Transcription
Hello, hello, hello, and welcome to the first ever Dan talk about the microbiome. Very excited about this, and we still have people signing in, kind of letting in. I can see the folks come in, so maybe I'll just delay for a few seconds and chitchat about something while people come in. Oh, so much to talk about, I don't even know where to start.
But let's get the recording going. And I've really left, I left the country and I went to Thailand. They lived in a monastery for a couple years, got my head together, came back. But you know, ever since Dad died, I feel definitely like, um, you know, I enjoy and have always had older male teacher role model people. And true to form, I have a new one now. His name is Dr. Richard Lord. He wrote this book called Laboratory Evaluations for Integrative and Functional Medicine. And Richard and I have been working together for a couple years, and it's an interesting relationship. You know, if he's the best teacher I've ever had, he's one of the most knowledgeable scientists in the field of functional medicine. He literally wrote the book that every doctor uses, right? Every doctor in functional medicine has this book on their desk, whether they've read the whole thing a hundred times or not, that may vary. But this is the book of clinical lab, really the only book of its kind. And to now have Richard as a mentor and teaching me is just the most phenomenal experience educationally of my life. And you know, I kind of thought that I had peaked in terms of teachers. I've had so many wonderful teachers over the years, and I thought I'd peaked in terms of knowledge. And Richard is just, Mondays are Richard day, and he just slaps me around every Monday, asks me really hard questions that he knows I don't know the answer to. And he's kind of thrown me back into student mode. So tonight is a hundred percent about Richard's work, and I am trying to represent all the amazing things that he has been doing throughout his career.
So I want to talk, I'm going to start at the end of the presentation here for, sorry, we're going to skip around. And one of the things that Richard did, in addition to creating the whole, the whole sort of concept of organic acids testing, is Richard developed this particular test called the GI Effects. And one of the main features of this particular test, the GI Effects test, was to look at the commensal bacteria, okay? And that's what we're going to talk about tonight. So commensal bacteria means normal bacteria. And so, you know, for all the history of functional medicine, there's been an obsession for every functional medicine doctor, and hopefully every patient as well, on how to understand the microbiome, how to understand the gut, and gut health. And you know, what, what Richard sat down and thought about, he's like a Stephen Hawking of functional medicine, right? Like Stephen Hawking, more like the Albert Einstein. Can you imagine Albert Einstein in the 1900s just sat down and realized that gravitational waves exist, and he wrote it all out in formulas, and we just proved that like a few years ago? You know, so like Albert Einstein could like literally see things that no one else could see. Sir Richard is like that. Ten, 15 years ago, Richard's like, "Hey, I think we should be able to measure the microbiome. That would be a cool thing to do." And he set it upon himself to figure out how to do this. And at the time, he was working in a lab company called Metametrix, and he was their chief scientist and their chief researcher. And they spent a decade, you know, figuring out, "How are we going to analyze and test the microbiome?" And this is the result of that, this one page right here, which is an assessment of the 24 key commensal bacteria that are the major players in our microbiome. Is it every one of the thousands and thousands of bacteria? No, it's not. It's the clinically relevant bacteria that really matter. And each one of these markers mean something specific and important, whether it's low, whether it's high, how they relate to one another. And that's what we're going to talk about tonight. So again, as always, Richard, he's like 10, 15 years ahead of the curve, pretty much all the time. And this test now is in wide use. It's one of the more popular functional medicine labs that's ordered by doctors throughout the world, really. And I want to talk tonight a little bit about the commensal bacteria and the importance of them, and my interpretation of Richard's vision for this test, and why he even put it together. And you know, this flies, in some ways, in direct conflict with a lot of the work that I've done in the past. And you know, you know, give me some credit for just saying, "Hey, you know, not that I was wrong, but that there's another level of evolution here in terms of how we can actually look at gut health." Okay? And I want to try to explain that in a moment here.
So, quick overview and the purpose of all this. Oh, and there's one other thing I want to say, say before I forget. Is there's a book that you all should read if you're interested in the subject at all. It's a really wonderful book. Let me just flash it up here. It's called I Contain Multitudes. Okay? I Contain Multitudes by Ed Yong. If you're curious about the microbiome, it's a really, really well-written book that gets into not just the human microbiome, but the microbiomes of all sorts of creatures, large and small. Anyways, one of the best, I think, easy-to-read books on this subject. I highly, highly recommend it. If you're interested, go out and buy it. I Contain Multitudes by Ed Yong. Okay? And that will give you some grounding in what we're talking about tonight.
