SYSK Selects: How The Human Microbiome Project Works

should know, a production of I Heart Radios How Stuff Works. Hey, and welcome to the podcast. And Josh Clark, I almost just forgot what I was gonna say your name. Yeah. Uh, there's Charles W Chuck Bryant piping in ye and there's the trio the Trifecta and it's terrible. Ikealy Uh do you think, well, we are getting a little heat off of it right now. It's just nice. Did you ever see that IKEA commercial about the lamp that was thrown out on the street. No, it was really good. Well

what happened to it? Was it like the monkey at the I Kea? No, it was like a lamp gets thrown out with like someone's just redoing parts of their apartment and the lamp is uh kick to the curve, computer animated, So it's it's a human formed not human formed. What am I saying? Anthropogin anthropomorphized and like looks up at the apartment that he was just thrown out of it and stuff like that. Does he go back to Sweden? I don't. I don't remember how it ends. Just remember

the lamp like turns at human. It was sad. It was like sad. I got teared up. Did you go buy one of those lamps? No, of course it didn't work. Um, so, I guess you're feeling pretty good since you're talking about lamps and everything. You know me and lamps I do. That means it's a good day. A clear signal checks in a good mood everybody. Uh, you know. One of the reasons why you're in a good mood because your guts are functioning properly. Yeah, yeah, ish, yeah, you know me,

it's day to day yeah with my stomach. Well that's exactly right. Things change very quickly because of your stomach, and your stomach can't affect your mood. As a matter of fact, the vast majority of the serotonin, which is a mood stabilizing neurotransmitter, is produced in your gut. Yeah. And the way that things like serotonin and other stuff uh is produced is thanks to our microbiome. Dude, Yeah, our microbiome. This is the most fascinating thing going on

in medicine science right now. Yeah. I get the impression reading various articles. When scientists talk about it, they all seem really pumped up. It's like the breakthrough of the century and this thing like just started. It's two and like this could remain the breakthrough of the century. Yeah.

And I mean, if you think about the timeline up in till the twentieth century, you were like a plant or an animal, right, And then it was literally like the nineteen fifties and sixties that they started saying maybe we should break things down a little further, and they came up with the five kingdoms, and I think they are now even as a six kingdom. Well, there's three domains, now eight kingdoms. There's eight, there's eight and three two of the domains are account for two of the kingdoms

as well. Bacteria and archia and archia used to be thought that they were the same as bacteria. Yes, then they started looking into them a little more and they're like, oh, these guys are made up of different amino acids and they have different characteristics. And our chia, for example, are the kind of um microbial life that you'll only find around undersea, hot water, sulfur events. Yeah, like volcano crazy places. Not not in your vagina or in your mouth. Well, no,

because they're extreme ophiles. And a vagina or a mouth isn't that extreme? Well it is because our kia lives there, that's right. So the fact that we figured out that our kia are different than bacteria, and not only that they don't just live in extreme environments, but also on the human body, that was something we can thank the Human Microbiome Project for. Yeah, and that wasn't I think they didn't even discover our key until the nineteen seventies.

So this all this stuff is brand new, right and exciting. And by the way, the three domains are bacteria, archia, and eukaryotes. Are us, yes, or eukaryotes because we have nucleus as nuclei. Yeah, let's talk about this man we we have before. I'm sure you remember in the fecal transplant episode, yes, because it definitely factors into it. You can um hoop shakes. Yeah, you can cure Claustradium difficile,

which is something where that it's a gut microbe. It's very harmful to humans that can colonize your guts after you take antibiotics, which is basically just like a slash and burn approach, which, again thanks to the Human Microbiome Project, UM, we're starting to understand we might want to use antibiotics because what we used to just think of is almost entirely bad are actually mostly beneficial, and even some of the bad bacteria a. Ka. Germs um are actually present

in our microbiome and normally live in harmony. It just appears that when the microbiome gets out of whack, that's when disease happens. Yeah, Like you may have E. Coli in your body right now? Yeah, I probably do, but it's not a big deal. If you're always talking about stasis home, keeping things balanced in life is the key, yes, and uh, it's definitely the key with your own personal microbiome, which we have learned is very individualized, which we'll get

