Jack and the Microbiome
Episode transcribed by Rev.com.
Associate Professor, Department of Ecology and Evolution, University of Chicago
Environmental Microbiologist, Argonne National Laboratories
Bacteria are everywhere. They have been on Earth for 4 billion years, and have permeated every environmental niche on the planet, including our own bodies! We are, after all, composed of 10 trillion human cells and 100 trillion bacterial cells. But how do you study the Earth’s microbiome, and what influence do these bacteria have on our daily lives? On this episode, microbial ecologist Jack Gilbert joins us to discuss a very exciting collaborative study, the “Earth Microbiome Project.”
Forrest Gulden and Joanna Rowell talk with Jack Gilbert about the Earth Microbiome Project
Forrest: Hello and welcome to the Groks Science Show, I’m Forrest Gulden.
Joanna: And I’m Joanna Rowell. You know Forrest, looking around this radio studio makes me wonder what the microbiome is like in here.
Forrest: Oh, wait, what’s a microbiome?
Joanna: Well, do you know what a biome is?
Forrest: To be honest I could use a reminder.
Joanna: Well, biomes are often referred to as ecosystems. According to the Internet, which is never wrong-
Joanna: Biomes are large naturally occurring communities of plants and animals occupying a major habitat.
Forrest: Okay, so a microbiome is a community of microbes.
Joanna: That’s right! A microbiome is the totality of microbes, their genetic elements and environmental interactions in a defined environment. And, make no mistake, microbes are all around us. In a single gram of soil there are thousands of microbes. Bacteria, which make up a large portion of the microbiome, have been around for 4 billion years, and have invaded every niche on our planet. Even our own bodies.
Forrest: That’s disgusting.
Joanna: You, Forrest Gulden, are composed of 10 trillion human cells, and 100 trillion bacterial cells. So you’re outnumbered 10 to 1.
Forrest: But human cells can be 10 times bigger than bacteria.
Joanna: Okay, so it’s a bit of a stalemate.
Forrest: For now.
Joanna: Come on Forrest, there’s no need to be paranoid. The vast majority of bacteria, something like 99% of them are perfectly harmless and they can even be helpful.
Forrest: Okay, fine. So what do you think the microbiome of the radio studio looks like?
Joanna: Well, there’s different people coming in here every day, every hour, breathing into these microphones and touching the buttons on the soundboard, so, I bet it’s pretty dynamic. The community of bacteria probably changes a lot over a week or so.
Forrest: You know asking you about the studio I thought it would kind of scare you. No, you scared me about that. I don’t even want to think about that.
Joanna: Well, you’re out of luck Forrest, because that is what our show is about today. Recently I had the pleasure of interviewing Jack Gilbert, a microbial ecologist from the Argonne National Laboratory, and the University of Chicago. Dr. Gilbert is involved in this enormous collaborative project, called the Earth Microbiome Project, or EMP. One of the first questions I asked him was, “What are the goals of this study?” Here’s what he said:
Jack: Ambitious, to say the least. The goals of the project are to characterize the microbial diversity of this planet. As you might expect, that’s fundamentally impossible. However, let’s not be daunted by impossibility. What we’re trying to do is systematically approach the problem of what structures microbial life. What I mean by that is bacteria don’t live in America, they don’t live in Russia or China, they live in this boundary intersection between environmental gradients. Bacteria will live at the intersection of the differences in temperature, and the differences of nutrient or food availability in an environment. Much the same as human beings will often put their settlements next to a river, cause the fresh water and also the farmland is good around a river. Bacteria will find a place in the environmental perimeter space that makes them happy. So we are trying to categorize and characterize the space in which these microbes live. So the Earth Microbiome Project is fundamentally trying to understand what structures microbial life, and how microbial life is structured along those gradients.
Forrest: Okay, so this team of scientists is hoping to map the distribution and function of microbes all across the planet. That really is ambitious.
Joanna: Yes, it’s very challenging. Scientists used to grow colonies of microbes in order to identify the species in a given environmental sample. But this strategy substantially underrepresented microbial diversity.
