You Might Also Like: Incubation

Summary

Podcast Summary: The Great Detectives Present Dragnet (Old Time Radio)

Episode Title: You Might Also Like: Incubation
Host: Adam Graham
Release Date: December 7, 2024

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Introduction to Viral Dark Matter

In this episode of "The Great Detectives Present Dragnet," host Adam Graham delves into the enigmatic world of viruses that remain largely unidentified, often referred to as "viral dark matter." The discussion begins with an exploration of the ubiquity of viruses in our environment and bodies, highlighting the vast number of undiscovered viral species.

Jacob Goldstein [00:04]: "Viruses are in the air we breathe, in the water we drink. They're in the ground we walk on... we're surrounded and permeated by viral dark matter, by viruses that we don't even know exist."

Interview with Ken Stedman: Exploring Viral Dark Matter

Ken Stedman, a professor of biology at Portland State University, shares his pioneering research into viral dark matter. His work involves collecting samples from extreme environments, such as volcanic hot springs, to discover novel viruses.

• Discovery Methods: Stedman explains the methodology of collecting samples from harsh environments like Boiling Springs Lake in Lassen Volcanic National Park, where temperatures reach 130-140°F and the pH is around 2, making it highly acidic.

  Ken Stedman [03:19]: "We just took about 200 liters worth of water from the lake and then purified all of the virus-sized particles in it, then determined what their genetic sequences were."

• Unprecedented Findings: Upon analyzing the genetic sequences, Stedman's team found that over 90% of the sequences did not match any known viruses, confirming the vast extent of viral dark matter.

  Jacob Goldstein [06:04]: "Does that mean that we don't know about 90% of the viruses that are out in the world?"
  Ken Stedman [06:12]: "That is exactly what it implies."

• Cruciviruses: A breakthrough discovery by Stedman and his team revealed a new class of viruses called "cruciviruses," which appear to be a hybrid between DNA and RNA viruses. This challenges the long-held belief that DNA and RNA viruses are evolutionarily distinct with minimal interaction.

  Ken Stedman [09:05]: "But we'd sequence DNA. And when I say we mostly... we have what we're now calling crucie viruses that appear to have evolved by DNA viruses and RNA viruses coming together."

• Global Presence: Cruciviruses have been identified in diverse locations, including Antarctic lakes, deep-sea sediments, and even within microbial ecosystems in various environments, indicating their widespread presence.

  Ken Stedman [11:30]: "Basically anywhere that we have looked, we found these cruciviruses, very low amounts of them, but seem to be very ubiquitous."

Transition to Shiraz Ali Shah: The Human Virome and Asthma

The episode transitions to an interview with Shiraz Ali Shah, a senior researcher at Copenhagen University Hospital Gentofte, who focuses on the human virome—the collection of viruses residing in the human gut.

• Copenhagen Prospective Studies for Asthma in Childhood (COPSAC): Shah discusses the long-term study tracking 700 children from birth to analyze various factors contributing to the development of asthma and other chronic diseases.

  Shiraz Ali Shah [17:16]: "So there's more and more evidence showing that if you are not exposed to a diverse array of good bacteria in the body... you're way more prone to chronic inflammatory or immune diseases in the future."

• Virome Analysis: Shah explains the complexities of identifying viruses in gut samples, noting that traditional methods often miss the majority of viral diversity. His team manually curated viral families from vast genetic data, uncovering approximately 250 viral families, most of which were previously unknown.

  Shiraz Ali Shah [23:29]: "What we first do is we assemble all the sequences like a piece of a puzzle... and manually look through 10,000 clusters of sequences, and out of those 10,000, around 300 of them were the ones that I could confidently say were viruses."

• Link to Asthma: A significant finding from Shah's research indicates that certain temperate bacteriophages (viruses that infect bacteria) present in the gut at one year of age are predictive of asthma development by age five. Specifically, lower levels of 19 distinct temperate phage families correlate with a higher risk of developing asthma.

  Shiraz Ali Shah [27:15]: "So Christina... found that it was the temperate bacteriophages that were predictive of later asthma... the children that end up developing Asthma by age 5, they had way more temperate phages in their gut at age 1."