So, throughout the GI tract, there are different neighborhoods or areas where the bacteria can grow. All right? And some of them that are potentially pathogens, pathogen, we mean disease-causing, can be harmless if other things are happening in terms of a robust community of bacteria. In fact, these various communities work together, they feed off one another in a symbiotic relationship, which is the strangest thing in the world. When you read that book by Ed Yong, you just flip out about how actually odd this whole thing is. As a simple example, we'll get into detail on this in a minute, is hydrogen-anoxic versus hydrogen-trophic. Right? So there's some bacteria that generate, create hydrogen, and there's some bacteria that consume the hydrogen that those other bacteria produce. So, in other words, you got bacteria in your gut that are commensal, normal, healthy bacteria, they're making hydrogen which perfuses your entire gut, right? That's crazy in and of itself. You've got this hydrogen gas floating around in your gut. And then there's other bacteria that feed on and use that hydrogen as their food supply. So the hydrogen-anoxic bacteria are making the hydrogen not for you, they're making it for their neighbor down the street, who's the consumer of that. And in fact, these kinds of bacteria, their existing together, they could care less about you, right? They have a relationship with one another. It's hilarious. Okay. The, the pathogen, and we'll get more into the pathogen thing because I think that's kind of the headline of this whole thing. But the basic idea is that you can't really assess whether an individual organism is a pathogen, i.e., whether it's bad for you, good for you, in isolation. You have to look at the context in which it exists and in terms of the rest of the organisms in your gut. Good news, you can use prebiotics and probiotics to replenish and feed the good guys. So there's solutions to all these things that we're talking about, tons and tons of solutions.
Oh, and just to clarify, because this is a popular topic right now in general, SIBO stands for Small Intestinal Bacterial Overgrowth. SIBO, Small Intestinal Bacterial Overgrowth. That's your small intestine right there, okay? And there are bacteria in your small intestine. What we're talking about now is not related to SIBO directly, although it's indirectly related. We're talking about the commensal bacteria in the large intestine, not the small intestine, in the large intestine, okay? There's complicated relationships between what we're talking about now and SIBO, but we probably don't have time to get into that.
So, here's a list of the commensal bacteria. Now, remember, a commensal means these are good guys. They're good when they're in the right amount, when they're growing in the right amount. And they have funny names like Bifidobacterium, Bacteroides fragilis. Lactobacillus, everyone has heard of. My favorite one, I think, is a Bacteroides. There's a Methanobrevibacter smithii, that's a pretty cool one. Maybe we'll talk about that in a minute. There's this Desulfovibrio. And this one's hard to say. I just call it Pygar because I can't pronounce the first word. But the first word is Desulfovibrio pygar. Okay? And some of these bacteria are super, super, super triple amazingly important. For example, the Pygar, we'll look at later, is implicated in the production and consumption of these gases, okay, that we were just mentioning before. Okay.
Now, how this gets a little crazy, crazy, and the way that I've categorized them here based on Richard's chart is to look at them in terms of their abundance. So, in other words, you know, you've got billions and billions and trillions of these organisms, and there's some that are really dominant, like the Bifidobacterium. There's some that are kind of obscure that you don't really have that much of, like the few so bacteria. And there should be, in general, a certain balance between all these organisms, okay? So you've got the high abundance bacteria, they break down carbohydrate and polyphenols, okay? And you've got ones that are inhibited by hydrogen. In other words, hydrogen stunts their growth. And then you've got the other ones that I mentioned, remember, they feed on hydrogen. All right? And you can imagine, depending on how much hydrogen is in your system, some of these bacteria are going to do great, some of them are not going to do great. And this is this whole idea of communities where they're interacting with one another, these neighborhoods or communities. They're, it's a, it's a live interactive process. And by the way, every single bite of food that you take completely changes the bacterial balance that we're talking about. Every single bite of food that you take changes its dynamic. In fact, back in the day, when Richard was at the lab running things, they would test people every single day and watch, you know, diet changes, and within two, three days of diet changes, you can get a completely different microbiome. And that's how crazy this is, because these organisms are bacteria, they die, and then they just come back with a vengeance depending on what you're feeding them. So, enough. And then this lower group here, at the low abundance bacteria, they contribute to the diversity, right? So you want a diverse group of organisms, just as we want a diverse society. You don't want to just have one kind of people, right? You want to have a variety of different bacteria. And then some highlights on these that I think are really important, and we'll come back, we can talk about this several times, is that many of these bacteria, some of the more important ones, they break down carbohydrate, okay? Can you wrap your mind around that? But they also break down these chemical compounds called polyphenols. So polyphenols, some of you've probably heard of. If you think of as antioxidants, right? So polyphenols are the reasons why we should eat fruit and vegetables every meal, every day, all the time. Polyphenols are not broken down by the human digestive tract. So what happens when you eat polyphenols or you take a supplement full of polyphenols, if your gut can't break them down, what the heck's going on? Well, guess what? The bacteria break these polyphenols down. Okay? The bacteria break these polyphenols down. In other words, if you don't have the right bacterial balance in your gut, and you eat fruits and vegetables, you're not going to get the polyphenols. They're just going to pass right through you. How crazy is that? A large percentage of the nutrients that you can derive from your food are dependent on you having these bacteria in the right balance. You can't even wrap your mind around that one. What is it, even that a polyphenol is going to pass through you unless you have these bacteria? It means that we developed with these bacteria in our guts. The only reason why we're alive and why we're here is because we have developed a sort of coexistence with these bacteria. It's not that they're nice to have and that it's convenient that we have them. It's an essential aspect of human life that we have these bacteria in the right amounts. It's not an optional kind of thing. So again, really like this idea of neighborhoods or communities. And these bacteria are alive, right? They're not just sitting there like dead, right? They're actually organisms. They have their own emotional needs, they have their own agenda. You know, they may like a neighboring bacteria, they may not like a neighboring bacteria. They may grow really well when there's this other bacteria next to them. They may get stunted by one bacteria. And they don't have like a sense of consciousness in the sense that they're trying to help us. They're living their own little bacterial lives, and they have their own needs that they want to, you know, come to fruition. And just like your neighbor across the street is probably not completely attached to your personal problems, right? These bacteria, in a sense, they're all fending for themselves in our gut and trying to interact and get along with each other. And it's a fascinating, fascinating story. And again, in that book I mentioned earlier, he talks quite a bit about it. And Yong talks quite a bit about these truly interesting relationships these bacteria have with one another, completely independent of the host. Okay? So, and there's bacteria in the mouth, obviously. There's bacteria that we're really talking about or in the large intestine. And as I mentioned, SIBO, very popular topic right now, slightly separate from what we're talking about tonight. Those are small intestinal bacteria. We're not really going to get into.
