Microbiome MASTERCLASS: An Essential Guide to a Healthier Gut

The microbiome has become a buzzword. Microbiome. Microbiome. Gut microbiome. Gut microbiome. And with good reason. But what exactly is the microbiome? And why is it so important? Well, let me start you off with a fascinating fact. Did you know that your body is just as much bacteria as it is human? What I mean by this is for every single human cell in your body, there is at least one bacterial cell. Basically, you're half human and half Wahoo Petri dish. And that's not even counting the trillions of fungi, viruses, and other microbes living on and inside you. Collectively, these tiny organisms make up your microbiome. And they don't just sit there. They shape your health, influence your mood, and even control your behavior. Some scientists have even gone as far as to call us meta-organisms, because we aren't just human, we're walking, talking ecosystems. Your microbiome is as much you as your heart, liver, or kidneys. Now, in this video, we are gonna explore together why your microbiome is so crucial to your health, citing some stunning science-backed examples. We're also going to talk about how to tell if your microbiome is out of balance. Scientifically, this is called microbiome dysbiosis, and the answer might not be what you expect. Then we're going to talk about what all those gut health buzzwords actually mean. Decoding terms like prebiotic versus probiotic versus postbiotic, fermented foods, and more. Then we're going to talk about the practicals—how to take care of your microbiome, including surprising ways your mind can directly influence your gut. Yeah, top-down control. Then we're going to talk about where the future of microbiome science is headed, including cutting-edge microbiome transplants—yes, you heard that right—and smart toilets. I won't promise you you'll be a gut health guru by the end of this video—if there even is such a thing. I'm inclined to think there isn't. But you will walk away from this video with a clearer understanding of what the microbiome is and practical steps to improve your health by focusing on your gut. So with that, let's dive in and digest some information together, starting with Part 1: Why is the microbiome important? Well, let me answer that question with another question, something I alluded to already. Why is your heart important? Why is your liver important? Why are your kidneys important? They're all Organs, pretty vital organs, and your microbiome is very much like an organ too. It's a combination of cells that serves critical functions in your body. You couldn't live the same without them. And the microorganisms in your gut, they help process nutrients, protect you from disease when you're healthy, and contribute to disease when you're unhealthy. They also secrete hormones that can impact everything from your skin to your bones to your brain. You may have also heard of something called the gut-brain axis. This refers to the lines of communication between your gut and your brain that influence health, disease, and yes, behavior. A dysfunctional gut microbiome is thought to contribute to neurodegenerative diseases like Alzheimer's and Parkinson's disease and mental health disorders. Like depression, anxiety, schizophrenia. Really, your microbiome controls basically everything brain and mind, or at least influences it. And here's one stunning example from New Science. A recent study suggests that the microbiome can influence food addiction behavior. Now, in this study, which I cover in more depth in another video on this channel, researchers found that a particular gut virish alters the behavior of gut bacteria, which in turn changes brain activity, human brain activity, and influences food addiction behavior. It's pretty wild, right? This is not a joke or an exaggeration. It's hard published science. In fact, don't take it just from me. In the other video, which you should definitely watch, we include an exclusive clip right from the senior researcher of the team that published this paper. So if you want more details and to hear from the horse's mouth, check out that video once you're done here. Anyway, I really love this example because addiction is something we associate with willpower, something ephemeral, a function of the abstract human mind. But if the microbiome can influence the mind, then isn't it fair to say it's part of who you are. In 8 short words, your microbiome is part of who you are. Tell me in the comments if you agree. Alternatively, and this is semi-joking aside, if you want to point the finger for your late-night ice cream binge on evil bacteria in your gut rather than a lack of willpower, well, I won't judge you for it. Anyway, moving on. Part 2: What are the signs of an unhealthy microbiome, microbiome dysbiosis. All right, you ready for a crappy answer in addition to that crappy pun? Well, an unhealthy microbiome is simply the microbiome