Implications and Future Directions

Both Stedman and Shah emphasize the potential significance of their discoveries in understanding human health and disease. While Stedman's exploration of viral dark matter opens new avenues in virology and evolution, Shah's findings suggest that the virome plays a crucial role in immune system development and the prevention of chronic diseases like asthma.

• Potential for Disease Prevention: Shah expresses hope that future research will enable the manipulation of the virome and microbiome to prevent chronic diseases.

  Shiraz Ali Shah [31:07]: "I'm hoping in the future that we have a much better overview... so that we can prevent maybe 10, 20, 30 years from now, we can prevent a lot of chronic diseases..."

• Environmental Factors: The studies indicate that environmental factors such as living in rural areas and consuming whole foods may promote a more diverse and beneficial virome and microbiome, potentially reducing the risk of developing asthma and other diseases.

  Shiraz Ali Shah [30:08]: "The ones that really live in a rural environment have a much more diverse ecosystem in the gut."

Conclusion

Adam Graham wraps up the episode by highlighting the groundbreaking work of both Ken Stedman and Shiraz Ali Shah. Their research not only expands our understanding of the vast and largely unknown viral world but also opens up possibilities for novel approaches to disease prevention and health optimization.

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Notable Quotes with Timestamps:

• Jacob Goldstein [00:04]: "Viruses are in the air we breathe... we're surrounded and permeated by viral dark matter."
• Ken Stedman [03:19]: "We just took about 200 liters worth of water from the lake... determined what their genetic sequences were."
• Shiraz Ali Shah [27:15]: "They had way more temperate phages in their gut at age 1."
• Shiraz Ali Shah [31:07]: "We can prevent a lot of chronic diseases by giving babies viruses or bacteria..."

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This episode of "The Great Detectives Present Dragnet" offers a fascinating glimpse into the hidden world of viruses that inhabit our environment and bodies, shedding light on their potentially profound impact on health and disease.

Transcript

[Jacob Goldstein]

Viruses are in the air we breathe, in the water we drink. They're in the ground we walk on. They're on our skin. They're in our bellies. They have us surrounded. And the wild thing is, we've only identified a fraction of them. In other words, not only are we surrounded and permeated by viruses, we're surrounded and permeated by viral dark matter, by viruses that we don't even know exist.

[Ken Stedman]

We have lots of viruses in us, and we have no idea what they're doing. And potentially in that dark matter, there are some answers to the questions on what are they doing there?

[Jacob Goldstein]

I'm Jacob Goldstein, and this is incubation. Today on our final episode of season two, we're going out to the scientific frontier to talk about all the viruses we don't know about in the world and in our bodies.

[GSK Advertisement]

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[Jacob Goldstein]

In the second half of the show. Today, I'll be speaking with a researcher who has recently discovered hundreds of families of viruses that live inside the human gut. And he's found a link that suggests some of those viruses could actually help kids stay healthy. But first, I'm going to talk with Ken Stedman. He's a professor of biology at Portland State University. He studies viral dark matter, which basically means he goes looking for viruses in wild places. To start, I asked him, how do you look for a virus that nobody knows exists?

[Ken Stedman]

Couple of different ways. All viruses that we know of by definition have to have a host that they infect. What we do is we'll go and collect samples in the craziest places we can find, usually volcanic hot springs, and then we bring them back to the Lab and see if they infect our favorite microbes that also happen to grow in these hot springs.

[Jacob Goldstein]

I've read a little bit about your work at Lassen Volcanic national park in Northern California. So tell me about what's going on there. Tell me about Boiling Springs Lake.

[Ken Stedman]

So Boiling Springs Lake I like to describe as the biggest hot spring in the world that nobody has ever heard of. It's a slight exaggeration. The low temperature in the Lake is about 130, 140 degrees Fahrenheit.

[Jacob Goldstein]

And so what does that mean for finding weird viruses?

[Ken Stedman]

Well, hang on just a sec. That's the temperature. I haven't told you about the PH yet, have I?

[Jacob Goldstein]

Wait a minute. If you like the temperature, you're gonna love the ph.

[Ken Stedman]

Exactly. So the ph is about 2.ph of.

[Jacob Goldstein]

2 means it's acidic. It's highly acidic. So not great for soaking is what you're talking about.

[Ken Stedman]

Not great for soaking. We've seen people walking up there in their swimming gear and we tell them, not a real good idea.

