A Geneticist’s Approach to Human Microbiomes

Penn State undergraduate Kassi  Bradburn  interviews assistant professor of biology  Emily Davenport about her unique approach to researching the complex relationship that human beings have with our microbiomes. Her lab uses high-throughput sequencing technologies and novel computational and statistical techniques to approach this material from a genomic perspective. 

HOST:
Kassie Bradburn, Penn State undergraduate  student double majoring in Forensic Science – Biology Option and Biobehavioral Health with a minor in Chemistry.

GUEST:
Emily Davenport, Assistant Professor of Biology at Penn State working to understand the complex relationship humans have with our microbiomes. Her lab uses 

Transcript

[THEME MUSIC]

Mark Shriver:

From Penn State’s Center for Human Evolution and Diversity, this is Tracking Traits

 [MUSIC FADES]

 Nina Jablonski: 

Hello and welcome to the Tracking Traits podcast. My name is Nina Jablonski and I’m the co-director of CHED, the Center for Human Evolution and Diversity at Penn State.

Mark Shriver: 

And I’m Mark Shriver, the other co-director of CHED. Welcome to the podcast. So Nina, whose research are we hearing about this time? 

Nina Jablonski: 

Well Mark, for this this third episode of our second season, we’re focusing on the work of Emily Davenport, an assistant professor of biology here at Penn State.

Mark Shriver: 

Oh yes, Emily; she’s working on human microbiomes. That’s a hot topic in science right now. It’s really attracting a lot of researchers. 

Nina Jablonski:

It absolutely is. There’s a lot of excitement and activity going on around microbiomes these days, no doubt about it. But the thing that makes Emily’s work a little different is that she’s approaching a wide range of diverse human microbiomes from the perspective of a geneticist, rather than a microbiologist. 

Mark Shriver: 

That’s a very interesting intersection, human microbiomes and genetics. Emily has to be discovering new things that no one’s had the chance to even observe before. Especially because this is still such a relatively new field. 

Nina Jablonski:

You’re right Mark, and this comes up in the podcast conversation; we’re only just beginning to scratch the surface of how much there is to discover in this particular area of scientific research.

Mark Shriver:

With that in mind, some of the questions that Emily is investigating in her work are about trying to understand what makes for a healthy microbiome, as well as looking at how the answers to that question can be very different for different people from different parts of the world.

Nina Jablonski:

That’s exactly right Mark, and this is something that is being misunderstood right now in the public sphere, where a lot of people are making claims about what they call “gut  health.” There are lots of products being developed and sold out there that claim to improve gut health, and proponents of these products often make loose references to the micro biotic organisms living in our digestive systems. But Emily points out that as of yet we really have no solid evidence about the efficacy of these things.

Mark Shriver:

That’s a very relevant and timely observation. Please remind me Nina, who interviewed Emily for this episode?

Nina Jablonski:

Kassi Bradburn conducts the interview. She’s an undergraduate student at Penn State double majoring in Forensic Science with a Biology Option and Biobehavioral Health with a minor in Chemistry. Kassi’s interested in human genetic evolution across different populations and the various impacts it may have on society. So this conversation is right up her alley.

Mark Shriver:

Oh I know Kassi well. She’s terrific and I’m sure she did a great job.

Nina Jablonski:

Absolutely. And as usual, the conversation covers not just the science, but also the human aspects of being a scientist. Finding your passion and mentors, and figuring out how to stay inspired even when things get tough.

Mark Shriver:

Sounds like another great episode. Let’s give it a listen.

Nina Jablonski:

Absolutely! Here’s Kassi Bradburn talking with Emily Davenport about A Geneticist’s Approach to Human Microbiomes.

[MUSICAL INTERLUDE]

 Kassi Bradburn:

Hi, Emily. How are you?

Emily Davenport:

I'm great. Hi, Kassi. How are you?

Kassi Bradburn:

Good. So welcome to the podcast. I was wondering if, in a few sentences, you could describe your research, which is going to be our main focus for today.

Emily Davenport:

Absolutely. Thank you so much for having me. So I am really interested in the human microbiome. So I'm really fascinated with all of the bacteria and [archaea] and viruses and all the other things that live in and on our bodies. So my research in particular tries to determine how those microbes live in our bodies, how they get there, what determines their abundance, and then whether they're important for health and evolution.