Forrest: So that’s not the best way to go study microbial diversity on any sort of large scale.
Joanna: Right. Now what researchers study is called the metagenome. The metagenome is the genetic material of all the organisms in an individual environmental sample. It can be analyzed using modern gene sequencing techniques which can tell us a lot about the microbial diversity and the function, what these microbes are doing. Let’s have Dr. Gilbert tell us more about how one goes about studying the global distribution of microbial life.
Jack: Perseverance and collaboration. Collaboration is key, we’re desperately trying to work with hundreds, if not eventually thousands of researchers around the world. People who have collected a soil sample or a marine water sample, or maybe they collected some leaf tissue or animal tissue from plants and animals. Maybe they’ve collected air samples or human samples from populations. Yet, they haven’t really thought about putting this data that they might create about the microbiology of those communities, in any kind of context. Like a global context. And it’s quite important that we enable those people to really put their data in the context of say, what do all the other marine samples of the world look like microbiologically? If we treat them all in the same way, if we do them all in this use, generate the data with the same experimental outline. Then we’ll be able to compare samples from Bolivia, and samples from China Sea and samples from the Great Barrier Reef and samples from the English Channel and the Arctic. They’ll all be comparable.
So fundamentally we want to enable people to generate data through us that is comparable across multiple scales, multiple environments, multiple ecosystems.
Forrest: Okay. So let’s say you map the distribution, diversity, and function of microbial life on this whole planet. What do you do with all that data?
Joanna: Well, the EMP researchers are using this data to make predictions about how specific environmental conditions affect microbial communities. For example, they’re studying the effects of the 2010 oil spill on the bacteria in the Gulf of Mexico. And they’re also making ocean-wide predictions of microbial life that extend to 2100. But that’s not all you can do, here’s Dr. Gilbert again:
Jack: Okay, so we’re generating a really big data set. A data set that fundamentally helps us to see what really makes a bacteria grow in a particular environment. Bear in mind there are hundreds, if not millions of species of bacteria, and those millions, if not billions of species, and I’ll keep on exemplifying the number of species of bacteria, they grow in every kind of environment we can possibly imagine. So we really have to understand that. One of the real big benefits of having this database is to be able to say “Hey, I’ve found this bacteria living in sludge from a factory in Wisconsin, where else is this bacteria found? And how do I think this bacteria got here?” Now if it turns out this bacteria’s found in the same sludge in China, in Australia, maybe in bogs or mangrove swamps in Brazil, then we have a way to find out that information. But also to say, “Well, what environments can this bacteria live in?” Which can help us as people, to maybe understand a bit more about why that bacteria might be found there.
Fundamentally, also, we work with agricultural specialists and aquaculturalists to try and understand why certain bacteria are found in certain environments that may be beneficial for their agricultural or aqua agricultural practices. For example some farmers think the top end of their field, plants grow really well there and they never get sick. Bottom end of their field plants will always get a bit sick and productivity’s always lower. Well, why is that? Normally, you’d say “Well, it’s because moisture and nutrients.” But when all of those controlled for? It’s probably because of the bacteria. And if the bacteria are different in the top part of the field and the bottom part of the field, and if we can show that this occurs in China, in Europe, in North America, in Australia, in different environments, then we’ll be able to really get a statistical solid feeling that those bacteria are important in the productivity and disease suppression of those plants.
Forrest: That data set’s theme is gigantic. So it must require a massive amount of computational power.
Joanna: Yes. And I asked Dr. Gilbert to give me an example that illustrated how much computational power this study requires, and here’s what he said:
Jack: So far we’ve generated well over 3 billion 60S reads. Which isn’t a huge amount of base data, if you will. The amount of sequence data that that actually comprises is maybe a few gigabases. No, gigabytes. I get my bases and bytes mixed up. So maybe a few gigabytes worth of data generated. Not a tremendous amount of problem, I can store that on my local hard drive. However, when I start to want to compare, this OTU, OTU number 1. When I say OTU I mean a taxa of bacterial species-
Jack: So the bacterial species number 1, I want to compare that and see how similar it is with bacterial species number 2. And then I want to compare bacterial species number 1 with bacterial species number 3. OTU species number 1, bacterial species number 100. Bacterial species number 1 with bacterial species number 1 billion, and everywhere in between. And also I want to do the exact same with bacterial species number 2, with bacterial species number 1, number 3, number 5, number 100, number 1 billion. And I want to do that iteratively so I compare every single bacterial species, with every single other bacterial species. What I’m doing, is I’m actually comparing a string of a 125 letters, with all of the other 125 letter strings in this 2 or 3 billion data set.
