they can make postbiotics and all these beautiful things happen. The short-chain fatty acids get produced. You can eat that through vegetables in general, especially the stocks, but especially in things like artichokes and asparagus and chicory root. There is a special prebiotic called inulin that actually seems to be the magical prebiotic that produces more of the bacteria that even help in weight loss, which is so interesting, because I think people are really interested in newer, natural ways to control our weight. One of the best ways is to get prebiotics like insulin in your diet.

Dr. Gabrielle Lyon [0:30:47]

I think it’s so fascinating to think that humans can survive and thrive on a multitude of different dietary patterns. I’ve been reading a lot about urolithin A, I’m sure you’ve heard about it, the timeline is by far and away, I think it’s going to be the next big thing. But one of the thing that’s so interesting about urolithin A is that it’s an ellagitannin, so whether you’re eating pomegranate, or you’re eating walnut, or whatever it is that you’re eating that has these ellagitannins, only 40% of the population can actually make this compound in the gut microbiome to help support mitophagy or whatever is the desired outcome. I’m curious is if you’ve ever read anything as it relates to our people ingesting things like chicory root or ingesting things like Jerusalem artichoke, but individuals don’t have the same microbiome response because of the current foundation of whatever it is that their microbiome is.

Dr. Amy Shah [0:31:54]

Yeah, and I think that’s where the problem is. For example, with the evidence of probiotics improving mood, for example, it’s so variable. The studies are like, some people get a huge boost in their mood. It’s stronger than antidepressants. In other studies, it’s not as strong, and we think that part of it is the host. You may have a very strong, diverse microbiome. So when I give you prebiotics or probiotics, your mood instantly changes. But if you’re someone who has a depleted gut microbiome, you may have different effects from it. It’s not just like, you add this and now you get this result. What we’re realizing is you really have to systematically heal the gut, improve the bacteria, both in diversity and number so that it can start functioning for you. When we talk about exercise, we always talk about in a way that it improves your physique, muscle mass, and your brain health. But one of the strongest things it does is it improves that gut microbiome, which is what we’re trying to really foster so that we can get all these effects.


Dr. Gabrielle Lyon [0:33:18]

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That’s through the influence on short-chain fatty acids. Does it matter what kind of exercise, or is it contraction of the skeletal muscle? What is it?

Dr. Amy Shah [0:35:57]

We don’t even exactly know what signals it’s getting from where. We know that the contraction helps. We know that the blood flow helps. We know that both weight training and cardio or whatever the opposite of that is will stimulate that change. But we don’t know exactly if there’s an optimal type of exercise. We do think that having a regular exercise regimen, so when we’re talking about whether we’re doing steps, or we’re talking about 20 to 30 minutes a day, that seems to be the amount you need to start changing your gut microbiome in a positive way as well. The other thing I see people really noticing when they change their gut microbiome is that their food sensitivities change. People who couldn’t tolerate dairy or certain food items are able to do that, and then their autoimmune issues improve. There’s much more than just mood and physique. It’s like your overall health in general will improve when you improve this.

Dr. Gabrielle Lyon [0:37:11]

That, of course, is so critical. The challenge, I think, becomes, and I’m really curious as to how you do this in your clinic, we had the head of Cedars-Sinai’s microbiome institute, Suzanne Devkota on, incredible. She is really paving the way on some of this. We were talking, and she said there’s so many different bugs in this gut microbiome that the testing that we have is really lacking. Obviously, we use some basic GI Map testing in our clinic, and we do things of that nature, but the question then becomes is, how do we really get a handle to look at a baseline? What are your thoughts? Where do you think the emerging evidence is going as it relates to clinical practice?

 Dr. Amy Shah [0:38:05]

I agree with you, the clinical practice piece of this is the most difficult because there is no good test. Let’s put it this way, there is no reproducible, gold standard when it comes to gut microbiome testing. Unlike just testing your vitamin D level, we can’t just know what’s going on. It’s symptomology based, and even the improvement really now is symptom based. You can watch the changes longitudinally. If someone is having more Bifidobacterium, for example, in their stool, you can pretty much know that they have more growing in their gut now. So from point A to point B can be helpful, but there’s really no good slam dunk test. I think that’s where the science is going, though, I think if we could. I’ll just give the example. Someone out there, if you could say, hey, Dr. Lyon and Dr. Shah started with this many colonies of Bifidobacterium, and we got them to double, triple, quadruple, quintuple that, that itself would be really great information for us because we know that Bifidobacterium is one of the short-chain fatty acid-producing bacteria. If I knew that I could change that by five times by consuming this or doing this, that’s I think where the science needs to move is to really give us better direction on bio-individuality in people and how one action can create better change. I think that’s where it’s going.