Kassi Bradburn:

That's really cool. Would you mind elaborating for our audience what a microbiome is?

Emily Davenport:

Yeah. So microbiomes are really complex ecosystems that live on basically everyone and everything in the world. So bacteria, archaea, viruses, single cell eukaryotes, fungi, all of these things that are microscopic, but live on every single surface is what makes it the microbiome. So your body contains a number of different microbiomes. Things like your gut, your lungs, your skin, your mouth, they all have different microbiomes. Different microbes live there. Basically, everything you are in contact with in the world also does as well. So your chair has a microbiome, the soil has a microbiome, the air even has a microbiome.

Kassi Bradburn:

Wow. That's really fascinating. So if micro  biomes are different within our bodies, are they similar when compared to other people or are they also very different?

Emily Davenport:

It's a great question and it's a big area of my own research, actually. So certainly, the microbiomes of each individual object or different places in your body are unique in terms of your gut doesn't look like your skin, doesn't look like the soil, for example. That being said, things look very different across individuals. So you can kind of tell that's something might be a gut microbiome, it looks like a gut microbiome, but your gut microbiome and my gut microbiome are going to look very different from each other. There's a very low percentage of species that we actually share in common at any one given time. That being said, they look a lot more similar than either of our guts do to the soil, for example.

Kassi Bradburn:

Hm. Nice. So let's backtrack a little. What got you interested in science to begin with?

Emily Davenport:

You know, this is going to be a very cheesy college essay answer, but I've always been interested in science. Ever since I was a little kid, my favorite class in school was always the science classes. When I was in high school, I fell in love with biology. An d in particular, I fell in love with microbes. There was a biology lab class that I remember very distinctly where we had to culture a microorganism from something, some surface in our school. I just remember that feeling of streaking something out on a plate and all of a sudden, watching a colony grow and thinking that was completely incredible. But all of a sudden, you can make these invisible organisms visible again. So that's kind of how I fell in love with it in the first place.

Kassi Bradburn:

That's really nice. I kind of have a similar story where it didn't happen until later, but it was an AP bio class and we were dissecting one of the animals and that's really what got me super fascinated into science and what it could do because evaluating what I was looking at on my table versus what my friend was, it was actually kind of different, even though it was the same species.

Emily Davenport:

Totally. What animal were you dissecting?

Kassi Bradburn:

We were dissecting pigs to begin with and then we ended up going with rabbits and we ended with sharks.

Emily Davenport:

Sharks. See, this is why I ask this question because everyone dissects such different things in high school. I feel like most people do a pig or they do a worm, but a shark, that is fascinating.

Kassi Bradburn: 

Yeah. It was actually kind of funny why we ended up doing sharks. The reason being was because there was a shortage of getting cats. Then I think one of the students had an issue with it because she had a pet cat and she was just not comfortable at all. So our teacher was like, "Well, can't do cats anyways. Let's do a fun animal," and she picked sharks, so…

Emily Davenport:

That is so fascinating. Supply chain issues also ruining AP biology classes around the country.

Kassi Bradburn:

Of course. Well, that's how you got into science. What got you specifically into microbiomes?

Emily Davenport:

So I went into college knowing that I loved microbes. So from on day one, I mean, I think I went through the typical progression that I thought I was going to be pre-med, realized very quickly that wasn't for me, but then fell in love with research. I knew I wanted to study microbes. So I was a bacteriology major, studied microbes all throughout undergrad, including doing some undergrad research. Back when I was in college, was a few years ago and it was pre-genomic era. So most of the people in my department who were doing microbial work, they had their favorite bug and their favorite gene in their favorite bug and they spent their entire career studying that, which is great. However, I didn't fall in love with any particular bug or process or pathway when I was an undergrad. So I was still kind of trying to figure out what I was going to do. So after I graduated, I ended up working for a couple of years and I ended up working at a genomics company, which was really brand new at the time. And during that experience, I really, really fell in love with genomics.

Emily Davenport:

So I really loved the idea of being able to look at an entire system, see what patterns exist, see if you know, things that we're noticing are abnormal or that it's totally normal. I knew that I wanted to do that going forward. Additionally, I had a bunch of friends at the company I worked at who were computational biologists while I was a wet lab biologist. And they seemed like they were doing all of the really cool stuff. So I knew I wanted to continue my education. So I knew I was like, "Okay, I want to do something with genomics and I know I want to learn how to code." And so at the time, everybody who was doing genomics, I thought, was doing human genetics.