This is one of the studies that Richard published a couple, three years ago. Just kind of interesting to see that you can have such profound effects on everything from gallbladder function to liver function to cardiovascular function based on these bacteria.
So now, here's that, here's that the main question for tonight. You know, is that in functional medicine, in functional medicine, in the way that I was trained, was to focus somewhat obsessively on finding pathogens or infections in the human gut and killing them. And not like namby-pamby around about it, but being quite aggressive and killing them dead. You know, like my, my first teacher in this area, Dr. Timmons, he was just no-holds-barred, find the pathogen, kill it kind of guy. If you could have met Timmons, you know, he grew up in a really rough part of Los Angeles. His dad was a cop, Highway Patrol. He actually became a Highway Patrolman for a while. He had several different black belts. He ran a bar. He's just a tough dude, you know? And Timmons, like, he was the kind of guy who's quiet and looked like a nice guy, but he was the kind of guy if, for any reason, you're in a bar and all of a sudden a fight broke out, you just hope that Dr. Timmons was right next to you because he would just clobber the guy. So his attitude, and he instilled this in me in my late 20s, early 30s, was, "Hey, find the thing that's causing the problem, find the pathogen, and just kill it." And so that has lasted for me for 22, 23 years as a very effective strategy. I'm not putting that strategy down. It built my entire career. I've helped thousands of patients with that strategy. All right? It's not a bad strategy.
But we're trying to take this now, and this is how Richard's been sort of, Richard the doctor, Lord has been training me, you know, upping my game and challenging me and saying, "Well, really, is it the pathogen that's the problem, or not?" And, you know, human beings reflexively want to blame someone or something for a problem. And aren't we in the middle of that right now with our country? Build a wall. How stupid is that? You know, just accusing victims of being perpetrators. How stupid is that? And we see that, well, sexual abuse going on now, these accusations against all these men, with the crazy attitude we have towards immigrants right now in this country. It's all just completely insane. In fact, you know, my father is Jewish, plus Jewish, my mom is half Japanese, half Portuguese. If you know the current political climate, you know, I, you know, would be either like hung out to dry and shot by a bunch of Nazi sympathizers or put in jail for being Japanese. Anyways, this is human nature. And I understand that you find something that's bad and you want to kill it. Okay? What we want to do is look at a more global, bigger picture here, right? And say, on a physical level within the human body, just as we probably should look at a bigger picture in terms of our overall culture and how it's kind of degenerating politically right now. But the bigger picture in the human body that I want to try to create here is, is a pathogen a problem in and of itself, or is it a problem that's generated by the host? And so I want to show a slightly different set of slides here, just for a second, just so you guys can see what I'm trying to talk about here. We go. I'm going to skip around a little bit, just to, there we go, that's the one I want.
So, here's the dealio, is that when we're stressed, dude, who, like in my case, the death of my dad, due to a divorce, due to a second or third baby that you might have, due to overwork. When we're stressed, the immune system starts to fail, and we have a weakening of the immune response in the gut due to that stress. And that's when we start to pick up pathogens, or if we already have these pathogens, that's when they start to flare up. This has been always my clinical model for almost 20 years, right? So we're basically stressed, that weakens the immune response in your gut, and then the pathogens flare up. So what's the real problem here? Is it the pathogen, or is it the stress? And I want to add to this is that as we become stressed, obviously the microbiome starts to fall apart, you know? So a component of this whole model then is that it's not only a weakening of the immune response, but it's an imbalance in these commensal bacteria that allows the pathogens to become a problem. In other words, if you have a series of digestive tract infections, to say Giardia and H. pylori, and a horrible Candida overgrowth, and your immune system is in wonderful shape, and your diet is really pretty good, you may not even know that they're there, and you may live your whole life and die with these infections and never have a symptom or problem because of them. Because the microbiome is so powerful, it can handle GI pathogens. It's when the microbiome becomes compromised, as when we become emotionally compromised due to stress and spiritual disconnection, that all of a sudden the pathogens flare up. And this is like, to me, a higher level way of looking at all this stuff that we're talking about.
Let's go back here, and I'm going to talk a little bit about some of these bacteria, and then, you know, come back on a bit to the bigger picture. And then I have a case or two that I want to show you, too, okay?