That’s a fundamentally, computationally, expensive task. It takes a lot of computing time to do this. It’s very hard to run it on a system which has, like your laptop or my iPad, which has a very limited amount of memory. We need a huge amount of memory and we need a lot of processors, and only then can we really get close to being able to do this. Now, those machines do exist, but they’re difficult to get a hold of. And they are expensive to get a hold of. So we are actually now starting to use a slightly easier approach, maybe a more collaborative approach, working with the community to get them to enable us to access their computer resources so that we can do these very big computational problems.
Forrest: You know, I am a big fan of citizen science, and it’s really fantastic that they’re involving the public in this project. It seems like a lot of fun.
Joanna: It does. The Earth Microbiome Project involves the help of many citizen scientists. The data are available and even analyzed as part of a public forum. A massive project like this one really requires a lot of help, and they are getting it.
Jack: The citizen scientists and also other scientists. Scientists that may have never thought about bacteria. Physicists, and chemists, and mathematicians who have compute resources sitting around. And yes, you’re right, people with their laptops at home. We’re hoping to develop software. In the mid-90s, I’m aging myself a little bit, we had a system called SETI, the search for extraterrestrial life and they passed out bits of data to people, and they would run on their computers when the computers were idle. And they have that screen saver which showed you passing through data. Now, they did the same thing with protein folding. They actually passed out the amount of information protein folding and people could do that on their computer. We want to do the same thing. But we want to take bacterial communities and compare them, and that takes a huge amount of data. So we’re thinking of pushing that out into these spheres so citizen scientists can play a major role.
Joanna: Having so many people involved really helps both with the data analysis and sample collections. Can you imagine sampling every type of environmental niche on this planet? So far, the EMP has over 60 thousand samples. And some of them are from very peculiar places.
Jack: We take them from pretty much anywhere you can imagine. It’s important to understand that we’re not trying to thin out the global map. We’re not trying to say “We want a sample from every hectare on the face of the Earth.” That would be technically difficult and also scientifically not particularly exciting. What’s more interesting is for us to explore gradients. So we started looking at samples, and they’ve been characterized for temperature, nutrient availability, for pH, for total organic carbon, for pressure, light availability, etc. And then we say “How many samples do we have from soils that are of a pH of 6, that cover the range of temperatures that those soils experience?” So, minus 40 degrees centigrade, up to plus 40 degrees centigrade. Can we find samples from those soils that comprise that gradient? If we can, then we characterize the microbe community. So by systematically characterizing the microbial community along these gradients, and the intersection of these gradients, we start to build up this really detailed picture.
Now, where is the weirdest places we’ve had them? Well, depending on what you call weird. So we’ve had deep rock sediment samples from communities that are living 2 or 3 kilometers below the surface of the ocean. Surface of the ocean floor, sorry. We have samples from volcanic islands. We have samples from hot springs. We have samples from African bushmen, from Puerto Ricans and Americans. I mean Americans, that’s strange. We have samples that come from air, from insects, from pretty much any environment you can possibly imagine and put your finger on, we try to sample it. We’ve worked with collaborators who can get us samples from those locations. We’re actually working with Jonathan Eisen now at the University of California, Davis. We’re starting to look at getting samples from the International Space Station. If we can do this, we’re actually maybe extending the remit of the Earth Microbiome to the Earth-Influenced Microbiome, cause it’s still in the gravitational field of the planet.