associated with poor health. How's that for a chicken and the egg scenario? Now, I know at first that answer will seem unsatisfying. Top of mind for many people is the question, how do you know if your gut is healthy or if it's quietly working against you. And so you want a list of signs and symptoms that you can look for to determine, are you in balance or out of balance? But because the microbiome can impact so many elements of our health and is so diverse among individuals and largely still a black box in science, it's very, very difficult to pin down a precise array of signs and symptoms. We can find interesting associations between certain gut bugs and states of health, but at the end of the day, it's all very individualized and empirical. Let me elaborate with an interesting example of a patient I knew. This patient lost over 50 pounds by cutting sugar out of her diet. She was doing great, and her sugar cravings actually vanished. But after 6 months, they came back. The cravings came back with a vengeance. So she asked herself, "What changed?" And what had changed is she'd reintroduced artificial sweeteners, like the occasional diet soda. And the crazy part was she wasn't even drinking the diet soda daily, just once or twice per week. But the cravings persisted every single day. And then when she cut out artificial sweeteners again, the cravings disappeared. Interestingly, thereafter, she tried instead a natural sweetener, stevia in this case, to see if it would have a similar impact as the artificial sweeteners. It didn't, suggesting this wasn't just a matter of sweet taste driving cravings acutely, but something else. And research shows that artificial sweeteners, like aspartame or sucralose or saccharin, they can mess with the microbiome and can lead to metabolic dysregulation. So could it be that the diet soda she reintroduced changed her microbiome to reawaken her cravings? And perhaps it was a microbiome shift from sugar elimination and sweetener elimination that made her cravings disappear in the first place. Pretty interesting. You can listen back to that if you want and really think about that patient case because I think it's a cool one. But here's the point I'm trying to make: The gut is central to health. Even if we don't know exactly what a healthy gut looks like in every person, the practical approach is to ask yourself this question: How can I treat my gut better to improve symptoms I care about? Then start your own experiments and observe your results. You might notice that gut-targeted protocols could alter your cravings, mood, sleep, body composition, and so much more. In a phrase, since the microbiome is so individual, you need to be your own scientist on your own body. And I'll give you some tools to play with in a moment, after we decode some of the jargon you should know. So, that brings us to Part 3: Decoding the Jargon: Prebiotic, Probiotics, Postbiotics, and More. Now, warning, this section will be a bit drier, kind of like a bad fiber supplement. But I thought it was warranted since scientists like to toss around terms like we're 12-year-olds in the summer having a water balloon fight. And of course, we love making the biggest possible water balloons. As a case in point, pneumo-ultramicroscopic silico-volcanoconiosis. That means lung disease contracted from the inhalation of very fine silicon particles from a volcano. It's basically the nerd equivalent of ego lifting at the gym. As many letters as you possibly can cram in a single word. Thankfully, these terms we're going to review aren't as bad. See what I did there? Kind of primed you with the harder term so we can go a little bit gentler. Prebiotic. What does prebiotic mean? Pre means before, and prebiotics are non-digestible food components that come before, upstream of gut microbes, and are thought to promote the growth of beneficial gut bacteria. Examples include inulin and resistant starches. Probiotic. Pro refers to promoting, and it's easy to confuse prebiotic with probiotic, but whereas prebiotics are non-digestible food components, probiotics are living bacteria that support gut health. Fermented foods like live culture yogurts, kefir, and fermented vegetables like sauerkraut and kimchi are probiotics. I have a whole different video on fermented foods if you want to check that out. And postbiotics. Post refers to after, and postbiotics are the things that come after or downstream of gut microbes and are bioactive compounds produced by microbes that ultimately execute on their health effects. Examples include short-chain fatty acids , enzymes, and peptides that support gut and whole body health. And since I mentioned short-chain fatty acids, these are very small fatty acids with fewer than 6 carbon atoms. They can be made from the fermentation of fibers or consumed directly from foods like dairy. The main short-chain fatty acids are acetate, propionate, and butyrate. Butyrate is