[Jacob Goldstein]

So you go to this hot, acidic lake and what, what do you do there?

[Ken Stedman]

We just took about 200 liters worth of water from the lake and then purified all of the virus sized particles in it, then determined what their genetic sequences were, what we call a metagenome. But basically all the viruses, what genes do they have in them?

[Jacob Goldstein]

So you're basically just what, pouring this acid into a machine and saying, tell me all the genes that are in here?

[Ken Stedman]

More or less, yeah. So one of the things about viruses which makes viruses incredibly unique is they have what we like to call, we call it a virion. It's the virus structure. So the lunar lander module kind of thing.

[Jacob Goldstein]

Right. Your classic virus looks like a little lunar lander with like a pod and then little legs coming out, right? Absolutely.

[Ken Stedman]

And it's relatively small. So what you do is phage.

[Jacob Goldstein]

Right. That's the classic phase. That's the class that lands on the bacterium and then inserts its genetic material.

[Ken Stedman]

Injects it. Exactly. But even if you think about, you know, SARS, COV2 virus that causes COVID19 also is a little bag which has genes on the inside of it.

[Jacob Goldstein]

Sure.

[Ken Stedman]

So you break open the bag and you throw it into the machine and then it gives you back hundreds of thousands of sequences, in our case now, millions of sequences with the newest technology. So millions of genes. Hundreds of thousands of genes. But they're not genes, they're gene fragments. They're little pieces. Now at first you just want to look at what those little pieces are relative to known sequences. The dark matter is going to be those little pieces that don't match anything, and the light matter is going to be stuff that does. 90 plus percent of the sequences that we got back of our hundreds of thousands of sequences didn't match anything.

[Jacob Goldstein]

And what did you think when you saw that?

[Ken Stedman]

Oh, it's like other environments, other people had seen very similar things. So you do this with seawater, you do this with things you find in soil. 90 odd percent, plus or minus, don't match anything.

[Jacob Goldstein]

Does that mean that we don't know about 90% of the viruses that are out in the world? Is that broadly what that implies?

[Ken Stedman]

That is exactly what it implies.

[Jacob Goldstein]

And it's not just in a weirdo boiling acid lake. How about just in the dirt? If I just went into my yard and dug up some dirt and sent it to somebody who could put it in one of your machines. What percentage of the viruses in my backyard are known to science?

[Ken Stedman]

Roughly 20%.

[Jacob Goldstein]

Wow. 80% are dark matter. Unknown. Yeah, I love that.

[Ken Stedman]

It keeps us employed.

[Jacob Goldstein]

Yeah.

[Ken Stedman]

Right.

[Jacob Goldstein]

So, okay, so you get this result back. It's 90% is unknown. And so what you just have is like a genetic mess that you don't know what to do with, because it's not like each little fragment is like, oh, that's a new virus. It's just these are weird fragments that we don't understand.

[Ken Stedman]

Yeah, exactly. They're weird fragments that we don't understand. But one of the other things that we found is some of the fragments that we could actually identify didn't look like sequences that we should have found.

[Jacob Goldstein]

Meaning not only are they different than anything that's been found before, they are like, too weird. They're like, wait, that doesn't make any sense. How could that even be?

[Ken Stedman]

Exactly.

[Jacob Goldstein]

Did you think you had made a mistake of some sort?

[Ken Stedman]

Absolutely.

[Jacob Goldstein]

Or that the machine was broken?

[Ken Stedman]

We thought that we had absolutely screwed up in this case. So we've got genetic material for viruses. You've got RNA viruses, you got DNA viruses.

[Jacob Goldstein]

Right. So basically a virus is just like a bag with genetic material in it. And there's some viruses have DNA and some viruses have rna. And even though these are like two types of viruses, sort of historically, evolutionarily, they're like really different from each other. Right.

[Ken Stedman]

DNA viruses and RNA viruses we always thought were completely different relative to each other. And if you think about the evolutionary relationship between RNA viruses and DNA viruses, there basically seems to be almost none.

[Jacob Goldstein]

Like, how big is the gap, sort of. Whatever. Evolutionarily, how different are DNA and RNA viruses?

[Ken Stedman]

So the difference between DNA and RNA viruses is probably billions of years, evolutionarily speaking.