So, there's different locations, right? For example, Bacteroides fragilis lives deep in these intestinal crypts. That's where it likes to hang out. And it's got an amazing little story to tell here. So, and there's some, I have a second here. This is that, this is just incredible. When I first learned this, I couldn't believe it. So I'm going to read this out because it's a little complicated. But this is a quote from the study that was done. "We report here that the prominent human symbol Bacteroides fragilis protects animals from experimental colitis." So, in other words, this bacteria prevents the colon from becoming inflamed. This bacteria, when its present, protects your intestinal tract from becoming inflamed. Again, up here in this study, "The human commensal bacteria Bacteroides fragilis corrects gut permeability." Let's say that again. You all have heard probably of leaky gut. What they're saying here is Bacteroides fragilis corrects, corrects gut permeability. It corrects leaky gut. That's deep. The right balance of that bacteria hanging out in these crypts in your large intestine repairs leaky gut and prevents inflammation. That's its job. And that's a pretty incredible thing for this bacteria to be doing. What if you run this test and your Bacteroides is low? How is that going to work? Not very well, all right? You're going to have some pretty major problems if this bacteria is low. You're going to have a leaky gut, and you're going to have a lot of inflammation unless you have this guy in there. And you can measure for this guy, you can test for it, and you can tell if you have a Bacteroides fragilis problem or not. That's the amazing thing about the testing.
So, symbiosis, you probably have heard of this term, right? We want to maintain the equilibrium. We want to have a good balance of the various bacteria, like I showed on the chart earlier, and a good healthy growth of all of the bacteria that are important. And if a certain microbe begins to dominate, then it can become a problem. And here we are with smithii and pygar. So this is again, just to show you some of the complexity of the relationships. Hydrogen-producing bacteria that we talked about earlier, they flourish by breaking down carbs and polyphenols to produce short-chain fatty acids, okay? And these are really important, obviously, for a variety of different reasons to support ourselves nutritionally, right? But one of the things that they're doing is, as a byproduct of their life cycle, is they're making hydrogen. And everyone has a general sense of this, right? There's certain foods that you might eat, like beans, that give you a lot of hydrogen gas, and you get gassy in your intestinal tract, right? But what's supposed to happen, if you have the right balance of bacteria, is that the hydrogen consumers like smithii and pygar remove the hydrogen. They pull it out of the system. They're feeding on it, it's their food supply, okay? And so what does that mean? Think about how deep that is. Number one, it means smithii and pygar have to have the hydrogen producers, or they can't grow. So if you're messed up or deficient in the hydrogen producers, smithii and pygar, you won't be able to grow. They can't get a foothold. And at the same time, think how cool this is. Smithii and pygar allow the hydrogen producers to flourish by removing the hydrogen. So, in other words, the hydrogen producers, if they make enough hydrogen, they just start to kind of kill themselves in a way, they can't keep growing. The smithii and pygar populations, by consuming the hydrogen, allow the hydrogen producers to continue, you know, growing and moving along. So again, this is the idea of these neighborhoods and the idea of community within these bacteria.
Now, as a really simple example, just from a clinical standpoint, let's say that, for example, it's calming. Let's say that you don't have enough smithii and you don't have enough pygar. And all of a sudden, you start to eat foods that stimulate the hydrogen producers, you're going to get really gassy. You're going to be like, "Oh man, every time I eat that food, I don't feel very good. This is not a good thing." But if you continue to eat that food for a few months, and the smithii and pygar populations start to come up, and they're breaking down that hydrogen, all of a sudden, that food that gave you a little bit of a first is now going to be something that really works well. So it's hard to tell from our initial reactions to a food where there's something good in the long run is happening or not. And again, there's these very strong correlations with pygar and cardiovascular disease, and with smithii and irritable bowel disease. And it's pretty incredible. The right balance of these organisms helps protect us against cardiovascular disease and IBD, and then using some of these bacteria that help prevent against weight gain.
So, here's a little breakdown, a little more detail on some of this. And we've got pygar and smithii, all right? And this is maybe a little technical, but it's kind of interesting. We think about here. So here's pygar. These are the chemical processes. You guys took biochemistry, this is kind of interesting. And here's smithii producing methane. Whereas pygar is producing hydrogen gas. And it's kind of interesting. So this slow release of hydrogen gas is what a mediator of healthy GI and liver function, needed for your kidneys and circulatory system to regulate properly. It reduces the risk of heart disease. It reduces the risk of ulcerative colitis. So a little bit of hydrogen gas is really, really important for your gut, your kidneys, your cardiovascular system, your also, you know, preventing inflammatory bowel disorders, etc. Now, if pygar is dominant and growing excessively, then you can have a problem with anaerobic bacteria. Smithii creates a four-fold reduction in hydrogen volume. So, in other words, if smithii comes up, your bloating goes down because it's consuming the hydrogen gas. It leads to a reduction in growth inhibition. It's kind of technical. And what's really interesting is that it helps produce methane. Crazy as that. But all the while, both of these organisms are removing hydrogen, which what allows the hydrogen producers to continue to grow. And the hydrogen producers then are allowing these organisms to do all their special things. If you don't have the hydrogen producers, then the smithii and the pygar are not going to be present, and you're going to have increased risk of heart disease, kidney problems, ulcerative colitis, etc. Okay? And here's some more detail on some of the studies on this. It's pretty fascinating. There's a ton and ton and ton of research on this that's been going on for the last 10, 12 years, maybe 15 years or so, and it's almost more than you could keep up on.