Dr. Gabrielle Lyon [0:39:45]

That would be incredible. It just made me think individuals that are on SSRIs when you talk about the psychobiotics. It would be so fascinating to see if there are any medications in the future over the next 10 years that begin to combine this psychobiotic with actual psychopharmacology. That would probably be pretty life changing for people.

Dr. Amy Shah [0:40:11]

There’s actually a really good study looking at SSRIs combined with psychobiotics showing that the psychobiotic has actually improved even the function of the SSRI. I think it’s in-patients that are being treated. Of course, everybody has to check with their own physician, but I think it makes sense to really try to boost that gut bacteria, especially the strains that will help your mood so that you can combine forces. For example, we know lactobacillus, like in the yogurts, for example, and cottage cheese, and then the Bifidobacterium, we know that akkermansia, there’s certain bacterial strains that are psychobiotic. Why not employ these in our treatment protocol so that we can help? Again, it’s individual, so you have to know how healthy the person is. They have to be eating healthy, doing the exercise, doing the work. But then on top of that, really increasing these bacterial colonies can help them.

Dr. Gabrielle Lyon [0:41:17]

If, for example, someone has low akkermansia, could an individual just take akkermansia and then push the needle? When you’re looking through a test that you’ve got this patient sitting in front of you, and they’re having GI issues, they’re having mood issues, are there a handful of strains that you’re looking for that when you’re low, you’re concerned, and you know exactly what you’re going to deploy?

Dr. Amy Shah [0:41:44]

The science is not there yet. We can’t really say, oh, just add some akkermansia, add some Bifidobacterium. This is still to be determined. What we do know right now is that if you increase your gut bacterial diversity and number, you will see the benefits. You can see the benefits in as little as three days and over a few weeks and months’ time. For me, what it says is, hey, if you can change your diet, you can change your exercise, you can concentrate on really improving your gut health by not taking antibiotics if you don’t need it, not using gut bacterial killers if you can do it. We do know that creates good outcomes. Where the data stands right now is that if you can figure out where your gut health is lacking, or where your diet or your exercise or your lifestyle is lacking and start to fix that and improve your gut health, you will see improvements in your mood. You will see improvements in your metabolic markers. But to say, we’re not 100% sure right now, based on the studies, which probiotic should I be taking if I’m anxious? What about if I’m just tired all the time? What about if I’m perimenopausal? We have that data about which bacteria can be different, but it’s not as easy as just giving them that bacteria.

Dr. Gabrielle Lyon [0:43:20]

I think that’s really important to point out. You’re talking about this in the book, there’s a whole list of different kinds of foods and strategies to help diversify the gut microbiome, which I think is easy to do and profound because it can create such a positive impact, we hope, in the body. Individuals that live together, do they have the same microbiome?

 Dr. Amy Shah [0:43:46]

We always say we’re the sum or the best of the five people we spend the most time with. That absolutely goes for gut bacteria. For example, twins who are separated at birth, their gut microbe microbiome looks nothing like each other. It looks much closer to their family that they live with than the biological twin. We know that there’s a lot to be said about the people you’re spending time with, sharing food with, sharing microbes with. In fact, so much so that athletic performance is based on gut microbiome. If you spend time sharing food with, sharing microbiome with someone who has the athletic prowess that you want, you will start to get some of that gut bacteria. So that opens up a whole world. How do I get close to LeBron James, even though I don’t live with him, if he gave you his gut microbiome, you could start getting some of the athletic prowess that he has. It’s really exciting. It really gives more credence to the fact that you are so much like the people you spend time with, and I think we tend to think of that as just like a mental health thing, but it’s definitely a bacterial thing. Also, it tells you, you have little kids, and I do too, as a mom, it’s very important to share food with your child if you’re healthy, so not sick, don’t have cavities or an open wound because you’re building especially in the early window of their immune system and their gut development. You can really strengthen it by introducing healthy gut microbes to it.