[GSK Advertisement]

Okay.

[Jacob Goldstein]

Okay. I was gonna say, like, it's, like, as big as the difference between mammals and reptiles, but it's way bigger than that.

[Ken Stedman]

Oh, it's probably more like the difference between, you know, bacteria and people. Bacteria and people, Exactly. Much more like that in terms of evolutionary difference.

[Jacob Goldstein]

Wow. Okay. So they're these profoundly different things.

[Ken Stedman]

So we sequenced a bunch of DNA, put it into our machine, said, hey, go get some DNA sequences. And then some of those approximately a couple of thousand sequences that actually match something in those sequences were things that looked like RNA viruses in terms of.

[Jacob Goldstein]

Their sequence, but it's DNA that you're seeing.

[Ken Stedman]

But we'd sequence DNA.

[Jacob Goldstein]

Yeah, but we.

[Ken Stedman]

And when I say we mostly. A graduate student working in our group, Jeff Deamer, he then started to try and put some of these pieces together. What he found was those pieces that looked like RNA viruses were connected genetically to sequences that looked like DNA viruses.

[Jacob Goldstein]

Okay. And connected, like, physically like that.

[Ken Stedman]

They were physically on the genome.

[Jacob Goldstein]

It was like the one piece, a chain of genetic material. Exactly.

[Ken Stedman]

And then what we did is we went back to the samples that we collected from Boiling Springs Lake, and instead of pouring them into the machine to get the sequences, we then made many, many copies of whatever this piece was. And this piece was to show they were actually connected to each other. So there are these what we're now calling crucie viruses that appear to have evolved by DNA viruses and RNA viruses coming together.

[Jacob Goldstein]

Okay. So we thought these were, like, totally different kinds of viruses, but now you have discovered this new kind of virus that's kind of like a cross between the two of them. Right. What does that mean? Like, what does it mean for how we think about RNA viruses and DNA viruses?

[Ken Stedman]

It means that there's communication between them and there's this recombination. So it's not billions of years of evolutionary difference, which is what we thought. Now it looks as if they can be exchanging genetic information with each other, which is really kind of revolutionary in terms of thinking about virus evolution. And what it means is we always thought DNA viruses evolved like this, and RNA viruses evolved like this, but if they can exchange genes with each other, that kind of throws a lot of what we think about virus evolution kind of out the window. Turns out that these viruses in and of themselves are just so different from any other virus anybody's ever seen before in terms of their shape in terms of their genes, what is in them.

[Jacob Goldstein]

So you and your colleagues found this crucivirus in the boiling acid lake. I know that since then, a number of other of these cruciviruses have been found. So just give me the landscape, give me what we know so far of like, where are they, what are they doing, et cetera.

[Ken Stedman]

We do not know what they're doing. Crucivirus has been found in Boiling Springs lake, Antarctic lakes, in deep sea sediments off the coast of Greenland, in Korean air samples, isopods off the coast of Oregon, monkey feces in dragonfly guts, soil just outside the lab at Portland State University. Basically anywhere that we have looked, we found these cruciviruses, Very low amounts of them, but seem to be very ubiquitous. So where are they? Everywhere.

[Jacob Goldstein]

Love it.

[Ken Stedman]

What are they doing? We don't know.

[Jacob Goldstein]

Are they in my body right now?

[Ken Stedman]

Probably in your body right now.

[Jacob Goldstein]

So these things are all around us, all over the world, possibly in our guts, and nobody knows what they're doing?

[Ken Stedman]

That is exactly correct.

[Jacob Goldstein]

I love it.

[Ken Stedman]

Me too.

[Jacob Goldstein]

So what do we know about what they're doing?

[Ken Stedman]

We're trying to figure out what they infect. We think they're infecting microbial eukaryotes. So things like fungi or protists, these paramecia things, you know, swimming around in.

[Jacob Goldstein]

Lakes, are those things also? Are there also organisms like that in our bodies?

[Ken Stedman]

There definitely are.

[Jacob Goldstein]

Is that part of the microflora?

[Ken Stedman]

Yeah, we have a eukaryotic microflora. Mostly these are going to be fungi, some kinds of yeasts, et cetera. But there are many other of these. And again, this is something which has been not very well studied. So you kind of put environmental viruses have not been well studied. These microbial eukaryotes have not been very well studied. So you put those two together. Extremely poorly studied.