So now, if you're thinking about how do you make all this work? We need prebiotics and probiotics, right? To keep the bacteria in balance. So prebiotic, defined as a food ingredient that is not hydrolyzed and not broken down by the human digestive enzymes in the upper GI tract, and it beneficially affects the host by selectively stimulating the growth and activity of the bacteria. Okay? So a prebiotic helps the bacteria grow. Probiotics are actual live organisms which provide a benefit to the host, potentially as well. But the real name of the game here is the prebiotic, because if you can seed your digestive tract with all the nutrients that these bacteria need, your need for probiotics is going to diminish, because you're growing the bacteria as they should be grown in your intestinal tract, okay? So we talked a little bit about polyphenols, remember? And where do you find polyphenols? In fruits and vegetables. And in fact, as you eat polyphenols, these good bacteria, and this is one of the main reasons why fruits and vegetables have to be eaten every meal, every day, if you want to have a good microbiome. Pretty straightforward. You can also buy polyphenols, you know, antioxidant supplements. You can buy inulin in the supplement form. But we're really trying to get people to do this with food. That's kind of the whole point, you know? And if you need to, when you're suffering, you're not doing well, you know, you can do the lab tests, you can do the supplements. But the point of this is that much of this can be controlled just with where you eat.
So when I, when I go to, um, so you just tell you about my shopping habits, you know, in case you care at all. Every Sunday morning, I wake up around 3:30 or 4:00 in the morning. I do my little meditation thing. I built a steam room behind my house now. So I have a steam room that's outdoors. You can't believe that. Got this outdoor steam room, it's all redwood and kind of nice. Do my steam. And I don't know, around 9 or 10, I make up his dime ago and I run down to the farmers market near my house. I used to ride my bike, honestly. Now I drive my car because I'm kind of getting lazy. But it's hard, you know, hauling 50 pounds of vegetables up this hill is kind of hard. So anyways, drive down to the farmers market, buy all my fruits and vegetables. But the one thing they don't have there, at that particular market, anyhow, is beans. So I have to, every couple, three weeks, go to Whole Foods and buy all of my beans. And the last time that I did this, the clerk, and she's like, this 25-year-old, she's just looking at me like, "Oh, you are insane, dude." Like, basically, she starts this conversation. It's like, "Really? Nobody really buys beans." And I have, you know, bag after bag of beans that I'm buying. And she's just trying to figure out, was I up to something weird or something? Like, "What are you gonna do with all these beans, dude?" But anyways, super, super important. Beans have the fiber that these bacteria need to grow. And beans are out of fashion, as evidenced by my local Whole Foods clerk, who just thought it was a little crazy that a human being would want to buy five or six different kinds of beans on one shopping trip. Beans are an essential component to the microbiome functioning well. I understand for many of you who may listen to this, that you don't tolerate beans. We want to get your digestive tract to the point where it's robust enough that, you know, you can handle them, okay? And then they become your friend, and then you get the hydrogen-producing bacteria, and then you get the pygar growing and the smithii growing, and pretty soon you have this whole ecosystem that's, you know, basically a result of you eating beans.
So, if you want the short version of this seminar, you want to kind of summarize everything I'm saying: vegetables and fruit every day, no matter what, with every meal. And then you need beans pretty much every day as well. How much on the beans? Somewhere between a half a cup and a cup and a half, okay? So half a cup to a cup and a half of beans. It doesn't matter what kind of bean. Could be lentils, black beans, pinto beans. You could do hummus, chickpeas. It really doesn't matter. Whatever works for you, whatever you like, and whatever you can tolerate and digest. But remember, if you have a poor reaction to a food initially, it may mean that your bacteria need a few months to adjust before they can start to grow out their populations. Because remember, you might all of a sudden start at your new food, and the hydrogen-producing bacteria are stimulated, and they grow really robustly, but you haven't gotten those hydrogen consumers to grow yet, right? So there can be some lag time while the smithii and pygar come up. You're waiting around for that to happen, you may not feel that great. So it can take some time to adjust to new foods, okay? You can also have, and there's tons of research on this now, this whole gut-brain connection. So these prebiotics can also have a really powerful impact on your brain. And then you can do things in the form of probiotics. I sell them, you know, I use them with patients all the time when we're desperate and we really need to kind of kickstart things back into shape. But the, the, the probiotics, even the best quality stuff, like the stuff that I sell, they're only going to last in your system for a couple of weeks at the most. They're not going to really come all the way down into the large intestine where we want. So you can use probiotics, I'm not against them, and I sell a lot of probiotics to my patients. But really, the whole point of this is to put the polyphenols, put the fiber into the intestinal tract in the form of food, so that you grow these probiotics on your own.
All right, and then I'm going to show you a little bit more here on the testing side. The test that Richard Lord designed is called the GI Effects. And again, it's been around for a while. Nothing new here. And it's got a lot of stuff going on, more so than just what we're talking about tonight. But I don't know, I don't want to confuse you. Totally don't have to look at the entire test. To me, it takes a bunch of other things. It's just kind of, but here's a part that we're focusing on tonight, the commensal bacteria. And this is the, you know, many other labs, well, all right, let me just after say, I'm not going to do, let me just show you other parts of the test. If they do do culture for bacteria, also they look for pathogens, you know, parasites, etc. But many other lab companies do that. But what's actually extra-special about this test, and it's run by a lab company called Genova Diagnostics, one of the kind of premier lab companies in function is, and they see, Genova Diagnostics GI FX stool panel, I guess the actual test itself. Pretty much every other stool testing company checks for infections and inflammation and all these other things. What's unique about this test that no one else has developed yet is these 24 commensal bacteria markers.
