Biomes Podcast Show Notes: Season 2 Ep 2 with Jack Gilbert

Microbiome Insights is proud to be the sponsor of season 2 of Ruairi Robertson's Biomes Podcast. 

In this episode Ruairi talked to Jack Gilbert from UC San Diego. Here are the key takeaways from the conversation: 

  • The pair discuss Jack's background and how he went from cataloging butterflies in the Natural History Museum to studying microbiomes in Antarctica to eventually playing a leading role in the Earth Microbiome Project.  
  • Microbial diversity and evolution. How microbes can adapt in order to survive in extreme and ever changing environments. 
  • How are microbes shared between people? What can we learn from microbiome research in the military and Amish and Hutterite communities. 
  • Are dogs the key to space travel and reducing asthma? What Jack is excited about working on next. 

 

Listen 

Links to Apple, Spotify, Podbean 

 

Full Transcript 

Ruairi Robertson:
Hello there and welcome back to the Biomes podcast. My name is Dr. Ruairi Robertson, and I am back with a second season of Biomes, where I chat with the leading researchers in the world studying the human microbiome. This second season of the Biomes podcast is sponsored by Microbiome Insights, who could be great partners for your microbiome study. So whether you're planning a study, applying for a grant or you're ready to ship samples for sequencing, the people at Microbiome Insights can help. They provide end to end microbiome sequencing and bioinformatics analysis, and their range of services enables industry and academic researchers to include microbiome analysis in studies across human, animal, agricultural and environmental applications.

Hundreds of researchers around the world rely on the expertise of Microbiome Insights, and they are offering free study consultations for all Biomes listeners. So to avail of this, go to microbiomeinsigts.com and tell them Ruairi sent you. In this first episode of the new series, I speak with Professor Jack Gilbert of the University of California, San Diego. Jack is an amazing scientist who has studied microbes from literally all over the world, from Antarctica to active volcanoes and even outside of this world, in the International Space Station.

In this episode, I talk to him about the amazing interactions that we humans have with the microbes that surround us. How we shape each other's microbiomes, and how those microbes shape us. As Jack explains, humans emit about 37 million bacteria an hour. And when we interact with other humans, these microbes are transferred to each other. He has studied these interactions in a wide range of contexts, notably in hospital settings, where he has shown how microbiomes of hospital wards can influence the health of its patients, and has developed exciting probiotic solutions for buildings to aid human health.

His research even spans to outer space, where he has reported how the evolving microbiome of the International Space Station could endanger astronauts, and is considering potential future strategies to help solve these problems. So Jack Gilbert, thank you very, very much for agreeing to have a chat with me all the way from sunny or not so sunny San Diego, I kind of had a bit of difficulty in trying to figure out a theme for a what I talk to you about because your research is just so wildly all over the place, and still relating to the microbiome but the microbiome of everything.

In fact, I watched one of your talks where you described yourself as a pediatric oceanographer at one point, so to describe the kind of breadth of the research you do in the field. So maybe we can just start off and you can give a little introduction to how you got to where you are, and how did you start off? And how did you get to this kind of crazy place you're in now?

Jack Gilbert:
I would say you could sum it up as academic ADHD. I love everything and I have so many questions I want to ask, and it's weird, as soon as we get a grant to work on something, I'm less excited about actually doing it. I love the ideas. I love creating research plans to develop those ideas. But my background is kind of weird. I did my undergraduate at King's College in London, and then ended up working for the Natural History Museum down in Kensington for a long time, about a year and a bit, cataloging their butterfly distribution patterns, so cataloging their collections, and putting them into a computational platform to look a biodiversity in Africa. And I absolutely loved that I thought it was going to be an entomologist from my whole life.