Emily Davenport:

So I decided to get my PhD in human genetics. At the end of my rotation during first year in the lab that I ended up joining, the PI was like, "Oh, hey. You know you can do genomics of microbes. That's the microbiome." I was sold. I heard that and I was like, "This is amazing. This is exactly what I want to do." So from there, I merged those two interests and so the bulk of my research these days is studying this relationship between the human genome and the microbiome, so genetics and genomics of all of the things basically.

Kassi Bradburn:

That's great. You really got the best of both worlds

Emily Davenport:

I really did. Yes.

Kassi Bradburn:

Yeah, that’s  all really awesome. So I know we've talked a little bit about it before, about how the microbiome has changed a lot from prehistoric times to where it is currently. So I was wondering if you have any idea of what you would expect microbiomes would look like in the future, let's say, 100 or so years from now?

Emily Davenport:

That is such an interesting question. Yeah. I mean, so we certainly know from current studies looking into the past that things have shifted over time. So, from ancient DNA samples and from populations that practice more traditional lifestyles, we know that the microbiomes look different than, you know,  people in industrialized countries. So what will this mean going forward as the world further industrializes, but also as things change in industrialized countries? So one thing is, there's been a lot of attention paid recently to industrial scale processes that affects our lives. So for example, throwing a bunch of preservatives in food seems like it might be harmless, but it may not be harmless to the microbes that are in that food. There's a bunch of studies that have come out in the last few years demonstrating that things like preservatives, things like artificial sweeteners, those kinds of things can actually influence the microbiome.

Emily Davenport:

So it'll be really interesting to see, you know, in 100 years what the state-of-the-art is on that. It's possible that we'll learn that some of these things that we eat every single day right now are actually maybe not so great for us in the long term or not so great for our microbiomes. So I'll be really interested to see if those practices shift and if that then has, like a shift on our microbiomes. Additionally, as the world gets more and more connected, what will globalization do to our microbiomes? Right now, there are some geographic patternings to the microbiome and will those disappear as people move around more and more, as populations, you know, mingle with each other, as cultural practices kind of merge into more similar things, or will people maintain distinct cultural practices, distinct diets, and distinct microbiomes? I mean, I guess we'll just have to see over time.

Kassi Bradburn:

Yeah. If I could live that long and see how it would change, I think that'd be really cool, but I don't think I'll make it past 100s though.

Emily Davenport:

Well, hey, never say never. I'm sure there are people out there working on that.

Kassi Bradburn:

I mean, yeah. There's already all of those things to see if you can live longer or just come back to life eventually. So who knows? Maybe that will become a reality.

Emily Davenport:

Yeah. Well, and then someone's going to need to figure out how to re-engineer your microbiome. It's one thing to cryogenically freeze yourself, but will your microbiome survive that? I don't know.

Kassi Bradburn:

Very good question. I don't think I want to live to see that answer though. You mentioned culture and I was just curious, how do you think culture influences microbiomes or geographic location?

Emily Davenport:

Those are great questions. There's a number of different things culturally that can influence microbiomes. So I study the gut mostly. So one of the things that affects the gut microbiome in particular to a great extent is diet. You can imagine different cultures have very, very different dietary practices. Some of that is tied with geography, what foods are available either historically or currently, but even still, you know people will move around the globe now. You take your cultural diets with you and it's a wonderful thing, but it does influence your microbiome. Additionally, different cultures have different, you know, interpersonal practices. You know, here, in kind of the US, with very Western cultures, think about child-rearing, for example. It's a very individualistic thing, right? You have the nuclear family and you have the parents that raise the kid and that's kind of it, other than school and stuff like that. But there are other cultures around the world where it's very much more so a community effort. Right?   Their kids, but your neighbor, your friend, the grandmother, the aunt are much more involved in child-rearing.

Emily Davenport:

You can imagine as your microbiome is establishing, having those connections with different people that all have different microbiomes could actually shape that in a different way. So those are just two examples, but there's a number of other things as well that could change the microbiome based on culture alone.