to with the project. Right, So, if you take human body and you scanned all the genes in it, Well you would find is there are about a hundred times more microbial genes than human genes in a genetic scan of a human body. Yeah, are are Human cells only make up about ten of the cells in the body. And here's another great stat We actually the healthiest person on the planet has between two and five pounds of bacteria pounds. Yeah, of your body weight, about up to

five pounds. Yes, what's crazy is is that that's even considering that microbial cells are anywhere from a tenth to a hundredth the size of an average human cell. Yes, you do. You know how many? How much five pounds would have to add quite a few. As a matter of fact, there's um an estimated hundred trillion microbes on an average human in person, just in on and a part of such a such a part of us and our our normal functioning that we're finding very quickly that

they're they're pretty much interchangeable. There, they are one with us and um as their host. We are kind of one with them. Yeah, like you have fungus on your skin, Yeah, no big deal. Right, Well, that's another thing too, we should talk about when people say microbe. Um, it's kind of a catch all word for yeah, any tiny, typically unicellular life. And that's the case here too. But it doesn't just mean bacteria. The human microbiome is made up of lots of bacteria and lots and lots of different

types of bacteria. Um. For example, the mouth may have up to five thousand different species of bacteria. Yeah, and they're not just lazing around in your body, like they are responsible for keeping your body in chat or you know, sometimes responsible for it being out of whack. But they're all they're all doing something or laying there waiting to do something. You also have a what's called a virume.

You have viruses in your microbiome, and they appear to be present to keep the bacteria populations from getting out of control. Like they're there to infect bacteria, to kill them off. And they it's kind of like, um, they're the lions to the gazelles of the microbiome. You take away the lions, you've got too many gazelles. Yeah, they all start to starve, they don't function correctly. They may even eat each other. You don't want to see a

gazelle eat another gazelle. So you have lions there, and the lions these apex predators keep the gazelle population and check and ultimately healthy. Paradoxically, the same thing with the virume in your microbiome. Yeah, I mean they we know they aid like gut bacteria aids digestion, and we'll get the gut bacteria more. I mean, they're discovering just all

kinds of things that affects uh, synthesized vitamins. Um. When you poop in the toilet and you look at your poop, which you should do by the way, like you know on a regular basis, Um, how much is it? Is it half? From a third to half? So a third to half of that is microbial biomass. It's not food, No, it's like dead and living bacteria that you're pooping out about half half. I saw something that was kind of mind blowing to um. It's it's really neat and accurate,

especially on a microbial level. To imagine your alimentary system, your digestive system as the inside of that is technically outside of your body. You have a hole, a trail running through the middle of your body that's technically the outside. Uh yeah, I guess I see what you mean, it's just chew on it from an Yeah, like the the inside of your digestive system is technically the outside of

your body. That's outside of your body. Yeah, it's confusing, it is, but once once your head wraps around it, it's like one hand clapping kind of thing and you're just like, whoa, that is neat. Uh all right, So that's I guess the briefest of overviews of microbes in bacteria, which we've talked about ad nauseum on the show in our Great Digestion podcast that was one of my favorite ones.

And then we've already talked about the poop shakes. Uh. So the National Institutes of Health came up with a plan, got some money together and said, let's try and do what the Human Genome Project did. Let's try and map out the micro the human microbiome, which is a very tough task because everyone is different. Yeah. Well, yeah, everyone's microbiome is different. And I just saw today it was released from the University of Michigan. They've kind of already

determined there is no such thing as a baseline healthy microbiome. Yeah, and that was one of the goals of this project. That was started in two thousand seven, was that UM to fight to establish a baseline micro biome like they didn't know what one looked like like. They knew that people had tons of bacteria and protozoa and viruses all over us and in us, But what is that's supposed

to look like? And when you figure out what it's supposed to look like, then you can figure out what what an unhealthy one looks like and then possibly how to correct that by adjusting this this microbial ecosystem back to a baseline. But I'm not surprised that they found that there isn't a baseline that is two different And that doesn't mean that they can't like learn a lot

and help us out a lot. What they're basically saying is you take a dozen completely healthy people and their microbiomes are going to be completely different still, and there was UM. There is one huge revolution in UM in the study of bacterial or microbial life that that made this project possible, same with the human genome, but UM

much more for this it's called metagenomics. And prior to the Evan and metagenomics, if you wanted to study bacteria, you had to find a bacteria that could be replicated, cloned, cultured, Yeah, in the laboratory setting, and UM disaccounted for just a very very small fraction of the number of microbes out there. What's more so, not only did you not have a representative sample, but you also didn't have UM any kind

of anything less than an artificial setting. So even if you did get these microbes, if you could replicate him in the lab, UM, they weren't gonna behave the way they would in their natural set, like on your body.