And then weirdly out of the blue on my lunchtime one day I can't remember when it was, somebody emailed me and goes, "Your name has come to my attention, we would like to offer you the opportunity to do a PhD, at Nottingham University, but it means you'd have to go and live in Antarctica for two years." And I was like, "What?" I was like, "Who is this?" So I followed it up and lo and behold, I don't know how my name got into the lexicon, but they offered me the PhD position. And so I spent two years working on microbes. And I told him I had no microbiology background really apart from an undergraduate course. But they said you can learn that, I'll be fine. And that, "You can learn that, it'll be fine." Has pretty much been the running theme for my entire career.

Ruairi Robertson:
Of course as with lots scientist. We'll figure it out.

Jack Gilbert:
Build the plane while flying it.

Ruairi Robertson:
Exactly.

Jack Gilbert:
And so it's been a huge amount of fun. I bounced around from microbiology in Antarctica, then I went to Canada to do a postdoc where I had to learn proteomics and protein characterization, X ray crystallography, that kind of stuff. I came back to England to work at Plymouth Marine Laboratory for about five years until 2010, where we were doing marine microbiology. And then I went to University of Chicago in Argonne National Labs in Chicago. I didn't know where Chicago was, that's how ignorant I was of US geography. I worked there for nine years.

Ruairi Robertson:
You only do the UK and Antarctica, but you didn't know geography of the US.

Jack Gilbert:
I'm like, Chicago is somewhere in the middle. Worked there for nine years. And then in 2019, I came over here for my midlife crisis retirement into sunny climate so I can surf.

Ruairi Robertson:
Butterflies, to oceans and now to human somewhat, which we'll get onto. I didn't actually know about that Antarctica bit. Tell us about what that was like and what you'd do day to day for science and what was it like living there.

Jack Gilbert:
It was crazy. It was a privilege. Is was me and 19 Australian guys who were part of the Australian Antarctic Research Division. It was only men because only one woman applied that year. So due to Australian regulations for gender reasons, you have to have two women there for the prolonged period of time, women needs support of other women. That's what we were told I don't know whether that would hold up under current gender regulations. So it was very isolating from that perspective, I was very young, I was 22 when I went down.

And it was a crazy experience. My basic role there was to find bacteria that bind onto ice and stop it from growing. So these ice inhibition bacteria. And that's a beautiful story, I actually got to go back to the lab, which I worked on during that period, I got to go back and see their work because my supervisor was retiring. And it's funny, 20 years on, they've done some incredible things with the science.

They found that some of these bacteria bind onto ice using this appendage, but they also bind on the same appendage to a diatom. And if six of these bacteria bind onto a diatom, they can use their flagella to swim the diatom up to the surface of a lake, bind onto the ice on the surface, where there's light, nutrient rich water to feed the diatom. The diatom then produces sugars which they consume. How insane is that? That's so cool.

Ruairi Robertson:
No way, really.

Jack Gilbert:
They hijack their own power plant facility and then take up to the top of the lake. And that's what blew me away. Is it took 20 years to uncover this and I just started it by finding this bacteria in this lake. And you realize you're just part of a cog in a machine in academia, right?

Ruairi Robertson:
Yeah, exactly.

Jack Gilbert:
There were 15 other postdocs and graduate students galore followed me and did all this incredible work. And I love that, I love being part of a larger story. I never really wanted to be the leader of XYZ, I always wanted to be part of a larger story, a collaborator that can build up this amazing body of knowledge. But I guess, long way of saying, I love doing everything, and I love being part of everything and collaborating on everything. And it's stood me in good stead so far.

Ruairi Robertson:
Well, you say that you love only being a part of it but really, you are a leader. And one of the big kind of things you're known for is the Earth Microbiome Project, and you lead this to try and catalog living microbes in huge number environments around the world. You were... Not trying to blow your trumpet or something but you are more like Darwin trying to systematically catalog microbes, which we don't know enough about in all kinds of regions of the world. So, tell us a little bit about that and how close are we getting to where Darwin was in his day?

Jack Gilbert:
Well, I always say if Darwin was alive today, he would have been a microbiome scientist right?

Ruairi Robertson:
Yeah.