actually, as a fun fact, derived from the Greek word for butter. And yes, you can get butyrate from butter as well. These short-chain fatty acids can provide energy to gut cells, reduce inflammation, and overall support metabolic health. And as another fun fact, I bet you didn't know that gorillas actually get a majority of their energy from digesting fibers into short-chain fatty acids. About 57.3% of gorillas' energy, according to one study, come from SCFAs. Thus, one could argue gorillas are actually on a high-fat diet, sort of. But unless you have a gorilla's colon, you probably can't pull off this fermentation feat. But now you do have an extra fun dinner party fact. Now, fermented foods. Fermented foods are those that have undergone fermentation, a process whereby microorganisms, like bacteria, yeast, or fungi, break down sugars into compounds like organic acids, alcohols, and gases. Basically, we let microbes digest part of our foods for us, and then we eat it anyway. Kind of like baby birds. Delicious, right? Examples include, as I mentioned earlier, kimchi, sauerkraut, natto, kefir, and for more on fermented foods, I have this video specifically devoted to it. So after you finish this video, watch that one. Now, fermentable and non-fermentable fibers. These terms are somewhat self-explanatory, but I'll explain them anyway. Fermentable fibers can be broken down into short-chain fatty acids and gases, and non-fermentable fibers pass through the gut largely intact, aiding in stool bulk and regularity for some people. But don't get trapped into assuming that fermentable fibers are better. That's overly simplistic. They're a double-edged sword since the gases made by the fermentation of fibers can cause some people really unpleasant gastrointestinal distress. For example, some people get terrible bloating when they have broccoli or cauliflower, which are high in oligosaccharides that can be broken down into gases and generate bloating. And sorry if this is TMI, too much information, but speaking from personal experience, no amount of prebiotic and potential health benefit is worth having the toot train going when you're on a date or trying to have an intimate experience with your partner. But that then begs the question, what can you do, or what can you do-do, to change the gut microbiome profile? Enter our last Shark Week term, fecal microbiota transplants, or FMTs. This is a medical procedure where fecal matter, yes, poop, is transferred from a donor to a host. The idea being to transplant the microbiome like you transplant any other organ. Now, currently it's only medically approved for Clostridium difficile infections, but I think it has far broader therapeutic potential. The issue is, it's not as easy as you might think to actually do. You need to prepare the donor with antibiotics to wipe out existing colonies in preparation to seed new ones. The delivery systems can be oral or rectal, neither of which are simple per se. And you do need to seed a new microbiome. To do this, you probably need multiple —regular donations—for many use cases, rather than a one-time dose. So how often you need a donation to truly establish a new colony, what dose, and how to store the samples are all open questions. There just aren't great protocols. In brief, FMTs are not, nor should they be widely practiced and prescribed now. However, my opinion is that they are a treatment that deserves further rigorous research because they have serious potential. So let's put a pin in that for now because there are other safer ways to get your microbiome in shape, which brings us to part 4, how to get your microbiome in shape. And technique 1, we're gonna talk about something I mentioned already, fermented foods. Fermented foods can increase microbiome diversity in some people and tend to be anti-inflammatory. Again, I have a video specifically on this topic that I'm going to refer you to for more. But one thing I'll add is it may be wise to introduce these fermented foods slowly to reduce chances of GI upset. Start with, for example, a half serving of fermented food—sauerkraut, natto, or kefir—per day and build up your microbiome resilience over time, kind of like you're sending your gut bacteria to the gym. Just like your muscles should adapt to lifting progressively heavier loads—that's called progressive overload if you're a gym rat—your microbiome may adapt to handling more fermented foods as well. So introduce them slowly. Honestly, depending on your starting point, it might not work that simply and cleanly, but I still think it's a fair analogy and mental model to get you started. Alright, 2. Fiber. I know I'd get skewered if I didn't mention fiber, so I'll go over it briefly. Honestly, I personally am not convinced that fiber is necessary for a healthy gut. And the data show that in some people, fiber can even be inflammatory. What I will say, and I'm sorry if this seems like a cop-out and