Kassi Bradburn:

Yeah, that's really cool because I'm half Asian and half European. So my mom was originally from the Philippines and then she immigrated to the US. So a lot of her culture, she brought back here and practiced with raising me. So I was kind of curious how maybe the merging of two cultures affects the microbiome. Because it's very different here and experiencing like, the mix versus like, seeing what my relatives over there are like and how my friends who have just been born and raised here in the US have been their entire time.

Emily Davenport:

Yeah. And, not my work, but there is a really fascinating study of Hmong individuals from Southeast Asia and what happens to their microbiomes as they immigrate to the US. It's really fascinating because it really depends what generation you are and then also how quickly you, as a first, if you were a first gen person, how quickly you integrate into your new culture. So many, kind of first gen immigrants, you maintain a lot of your home culture, right? You maintain home diets. You maintain a group of friends that if you have that in your area, and that can maintain your microbiome more  so than if you immigrate to a new place, you all the sudden adopt new dietary practices, new medical practices, new all of that. You know, that can actually influence your microbiome much quicker. So, super interesting question.

Kassi Bradburn:

So while we're on the topic of diversity and evolution, how is your research related to this?

Emily Davenport:

So I can  mention I'm really, really interested in the diversity of the microbiome in general. Like, I'm really interested in understanding what is the baseline level of normal across human populations? So a lot of people think that there might be a, quote unquote, “healthy microbiome”  and I don't necessarily think that exists. What is healthy for you might be different than what is healthy for me. Then someone halfway around the world might have a microbiome that's healthy, but looks totally different. And so, I think you know, it's really important, as this is a fairly new field, to establish what is normal, and what is the range of normal across the whole world. We've done this in my own lab and in my work in a couple of different ways. So we've studied multiple different human populations, many of which practice different lifestyles. Currently, one of the things that we have going on in the lab is we are studying Nepali populations that practice different subsistence strategies.

Emily Davenport:

So some Nepali populations that we study are nomadic hunter/foragers, some are small-scale agriculturalists, and some are kind of in that transition from hunting and gathering to small-scale agriculture. And so, you know, by studying very similar populations of people, similar underlying genetics, similar environment, but now by varying these different lifestyles, we can get a better idea of how lifestyle alone influences the microbiomes of these individuals that are very understudied in scientific literature.

Kassi Bradburn:

Yeah. That's really cool. Especially since, as you mentioned, they're not as studied in scientific literature. So I think getting into groups like that and bringing them into the scientific community and increasing the research for those types of populations is very important.

Emily Davenport:      

Absolutely. Like many fields, the biggest money and power structures in science are in westernized countries, the US, Europe, things like that. So it makes sense, especially for a new field, but a lot of the studies are on populations that are convenient for those people to study AKA a lot of white people, but the microbiome field and certainly human genetics as well, there's huge efforts right now in diversifying and studying people all around the world that have different genetics, that have different lifestyles, that live on different continents. And t hat's really informative because how are we going to understand what's normal unless we understand what everybody looks like?

Kassi Bradburn: 

Of course.  

[MUSICAL INTERLUDE]

Kassi Bradburn:

So how quickly can microbiomes change as it pertains to evolution? So is it like they change every single day? Do they change, like  over the years? What's that like?

Emily Davenport:

There's so many layers to this question, which you probably don't even realize as you're asking, but there's so many ways I could go with this. So the microbiome itself is composed of bacteria and archaea and all that. Those single cell organisms can actually evolve inside of your own body. Right? So they double extremely quickly. Like, E-coli has a doubling time in the lab of something like 20 minutes. And so you can imagine, you know over the course of a day or a week or a month, you get many, many, quote unquote, “generations”  of E-coli that live in your body and can genetically adapt and evolve to the conditions in your body. So evolution can happen quite quickly within a host system if we're thinking about evolution just in the microbiome itself. Another level, of course, is evolution of the host and the host in concert with the microbiome or what people often call the halobiont. 

Emily Davenport:

And so evolution at host scales happens a little bit more slowly, right? Because our lifetimes are a little bit longer than E-coli. And right now, there is a really active debate in the field about number one, whether this happens in humans and other mammals and big species like that, and two, how quickly it might occur. You can imagine scenarios where it can happen really fast. Like if your microbiome can, you know give you some kind of competitive advantage in an environment, maybe that is a really great selective pressure that results in evolution very quickly. But there might be many scenarios where there's not really a role to play of the microbiome. And so it's not really playing a great role in evolution. And that's definitely something that it's a very open question in the field and hopefully one we will be able to answer soon.