Jack Gilbert:
And for me that holds true because microbes and their potential to evolve and adapt, and manage the environment around them, they're phenomenal, they are just incredible. What he was inferring from finches and earthworms now we are observing in microbes on a regular basis. And so that was awesome. Yeah, we started the Earth Microbiome Project in 2010 and there were about 20, or 30 of us locked in a hotel room above Salt Lake City doing some pretty heavy drinking but pretty cool theorizing about what could you do if you could sequence everything.

And out of that came Rob Knight who's obviously the super 50,000 pound gorilla in microbiome science and one of my close friends and colleagues here at UCSD and Janet Jansson, who's up at Pacific Northwest National Lab. Rob had all of the expertise and technical experience, I was just a wonderful cheerleader and absolutely loved doing it and had some funds to help kickstart the program. So for me, it was always a part of being part of that group the resulting 450 other scientists that we collaborated with who also played major roles.

So not so much of a leader, more of just a herder of cats in getting the program to actually work properly. But it was, for me, a phenomenal honor to be part of such a large group of people doing some pretty cool science. And it's still ongoing. In 2017, we published the first paper with 27,000 samples processed, we're now up to about 160,000 samples processed and data is available, it's publicly available on multiple forums. And people can now use that. They can take their microbiome data from their study and put it in context to the global microbiome. And that's important if you want to understand ecological trends.

But when will we be done? Never probably, because microbes are evolving. And our main goal is to understand how they interact with each other, how they manipulate their environment, and what that actually means for the globe, and how the globe is responding to the current crises, such as climate change which we are affecting it. And so yeah, we're in a continuous discovery pipeline and I think Darwin would approve of that, right?

Ruairi Robertson:
I definitely think so.

So give us a few examples of the kinds of cool places that you have data from in the Earth Microbiome Project. Where is the equivalent of Darwin's Galapagos Islands, where you have this huge diversity that you didn't know much about before? What are the kind of cool places?

Jack Gilbert:
This is what's fascinating for me, we did a lot of work on this in 2008 to 2011, approximately so about a decade ago now. And we actually found out one of the most diverse places on the planet. If you look at it from the data, it's actually the English Channel, which makes no sense, it's totally irrational. But when we sequence really deeply in the English Channel, you find all of the microbes more than 60% of all of the bacteria we observed in any other environment in the ocean, globally. So that suggests that we shouldn't think more of... It's not like the Galapagos Islands is the most diverse place in the world, we don't really have that simulacra in microbiome science, because microbes are distributing around the world so regularly.

In terms of numbers, the most diverse bases are soil and sediment because they're the ones that have the most niche structure. The little individual niches on a within say, a gram of soil is so many surfaces, which bacteria can colonize. Interestingly for any gram of soil, only about 20% of the surfaces of the soil grains are actually colonized by bacteria, 80% is just a blank desert with no biological material. But it's a phenomenally rich, complex environment. But because microbes can move around the world, maybe Baas Becking was potentially correct and everything is everywhere, and the environment selects.

I don't think that's true in any given moment, in any given day. But if you look at geological time, or at least thousands of years, then I think it's very true. We are living in a microbial world, they permeate everything, and they're just adapting to whatever comes along. Be the chunk of ape, or buildings that we are now creating, our built environment which is a massive selective pressure against microbial evolution and changing the paradigm for many of the microbes that we've come to know and love or hate.

Ruairi Robertson:
That's amazing. And I want to come on to that, into the buildings next but say you did go back and sample some of these places. We all know that microbes evolve really, really fast, much quicker than we as humans evolve. So, how long would it take for you to go back and see completely new species if you were to go back to some of these places that... Obviously that depends on the environment and climate change and things like that but how fast are these actual changes happening to these kind of communities that you're sampling?

Jack Gilbert:
I would argue, we'd have to define the parameters of your investigation, right?

Ruairi Robertson:
Exactly.

Jack Gilbert:
What's the species?