kicking the can down the road, but most "experts"—heavy quotes there—will suggest you do need fiber for a healthy gut. Whether or not I'm convinced by the data is actually immaterial for for our purposes, but I think it's fair to acknowledge the majority opinion is that one, that fiber is good for the gut. That said, it's also important to point out science is not a democracy, although it operates like one sometimes, unfortunately. Anyway, what I can say with certainty is that there are those who respond poorly to fiber and do better, at least over shorter time courses, with fiber elimination. For those individual human beings, I think it's a fair and legitimate choice to eat a lower fiber diet. You can't blame people for doing what makes them feel better. And again, in my opinion, it's possible to have a healthy functional gut without eating loads of fiber. That said, for most people, based on the majority of the data I've seen, I would say eating a diverse array of real foods Rich in fiber, not fiber supplements per se, is more likely to offer benefits than harm for your average person. But one cannot make a blanket statement about fiber being good or bad. It is highly individual. And I'm sorry if that answer is like a bad bowel movement, unsatisfying. But for more on this hairy topic, please feel encouraged to see my full video on fiber facts Myths. It's also linked in the video notes. I thought that deserved its whole separate video. Now, like a good bowel movement, let's move on. Processed foods. More important than your gross fiber intake is, in my opinion, avoiding the broad class of foods known as ultra-processed foods. Given the lack of a long-term safety testing on the vast majority of additives in our food, it's almost certain that some or many contribute to gut dysfunction and thereby poor health. As a case in point, one study showed that the most common food dye in the world, Red 40, can contribute to inflammatory bowel disease in predisposed mice by altering the activity of an inflammatory molecule, IL-23, that is also the target of medications used in humans to treat inflammatory bowel diseases. Now, can I say for certain this mechanism is at play in human beings? No. But that's actually the point. It's very hard to prove causal connections in human beings, given that you can't practically conduct randomized trials, and confounders in our food environment are more plentiful than chocolate at Willy Wonka's Chocolate Factory. So in my opinion, the precautionary principle applies. And I haven't met anyone who thinks your gut wouldn't be better off by reducing ultra-processed food intake and eating as close to possible a real whole foods diet. Now, there are some well-formulated gut-friendly processed foods. So I wouldn't say it's a hard rule that you can't eat processed foods. But for beginners, I think it's a good guideline. The simpler the ingredients, the healthier the gut. Okay, moving on. 4. A carnivore reboot. Another topic that's arisen in this space is that of a carnivore diet gut reboot. The idea is actually pretty intuitive. If you think you have microbiome dysbiosis or an unhealthy gut, you can try to starve off the bad bacteria by going on a carnivore elimination diet of only meat, fish, and eggs for 6 to 8 weeks, and then slowly you can try to build back a a fresh, healthier microbiome by slowly reintroducing things like fermented foods. The idea is to build back slowly and see how far you can go. Anecdotally, I've heard this works for some people, but it has not been rigorously studied. It just makes sense on a high level. I'd love to see some protocols on this developed, but they haven't been yet. Nevertheless, I thought I'd share that possibility. Alright, 5. A word on antibiotics. This is a topic on which I don't want to mislead people because antibiotics can be lifesavers. And sometimes we do need them. But other times, the cons may outweigh the pros. What I would say is antibiotics can screw with your microbiome and lead to really unpleasant side effects, some of which may never go away. I speak in part from personal experience. When I was a newborn, I had a terrible fever at about 106°F, and I received intravenous antibiotics, which we now know massively increases your risk of developing inflammatory bowel disease like ulcerative colitis decades later, which I did end up developing at age 21. Thus, we—me, my parents, my medical team—think my early life antibiotics may have screwed up my microbiome. Possibly for life. And I'm not saying it was the wrong medical decision for me at the time. I'm just saying antibiotics can cause harm. That is actually not controversial. Nor is it controversial for me to say to you, you should ask your healthcare team about the real risks and real side effects of any medication, antibiotics and beyond, you may be offered so you can partake in the cost benefit analysis, and make an informed decision for