Kassi Bradburn:

What are some of the practical and ethical components that you've faced when dealing with your research?

Emily Davenport:

So humans, of course, are tricky and there's a lot of ethical considerations. In some ways, a lot of the work that I've done has not been too fraught. I typically will sample from places that aren't invasive, so fecal samples, saliva swabs, things like that, where people are pretty happy to part with their fecal samples. That being said, with humans, there's a lot of privacy concerns and especially because the microbiome field is so new, it's really hard to anticipate what the long-term consequences might be of putting information out there that we just don't know the consequences of it. So because a lot of my work intersects genetics and the microbiome, I'm very, very careful in that regard. Genetic information, for sure, if gotten in the wrong hands, can be very bad. It can result in discrimination and higher insurance rates and all sorts of crazy things. So we're very careful when we collect samples and collect data to make sure that is de-identified, stored on secured servers. It's available for scientific use, but only for scientists that will assure keeping up privacy standards and all of that.

Emily Davenport:

We're not as stringent with the microbiome data as that. However, we do, of course, make sure that people are de-identified, we make sure that people understand when they are consenting to these types of studies, what exactly this means. I think, yeah, in general, I think this is an area where we need to do a lot of thinking as a field to make sure we're doing the right thing. Right now, there's this big push in science for open science where we collect data. We're getting grants from the government to collect data. We should make that data public so other scientists can use it. That's wonderful and I totally agree with that. However, when there are humans on the other side of that data, right, there has to be a middle ground where that data is available, but also, you're protecting the identity of those individuals so that they don't get into any trouble later. So it's a difficult question and one, I think, that the field will be grappling with for a long time.

Kassi Bradburn:

I mean, human studies of any sort, there's always going to be that underlying question of whether or not this should occur.

Emily Davenport:

Yes.

Kassi Bradburn:

If it's a live study and someone can pull out any time, can they still pull out even if their information is out there?

Emily Davenport:

Yeah. Especially with more and more studies happening across the world. If researchers are going into a place where they are not originally from, maybe they don't speak the language, is it being communicated to the study participants what they're agreeing to? The last thing you'd want is to go somewhere, get some samples, and then those participants not realize, "Oh, hey, my microbiome data is now going to live out there on the internet forever and anyone can get it." Some people might be fine with that, but other well might not be. And so yeah, making sure all of these things are thought about at the beginning is really important.

Kassi Bradburn:

That does make me wonder though, because there are people who decide to donate their bodies to science after they pass on. So how would that work with research like yours?

Emily Davenport:

That is an interesting question that I will admit, I have never thought about, at least in the context of microbiomes. One thing I do think about, so because I wear this dual hat of both a microbiome scientist and a human geneticist is if you make a decision as an individual to release your genetic data, in some ways, you are sharing stuff, not only about you, but about your relatives as well. If I release my genetic data, half of my genome came from my dad, half came from my mom. I have kids. If I release my genome, half of their genome is my genome. So I can make that decision, but there's also long-term effects on my relatives. So if someone donates their body to science, is that genetically fraught considering your relatives, but also microbiome similar, right? I could release that information, but is there going to be negative consequences down the line for my kids or my grandkids or my siblings, things like that.

Kassi Bradburn:

Yeah, of course. So I'm in the forensic science club and we had an opportunity to go to one of the autopsy labs here on campus. We discussed all of the people that were donating their bodies to science. So we got to see... She talked about this company in Germany, I guess, where they make really thin slices of your body. Then you can see all the organs. She started with some of the ones that they had in her lab. It was really, really cool. So it makes me question how, not just like in terms of the anatomy, but other research studies where this could be relevant, how that would work. So thanks for answering that.

Emily Davenport:

I mean, one thing that could be kind of interesting about this is it's really easy to study what our microbiome looks like right now. If we want to go study a population right now, takes a while to set up the study, but you can go, you can fly, you can study them, whatever. But especially in the context of industrialization and thinking about how the microbiome changes over time, it'd be really interesting to know what the microbiome looked like 25 years ago or 50 years ago or 75 years ago. So if some of these things exist, people could mine that to actually study what our microbiomes look like in the recent past. People are doing a really good job right now studying ancient microbiomes, but I think there's not as many opportunities for more recently, yeah, more recent microbiomes than that.