Now, I want to talk a little bit about the technology behind the test because it's important. You see, we're up here at the top, it says commensal bacteria by PCR, Polymerase Chain Reaction. So that's a DNA probe that's developed to look for the DNA of these organisms. So I don't know how long ago it was, it was back around 400 years ago, three, four, five hundred, I don't know. I think it was in the 1600s, Leeuwenhoek developed the microscope, right? And that was a big deal, man. It's an interesting story, and he tells it in the book, and I've read this before. When, when he invented the microscope, and he built these lenses, right, that no one else had ever built, obviously, and he could all of a sudden see bacteria. But what the heck? He didn't know what they were. No one had ever seen a bacterium before. And he started to write all these scientific reports about these bacteria that he was observing, and nobody believed him because no one else at that time could build that good quality lens. Isn't that cool? And so there was a long period of time where that scientist that developed the microscope, everyone thought he was crazy because other people would look under their microscopes with their crappy quality lens and not be able to see anything, and he's seeing this whole world of bacteria. Anyways, what has superseded the microscope is the idea of testing for DNA. And this is very important from kind of a strategy standpoint in terms of why these tests are so vital.
So when you do a microscopic exam for a pathogen, you've got a human being looking under a microscope trying to find things. And that works out very well. And I still do that in my practice. And for if you've seen a functional medicine doctor, you almost certainly have done a stool test where they did that kind of test. We're not against that, and that is old school, but still valid and still really helpful. And I run those panels on just about every patient, okay? But in order to look at the commensal bacteria, if you try to take a stool sample and then put that bacteria, put that stool sample in a petri dish and grow out certain bacteria in a petri dish, the big problem is that when you're growing something in a lab, the organisms are exposed to oxygen. All right? And these organisms are what are called facultative or functional anaerobes, meaning that they exist in your large intestine in an anaerobic environment, without oxygen. So the standard way that we've been looking at the, where the culture is very inaccurate and doesn't represent what's actually happening in the human gut, because you're doing a stool sample, then you're growing it out, but you're growing it in the presence of oxygen, you get completely different results. The PCR test, the beauty of it is it's looking for the DNA of these organisms in the stool sample. And DNA doesn't lie, right? This is the exact same technology that they use when they want to throw someone in jail for the rest of their life for murder. They say, "Hey, we found your DNA at the crime scene, and your DNA was on the murder weapon." And then, you know, blah, blah, blah. It's enough of an accurate testing technique, DNA sampling through PCR, that we literally put people in jail for the rest of their lives. We're very sure that that's what's happening with these DNA probes that are used on the GI Effects test. You're looking for the DNA of these individual organisms. And that is very, very important because the DNA is going to be a very accurate representation of the concentration of that bacteria in your intestinal tract, whereas the microscopic exams or the cultural exams that we do are not going to accurately reflect the actual bacteria level that's growing in your gut, okay? So it's really important.
Now, this is a complicated technical thing to do to develop these DNA probes for each one of these organisms, there's 24 of them. This cost a lot of money and took a lot of time. But they did it at Genova or at Metametrix, and then Genova bought Metametrix. And there is no other company right now that has 24 commensal bacteria. There are other labs that I use on every patient, and they have some commensal bacteria, maybe six or eight or ten. There's some labs that have PCR for pathogens, and I use those tests too. There's some labs that test the entire microbiome, which gives you a complete understanding of all the bacteria. But that's not clinically relevant. And what I'm interested in as a practitioner is lab data that's clinically relevant, that's actionable, right? No one has so far copied this test yet. And there is no one else that's attempted to look at the microbiome, the commensal bacteria that are functionally important, the ones that there's research behind, that we know that there's a clinical effect of their population, okay? And so again, we'll just look at this, and you can see there's 24 of these little guys here. And the way that the report is generated, it's a little confusing, but it's with exponents because the numbers are so big. So when it says 3.2 times 10 to the ninth, that's a three with nine zeroes after it. That's a big number, right? And so you can see again, these organisms exist in huge quantities per gram of stool because they're tiny little bacteria, right? Of course, there's going to be trillions of them because they're tiny, tiny little guys. And let's see, and here's some of the ones that we talked about. And I can show you again here. Here's your, let me blow this up a little bit so you can see. Here's your pygar, right there. There's one. Everyone's heard of E. coli is measured. This one is really interesting. This is like one of my favorite ones. It's kind of named for what it does. And any of you guys that are into leaky gut, let me see, hang on a second. Sorry, let me make this easier to see. There you go. Akkermansia muciniphila. Let me say that again. Akkermansia. It's hard to pronounce these. Akkermansia muciniphila. That guy, mucin, the word mucin in muciniphila is a mucin lover. So what does that mean? It goes along the intestinal tract lining and it chomps away at the surface of the gut lining and chews it up. Mmm. It's kind of like a lawnmower, you know? Like if your grass is growing too much, it's a good thing that you mow the lawn. It's in your gut lining, mowing the lawn all the time. And what would you think would happen if there was too much of this guy? You would have leaky gut, right? Because it would chew up. Imagine if you kept mowing your lawn and you kept mowing your lawn and you pushed it down really hard, you know, eventually you would chew into the grass, right? So you get too much of this guy, you can have leaky gut. But the right amount of this guy is critical for the maintenance and health of the intestinal tract lining cells. How amazing is that? There's a bacteria, there's an organism that we consume, that is living in us, right? That is responsible for kind of tuning up and mowing the intestinal tract lining cells. It's like a little gardener guy that's that's circulating down there.
