What Makes a Happy Community?

4/12/23 Podcast

Duke CEE faculty member Andrew Jones investigates how and where bacterial communities thrive in the built environment—and imagines a future water smart grid that’s accessible to everyone.

podcast cover art: magnifying glass and bacteria
What Makes a Happy Community?

Featuring

Akhenaton-Andrew Dhafir Jones Profile Photo
Akhenaton-Andrew Dhafir Jones Profile Photo

Akhenaton-Andrew Dhafir Jones

Assistant Professor of Civil and Environmental Engineering

Research Interests

Biofilms, cardiovascular infections, infectious diseases, biomaterials, antibiotics, porous media flows, fate and transport of nanomaterials in biofilms, water quality sensors, environmental systems analysis, environmental equity,…

Transcript

Miranda Volborth: Civil and Environmental Engineering faculty member Andrew Jones is interested in a lot of different stuff. Bacteria and how they form biofilms, developing new techniques to breach the barriers of these biofilms, how these bacterial communities can impact human health, the future of the grid and the environmental justice issues involved with that future. Meet Andrew Jones on this episode of Rate of Change, a podcast from Duke University, dedicated to the ingenious ways that engineers are solving society’s toughest problems. Hope you’ve had your coffee today so you can keep up. We’re going to start with Andrew telling us about growing up here in Durham, while his dad was a grad student at Duke.

Andrew Jones: Which hotel is that? The Hilton that we normally put faculty up in off of Main Street, used to be a giant open field. And that’s actually where I learned how to ride a bike and fly a kite, because Duke lovingly has all these trees right around the main quad, which means that as far as flying kites go, it’s kind of out. Riding a bike, actually I think I might have ridden a bike there. Anyway, I also have a really good memory of climbing a magnolia that still exists over in the Sarah P. Duke Gardens.

Miranda: I know the exact one you’re talking about. Yeah, magnolias are the best climbing trees.

Andrew Jones: They are. They have nice low branches and…

Miranda: Yeah. And you said your family farmed here, right?

Andrew Jones: My mom’s entire family, they were from, I guess about an hour north of here, Caswell County. My grandfather had a fairly large farm. My aunts, all my great aunts who descended from him had small farms or large farms, depending. My mother, even though she was born and raised mostly in Cleveland, she would spend her summers down here picking tobacco. She claims that she even got a small nicotine addiction and that’s where it started. She’s since given up cigarettes, but that’s where it kind of started, was picking and handling tobacco. And if I want to tie that into the research that I do now, one of my students was very curious about nicotine’s relationship to antibiotic resistance and relation to, because there are oils on tobacco leaves. And so you have the oils coming off the tobacco leaf, you have the pesticides and herbicides, all the pesticides we spray on tobacco leaves and how that might influence the skin microbiome.

And that’s one of the projects that we’re looking at right now, is just looking at how the skin microbiome just hangs around on our skin in an in vitro situation. So instead of having to do a mouse model or a pig model, we have 3D printed skin, and we’re looking at three different bacteria that we know exist on the skin and how they interact, how they will relate to each other, and how this differs from when we look at these same bacteria on the standard agar plate model, which is what everybody uses. They basically take gelatin and they make an agar plate, and that’s how they grow bacteria, and that’s not really representative of the way our skin works. Our skin is not as wet as agar.

Miranda: Hopefully.

Andrew Jones: It’s pretty dry. It is more porous than agar, right. That’s how we have pores on our skin. We have higher temperatures. We have more oil on our skin than agar does. So just looking at how bacteria will differ between that platform, the agar platform, and these 3D printed skin that we are able to produce is going to hopefully open up some new doors for studying the more advanced stuff, like how nicotine and other oils from tobacco leaves might affect your skin microbiome. And then affect your health down the line. Or how pesticides and herbicides might affect your skin microbiome, which will eventually affect the rest of your health down the road.

Miranda: I have so many questions about this. What are you 3D printing the skin from?