But also we’re starting to maybe explore those human habitats a little bit more. Now we’re working in homes and on hospitals, trying to understand the bacterial community in those homes and hospitals. Now that’s all part of the Earth Microbiome Project. It comprises the greater, the Earth that we as humans interact with.
Forrest: Samples from the International Space Station. That is pretty wild. And maybe you’re right, it could be kind of interesting to study the microbiome of this radio studio.
Joanna: Okay. So next time we’re here, we’ll take swabs from the microphones, the headphones, the soundboard, the record player, the doorknobs, the floor, the logbook, the ceiling, the records-
Forrest: Wait, wait. No that’s too much, that sounds like a lot of work.
Joanna: Well, okay fine. But that’s the type of thing that Jack Gilbert and his colleagues are doing as part of the home and hospital microbiome project.
Forrest: The home microbiome project? Is that what I think it is?
Joanna: Yes, it is. It’s just what you would imagine it to be. Studying the microbiome of our houses and our apartments.
Jack: So the home microbiome study was an interesting idea. We sat down and we thought “What is it about homes, and about human populations, indoor environments, which is interesting from a microbe ecologist perspective?” I’m a microbial ecologist, a card carrying ecologist. And I wanted to know explicitly why I should bother working in an indoor environment. I mean where there are no lakes, there are no rivers, there’s no green system, there’s no soil, there’s just surfaces and door handles and light switches and people. And animals. But not a huge amount of interest for what we would normally consider an environment. So I started to ask myself some very serious questions about that, and one of the questions that came to mind was “Well, what happens when people move into a new space?”
Explicitly, you have a huge number of skin cells in your body and you’re shedding those skin cells all the time. And every single one of your skin cells can have millions of bacterial cells on it. So when you shed say a billion skin cells a day into an indoor environment, each one of those billion skin cells has a millions bacterial cells. You do that math, you suddenly end up with an inordinate number of bacteria shed from your body into this space in which you are living. Right? So you spend a lot of time in your house. It’s a really rich environment for your skin cells and for you. So we wanted to say that, “Well you move into a new house or a new apartment. Somebody else has been living there. Well how long does it take that apartment or that home to start looking like you, microbially?” So we sampled people’s hands, their feet, their nose, and also the surfaces of their home, their kitchens, their bathrooms, and their bedrooms.
And we said “Well, how rapidly does it occur?” So we started sampling the days they arrived and we sampled every day for about 4 weeks. And we said “Well, at what point do surfaces start looking like the people that just moved in?” And it got around say 5 or 6 in some sites, in some houses. Importantly, the people that were living in that house redefined how and why the surface started to look like you. If you’ve got small children, I have 2 small children, and they do like to dribble and drool. And spread their mucus over surfaces, especially floors and counter tops. And they actually did show an amazing transition, their oral microbiota, amazing microbiota, is very similar to surfaces a lot faster on the floors and counter tops than say on the light switches and the door handles, which they were barely touching. Whereas stay-at-home mothers or stay-at-home fathers who were living in the house, they had a much bigger impact on the microbial diversity of the house than the partner who went out to work.
These ideas might be axiomatic, these might be obvious. But we never really had rate measurements before of how quickly these things happened. Now we have these rate measurements which can tell use explicitly why and how people microbially interact with that space and what that means for the development of health or epidemiology.
Forrest: So our homes look like us in terms of the microbes that are present. That makes me wonder if you could ever identify a person based on their microbial signature. Sort of like a fingerprint.
Joanna: I had the exact same thought. Apparently it’s not as hard as you might think.
Jack: It’s actually scary easy. What we found that was remarkable was even within the first few hours of moving into a house or being in a space, we could tell that someone had been in that space. Now, when I said that it took 5 to 6 days for that microbial signature to appear, I’m talking about absolute dominance. I’m talking about that the surface of the floor looks like the soles of your feet. Especially in bedrooms and bathrooms where you’re mostly walking around without socks on. That transition was quite dramatic after about 5 days. But even immediately we could tell that somebody had been in that house and if we’d sampled that person we could make a direct link between that person and the immediate microbial signature they left behind.