Dr. Gabrielle Lyon [0:46:00]

I think what I’m hearing you say is Tom Brady is going to be wondering why people are always stealing off his plate after this podcast comes out.

Dr. Amy Shah [0:46:08]

Yes, exactly. Or his toilet.

Dr. Gabrielle Lyon [0:46:12]

Yeah, that or Tom. But it also makes me think, it should inspire individuals within a home to be the healthiest version of themselves because it’s not just the individual, but the individual’s impact on say, a spouse or a child. The next layer to that makes me think, our military. Our military spends a lot of time, close contact and gut health or microbiome assessment is not something that’s done. We’re definitely working on changing that. Then the next layer is athletic performance and first responders and those people that are all, as it relates to being in part in a team, also makes me think, mood challenges, just all of the things, potentially, this gut microbiome, this mood-gut connection, which you talk about, may be even exponentially more impactful than we are aware of. There’s a lot of talk about PMS and training and gut health. Is there a role that gut health plays in perimenopause, mood changes, PMS, or even andropause?

Dr. Amy Shah [0:47:27]

It’s very eloquent, the gut-immune-hormone-brain connection. It’s not eloquent at all, I’ll just say it. In the studies, they talk about this as it’s a neuro-endocrine immune interaction that’s happening in the gut all the time. When you’re looking at what we talk about as hormonal imbalance, or we’re talking about what’s happening to the liver and the gut during perimenopause, it’s that interaction. As you may have heard, and a lot of people have heard, your estrogen levels and how you detox estrogen out of your body has a lot to do with the gut bacteria that’s present. We have this thing called estrobolome in our gut that helps us with our estrogen balance.

For example, for me personally, I’ll tell you, that what I thought were all hormonal symptoms, because I was a young busy mom and I thought, oh my God, my cortisol is off. I’m estrogen dominant. I was reading all these things online, nothing I have learned in medical school. But I realized after years of looking into this, that it was my gut that was really imbalanced. When I started to fix that, the hormones, the immune system, the skin, the metabolism, all kind of fixed itself. So starting with that is where I would tell people to start. If you’re feeling tired, if you’re feeling like your hormones are off, that’s where you should start because most of the hormonal symptoms that we’re feeling are coming from that gut interaction with the hormones. Absolutely, perimenopause is a doozy, and we need to talk more about it because not enough people are talking about menopause and perimenopause and what happens, not only just to our gut, but to our moods or metabolism, to our entire bodies during this time.

Dr. Gabrielle Lyon [0:49:32]

This is a really tough question, and you can say pass or whatever you want to say. Oftentimes, when we think about body composition, I personally think about calories in, calories out with an appropriate macronutrient balance. It would be challenging to not address or not acknowledge that gut microbiome probably plays a role in whether it’s calorie absorption or calorie utilization. I’m curious as to what percentage of obesity or these kinds of difficulty losing weight is related to the gut microbiome versus say, a calories in, calories out? It’s obviously probably all together, but I’m just curious in terms of hierarchy of importance.

Dr. Amy Shah [0:50:30]

I’ll give you an example from the research because I think this can frame the conversation. If you give mice gut bacteria from an obese human, and you give the other group of mice, gut bacteria from a lean human, and you let them eat freely, the mice that received the obesogenic gut bacteria become obese. The mice that received the microbiome from the lean individuals stay lean. They’re allowed to eat freely. They’re allowed to exercise freely and do whatever they want. It just tells you, oh, whoa, there is a complex communication happening. Like we’ve said, it’s like the hormones and the immune system and the nervous system are all communicating through this, if you think about it, kind of a central command center. To me, when you hear that, and I’m a believer, too. If you change your diet, you’re eating the appropriate calories and macronutrients, staying away from ultra-processed foods, that you too can change, that anyone has the ability to change their weight balance. But when you hear that, research is just mind blowing to me that there’s interplay. What’s happening is there’s genetic changes that are happening on the epigenetic level. There are hormonal signals that are being sent, and there’s these anti-inflammatory, like the short-chain fatty acid thing that we’re talking about, that really is a central player in weight as well. That just tells me there’s a whole world out there that we haven’t explored yet for weight loss, and these GLP-1 agonists are just the beginning of gut-based hormonal modulators of weight.