Now, there's good news and bad news in this bigger picture of things. Most of the reports that I've looked at say that, you know, the way that we get these bacteria typically is through, you know, the responsibility of the mom, right? When you're born and you're a vaginal delivery and you go through the vaginal canal, your head is mushed through the vaginal canal, you pick up a whole bunch of bacteria there. And then again, if you're a vaginal birth, you're not a C-section birth, your head is kind of mushed in and around your mother's anus, and you get a whole bunch of bacteria directly from her that way. Subsequent to that, as she starts to breastfeed, and Yong talks about this in his book, it's pretty interesting. As she starts to breastfeed, you, if you were breastfed, there's a whole huge percentage of the contents of human breast milk that are not designed for the baby. These special compounds are designed to feed the bacteria in the baby's digestive tract. Let me say that one more time. Human breast milk contains a large percentage of nutrients that are strictly designed not for the baby, but for the bacteria to grow in the baby's gut. So if you have a vaginal delivery and your head gets mushed against your mom's anus and you get bacteria from the vaginal tract and from her anus, and if you then are breastfed, you're going to have a microbiome that's in place around the second year of your life. If you are a C-section, you were a C-section, if your mom didn't breastfeed, if you were put on a large number of antibiotics, then your microbiome is going to be struggling to develop, you know? And so a lot of this is determined in the first couple years of life. And unfortunately, you know, more and more we do C-sections for a variety of reasons, and maybe sometimes they're, you know, absolutely critical and they save the mom's life, so you don't have a choice. More and more women don't have the ability or tendency to breastfeed, perhaps as much as they did a thousand years ago. And more and more we take antibiotics when we're quite young. So the microbiome is susceptible to these alterations, and it's very sensitive in the early years of life. But that's basically the original design, in a sense, for all this stuff.
Now, we'll go back and summarize a little bit because I don't want you guys to get the impression that I'm anti-pathogen testing, you know? But I just want to open up this idea of, number one, if there's more than just pathogens that we want to look at, we also want to look at the microbiome itself. And we want to do specific interventions to correct the microbiome. So for some of these bacteria, there's specific supplements. Some of these bacteria feed on sulfur. I honestly didn't believe this when I first read it, but yeah, they do. They feed on sulfur. And so if you're low in sulfur-containing foods and you're low in sulfur in general in your system, you can take a sulfur-containing supplement and it'll bring up the numbers of that particular bacteria. Some of them feed on the nutrients that are found in chicory, and you can eat chicory, and that'll cause some of these guys to grow. Some of them will respond, at least partially, to specific probiotics. You can take specific probiotics and try to get the bacteria that are low back in balance. What really doesn't work, though, is just a completely guess about all this, right? So if you're taking a really specific strain of probiotic for a year after year, or you have this chronic digestive issue or microbiome concern, and you're not understanding exactly what the bacterial balance is and how to correct it, you can really chase things around for a long time and not get the benefits that you want. So the technology is now available, you know, it's, you can measure these 24 different bacteria and start to see what the relationships are and which are the ones that you might want to boost now or or decrease, right? So for example.
You can see here on this example test, there's several of these bacteria right off the bat that are high. So if a certain number of these bacteria are high, you're probably already thinking, "Well, how could that even happen?" Well, typically that is going to mean that there's going to be some of these bacteria that are out of balance or low. All right? Because they're all competing for space. And so it's not just a matter of bringing the low ones up. The goal here, and I can show you just graphically on the test, the goal, the ultimate healthy microbiome, is to have a robust and healthy growth amongst all these bacteria. And I didn't draw that very well. Hang on, let me do that one more time. It should be like this. All the bacteria should fall into this general category here, not too high, not too low, but a robust and healthy growth of all these organisms.
Because remember, that means that you have a wide diversity of organisms. That means that you have the cardiovascular prevention, the obesity prevention, you have the health of the kidneys in mind, you have the reduction in leaky gut problems, the reduction of inflammation. When all these are laid out, and what we see is we look at these tests, you know, by the hundreds, is that's very, very rare to have. And that the imbalance in this microbiome can then be a trigger, along with stress, to create the pathogen-related problems. So in terms of sequencing, the way I look at this now is to start with an analysis of the pathogens and make sure that the major infections are handled and that the stress response is improved. And I'll show you here in terms of my treatment plans. So we do an assessment for adrenal hormones, neurotransmitters, sex hormones, this kind of stuff. We get that sorted out, get the person de-stressed, get the diet working well, testing correct for any of the GI pathogens, okay? And then start to look at, once the pathogens are under control, how are we really going to fix this problem long term? How are we going to be able to get the microbiome to work well?