Ruairi Robertson:
Well there you go, yeah it depends.

Jack Gilbert:
If you take, say a hydrothermal vent, we see a very, very selective environment, high temperature, high pressure, zero light, lots of sulfur. So lots of sulfate reducing potential. Are the organisms that we saw there 10 years ago, the same as the organisms we see now? Well, most of those vents don't last 10 years so it's hard to say, isn't it? But I would argue, from what we can tell, if you look at strain level or genotype level organisms, this is a microbe with a unique genotype, not just one or two snips, a single nucleotide polymorphisms, but enough genetic manipulation to say, "Yeah, that can do something different." It has a different functional phenotype, maybe very similar to its strains siblings, but it has the potential to do something different.

What we find, we find those cropping up all the time. When we looked in 2018, 2017, we started this project in 2010 but we were looking at the oil pollution that came out of the Macondo wellhead explosion in the Gulf of Mexico, in 2010. And we found that the genetic diversity of the microbes in the sediment that were responding to the Macondo oil explosion was phenomenal.

A lot of these bacteria, the genotypes were found all over the Gulf of Mexico, we could find in sediments that had no oil associated with whatsoever, but they were very low in abundance. And then around the oil head, they became super abundant. And each one had a unique adaptation to degrading one type of polyaromatic hydrocarbon. So they were nibbling and nibbling. Each one was nibbling away at different parts of the crude oil which had seeped out. And that to me was crazy. These guys are hanging around waiting for something to happen. Well, each one of them is also undergoing genetic mutation and therefore has the potential to alter its phenotype in response to the world around it. And that's the beauty of microbes as you said.

Ruairi Robertson:
That's phenomenal, that's brilliant. So you moved on then you kind of had looking at the bigger environment all around the world and then you kind of wanted to start looking at closer to home, and honing things a little bit. And you've some published some really interesting stuff on the microbiomes within the buildings around us in various different settings. One of which is in hospitals. And I know, there's some really interesting anecdotes and studies showing how the microbiome of the hospital buildings can actually influence infection rates in patients. Tell us a little bit about that, and why the kind of microbiomes of hospital buildings might actually be important for the humans within those buildings?

Jack Gilbert:
Yeah, the key takeaway from all of our studies here, we published a study in 2017 that basically demonstrated that what we'd found before that, when a human being enters a room, they shed so many bacteria that they basically...Their microbes, the ones that can survive in a building, which are very, very few, about 99% of bacteria that leave your body die. But the 1% that do survive, they are your microbes, and they colonize the space that you're in. Each one of us is emitting 38 million bacterial cells an hour, according to Jordan Peccia at Yale who did some phenomenal work in that space.

The outcome is the patients enter a room and their microbes leave their body. And what happens to the ones that do survive is very interesting. What we found through extensive metagenomic analysis of over 100 samples and then reconstructing the evolutionary selective pressure upon operons that were associated with antibiotic resistance is that the bacteria that were in the room were being selected for antibiotic resistance, but not by the antibiotics the patient was getting. And that was really interesting to us. So it didn't matter what antibiotic the patient was receiving, the organisms were being selected for antibiotic resistance genes that had no relationship to that antibiotic.

And we hypothesize, based on the evidence that we received from there and recent studies that we've been doing that haven't been published, that the bacterial operons that are associated with antibiotic resistance are also associated with survival in extreme environments. So you've got things like Staph aureus, Strep pneumoniae, Pseudomonas aeruginosa, and they're leaving the bodies of these patients ending up on cold, dry, harsh surfaces where there's virtually no moisture, they're surviving, but they're surviving on the edge of survival. And so the selective pressure of that survival environment is also enabling these organisms that just so happen to contain the antibiotic resistance genes on those operons to survive and thrive. Well thrive is hard, but they are definitely surviving.