So what metagenomics did UM was you can now take like a representative sample, say like a clump of soil or a swab of somebody's earfold, and get all of the microbe microbes in there, and then basically just do this rough scan of them, separate all the DNA out at these enzymes that go and clip coherent fragments of this DNA out, and then you take it and you put it into what's called a model organism, and that model organism starts to replicate as cells, and then each

cell displays a certain characteristic associated with a different microbe. So all of a sudden you can start studying the different cells and say, oh, well, this has to do with this microbe, and this means that this protozoa is present, and so on and so forth, and now you can get a truly representative sample of what's in a microbiome. And without metagenomics like this, none of this would be possible.

But now we're starting to find all sorts of new uh not just information, but even new species of bacteria and protozoan. Fun guy, from the study of this stuff, which is a great thing. It is a great thing, and we'll explain why it's a great thing right after this break. Okay, so we're back. We're back, and uh.

We were talking about the microbiome project, which is being rolled out in phases, the first of which obviously is to get as many of those samples via this new technology and basically just get a big reference set, throw them out on the table like a like a crawfish boil too, in the hopes of establishing that baseline, well not just a baseline, just basically cataloging everything with the ultimate goal of seeing what this means to our body

and how these different things interact. So they put the word out on the street and I H said, Hey, we need some volunteers. Do you think you're a very healthy person. It's so come volunteer. And six people who consider themselves very healthy showed up and said, I'm a healthy person, and they were just made to learn that half of them weren't healthy. Yeah apparently, Um, like yeah, over half were rejected out right. And that doesn't mean

they're like super unhealthy. It just means for the purposes of this they needed the healthiest of the healthy people. And I read that even even still of the ones that were accepted, the two and forty two that made the cut, Um, those people still had to have periodontal disease and cavities treated first, and then basically they had to be treated for that stuff and then they were deemed fully healthy. But like, that's that's how the level of health they needed for this study, or that they

wanted for it. Yeah, And it surprised me they only got um subjects from two cities. I thought it would have been like spread out, but um, Houston, Texas and St. Louis, Missouri or where the final subjects came from, and they haven't been And they were all white too. They were white men and women aged eighteen two forty I believe, And um, they were in the they were the picture of perfect health. After the dentists got finished with them,

people are wondering. I don't know, but um, it's not that this has been that the Human Microbiome Projects has been criticized for it. It's more just been like you, so you guys got a swab of just these just a small fragment of humanity. Yeah, maybe there's so much starting point right, Well, yes, because they can't include like every ethnic group in race when you're just starting out right, Okay, But I mean it is surprising that we just went

with called Asian only. Uh. So they finally get these healthy people, Um, a couple of hundred scientists, eighty different institutions. It's a big group thing. It's not just like one university that's running the show. Uh. Budget of about a hundred and seventy million bucks to start out with, and a bunch of uh cotton swabs, Yeah, lots of them, over eleven thousand cotton swabs, generic cotton swabs. Right. They they they swabbed each man in fifteen locations, women in

eighteen locations. Three of the locations were in the vagina. Men don't have vaginas, they don't but men have ears and armpits and folds mouths. Uh. So there's up your nose stool stool samples they're they're getting, as you know, they're swabbing all the moist places, right uh and yeah, that's exactly right, and not just moist places. But I think that's where you're gonna find the gold. Sure you know. Yeah, well, no, it's true like your four arm actually uh is typically

pretty dry. Um, but it has one of the most diverse array of bacterial species in your whole microbiome. Uh. You have about an average of forty three. Yeah. And people, when you hear this, don't think that didn't get the reaction now is expecting? Well, that seemed low to me, Yeah, because I'm used to hearing like thousands, thousands of bacteria, not necessarily species. It's um, although I think the mouth