And one of the key reasons why this happens is that the microbial signature is transient. And what I mean by that is you touch a light switch, light switch to this office, you touch that light switch, you leave your sebaceous material on there. Now you’re sebaceous material, oils, may dry out very quickly. And the bacteria will start to die off when they have no more liquid to survive on. Some may persist as spores, but on the whole they’ll die. Now if you frequently touch that light switch, then you’re actually building up a residue base of oils on the surface of the light switch. Then it gets into the little rivulets on the light switch, the texture that helps you to grip the light switch when you turn it on and off. Or it gets into the fine scale pores of the metalwork on your door handle, or the surfaces, you can feel on any surface of any table, it’s not flat. There’s many little valleys and rivers. And things get into there and they grow. So it can build up over time.
But in the immediacy, we do see those signatures. It opens up some very interesting questions, like can we use this to track people? Theoretically yes, there’s no reason why not. But we’d have to build up the same kind of database that J. Edgar Hoover did with fingerprints for the FBI. Imagine a microbial fingerprint database. A national one held by federal agencies which would allow them to track people’s movements through spaces without ever really finding, it doesn’t matter how many clothes you’re wearing you’d have to wear a complete body air suit to rob a house. You could walk into a house and we’d be able to detect you within minutes.
Joanna: Maybe there would be products that would like spray different microbes around.
Jack: Surfaces? Well you can imagine that-
Joanna: Roaring trade.
Jack: Exactly, yeah. Black market for masking your signature.
Forrest: So, Joanna, I think you have a wonderful career ahead of you producing bacterial sprays for burglars.
Joanna: I like to think that I have some good ideas now and then.
Forrest: So if your house takes on your microbial signature and this only takes around 5 days to happen, does this mean that people who spend a lot of time together, such as married couples, start to resemble each other?
Joanna: Dr. Gilbert and his colleagues explored this very question.
Jack: Yeah, well another interesting fact is we found that people who interact more, physically, they share their microbiome more. We can see this in, for example, 3 people living in the same house. The couple, and their lodger, shared very different microbiome signatures. The couple, their microbiome signature overlapped quite significantly. We could see that they were interacting and they shared lots of their microbes. And they looked quite similar, despite different sexes, different ages, different diets. Whereas the lodger, this separate person, who wasn’t physically interacting with, hopefully not, the male or female partner who lived in the house, looked very different. There was no significant similarity. So we could tell people who were interacting as well. That opens up an entire new avenue for security potential, but also for maybe divorce lawyers and many other things.
Forrest: I think you might have more customers for your microbiome masking spray: unfaithful husbands and wives.
Joanna: And another possibility, you could develop a probiotic spray. Did you know that when you sterilize a surface, you kill the existing population of bacteria and then microbial weeds take over. So it’s actually better to have a strong community of harmless bacteria, because it diminishes the chances that dangerous bacteria will colonize a particular surface. So, after you clean your kitchen counter you could spray it down with probiotics.
Forrest: That sounds great, I guess?
Joanna: Well it might help keep us healthy. Speaking of health, Dr. Gilbert and his colleagues are actually now beginning to study the microbiome of a hospital. This really exciting study is happening right here, at the University of Chicago campus.
Jack: In the hospital microbiome project we had the unique opportunity, same as with the home microbiome project, where we were looking at people moving into a new house and the influence they had upon that new house. How long it took them to master the existing microbial signature in the house. In the hospital microbiome project we’ve uncovered a new hospital being built, on our very ground in the University of Chicago, and this new hospital is a hundred million dollar hospital. Is being built to house many different types of sick people. Including very transient surgical patients, to people with cancer, or transplants. So we wanted to say “What did the microbiome of this building look like before these sick people and doctors and nurses moved into the infrastructure?” And then, “How did it look like after they moved into the infrastructure for a year?”