Kassi Bradburn:

For people who aren't super interested in science or interested in microbiomes and things like that, what do you hope that they'll be able to take away from your research and your research findings?

Emily Davenport:

I think the number one goal is that it's complicated and not to worry too much about finding that healthy microbiome. I think there's a lot of stuff out there just in the popular media and in the zeitgeist about the microbiome. You know, people are really into probiotics and, "Oh, what kind of food should I eat for a healthy microbiome?" and all of that stuff. And what I would reassure people is that, like we really don't know yet. You know, we're learning more and more every day, but there's clearly not one healthy microbiome. There's not a magic pill you can take to get the perfect microbiome. I think as long as you make the good lifestyle decisions you know you should be making, that's as good as you can do and to not worry too much about the rest.

Kassi Bradburn:

Yeah. I know, there was this Netflix movie that came out, To All the Boys I’ve Loved Before, which was based off of a book series, and one of the characters in it was drinking this little yogurt drink called Yakult, which is really popular over in Asia and it's kind of like a probiotic drink and people became super fascinated with it. And it was just like the fascination with, I believe it's kombucha? It was flying off the shelves. I was just so curious, because I was like, "I just like this drink because it tastes good," and all of these other people were like, "I'm drinking this because it says it's going to be good for my gut. It's like a great cleanse," all of this stuff, so…

Emily Davenport:

100%. There's so many products on the market that say that and very, very few of them are actually backed up with scientific studies that prove that's the case and that it matters long-term. So yeah, definitely. I mean, people ask me this all the time and my advice for people is I don't think it's going to hurt you. Probiotics, I think, aren't going to hurt you, but they also may not help. So if you like the taste of something, if it makes you feel like you're doing something good for yourself, that's great. But it may not actually go beyond that.

Kassi Bradburn:

It's kind of interesting because you're looking into the gut microbiome and then there's nutritionists and things. I feel like sometimes you're saying two different things, like the nutritionist is like, "Yeah. This stuff, it's great for you. Great for your gut," and then someone studying the gut microbiome is like, "I mean, yes, but it might not work for you." 

Emily Davenport:

Yeah. I mean, I think this is often a function of the fact that both of these fields, both nutrition and microbiome science, are incredibly complicated. Nutrition is one of those things that people are still struggling to understand and the microbiome, people are still struggling to understand. And then certainly, the intersection of the two is complicated squared. And so yeah, we don't really understand how either of them work for sure and certainly across individuals and all of that. And so yeah, it's complicated. There's also things that might make logical sense, but then when you actually do it, you see opposite effects. So there was a really great study out that some people here at Penn State did, I think this came out a year or two ago, where they were doing a mouse study and they were giving the mice this indigestible fiber and the current feeling in the field is that indigestible fiber is great for your microbiome because they're able to use it and you get a more diverse, stronger microbiome.

Emily Davenport:

However, in this study, what they noticed is that actually, yeah, the microbiome became more diverse when you gave them this fiber, but then their mice were developing tumors. So just because something's good for your microbiome doesn't necessarily mean something is good for your body and vice versa. And so it's just really complicated. There's going to have to be a lot of studies done to figure out all of these different effects from all the millions of different food items that are out there.

Kassi Bradburn:

Yeah. It's crazy how complex something that, you know on the outside just seems so simple to us, but when you dig in deeper, it's like so many different theories and so many different pathways that are yet to be explained.

Emily Davenport:

Oh yeah.

Kassi Bradburn:

So what would you see as your future plans for your research?

Emily Davenport:

Totally. So I just started here at Penn State in 2019, not long before the pandemic. So we have a lot of stuff that is ramping up at the moment. So I'm definitely continuing my work, integrating host genetics in the microbiome. In particular, we've got a couple of studies where we are looking at host gene expression and the microbiome in physiologically relevant samples. So we've got samples from all along the digestive tract and also from the lung where we have the host tissue and the mucosal layer in those tissue samples. So we're able to look at these interactions between host gene expression and a microbiome in a really physiologically relevant way. So we're really excited about this because I think it's going to shed a lot of light on the host physiological mechanisms that interact with the microbiome in ways that we can't get at with just straight genetic studies alone. Additionally, we do have these studies looking at different human populations and also evolutionary microbiome work, so looking at these different Nepali populations and seeing how their oral microbiomes shift with subsistence strategy and whether or not that influences their health.