 Dr. Gabrielle Lyon [0:52:29]

The GLP-1 agonists or Ozempic, we’re hearing a lot about it; semaglutide also known as Ozempic, also known as Wegovy. Do you use them in the practice? Do you have a stance on the effectiveness, the input on the gut microbiome? What are your thoughts?

Dr. Amy Shah [0:52:53]

I think it’s so interesting because it stimulates GLP-1, and what GLP-1 is exactly this conversation that we’re having is that our gut sends signals to our brain that we’re full or hungry, and we stop eating. What I love about it is that it’s turning our attention to saying like, oh, wait, it’s not just don’t go to the McDonald’s. You can’t just tell a patient, stop doing what you’re doing. It’s about the hormonal signals that they’re getting, and in a lot of people, it’s altered. If we could give them a gut microbiome transplant, amazing. But until then, there are going to be medications and other things that can do this. I don’t have a moral stance on it because I’ve realized that as a physician, I can’t have a moral stance on people who are carnivores or vegans or vegetarian or gluten-free. It is a medical choice that you make with your physician. If someone comes to me, and they say, I’m taking this, I don’t say to them, you’re taking the easy way out. I’m not giving it out like it’s an easy solution for everyone. I think that it’s super individual. But like a lot of obesity medicine that physicians have pointed out to the general public is that you wouldn’t deny blood pressure medication to someone who’s tried everything but can’t get their blood pressure under control. You wouldn’t say, oh, sorry, you need to try three more diets before I’ll put you on a medication. It’s the same thing with someone who had a heart attack. You can say, yes, change your diet, change your exercise, but I’m also going to give you aspirin. So I think it makes sense to put it in the arsenal for patients who are obese. Should the general public use it? That’s a different conversation.

Dr. Gabrielle Lyon [0:54:46]

I think that what you’re pointing out is true. As a physician, it is definitely not our place to judge. Second of all, the idea that these GLP-1 agonists that were targeting weight loss focused on the gut above and beyond just the impulse to eat, whether it’s hunger or cravings. I think that these drugs are very beneficial, whether it’s semaglutide or tirzepatide. I think that these drugs are definitely going to pave the way and highlight a lot about what you’re talking about, this gut-mood, gut-weight connection as a central focus, this gut microbiome, which ultimately is what is going to be leveraged in these medications, or at least in part. I do want to mention, people are saying, oh, well, I am concerned about trying Ozempic or concerned about trying semaglutide because of its effect on muscle mass. I have scoured the literature, and I have not found one mechanism of action that shows that this GLP-1 agonist negatively affects skeletal muscle mass. If you are training, as Dr. Amy was talking about, if you are eating a protein-optimized diet and taking semaglutide, obviously check with your physician, but there is typically no reason why an individual would be also losing muscle.

Dr. Amy Shah [0:56:18]

I’m curious about your take in general. That’s actually a really good point because I think that’s one of the projected downsides of using it in a non-obese or just using it in general. But what are your views about the GLP-1 agonists? I’m curious.

Dr. Gabrielle Lyon [0:56:37]

We use them all the time in the practice. I think that they are very advantageous. I think that there is a possibility to help reset hunger cues. Browns, white fat, I think that they’re also very promising as it relates to changing body composition with the right strategies.

 Dr. Amy Shah [0:57:01]

I talk a lot about these natural ways to control your appetite, for example, releasing GLP-1, but also CCK, neuropeptide-Y, and leptin. There are actual studies that show that you can augment the release of all of these satiation hormones. I talk a lot about what are the things you can be doing, the supplements, the foods, the activities, that you can feel more satiated? Something as simple as sleep increases your leptin levels by many fold. Getting adequate sleep should be the base of somebody who’s trying to improve their body composition.

Dr. Gabrielle Lyon [0:57:53]

Absolutely. When you and I were on call, though we weren’t on call together, remember night float? I had to say, I don’t know if you guys ever had night float, it’s where you’re up all night. It’s part of the deal in training. I am telling you, I could not regulate my hunger at all. I didn’t care if it was protein. You’re up and not getting to sleep, even though your quote, supposed to be sleeping during the day. It doesn’t really happen. I’m curious as your time in clinical practice over a period of time, has there been anything that you’ve changed your mind on that has just totally shocked you? Again, Amy, what I love about you is that you are a clinician in clinical practice.