So the potential for those to re-colonize people who are susceptible is great. And so we're doing a double whammy. We're working with people who develop phages to kill off the bugs inside the patient. But we're also working on strategies to alter the building environment, potentially by adding bacteria back in bacillus subtilis spores, for example, to just saturate the environment with good bacteria or benign bacteria that can out-compete these bugs that can survive when they leave our body in that space. So it's biological control in a hospital. And we think that's much better than sterilizing everything. So if you sterilize everything, the patient doesn't stop emitting bacteria into the environment so if you sterilize the surface, two or three minutes later, the patient's bacteria recolonized it.

Ruairi Robertson:
Yeah, I think there is evidence of that isn't there? I read some interesting anecdotes, at least anyway, that hospitals that had installed this kind of antimicrobial flooring, hoping that it would reduce infection rates, but actually it increased infection rates, because it led to those bacteria-

Jack Gilbert:
They can select. As you pointed out earlier, the bugs find a way. It's like very Michael Crichton, the life will find a way, but microbes do they find a way around what we're trying to do. I often say that if you really, really want to be super sterile, the best thing to do would be covering every surface in copper. It's very hard for microbes to evolve a mechanism to survive or resist copper oxidation from the divalent metal iron getting into this, it should wipe out everything. But covering the entire surface of a hospital in copper would be incredibly expensive and almost potentially... but it may lead to resistance, it would be crazy if it did but that's the exciting piece. So we need other solutions, things are working quite well, but we need other solutions.

Ruairi Robertson:
So tell us the practicalities of that. How do you fill a hospital potentially, with these kind of healthy or kind of non disease causing microbes in order to do that? Are you spraying around the place?

Jack Gilbert:
Yeah.

Ruairi Robertson:
Really?

Jack Gilbert:
Well research is already doing this. I mean, you can buy products on the market on Amazon, whatever your favorite online retailer is that contain bacillus sort of spores in them. So you can wash home with bacillus spores if you want. This is just standard cleaning products, spray bottles, floor cleaners. And the issue is we just don't have a huge amount of evidence to suggest it actually does anything. Now there is a group in Italy and one group in Florida that have done limited clinical studies and demonstrated that the addition of these bacillus spores, compared to standard cleaning tends to reduce the abundance of antibiotic resistance genes in the environment but they're very small. Now we're doing much larger studies replicated at much larger level to demonstrate its efficacy, we hope, as a potential strategy, but it's one in a tool box of arsenal.

One that is interesting is we've also just recently demonstrated that SARS-CoV-2 like the flu virus binds to the outside of some of these bacteria which can survive in the outside of the body. So if SARS-CoV-2 finds its way into someone's lungs, and that person has Staphylococcus aureus in there, and it's asking me to combine on the outside of Staph aureus, then when both of those are released into the environment, the SARS-CoV-2 can survive longer outside the body on cold dry surfaces, because it's bound on to this bacteria, which can also survive. And then if that's re inhaled, the bacteria finds a neat little way of getting back into the body because the SARS-CoV-2 can help the bacteria to invade human cells, because you know, the lock and key mechanism of the spike protein. It can also help the virus because then the body goes into parallelisms of an immune response to deal with the Staph aureus and leaves the SARS-CoV-2 alone.

So there's a great researcher Jason Rosch at St. Jude's hospital who did this work in flu and demonstrated it quite effectively that flu rate through transmission is much greater if ferrets have particular types of bacteria in their lung because of this transmission potential, and we're now demonstrating that in SARS-CoV-2. And so it may be that if a SARS-CoV-2 Staph aureus conjugate lands in an environment flooded with bacillus spores, it may not survive, and may not have the greater potential to cause transmission. And so we think there may be benefits even to the current pandemic of doing this. And that's exactly what we're researching now.

Ruairi Robertson:
Wow, amazing. So how does that work then? So we're kind of honing in on ourselves here, we started like earth then hospital, and they were coming a little closer to home. In the home itself you know. Oh I made you choke on your tea. I'll give you a minute.

Jack Gilbert:
Sorry about that.