[Jacob Goldstein]

Very dark. Very dark matter.

[Ken Stedman]

Very dark matter. But at the same time, really exciting because there's so much to discover.

[Jacob Goldstein]

Like why does microbial dark matter matter, besides being cool?

[Ken Stedman]

I think it's a area where we can make discoveries. There's so much we don't know. We have lots of viruses in us and we have no idea what they're doing. And potentially in that dark matter, there are some answers to the questions on what are they doing there. So I think that that's a very important thing to think about.

[Jacob Goldstein]

Not just how are they making us sick, but how are they keeping us healthy? How might they get out of balance at times and contribute in indirect ways to sickness certainly seems plausible. We know that happens with the bacteria in our gut.

[Ken Stedman]

Yeah, I think that that's a very reasonable thing to think about. And then just in a larger ecological sense, understanding the ecology, there's still so much that we don't know. I think understanding the viruses role in not just us, but also in life on our planet. I think understanding that dark matter will really help us understand what's going on with all of these different viruses.

[Jacob Goldstein]

I appreciate your time. It was a fun conversation for me.

[Ken Stedman]

Yeah, it was a fun conversation for me too.

[Jacob Goldstein]

I learned things, so thank you for that.

[Ken Stedman]

Good.

[Jacob Goldstein]

Ken Stedman is a biology professor and extreme virologist at Portland State University. His work and his team's work are expanding our idea of what a virus can be in a minute, discovering hundreds of kinds of new viruses that live in the human gut.

[GSK Advertisement]

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[Ken Stedman]

I'm going to go.

[Jacob Goldstein]

Out on a limb and say the most underrated viruses are phages. Phages are the viruses that infect bacteria. They're the most abundant biological entity on Earth, and they're killers.

[Shiraz Ali Shah]

Every other bacterium on Earth gets killed by a virus every day.

[Jacob Goldstein]

Actually, that's wild to think about.

[Shiraz Ali Shah]

Yeah, it really sucks for them.

[Jacob Goldstein]

Shiraz Ali Shah studies the phages that live inside people. He's a senior researcher on a project Called copsac, the Copenhagen Prospective Studies for Asthma in Childhood, the project is following hundreds of kids from birth into childhood to try to understand the causes of asthma. Shiraz focuses on the human virome, the universe of viruses that live in the human gut. And he told me that studying the virome from birth is really important.

[Shiraz Ali Shah]

In the first year of life, the baby has an immune system that has not yet matured, so it does not know how to distinguish friend from foe. What happens in the first year of life is that the immune system is still trying to get to know what is it supposed to attack and what is it not supposed to attack. And it seems that. So there's more and more evidence showing that if you are not exposed to a diverse array of good bacteria in the body and on the body within the first year of life, then the immune system is not properly trained and then you're way more prone to chronic inflammatory or immune diseases in the future. Like asthma, like asthma, like allergy, like asthma, even stuff like depression, anxiety, inflammation linked. Heart disease. Most definitely. Cancer? Most definitely. Diabetes? Most definitely, yes.

[Jacob Goldstein]

So, okay, so now you're getting into some of what you study, Right? Tell me about your work on this.

[Shiraz Ali Shah]

So this is a place called copsac, Copenhagen Perspective Studies for Asthma in Childhood.

[Jacob Goldstein]

It's a place where they're trying to understand how asthma works in kids.

[Shiraz Ali Shah]

Exactly. Okay. And so the way that they do this is basically they have a bunch of kids that were born in 2010 and they've been following them since the moms got pregnant. And today they're like 15 years old. Right. What they're doing is they're recording as much data on these children as possible as humanely possible. Like where do they go to daycare, how many siblings do they have? But also blood tests, you know, which chemicals do they have in their bodies, in their pee, what bacteria do they have in their poop, in their lungs, et cetera, et cetera. So we have like gigabytes upon gigabytes, also their own genes, their own genomes. We also have.

[Jacob Goldstein]

And so just to, just to be clear is the idea of doing all this and starting before the child is even born is the question they're trying to answer, why do some people get asthma and others don't?