Dr. Amy Shah [0:58:33]

I think what you’ll appreciate about this, is because I think you talk a lot about this, is that when I was growing up, I was vegetarian. That’s how I grew up. I was born into a family that was following a lifestyle practice called Jainism.

Dr. Gabrielle Lyon [0:58:56]

I’m actually very familiar with that.

Dr. Amy Shah [0:58:58]

Yeah, so no harm to any animals or plant life if you can. I really did start to look more into being a vegan or being more plant based. I think what I realized that for myself personally, when I started to add more protein to my diet, I found it really difficult to find a lot of vegan non-dairy plant sources. There are so many, and you can be very creative, and not to say that there’s so many even bodybuilders. What I did is I just I said, you know what, I’ve never eaten meat. I don’t want to eat meat, but I think that for me, now that I fixed my gut health, I can start incorporating dairy sources of protein, some egg sources of protein, and go to the lacto-ovo. I’ve changed my stance on dairy. I’ve changed my stance on eggs because I’ve realized wow, even the American Heart Association says, you know what, if you’re vegetarian and you want to eat eggs, that’s actually really healthy. It’s heart healthy. They’ve changed their stance, and for them to say that is a big step. It’s the same with dairy. Low-fat dairy, or just dairy in general, has had a really bad reputation over the years. People say, don’t eat dairy; they’re so inflammatory. I think what I’ve realized is that the data doesn’t really support that.

Dr. Gabrielle Lyon [1:00:31]

It doesn’t support that at all. We eat dairy all the time in our house, and we eat low-fat dairy. We do try to keep our overall fat content, or at least I do, low. The kids are–

Dr. Amy Shah [1:00:43]

They’re on their own journey. Even with gluten, I don’t feel like everyone needs to be gluten-free and not everyone needs to be dairy-free. It’s just ridiculous to tell an entire population of people, in my mind, based on very little or no data to say that they should be on gluten-free diet just because, that kind of thing. I saw much change in nutrition over the last 20 years. I think that to stay ahead of the trends, it’s really hard because things are changing all the time. But those are a couple of things that I’ve changed in my life.

Dr. Gabrielle Lyon [1:01:24]

I love that. What I’m hearing you say is there’s a lot more flexibility that perhaps start with the anchor of your own health, whether it’s gut health, whatever, and there is more flexibility as it relates to those kinds of things.

Dr. Amy Shah [1:01:39]

Yeah, and I think that if your goal is to be happy, to look better, especially through your older years for women, your goals might look different than they did when you were 15, 16, or 25 even. Change that with your goals in mind. My goals are good, better gut-brain connection, so improving my gut health, improving my brain health, improving my muscle mass as I age, and really keeping myself primed for longevity.

Dr. Gabrielle Lyon [1:02:16]

I love that. As it relates to gut health, do you believe or have you seen in your clinical practice– we use a lot of Xifaxan. I think there’s a lot of good data, and that this is a medication for SIBO, which is not actually systemic; it’s local. Do you think medications like that are effective, or you like to see a more natural approach to somewhat of a gut microbiome reset?

Dr. Amy Shah [1:02:47]

That’s a tough question. I think that we don’t yet have an exact protocol for everyone. I think that gut health is like nutrition, in that there are some people who are going to respond immediately through dietary changes. There are people who are going to need medication. there are going to be people who need a combination approach. I think the best things that people can start with is changing your diet, improving your circadian rhythm alignment, so getting sleep, getting sunlight, getting movement, and then fasting. Those are things that everyone can do to start and then see what’s left. There’s going to be people who need medical treatment for their mood, SIBO, or GI illnesses. But I think we start with the base and go from there. For me, whenever I go back to the base for myself or for the people I work with, you really fix those things first, and then we move on from there.

Dr. Gabrielle Lyon [1:03:49]

You fix those things first, and let’s say an individual has some kind of pathogen, whether it’s a bug like Entamoeba histolytica or something like that, would you still say let’s look at the fundamentals, or are you going to treat and then build the fundamentals as you’re doing it? Do you think that the body can rid itself?