Ruairi Robertson:
No, no, you're all right. All right. It's the thought of all these spores and everything. So you've looked in the home as well, you've said that we're all emitting 30 million cells an hour or whatever it is, when we go into a room, so how much of that then in a confined environment, like in a home is actually transferred from individual to individual? So say, I have a new roommate that comes in and lives with me, am I actually transferring that much and how is that transfer happening? Is it airborne? Is it through surfaces? And how much are we exchanging?

Jack Gilbert:
Yeah, when we look at, say people that become roommates, there is a certain degree of microbial exchange. And we looked at this in Air Force cadets. So these are people who come from all over the country, to a Air Force Academy, sorry, that tea really did a number on my lungs.

Ruairi Robertson:
Haha, it's alright.

Jack Gilbert:
Tea is very dangerous. And they came from all over the country, they stayed in, and you get the same duplex room, so the room is like a dormitory in a university. It has two beds, two tables, and they use those rooms, but they all eat the same food because it's the military, they all do the same exercise regimen, they all have the same haircuts, they all wear the same clothing, it's very, very prescribed. And in that study, which was led by the military, we noticed that these young, very healthy people tend to only exchange about 5% of their microbes. So they'll only become about 3% to 5% microbially, similar. Otherwise, most of microbes just mix in the environment. We don't fundamentally understand the mechanism of that transmission, we hypothesize it's through that shared activity and then inhaling it.

Jack Gilbert:
On your skin any microbial contamination, let's call it that, that you pick up can easily be washed off with hand washing and then your own microbiome will bubble up through the depths of your skin back to the surface. For example, if you and I shook hands, we did this for NPR once with...what's he called? The physicist who's on the TV all the time for Cosmos, Neil deGrasse Tyson. We had him shake hands with somebody, and then we swab their hands every minute for about five minutes. And you can see the microbial evolution of his microbiome coming back to his hand. There's a bit of contamination to begin with, and then it resurfaces, it restructures itself. And so there's always this, if we clean someone's hand that their skin will come back to their own microbiome, and eradicate whatever signature existed previously.

Prolonged exposure will have a big impact. If those two people are physically interacting, that changes everything entirely. Swapping saliva as it were and physical conjugation can have a dramatic effect, leading to a higher degree of similarity. But even married couples will retain unique microbial identities over decades of cohabitation. And so there is an element there that your microbial self stays, who you are you just swap a certain amount. Rob Knight did a wonderful study once where he looked at couples living together that either had dogs or babies or nothing. And couples with a dog were more microbially similar to each other, i.e. They shared more of each other's bacteria than couples with a baby or couples without a dog. So there's something else going on there that we can't quite tell.

Ruairi Robertson:
It passed to the dog somehow.

Jack Gilbert:
Right, those are the super transmitters, like a great vector for microbial transmission, we don't know. But that kind of understanding of where, how the microbes are transmitted is just something we... It's very hard to determine, even in animal models because it's hard to track the movement of all of these microbes, we've mathematical algorithms to do it, but they're not perfect.

Ruairi Robertson:
Right. That's interesting so you retain a lot of your own microbiome. So presumably, there's something ingrained from earlier in life that forces you to kind of have your own microbiome or maybe not earlier in life, there's something about your body that brings it back. So what do we know...

Jack Gilbert:
Well, you're an ecosystem, and your immune system is kind of unique, as well. And so the combination of having that... Darwin would be proud. You are an island, you're colonized as an island, and whatever that starting colony is will shape how your ecosystem develops, and your immune system shapes that as well. So that partnership between the immune system and microbiome is going to be continuously shaping and structuring who you are, and you can change that dramatically over your life through diet, antibiotic therapy, et cetera. But for the most part, it's always going to bounce back to who you were originally.

Ruairi Robertson:
Amazing. And so if there is that transfer between people, do we know enough yet what the implications for that are? Say there is this 5% transfer, you're saying or more if you're physically interactive with people, is there any evidence to show that, that actually has any implications for health or it's not enough to influence this island or this host?