[Shiraz Ali Shah]

Exactly. Because even though asthma is such a common childhood kind of disease, it's very poorly understood. And this is not only the case for asthma, it's also the case for all the other chronic diseases basically that kill adults, like cancer, heart disease, diabetes, you know, chronic respiratory disease, multiple Sclerosis, you know, all of these. And so maybe by collecting all of this data on the children, we can start predicting based on the data, who's going to get which disease. And based on that, maybe we can figure out, okay, if we do this, this and this, maybe we can avoid that and that and that chronic disease. Every time the kids visit us, and they do so once a year, we take as many samples as we possibly can.

[Jacob Goldstein]

Right. So you have this whole poop library going over the kid's whole lifetime that you can sort of examine over time.

[Ken Stedman]

Yes.

[Jacob Goldstein]

And how many kids are in this cohort?

[Shiraz Ali Shah]

So we have two cohorts. What I'm going to talk about today, the data is from the COPS Act 2010 cohort. So they were born in 2010, they're like 14 years old now. Right. And the 2010 cohort is 700 kids.

[Jacob Goldstein]

So the cohort you're following is 700 kids who were born in 2010. You're coming into this as a person who has been studying viruses that attack bacteria for our purposes here. And so when you get there, what do you do?

[Shiraz Ali Shah]

I get there and then my boss, he basically explains me some of the studies that they've been doing on the bacteria in the gut so far. And one of the major studies that they did just like one year before I came was that they found that in one year olds, when you're basically still a baby, the bacteria that you have in your gut when you're a baby end up determining whether or not you get asthma as a five year old. And I was like, what? I mean, how is that even possible? And so what the general picture is that if you have only a few different bacteria in your gut when you're one year old, then you have a much higher risk of getting asthma as a five year old. Right. But if you have like loads and loads of different bacteria in your gut when you're one year old, then you're much more protected from asthma as a five year old. And so basically that got me thinking, wow, that means that most bacteria are actually good for us. I mean, there are a few bacteria, maybe 100 species in total, that can cause infection.

[Jacob Goldstein]

Sure.

[Shiraz Ali Shah]

But the total number of bacteria in nature is like 100 million species at least. So those other 100 million are not causing. It's just one out of a million bacterium that is bad, and the other.

[Jacob Goldstein]

One in a million gives them a bad name. And in fact, they're keeping us healthy. So go on.

[Shiraz Ali Shah]

So I was thinking, okay, if that's the Case for bacteria, then what about viruses? What if it's the same for viruses? What if the only viruses that we know about are the ones that cause disease and there are loads of other viruses that are actually good for us? That's what I was thinking back then. But the funny thing is that this other guy called Dennis Nielsen, who is a professor at Copenhagen University, because he's an expert at figuring out which viruses are in his sample, he basically said, okay, you guys found this thing with bacteria. Why don't we look at the viruses in the gut and maybe we can find something similar or even cooler? And so when I started cop sec, this data set is already in the process of being generated. Dennis has taken 700 fecal samples, extracted viral particles, and then he has basically put them through a sequencer, and we're getting in sequences from each child.

[Jacob Goldstein]

Sequences, meaning genetic sequences. That allows you to determine what viruses.

[Shiraz Ali Shah]

Yeah, exactly.

[Jacob Goldstein]

So you get there in 2017, and another researcher is already just starting to look for what viruses are in the fecal samples of these kids in the study. How do you get involved? What do you do?

[Shiraz Ali Shah]

What happens back then? What people used to do when they got gut Virome data is that they would then take all the DNA sequences that came out of that, and they would then blast it is what it's called, against a public database of viruses, viruses that scientists have already discovered and know about, so that you can figure out which viruses are in those samples. The problem is that most of the viruses in the human gut at that time were unknown to science.

[Jacob Goldstein]

I love it.

[Shiraz Ali Shah]

So by doing that exercise, you're only going to get a list of contents of maybe 10 viruses, whereas the actual diversity in each sample is going to be like maybe 10,000 or maybe 1,000 or something.

[Jacob Goldstein]

Right. But the problem is you don't know what you're looking for, Right? You just have this random strings of genetic material. And if you're trying to find newly discovered viruses, well, how do you even do that? In fact, how do you do it?