I'm going to show you one more example of this. We'll wrap up with this thought. Here's a case study from my practice, so you can see how this rolls out. And I always try to show you all the big picture, so it's not just about microbiome. So we do a stress test and we look at cortisol. How's cortisol related? Cortisol controls secretory IgA, which is the immune response in your gut lining. It's pretty important to keep these bacteria going. And you can, if you've got stressed enough, you could screw up your microbiome just from emotional stress, if you worry enough. When I, when I was in college, one of my closest friends, Elizabeth, she was so funny. I love Elizabeth. We were study partners because she was like the smartest person. You know, I'm pretty smart, but Elizabeth was like twice as smart as me. So, and for some reason, she liked me. So we would always study together. But every time we had exams, and this went on for like four years, she would have these horrible diarrhea problems. Like, oh gosh, Elizabeth, just don't even tell me about it. I don't want to know. So anyway, stress can mess up your microbiome, as I learned from others.
And here's another, just to mix it up a little bit. Here's a pathogen screen. So we're worried about things like H. pylori. Still okay, that can be a major infection. It can just be devastating to people. We just had a case this week in the training program of Entamoeba histolytica, horrible infection that has to be dealt with, okay? So we're not against pathogen treatment, but that is a part of this. And then you can even have opportunistic bacteria like Citrobacter, Klebsiella. So these things, you want to eradicate. These are the bad guys you want to get rid of. All right.
And then the last part of the testing that we do is to look at organic acids. And I'll show you just real quick here where we're measuring things like fat-burning and carb, carb-burning energy production. We measure neurotransmitter capacity. Metabolism is really a big important part of this test. Wow, look at this one. This is a good one. All the neurotransmitter markers are messed up. So that's someone with a major brain problem. And this marker right here is part of the gut-brain connection. If your quinolinate is high, it means that there's inflammation typically in the gut that's damaging the brain, okay? So there's gut-brain connections here as well. And of course, your microbiome is intimately connected to your brain and your nervous system and your immune system in all kinds of ways. Other things that are important are on the organic acids, liver detoxification capacity.
And then I want to show you this last thing, and then we'll wind up on this final thought here because this is just kind of cool. If you're doing organic acids testing with your doctor, see where it says phenol acetate, you know, propionate, para-hydroxyphenylacetate. You see this is going, see the phenol, phenol, phenol. What do we talk about being polyphenols? Remember, you eat your fruits and vegetables, the polyphenols stimulate the growth of the healthy bacteria. Hey, that's what we're measuring here. These are the phenols, right? The the urinary byproducts of the phenol process, which is telling you about the bacterial balance of your gut. So there's other ways you can measure. Like you can basically, this is a test to see, are you eating enough vegetables or not? Are you eating enough vegetables and fruit such that your bacteria are growing properly? So you can see this on organic acids testing. And then if this is all messed up, like it is for this person, ouch. Look at that. That's like, slap you around, you better start eating your vegetables kind of situation. Or you're never going to get better, you know? So you can measure these things, the direct, the bacteria directly. You can measure how well the polyphenols are stacking up. Actually, look at this person. This is really messed up. I didn't choose this one on purpose, but these are low, and this one's really low, too. And why would you want to take a gazillion supplements for the rest of your life when the answer is just lying in fruits and vegetables and beans, you know? So I think if anything, this is kind of a call to arms for us to really sort through our diet and make sure that we get that figured out as part of the other two overall treatment plan, and you're not just stuck in a functional medicine, you know, spiraling nightmare of endless supplements and and digestive problems that you can't figure out.
And the general sequence then still the same in terms of how I work with patients. We deal with the stress component and fix all that stuff as best as we can. We take care of the pathogens first, and then look towards balancing the microbiome. If you have a histolytica, there's no point in messing with your bacteria that are healthy until the pathogen is dealt with. The the big picture here, though, and I'll end on this thought, is that the ultimate correction of the microbiome is what resets this system and prevents the problem from just coming back, right? And that's really what we're after.
I saw a quick announcement too about the coming new year. Obviously, I'm really into the microbiome. If you guys want to fear patient of mine already, you can order the test and we can analyze it for you. If you're not a patient, you're welcome to join us in the new year, become a patient, and you can get your microbiome tested. I believe that, you know, in the future years, this test is going to be just like a genetic test. You know, people do 23andMe, they want to know their genetic background, and and that it should be just a basic screening test that everyone does, you know, you should know what your microbiome is like. And even if you're not sick, you know, especially if you're not sick, right? It's really more helpful.
And then just like the quick announcement about the new year. So we're going to continue on on a monthly basis with a free patient webinar series next year. A lot of good things that I want to start to talk about. And then on the doctor side, we're going to have a free doctor kind of clinical application webinar series throughout 2018 as well. And not only focusing on the microbiome, but also the other things that Richard Lord is teaching me now. So really, um, you know, he gets to hang out in his house on the lake and, you know, feed the ducks and talk to me. And I'm the one out there, you know, my role now is to communicate all his information to you all. And it's a pretty exciting place to be at for my career. So next year is a really big one. We're going to have a lot of information coming at you guys. If you're interested in attending these things, you can tell your friends, of course. Everything is recorded, so you can listen to this again and again if you want. And if you want to get in touch with us, you can reach out. Reach me at my clinic, Kalish Wellness dot com for patients. And for doctors, we're at Kalish Institute dot com. I have a good evening, everyone. Bye now.