is going to top that. From what I remember, I said like that it's like up to five thousand species. I believe it. Yeah, um, But I think one of our goals here, and the goal of scientists, is to stop people from like changing the tide of how you even think about the stuff. So when you hear that all the bacteria in your mouth and under your armpit. Don't think gross, think awesome. Well yeah, for the most part, Yeah, you know so. Um, the project, I guess is still

very much in its nascent stages, Chuck. Basically they project itself. Yeah, they did the initial leg work, and then they did the second phase, which is sequencing these things, which again, like I just painted the broadest picture of metagenomic sequencing. It is one of the most involved, insane complex processes I've ever like tried to understand. It's more complex than the breathalyzer. Remember that it used like kryptonite somehow. Yeah,

that was very surprising. Yeah, if you don't know we're talking about, go listen to our Breathalyzers episode. It was really those are complicated missions. I thought there were fairies inside the little box that just pretty much smells like beer. Yeah, metagenomics is it's better to just kind of understand it, like little fairies performing magic than to really dive into it. But um, the point is this project. They have all this data. Now, now they have to sort through it.

They have what the problem of big data, whether it's just an overwhelming amount of data, like truly some bytes of data three point five trillion bytes of data, which is about a thousand times more than the Human Genome project. And at first you're like, oh, wait, that doesn't make sense. We're talking about bacteria, and you go, oh, yeah, that's right. We have about a hundred two times the genes in our microbiome than we do in just the human genome.

So yeah, that's a lot of data. And now they're starting to figure out how to how to sort through it. All right, So I guess after this break we can talk about some of the things we have learned thus far. Okay, we're back, all right, So now I guess we can talk about some of these great findings, some of the newest findings in the last what ars it? Well, they started two seven seven years old, and it seems like the first crop of like amazing stuff started in about

two twelve. Yeah, so after they had categorized things and got like thrown all the crawfish out on the table right in the corn. Yeah, the little corn is good. Have you ever done that? I've had that before. Yeah, it's good stuff. It's fun go to a big party. There's a place in um on Buford Highway called um the Crawfish Shack. I've heard of that, but I haven't been. Did they do it like that? Did they just dump it on the table and it's all picnic tables. No,

it's in the bowls and stuff like that. But um, but it's all picnic tables inside and um, just huge rolls of paper towels and it's dude, that place is so good. Yeah, I guess you can't do that as a restaurant. But if you go to a true crawfish boil at someone's home, you have the picnic table covered with the plastic thing and you just dump it on the table and everyone just stands around like a bunch of animals, right, getting drunk and eating, like sucking the

heads of crawfish. But my my family used to do something similar to that when I was a little in Toledo. We would eat um my dad called it garbage pail stew. Are you familiar? Is it like all the leftovers? No, it's like you use a trash can to make it. Oh, I've never heard of it over like a flame, and obviously use a new trash can, like a brand new one. So I guess when dad got a new trash can, we would have garbage pails stew anyway, the metal trash can.

It was, Yes, it was more like a the plastic just added just trying to like one of the old timing ones. What kind of flame you got in your house? And I don't remember what he cooked it on. Interesting, I don't like in my in my mind's eye, I can't look down. I can just see you just see the kind of the top of it. But anyway, it was like a Yankee northern Midwestern version of it. So there's like lots of cabbage in it and like kill

Bossa and stuff like that. But it was essentially the same thing and you would eat it on like like newspaper. I can't wait to get emails from people who were like, we did that same thing. I've looked around, I'm never seen it since. I'm sure that, yeah, that sounds like a thing that although your dad is very unique person, insane is the way to put it, all right, So back to the project and the findings. Um. One of the things they've learned is that periodontist this is gum disease.