Dr. Amy Shah [1:04:10]

I think it depends on the situation, like H. pylori, for example, you have to treat it. I just think of that, and it’s like, there are certain things that you can’t really just let them write it out. SIBO is a tough one. I’m not sure. That one is really dependent on the person sometimes just doing a diet overhaul. But if it’s something that’s been going on for years and years, or there’s some part of their diet that they’re not willing to change, for example, I had a patient who was doing an amazing job with their diet and lifestyle but could not quit the alcohol. Alcohol was regular, and we now know that even at small doses, even at moderate amounts, it can damage the gut microbiome as well as create negative brain changes, and muscle, all kinds of changes, and so we couldn’t get past that. There was a role for medication, but there’s other people who can really just change their entire gut microbiome through a rapid and extreme change in their diet and lifestyle. That Nature study is so landmark. There’s a Nature study that says that they took two groups of individuals, and they had them rapidly change their diet over a course of 14 days. They started to sequence their microbiome every day, and they saw that by day three of a completely different lifestyle and diet, that group had already started to change their gut microbes. It’s really quick, and you can start to see the changes almost instantly.

Dr. Gabrielle Lyon [1:06:04]

That’s incredible. That’s where it’s wonderful that you’re a physician, and you have the capacity to prescribe if you needed to, or if you didn’t, and you were going to try a natural approach. For those listeners, SIBO is small intestinal bacterial overgrowth. It’s something that I’m sure Dr. Amy sees all the time. I see it all the time, and it really does affect the way people feel and absorption, all of those things. That’s really helpful that it is individual, and it’s very much as the individual. Last question, I know that you’re in the middle of clinics, I want to make sure that we keep you on time. We had a little tech difficulties here; who knows why, but it happens. Why this book? Your first book, which I love these titles, Why Am I so Effing Tired?, and now this book, Why Am I So Effing Hungry?, was there something that happened or something that you saw where you said, I’ve got to figure this out? Is there a moment?

Dr. Amy Shah [1:07:03]

My moment was when I was early in my practice, and my kids were really young; they’re toddlers. I just felt out of control. I was tired all the time. My hormones felt out of whack. I felt like I was always in this constant fight or flight mode. I had a very serious car accident one day when I was going to pick up my kids. After that, I had to pause because the car was wrecked. I couldn’t go to work. I was injured. Thankfully, I survived that accident, but what that taught me is we don’t have our whole lives. We may have just today. Today might be your last day or tomorrow. I thought to myself, I need to fix my life. I need to be doing what I really want to be doing. I need to feel the way I want to feel. I need to live the life instead of just saying, oh, well, I’m too busy to even make a change. That really got me to thinking, what is it that I really have learned over the years that I want to share with people? Those books really came out of the fact that I was tired all the time, here’s what I did to change it. Then this brain-gut-immune phenomenon that’s going on over the last 10 years really changed the way I think about the future of health. I felt like there was no place where it was put together for someone to say, hey, let me go and try some of these things to improve my mood, to improve my hunger, to improve my body that they might not get anywhere else.

Dr. Gabrielle Lyon [1:08:53]

Well, I love it. The book is very well done. Where can people find it, find you, all the things?

Dr. Amy Shah [1:09:00]

Oh, thank you. First of all, I’m so happy that we’ve virtually connected. I feel like we are so connected, but we don’t get to connect as much in real life, so it’s been a pleasure. Thank you for having me and for taking the time. My website is My Instagram is fastingmd. My other social media is @amyshahmd.

Dr. Gabrielle Lyon [1:09:28]

We’ll link all of this stuff, and I’m going to see Amy in real life in a few weeks, so maybe we’ll even jump on a live if you guys have questions. Dr. Amy Shah, thank you so much for making time. I know how busy you are. I greatly appreciate it.

Dr. Amy Shah [1:09:44]

Thanks so much for having me.


Dr. Gabrielle Lyon [1:09:48]

The Dr. Gabrielle Lyon podcast and YouTube are for general information purposes only and do not constitute the practice of medicine, nursing, or other professional health care services, including the giving of medical advice. No patient-doctor relationship is formed. The use of information on this podcast, YouTube, or materials linked from the podcast or YouTube is at the user’s own risk. The content of this podcast is not intended to substitute for professional medical advice, diagnosis, or treatment. Users should not disregard or delay in obtaining medical advice for any medical condition they may have and should seek the assistance of their health care professional for any such conditions. This is purely for entertainment and educational purposes only.