yourself. Reasonable, right? All right, 6: Your mental health changes your gut. This is really cool. While we all intuitively know our gut feelings can impact our mood, our guts and brains have a bidirectional relationship. What I'm really trying to say here is your mind can talk to your gut and influence your gut and microbiome health. Let me give you two examples from recent scientific literature. A recent study showed that the brain can alter levels of a molecule called indole-3-acetate, or IAA for short, that can effectively poison stem cells in the lining of your intestines, contributing to poor gut health and gastrointestinal symptoms. Specifically, psychological stress activates the fight or flight branch of the nervous system and causes changes in microbiome function. This increases levels of the indole-3-acetate molecule, which in the gut harms the energy-producing mitochondria in intestinal stem cells, leading to stem cell failure and contributing to poor gut health. And this IAA molecule is actually elevated in patients with mental health conditions who likewise have higher levels of gastrointestinal upset. It's pretty cool. And if you want more on the science, you can see this video. Now, moving on, another recent study found that stress changes activity in the brain. No duh, right? But this can cause a brain region called the central amygdala to signal via the vagus nerve, the 10th cranial nerve, from the brain to glands in your intestines called Brunner's glands. And Brunner's glands secrete mucin, which helps feed bacteria. And stress, via this brain-to-gut axis, inhibits Brunner's glands, which starves off specific good gut bacteria. Altering the microbiome and leading to bloating and other unfortunate symptoms. If you want more on those data, see this video. If this blows your mind, tell me, or even just drop a mind-blown emoji in the comments. Help out with the algo. But what does this mean practically? Practically, this means that relaxation techniques like breathing exercises, yoga, meditation, and sex, and user-specific relaxation techniques, like for me, watching a Harry Potter movie, can actually be a gut health hack. Pretty cool, right? All right, finally, part 5: the future of microbiome science. I want to end with some forward-looking thoughts about what I imagine the field will look like in 5, 10, or even 20 years, and what research I'd like to see prioritized. I've already mentioned fecal microbiota transplant protocols, so I'll jump over that. But another thing I think we will see developed is more accessible and widespread access to personalized microbiome testing protocols to inform individual approaches to your microbiome. Specifically, I'm imagining microbiome analyzing toilets, linked to an app on your phone that tells you how your microbiome is changing day to day, movement to movement, as a result of dietary and lifestyle interventions. That would be an incredibly cool and powerful tool. And I think it's coming quick, kind of like a bowel movement after too many laxatives. I also think the field is rapidly broadening to include factors beyond just the composition of the bugs in your gut. In fact, more important are the compounds, the metabolites, the bugs in your gut create. That's because the same bugs can serve very different functions in different ecosystems, and you are a unique ecosystem. So I think we're transitioning to have our focus on what is called the microbial metabolome, the sea of metabolites produced by your microbiome, including complex arrays of secondary bile acids, various signaling molecules, and hormones that can impact everything from calorie balance to brain function. The science of the microbiome is still evolving, that's for sure. But one thing is clear, your gut is a central player in your health, your metabolism, your mood, and your behavior. While researchers continue to unravel its mysteries, you do not have to wait for all the answers to start optimizing your gut today. The best approach: experiment. Experiment, observe, and personalize. Your microbiome is as unique as your fingerprint, probably more so. So the key is figuring out what works for you. And if you want to stay ahead of the latest research, hit that subscribe button, please. I really enjoy synthesizing and communicating information in as clear, engaging, and as nuanced a manner as possible for you. And I can only do this and only have this opportunity because of my community's engagement, your contribution. The more of you who join our Metabolic Health Army, the more I can scale this up, scale what I do. And reach more people and fire up more initiatives like teaching other doctors and medical students about the importance of metabolic health and hopefully have a positive impact on making metabolic health mainstream. So if you can do me one kindness, it would be to subscribe. Subscribe and engage. Thank you and have a lovely gut-healthy day. Stay curious.