Some bacteria are elevated if you have periodontists. So that's gonna give you a little insight to maybe how you can better take care of your mouth. What kind of bacteria you need in there? What kind of you don't? Yeah, exactly, And like for example, strip to Caucus mutans is responsible for cavities, um, so you wanna take care of your strep to Caucus muticans mutans. The thing is, Chuck, that reading this made me wonder like, are we gonna go

the other direction now? Where it's like, we understand that you can't just use antibiotics to get rid of everything, But if we identify bacteria that's like, oh, well that one gives you cavities, Let's get rid of all of that and find some sort of medicine that just gets rid of that. It could make things even worse than

a whole other direction. Like one thing that I I figured out from this is that the the microbiome appears to exist in balance, like stuff that should make us sick E. Coli um, kinds of strepped staff, that kind of thing, like it exists on a healthy person's microbiome and it's just hanging out there. So it doesn't mean that they're inherently disease causing for us, or that they're they're inevitably disease causing um apparently if they exist in

harmony with their neighbors. That's the way it's supposed to be. And we can't just root out just ones that make a sick and get rid of those because I think

it will have repercussions. But they might. We might have a future where instead of an antibiotic you take, you actually take a bacteria that will attack the other bacteria the bad stuff, right, or you can write exactly like that that as long as we're not intervening and going after a specific bacteria, if we can aid the bacteria like you say that will fight it naturally, like by eating some sort of sugary paste, you know, or probiotics, I mean that's what that is, right, Yeah, and that

I mean, that's that's an issue that's being um examined in more detailed thanks to the microbiome. Like do probiotics work? Uh, And apparently the jury is still out in fury. They should work, but it depends on, you know, whether these things are actually colonizing your guts. And also I have the impression that it's like you don't really know what you're doing when you're adding like all these new people

of the neighborhood. Yeah, and because everyone's microbiome is so different someone probiotics for one person might be great and for another person might not do anything or make things worse. I don't know. Yeah, which is another goal of the Human Microbiome Project that if we start to understand, you know, what a call any Maybe there's not a normal colony for everybody, but what an individual's normal colony looks like, then you can take blood or samples and make adjustments

based specifically on what you need. Right there, it could be the end of pharmaceutical drugs conceivably. I know they're doing a lot of research into, um, how your gut bacteria affects ob cit and your weight. Um. They have found obese mice and transferred micro microbes from their gut

into skinny mice, and the skinny mice gained weight. And Um, there's just type in gut bacteria and obesity, And there are a lot of studies going on now thinking that maybe correcting your gut bacteria could actually help you help your metabolism, you know, straighten out right, Like they think the bacteria itself directly informs how the body uses their

stores energy. Yeah, yeah, Um, the one that blew me away was there's a type of um bacteria that helps that helps break down milk in humans and typically it's in the gut, but um as a woman advances in pregnancy, Uh, some of it moves down to the vagina. And they at first, the researchers who found this were like, what's the deal with that? And then they figured it out.

They think when a baby is born um and it passes through the vagina, it basically it's becomes covered in this bacteria, ingests some of it, and that bacteria goes down and colonizes the baby's guts and prepares it almost immediately to start breaking down breast milk. Yeah, evidently brand

new babies are just sponges. And like they're experimenting with cesarean sections to just swab Like after you have the cesarean section, you bring the baby out, swab it with with vaginal mucus and basically it just looks right into the skin and maybe have the same result, right, or swab their mouth or something like that. Yeah, um another way, And I guess that's kind of related to is um

with the immune system. Apparently the microbiome acts as kind of like a teacher to the early immune system and says like, hey, these are the good ones, these are the bad ones. Um, why don't you go ahead and produce some T killer cells or killer T cells, but not too many, um, and uh, we'll just go ahead and keep the homeostasis going. And they basically like teach a young immune system how to operate at an optimal level.

And they found that by engineering mice that are like totally germ free, their immune systems have a tendency to go crazy, like they'll become inflamed in the presence of what are say, um, non harmful fung gui. Um, They'll they'll become so inflamed that they'll damage the surrounding tissue or they'll have like irritable bowel syndrome or Crohn's disease.

They think also is a a flux state of the microbiome in the gut, so apparently it directly impacts the immune system as well, which my friend lends a lot

of weight to the hygiene hypothesis. Yeah, that's that's basically the notion that, uh, here in the West and even in developing countries now children are seeing such a decrease in infection when they're when their kids that when they grow up they have an increased number of allergies and maybe autoimmune issues, and um, you kind of see it playing out, you know, like it it's a real thing. Like if you're slathering your child with pure l you're

not doing the many favors right. So they may have asthma later on because of that exactly, And they are becoming they're coming to think that it's because of the the just a stunt to growth of the microbiome. Yeah, and I think they've found now even they think they have a direct link between your gut bacteria and allergies. So if you're if you get hay fever, it may