Emily Davenport:

We're also getting into some evolutionary work. So there's this hypothesis in the field right now that we, as humans, have co-evolved with our microbiomes over long evolutionary timescales and that in Westernized, industrialized countries, we are changing our lifestyles so drastically that we're kind of  breaking apart these ancient bonds that we've had with our microbes. That sounds really good in theory, but we don't know that that's true. So we're actually looking to test this both in humans, but then also in model organism systems and see if those species that we have co-speciated with and co-diversified with, are those actually relevant for human phenotypes and health? And how are those things determined? So we're also are doing that as well.

Emily Davenport:

And then finally, we are doing a lot of methods development work for the microbiome field. So the microbiome field is a fairly new one. It's really only 15-ish years old, something like that. There are so many times where we ask a question and we don't have the tools to answer that question. And s  o every time we come up against one of those walls, we try to create a new tool or method to solve it. So yeah, those are the three big areas of stuff we are working on in the lab, but there's a smattering of other things in there as well.

Kassi Bradburn:

Yeah. Lots of big ideas and I hope that they all get fulfilled and continue on.

Emily Davenport:

Thank you.

Kassi Bradburn:

Is there any advice that you have for future scientists and researchers?

Emily Davenport:

Yeah. A couple of bits of advice. First of all, just jump in and try stuff. You never should wait. If you're an undergrad, these days, high schoolers are doing research. Whenever you're like, "Oh, hey, this might be fun," give it a try. You never know if you're going to like something until you try it and you're never too young to try and learn. And then the second bit of advice, and I think this is true no matter if you're a scientist or otherwise, is to find your people. Find your peers, your mentors, people that are in your corner, people that you can talk to, people that when you have a conversation with them, you get excited, they get excited, you have a burst of ideas. They challenge you, they support you. Finding those people, I think, is really, really key because science does not happen in a vacuum and most of life doesn't happen in a vacuum. And if you can find people that are in your corner and make your science better, that's really the best gift.

Kassi Bradburn:

Yeah. Definitely those good support systems help you through the tough times, the good times, bad times, and the easy ones.I will also have to admit, joining research or just putting yourself out there into it, I would also recommend because I was afraid to do so as a freshman. So I didn't actually join Shriver Lab until my junior year, towards the end of it, because I got recommended it by one of my friends who actually joined their lab her freshman year. So I fell in love with it. I've been so happy. No regrets about joining it besides maybe getting into it sooner so I could have had more time with all these people.

Emily Davenport:

You are not alone. So I teach a couple of sections of freshman seminar every year and I hear the exact same thing from the freshman I teach. They're like, "Oh no, I'm not ready. Who's going to take me? I don't have the required classes." The thing about science, as you know, is you are doing something for the first time when you are doing something. You are figuring stuff out for the first time. So yeah, you can take a lot of classes and whatever, but when it comes down to it, you just got to get in there and do the science and you're going to be learning along the way when you do that. So definitely 100%, don't wait. If you are interested as a freshman, don't wait. At the same time, if you did wait, that's also okay too. You can jump in as a junior or even a senior and get that experience and you're totally fine.

Kassi Bradburn:

Yeah, of course. I mean, and also you may just need the time to find exactly what interests you and it doesn't have to relate to your major.

Emily Davenport:

Totally. Yep.

Kassi Bradburn:

I'm in the Eberly College of Science and Health and Human Development. I am nowhere near liberal arts, but that's the research I'm doing. It's very fascinating for me.

Emily Davenport:

That's amazing.

Kassi Bradburn:

Yeah. So what have been some obstacles that you have faced with your research, especially since one of them is it's a human research or human-related research as well?

Emily Davenport:

Yeah. I mean, certainly with human-related research, for me, the biggest thing has been trying to replicate studies. It's really difficult to collect both genetic data and microbiome data on large groups of people. So trying to figure out ways to replicate stuff is just really costly, expensive. People are all trying to work on their own stuff and stuff is difficult to share, things like that. That's been a really, really big challenge. I think the biggest challenge, honestly, it's just lack of time. I feel like there's so many things to do. There's so many things to learn and there's only so many hours in a day, so trying to figure out how to narrow down what's the most interesting or most important thing to study has been a challenge.