So what we’re doing is we’re sampling that building on 2 floors in 10 patient rooms, in 2 nursing stations and all the patients and all the nurses and all the doctors. We’re sampling them every day for a month before the hospital opens and then every day for 365 days, so a year, after the hospital opens. We’re building up the most detailed longitudinal, or time series analysis, of the change in the microbial diversity as all these doctors and patients and sick people move into this infrastructure. Specifically, we want to know how do bacteria move around in this environment? Why do they shift? And does that have any influence upon the build up of specific bacteria in this ecosystem? So fundamentally it’s a investigation. It is also a wonderful opportunity to explore an environment which is very well controlled, reasonably sterile, but also has a unique function in looking after people, in trying to keep them healthy and safe. So we have an opportunity to explore the relationship between bacterial diversity and health.
Importantly we’ll be looking at 2 floors. The top floor, the 10th floor, has cancer patients and people who have undergone recent transplants. They may spend weeks if not months in their rooms. On the 9th floor, floor just below it, we’ll be looking at elective surgery patients. So patients who are just there for 1 or 2 or 3 days. Those 2 different time frames, weeks to months, to just a few days, represent really unique opportunities for us to determine how much the person microbially influences the space when they’re in that environment, and how long it takes them to have a significant impact, a significant exchange microbially with that environment.
Forrest: That’s awesome. It certainly is an amazing opportunity to study the distribution of microbes in an indoor public place.
Joanna: I agree. It’s fascinating to imagine the invisible world of bacteria that we live in, and that we leave a trail of them wherever we go.
Forrest: Also kind of horrifying. But I imagine that this radio studio is starting to look a bit like Forrest and Joanna right now.
Joanna: Yeah, I mean as strange as that sounds.
Forrest: And it sounds strange.
Joanna: It’s true. And you know microbial sleuths might be able to tell that we were here.
Forrest: Although, you would also be able to tell by turning on the radio, or by going to our website, groks.net.
Joanna: Details, details. Well Dr. Gilbert was kind enough to stick around and play our game, the Grok-a-Tron 5000. Grok-a-Tron 5000, previously known as Deep Blue, is our super computer, and it had a few questions for Dr. Gilbert. It asked for each of the following famous people, or characters, what type of microbiome would they be found in? For example, they could be found in desert soil, rainforest soil, the kitchen counter, etc. Let’s hear how he responded. The first one is Prince Harry.
Jack: Desert. Afghanistan, he’s a soldier. So he’s probably going to be found in one of the warring parts of the world.
Joanna: Okay. What about the pop star Lady Gaga?
Jack: Lady Gaga’s got to be in, she’s the freaky one isn’t she? I’d say her ability to survive severe abuse by the press, as well as her unique ability to undergo graphic changes in her wardrobe would probably place her as an ideal opportunist in an Antarctic environment. Whereby she could eliminate the competition and survive unhindered.
Joanna: Wow. That’s a great recommendation for her. What about another young pop star, Justin Bieber?
Jack: Justin Bieber? Wow, I don’t know he probably would be, does this have to be terrestrial or can I go indoors?
Joanna: Oh, sure.
Jack: Be found in the bathroom somewhere. I don’t know. Justin’s-
Joanna: I feel like he’s in a very comfortable environment.
Jack: Yeah, probably.
Joanna: His needs are being met.
Jack: His needs are being met. Let’s put it that way, let’s leave it at that one.
Joanna: Okay. What about the fictional character Sherlock Holmes?
Jack: Sherlock Holmes, wow. Definitely tropical forest soil. He’s very complex, has a huge number of interactions and an ability to understand his environment in a way which most other microbes would never have the opportunity to explore.
Joanna: And finally, the actor Charlie Sheen?
Jack: Charlie Sheen? Geez. Probably in a hydrothermal vent somewhere [rushing 31:10] off his nut.
Forrest: Well on that note, it’s time to end today’s episode. I’d like to take this opportunity to thank Jack Gilbert for being such an amazing guest.
Joanna: Yes, I had a lot of fun speaking with him.
Forrest: You can find more episodes on our website, groks.net. We’re also on iTunes, prx.org, archive.org, Facebook, and Twitter. So you can look for us there.
Joanna: From everyone at Groks including myself, Charles Lee, Frank Ling, Elise Covic, and Forrest Gulden, have a fantastic week and keep on Grokin.
Transcribed by Rev.com