Jack Gilbert:
We don't have any evidence to suggest it influences health. There's lots of data that suggests that interacting with fellow siblings, for example, that have gone to school can influence your immune response as a child. Fantastic work from Susan Lynch, in University California, San Francisco, and groups in Germany. Trying to remember her name, that's terrible, because she's really good friend of mine. But anyway, I'll remember it later later. They have demonstrated quite effectively that children growing up in a household that have older siblings that go to school will have a stronger immune response, and are less likely to develop asthma or allergic disease than children who do not have older siblings or at school. So there's that element that interacting with those children that have that other microbial exposure could be playing a role. But it's all circumstantial to a certain extent, we cannot pick the mechanism that underlies that interaction. But the work we've done with the Amish and Hutterites, looking at asthma effects has demonstrated that children interacting with furry animals, and to a certain extent Susan Lynch's work with dogs and cats. Children interacting with furry animals very early in life can have a profound effect on their immune response.

So there's an element of that, if you grew up with a dog, and you can physically interact with it under the age of one, you'll have a 13% reduction in the likelihood of developing asthma. If you grew up on a farm interacting with farm animals, you have a 50% reduction in the likelihood of developing asthma, which is phenomenal. So maybe interaction with humans can be beneficial, but interacting with furry pets, that or furry farm animals that might be even better. So worth thinking about.

Ruairi Robertson:
And so what are these other kind of unique environments you've looked in? We know that if we have exposure to animals, we have exposure to other people, that's probably a good thing kind of increasing this diversity. But there's some cases where people are exposed to a limited environment, one of which I suppose is the International Space Station, which I think you've looked at as well. And that I suppose, is a really unique environment to look at, because these people are in a confined space for six months, a year with only, I think, five other people, and not any real exposure to the outside world and these other external organisms that you're talking about. So what happens there? We know there's long term implications for health for these people. Maybe not long term, but there is implications for when they come back.

Jack Gilbert:
Yeah.

Ruairi Robertson:
Is some of that to do with their changing microbiomes or how much their microbiomes change when they're up there?

Jack Gilbert:
We try to understand that and it's really complicated. And the complication is, these are really small groups of humans and so we don't have any statistical power to actually assess what's going on. So all the human studies actually on the International Space Station are really limited, and really hard to actually infer anything from. However, our main interest is, does the environment shape microbial evolution? And so we're currently sending up more materials up to the International Space Station a couple of months time on a SpaceX resupply, because we want to do time lapse, or time lapse observations and microbial evolution in that space. We already know that if we space fly isolates of fungi or bacteria, and we bring them back down to earth, there'll be more pathogenic than the same organism that just stays on earth for the duration of that exposure. So, if we infect nematodes with those bacteria or fungi, more nematodes die if the organisms have been space flown.

We don't know why though. We however hypothesize that the combined effect of being in this cold, dry, harsh environment may be combined with more radiation exposure from the cosmic rays and the sun maybe also zero gravity is somehow shaping these organisms evolutionary process or their epigenetic process in a way that has an impact upon their pathogenicity or virulence. But we're really early stages of trying to figure that out. So our main issue is, say you got an astronaut and she has to fly to Mars and she's going to be there for six months in a spacecraft, with maybe three other people. But she's going to be there also with 30, 40 trillion bacteria in her body and 30, 40 trillion in the other ones. And those bacteria leaving her body ending up in this environment that is shaping pathogenicity, if she does become susceptible to an infection, is there the opportunity for these built environment microbes in the spacecraft to reinfect her because of this heightened virulent activation? Whatever's driving it, right?

And so we're really interested in understanding is it possible to ameliorate that, and so maybe taking up a similar strategy for hospitals and imposing it into spacecraft could be a way of just preventing that from happening by preventing these organisms from ever establishing in the International Space Station. But then the question is, does bacillus mutate into some horrifying monster spacecraft bacteria? I'm currently having those epistemological fights with NASA to say like, "It's going to be fine." "Well how do you know?" "Well, I don't know."