[Shiraz Ali Shah]

So what we first do is we assemble all the sequences like a piece of a puzzle and get extended so that you get larger and larger fragments of DNA that must have come from the same virus.

[Jacob Goldstein]

You have this weird set of little chains and you need to put together like, ah, here is a virus and here is a different virus.

[Shiraz Ali Shah]

Yeah, exactly. And so that's then what happens. Now we got a bunch of DNA sequences from each child. So that. Then what I do is I annotate all the protein coding genes on These strands of DNA, so that I know which proteins are encoded on each DNA fragment. And by looking at those proteins, what they encode, what kind of functions those proteins code, I can start making qualified guesses in terms of, okay, this one must be a virus and this one must not.

[Jacob Goldstein]

Are you like actually looking at sequences and like, looking like one looks at jigsaw puzzle pieces on a table?

[Shiraz Ali Shah]

Yeah, I guess you could say. I mean, I can look at the protein coding genes that are encoded on each cluster and I manually look through 10,000 clusters of sequences, and out of those 10,000, around 300 of them were the ones that I could confidently say were viruses. And they correspond to viral families.

[Jacob Goldstein]

So when you're saying you're manually looking through 10,000, is that like years of work?

[Shiraz Ali Shah]

Yeah, it took five years, actually. Four years. Yeah.

[Jacob Goldstein]

And so you do this work, you spend four or five years going through this data. How many viruses do you find that live commonly in the human gut, in.

[Shiraz Ali Shah]

The children who we looked at? And that's all we can really say anything about. There are 10,000 species of viruses distributed in around 250 viral families.

[Jacob Goldstein]

So you discover all these new viruses. Does that mean you get to name them?

[Shiraz Ali Shah]

Super good question. So this is, and this was actually a huge issue for us. So now we're finding 250 new viral families. How are we going to present this in a paper?

[Jacob Goldstein]

Right. It can't just be like A, B, C, you're going to run out of letters.

[Shiraz Ali Shah]

Exactly. And so a lot of different suggestions were on the table. Pokemon was one of them.

[Jacob Goldstein]

Did you have a Pikachu in mind? That's the first question. Who gets to be Pikachu?

[Shiraz Ali Shah]

Yeah, exactly like Pikachu. Veriday, you know, Charmander, Veriday, et cetera, et cetera. And then a colleague of mine, Jonathan, who's the third author of this paper, he suggested why not just name them after the kids?

[Jacob Goldstein]

The kids in the study? The kids whose poop had the viruses in it.

[Shiraz Ali Shah]

Exactly. So we shuffled all the names and then we just distributed them over the 250 viral families.

[Jacob Goldstein]

So what are some of the names?

[Shiraz Ali Shah]

Christian Verde, Lucas Verde, Josefine Verde. Yeah.

[Jacob Goldstein]

So you do this work, you identify all of these previously undiscovered viruses that live in the guts of these kids. Do you then start to try and understand the health implications of different viromes, et cetera.

[Shiraz Ali Shah]

That was the entire purpose of this exercise. Right. So those bacteriophages, which were also by far most of all the families, the.

[Jacob Goldstein]

Viruses that infect bacteria. Okay.

[Shiraz Ali Shah]

Exactly. Those bacteriophage families can be divided into, like, two broad categories. There are the virulent bacteriophages and the temperate bacteriophages. Right. The virulent bacteriophages, they just kill the bacteria.

[Jacob Goldstein]

Okay.

[Shiraz Ali Shah]

Whereas the tempered bacteriophages, they integrate themselves as prophages on the bacterial DNA.

[Jacob Goldstein]

So first you look at the viruses that infect bacteria, and then you divide those into two categories and you say there's the viruses that just destroy the bacteria and there's the viruses that infect the bacteria but don't destroy it.

[Shiraz Ali Shah]

Exactly.

[Jacob Goldstein]

Does that tell you anything clinically?

[Shiraz Ali Shah]

Yeah. So Christina, who is the first author of that paper that came out in Nature Medicine earlier this year, she found that it was the temperate bacteriophages that were predictive of later asthma. For some reason, the children that end up developing Asthma by age 5, they had way more temperate phages, bacteriophages, in their gut at age 1.

[Jacob Goldstein]

And so the key data set is you're looking at the virome of the kids at age 1 and trying to understand, is it predictive of Asthma by age 5? And what answer do you and your colleagues find to that question?