Kassi Bradburn:

Yeah. And with the topic as broad as the gut microbiome, I can imagine how difficult it might be just to having to narrow it down to smaller parts.

Emily Davenport:

Totally.

Kassi Bradburn:

I know that right now, it is a small field of research and, as you mentioned, I think you said the past 15 years, this field has been doing research and everything. So how has your research been unique to others within the field of the microbiome?

Emily Davenport:

So I inhabit this really niche space of being both a human geneticist and a microbiologist. So most microbiome people, as a field was getting started, understandably were microbiologists. There was actually a pretty good amount of computational biologists in there too. But really, when I got started in grad school, there were no studies intersecting human genetics and the microbiome and those have risen more and more within the last five years, there have been more and more of these studies, but I really think it gives me a unique perspective on the microbiome because I think I can bring in tools and analysis techniques and approaches that are really common in the human genetics field to microbiome research. The human genetics field was a little bit ahead of the microbiome field in terms of using next gen sequencing technologies and really doing genomics and all of that stuff. So I've tried to take the lessons learned from human genetics and then impart them on the microbiome field. I think that really, that's a unique space that I inhabit with only a few other people.

Kassi Bradburn:

Yeah. So for people who I guess are in high school or starting out as a freshman who might be interested in the field of microbiomes, what would be some classes that you recommend they take or topics that they look into to see if maybe they do want to continue down this path?

Emily Davenport:

Good question. There's no one straight path. The fun thing is that there's microbiomes of basically anything, humans, plants, the built environment. A nything you can think of, there's a microbiome associated with it. So certainly, whatever field you think you're into, like if you're into plants, maybe go into botany. If you're into humans, go into biology or anthropology. You can pick from there. Then once you're there, many universities, including Penn State, now are offering upper level microbiome courses in those areas.

Emily Davenport:

I think it's also really useful to learn some skills that no matter what kind of science you're going to do would be useful. Statistics is always good. If you can learn a little bit of programming, a lot of microbiome stuff is big data. So if you can learn how to program early, that's always good. Any of that kind of stuff, it's going to be really, really key. But there's no such thing, I don't think, at most universities as a microbiome major or anything like that. So doing the best you can to cobble courses together in your field of interest and then also pick up some of those other skills is going to be really useful.

Kassi Bradburn:

Nice. Because we are, excuse my pun, part of this great community...

Emily Davenport:

Har, har, har.

Kassi Bradburn:

Yes, and on my way to classes today, I was seeing all the tour groups and I know this is one question almost any tour guide gets asked, so I figured I should also ask you this and that is, why Penn State?

Emily Davenport:

Oh, why for me?

Kassi Bradburn:

Yeah. Why did you decide, I guess, to bring your research here?

Emily Davenport:

Yeah. So for me, Penn State is really, I'm not kidding, the ideal place for me to do my research. So Penn State has a wonderful microbiome center. We are growing and growing and there's just an amazing group of people to work with there. Additionally, Penn State has a phenomenal genomics group. So those are the two main areas of my research and having people in both of those groups that are so strong, so close by, has been really, really huge. It's also, it's a beautiful place to live. It's a wonderful place to live. I'm a big runner. So I like being outdoors and being able to get to trails super easily. So yeah, I can't think of a better place to do my research than here, we are.

Kassi Bradburn:

Oh, I'm glad that you are here and that I can meet you and be part of this podcast.

Emily Davenport:

Thank you so much.

Kassi Bradburn:

Yeah. Well, that's all the questions I have. Thank you again for joining me today.

Emily Davenport:

Wonderful. Thank you so much, Kassi, for chatting with me today. It was really fun.

Kassi Bradburn:

Yes. Until next time.

Emily Davenport:

All right. Bye, Kassi.

Kassi Bradburn:

Bye.

[MUSICAL INTERLUDE]

Mark Shriver:

Tracking Traits is a production of Penn State’s Center for Human Evolution and Diversity. Our producer, audio engineer and musical theme composer is Cole Hons, and our logo was designed by Michael Tribone of mtribone design. 

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