be because of your gut bacteria. And it makes just uttering complete sense too, Like your body has been exposed to these things early on, learned that they're not harmful and no longer produces antibodies as a result of their presence. Because that's all analogy is. It's a a m it's a case of mistaken identity. Your immune system thinks that pollen or something is a harmful for an invader and

launches your your immune response. Pretty cool. Uh. Some of the other interesting things they found so far is that there wasn't a single microbe that everyone had in the study. Yeah, which is pretty interesting. Um, And that microbes are most similar on the same site of different people. So like you and I have more similar microbes in our armpit than even there were different people. Right then, you You're microbes in your armpit has to do with your belly button.

Ours are more similar than the ones in different places on your body. Yeah, that's pretty neat. And different microbes can do completely different things, like the way you digest food might use one microbe and I might use another, or that same microbe might have a completely different function in you than it doesn't mean right, so so personalized. It's like it feels like the beginning of like hyper personalized medicine. I think it is in the future. I

definitely think it is. I think it's also the beginning of a kindler, kinder, gentler approach to treating disease at all. Disease Like it's entirely possible, especially if you take a brain based view of mental illness. It's possible that every bit of disease can be cured by by understanding the microbiome,

even cancer. Apparently, they found from this that some types of cancer managed to cloak themselves by taking like um resin or residue from certain types of bacteria and basically sneaking past your your immune system and going and lodging itself into cells and hijacking them and creating tumors. But it cloaks itself by getting buddy buddy with certain kinds of bacteria. Cancer is a jerk. Yes, cancer is a

big time jerk. You know, we've kind of covered it here and there, but uh, I could see more specific cancer podcasting out, you know what. So like, so far we've done too that specifically got into the microbiome, but we've never done like a microbiome one. So I think we should come back like a year from now and even more stuff is out and do like the microbiome. Yeah, it seems like they're they're making breakthroughs at a pretty rapid pace. So in a year they might everyone might

be skinny. Yeah, because of the microbiome pill. Have you seen a picture of like an obese mouse next to like a skinny or normal eyes mouse. Yeah, it's pretty depressing. It is um sad mouse. Okay, So I will see you here at the end of next April. Uh, God willing for the microbiome? One deal, all right? If you want to learn more about the human microbiome, you can type that well those words into the search bar at how stuff works dot com. Uh And I said how

stuff works dot com. So it's time for the listener mail, Josh. I'm gonna call this response from a creationist. Okay, we got a few of these. Hey, guys, listen to your podcast on natural selection and really enjoyed it. I'm a biologist who is a Christian and creationist. Natural selection is not what we disagree on. And when I say we, I mean most creationist, but of course with every group they are outliers. We agree with micro evolution, changes that

occur within the species, not macro evolution. Species developed into a completely different species, which is what most people tend to associate with evolution. The only major differences between creationists an evolutionists is that we believe the Earth is between six and ten thousand years old um and again excluding the outliers, and that all organisms were created in their

basic form by our God. For example, we believe that everyone came from Adam and Eve, who through methods of natural selection, evolved into the many nationalities we have today. Same thing with animals. We believe that a small number of species were created by our God, and all the forms we have today evolved through natural selection. So the only main difference that we have with evolutionists is the

ultimate origin of species. The areas of evolution that we can see clearly occurring in front of our eyes we agree with. It's the areas the evolutionists theorized about that we don't agree with. So while there are differences between creationism and evolution, they're actually more similarities. And that is Eric from South Bend, Indiana. Thanks a lot, Eric, very salient points biologists. Yeah, I love it when like experts come out of the out of the would work, especially

when they're experts with a twist. Yes, and we love being refuted and refuting and reading refutations and uh, we'll always read these things refutation life. That's right. If you want to refute something we've said, or agree with us or whatever. If you just want to get in touch about anything, you can tweet to us at s y

s K Podcasts. You can join us on Facebook dot com slash Stuff you Should Know, or on Pinterest or on Instagram, and if you want to send an email to Chuck, Jerry, and Me, you can address it to Stuff podcast at how stuff works dot com. Stuff you Should Know is a production of iHeart Radio's How Stuff Works for more podcasts for my heart Radio because at the iHeart Radio app, Apple Podcasts, or wherever you listen to your favorite shows.