[Shiraz Ali Shah]

What we find is that there are more temperate phages in the kids who end up developing asthma later. Then we look at the temperate phages specifically, and we look at which families of temperate phages are predictive of disease. And then what we find, which is kind of surprising and funny, is that 19 of the 250 families we had in total, 230 of them were tempered. 19 of them. If you look at the amounts of the those 19 families in the children, you can actually distinguish between kids that end up developing asthma as 5 year olds or not. And what's interesting is that the kids that develop asthma as 5 year olds have less of these 19 families than the healthy ones.

[Jacob Goldstein]

Aha. So is it right that these 19 families of viruses seem to maybe be protective against asthma? Like having more of these particular viruses is correlated with a lower risk of asthma?

[Shiraz Ali Shah]

Exactly.

[Jacob Goldstein]

That's very interesting. Now I get nervous that even though it passes some set of statistical tests, this is going to be a fluke finding. You know, it's going to be due to random chance. And so what I really want you to do is go run this test on some other kids at age 1, make your prediction, and have it come true by age 5. Is that a reasonable thought?

[Shiraz Ali Shah]

That is super reasonable, I have to say, Jacob. And this is also something that Nature Medicine asked us to do, and we said, well, nobody else has Virome data for so many children. Unfortunately, such a cohort does not exist. You know, Cops Act 2010 is one of the most deeply phenotyped cohorts in the world, so we were not able to replicate it in another cohort.

[Jacob Goldstein]

Yeah, yeah. So you have this finding that a certain family of virus seems to be protective against asthma. Are you able to understand anything about what causes a kid to have or not have this apparently protective family of viruses in their gut?

[Shiraz Ali Shah]

Super good question. I don't know. I think it has a lot to do with different environmental factors that end up determining, for random reasons, which viruses end up in the guts of these children.

[Jacob Goldstein]

I mean, when you say you don't know, does that mean there's no way in your data set to investigate the question?

[Shiraz Ali Shah]

There definitely is. And this is what we're doing. It's ongoing, basically. Right. So what we do see is that there's a huge correlation in, for example, where the kids live, whether they live in a rural environment or, like, a city environment.

[Jacob Goldstein]

Okay.

[Shiraz Ali Shah]

The ones that really live in a rural environment have a much more diverse, you know, ecosystem in the gut. In terms of the bacteria. We haven't looked at the viruses directly yet, but we have an intuition that the same might apply for viruses as well. Also, there's. There are huge, you know, kind of links to the diet, the kind of food that you eat, whether it's very processed food or whether it's like whole foods. Whole foods are generally associated with a way, way higher diversity. So if you want to increase your chances of having the good viruses in your gut, then it's a good idea to live, you know, rurally or at least spend some time in nature. It's a good idea to eat whole foods instead of processed foods, et cetera, et cetera.

[Jacob Goldstein]

Okay, so that's based on, like, what we know about bacteria and what you suspect is true also for viruses. Let me. Let me ask you this. When you think about the future, what do you hope we know about the virome in 5, 10, 20 years that we don't know now?

[Shiraz Ali Shah]

I'm hoping in the future that we have a much better overview in terms of what kinds of chronic diseases are caused by deficits in which viruses, but also in bacteria, so that we can prevent maybe 10, 20, 30 years from now, we can prevent a lot of chronic diseases that cause a lot of problems today that those can just be prevented by giving babies viruses or bacteria or even adults.

[Jacob Goldstein]

Thank you. So much for your time. It was great to talk with you.

[Shiraz Ali Shah]

Good to talk to you too.

[Jacob Goldstein]

Shiraz Shah is a senior researcher at the Copenhagen University Hospital Gynthofte thanks to both of my guests today, Shiraz Shah and Ken Stedman. Incubation is a co production of Pushkin Industries and Ruby Studio at iHeartMedia. It's produced by Kate Furby and Brittany Cronin. The show is edited by Lacy Roberts. It's mastered by Sarah Bruguer. Fact checking by Joseph Friedman. Our executive producers are Laci Roberts and Matt Romano. I'm Jacob Goldstein. Thanks very much for listening to this season of Incubation. I hope we'll be back next year with season three.

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