Ruairi Robertson:
There's definitely going to be a movie made about that, this scientist who says everything's going to be fine and suddenly.

Jack Gilbert:
Maybe space zombies and everything is going crazy on Mars.

Ruairi Robertson:
Yeah. Maybe that. Although it is worrying, I know, there's talk of this kind of colonization of Mars and all these other places and really, that could be our downfall is the microbes that we bring up with us, rather than us being the architects of our own downfall through I don't know..

Jack Gilbert:
Well, that's why I think we need to take dogs into space. Laika was the first one, she didn't survive. Well, we need dogs in space with the people. Why can we have dogs in the International Space Station? They'd love it.

Ruairi Robertson:
Floating around.

Jack Gilbert:
When we go to Mars, we should have dogs there.

Ruairi Robertson:
Yeah, that'd be a great idea.

Jack Gilbert:
I think it's awesome.

Ruairi Robertson:
You can suggest to NASA on your next-

Jack Gilbert:
Oh, I already have they poo-pooed the idea.

Ruairi Robertson:
I think we'll leave at that. I don't know, what do you see... I was about to ask you, what is the future but I feel like we're talking about the future already with all these space, things. What are you excited about next? You've done Antarctica, you've done the earth? You've done space?

Jack Gilbert:
I'll tell you the two things I'm most excited about. As you can tell, I generally get very excited about all of it. But what I really want to do, we've done a lot of observation for last 10 years, we've built some phenomenal hypotheses. The two things I'm most interested in doing are precision therapies for humans. I really want to get to the stage where... We've identified, say, a bacteria released this chemical this metabolite, into the bloodstream of humans, it can be an indicator of disease. But could it also be a therapy? We found certain bacteria release certain metabolites into the serum, which actually alter the allergic response of immune cells in children's lungs, and prevent them from developing asthma. It is a hypothesis we've got mouse work that was suggest it, I really want to get to the stage where we can test that in a clinical trial.

And I'm maybe one or two years away from doing that. But if I take this metabolite, and I can inject it into children's blood streams early in life, who are susceptible to developing asthma, can I reduce their chances of developing it? You know, 12% of the US population can develop asthma in their lifetime. That's insane-

Ruairi Robertson:
And growing.

Jack Gilbert:
And it's... Yeah it's growing and it's a debilitating disease that we may be able to prevent. So I'm really keen on doing that. And many other diseases, but come back to environments, we're working extensively now with groups like one of my colleagues, Jeff Bowman and Sarah Allard at Scripps Institution of Oceanography and colleagues around the world as part of a new consortium we've built up like an Earth Microbiome but focused on mangroves. Mangroves suck up so much more carbon five to six times the amount of carbon as terrestrial forests, and they're nurseries for fish so they are important for re-establishing fish stocks, and they clean up all the pollution coming off the land, so they prevent the degradation of coral reefs. These are incredibly important environments and so we working to build microbial probiotics. So specific microbial organisms that can be placed into the root systems of planted mangrove trees to promote their growth, to ameliorate and remove pollution so we can actually re-establish mangrove forests around the world.

And those are just two examples, we're translating our science now. That's what I'm most interested in doing. That's the legacy I'd like to leave when I shuffle off this mortal coil is that we've actually develop some therapies for the earth and for humans that will actually have lasting impacts on the health of our planet and our population.

About Microbiome Insights

Microbiome Insights, Inc. is a global leader of end-to-end microbiome sequencing and highly comprehensive bioinformatic analysis. Based in Canada, the company’s diversified suite of services enables industry and academic clients to include microbiome analysis in studies across a range of human, animal, agricultural, and environmental applications. Our award-winning team has worked with over 50,371 samples from industry and academic clients and has a reputation for providing friendly, efficient service.