Andrew Jones: So, a combination of different gelatins and different cells. So, we can actually use epithelial cells and epithelial tissue to print structures. So that was kind of, it’s a really recent innovation. We didn’t do it in our lab. Right now, the most interesting structure we have is, well, a 3D coupon of skin, so like a cube, basically. But it has more porosity than agar, as I said. It has the ability to have cells growing inside of it. It’s multiple components, so we have different gels that we’re actually embedding these cells inside, so there’s a little bit of different stress and strain, because if you look at our tissue, our tissue is not one uniform homogenous tissue.

Miranda: Yeah, I’m just kind of trying to imagine what that process would look like. A 3D printer squirting out kind of…

Andrew Jones: It’s squirting out a combination of cells and inks. It literally is like a syringe, either your pastry syringe or the syringes that you get vaccines out of. It exists. So, it applies pressure and squirts it out, but it squirts it out at a nice slow enough rate and occasionally with a UV light so that we can, I guess, solidify or cross-link the material so that it’s more of a solid than a liquid.

Miranda: That is wild. I guess, I don’t think about the microbiome on skin, although I know that it is there. I think we usually think about the microbiome being in your guts or inside of other really wet kind of things. Are there other places around us that kind of host these microbiomes that people might be surprised by?

Andrew Jones: Everything has a microbiome. Yes. So, on a project with Claudia Gunsch, Duke University just got the… What is it? An engineering research center funded-

Miranda: PreMiEr?

Andrew Jones: Yeah.

Miranda: Andrew is referring to the engineering research center for Precision Microbiome Engineering, PreMiEr. This center is aiming to develop diagnostic tools and different approaches that prevent the colonization of harmful bacteria in the built environment and encourage beneficial microorganisms to thrive. PreMiEr is led by Duke CEE Professor Claudia Gunsch, and it’s supported by a $26 million grant from the NSF. Andrew is one of many researchers from multiple institutions collaborating on this new center.

Andrew Jones: And that is entirely designed to study the building microbiome. It’s when we think about the spread of COVID on an indoor environment, part of that thinking is, well, that is an indoor microbiome. That’s a combination of us walking into a room, exhaling whatever we have in our mouths and our lungs, and spitting that out into a room that will stick to a surface. I mean, we originally thought about COVID, I think in the early days, everybody was wiping down their surfaces. Because the thought was maybe COVID was spread through surface contact. Turns out it wasn’t. If we really think back to how human evolution worked or evolution worked, bacteria were first.

They’ve been here for millennia, and so they know how to colonize basically any environment, dry, wet, hot, acidic, volcanic. They are everywhere.

The biggest challenge with the bacterial side of the microbiome is that we can’t culture most of those bacteria. We don’t know what things make them happy to grow them in large quantities that we can see them under a microscope. However, they’re there. The recent innovations have been that we can use 16S RNA seq, which is a way of just amplifying a chunk of DNA and being able to amplify it enough so that we can see at least what DNA was there. And that’s allowed us to start seeing certain things. But the biggest challenge was really just growing those microbes in a controlled, repeatable environment, the way that we like to do science. Well, that’s harder. Because if we’re thinking, trying to grow the bacteria inside the sound booth, right? Well, what makes them happy to grow it? Is it the styrofoam that makes them happy? We don’t know. And we have to just keep tossing things at it and trying to figure out what works.

So that’s kind of the big challenge, but also the big opportunity is that we have new tools, new technologies like the 3D Bioprinter where we can start saying, “Well, what’s going to make this bacteria happy?” One of the cool findings that we found so far with just the 3D Bioprinter, is that Propionibacterium acnes, also known as Cutibacterium acnes, also known as the bacteria that causes acne, that bacteria likes growing on our 3D printed skin constructs a lot better than it grows on agar.

One of the other fascinating studies that happened that I was talking about when the PreMiEr grant was going through review was, I think it was a 2019 study where somebody went around and sampled hospitals. Just clipboards, the paper in the hospital, the different surfaces of a hospital, and then they just took those samples, put them under a SEM, so scanning electron micrograph, which allows you to get micron level images, and they’re normally in black and white, but they were able to find biofilms on those surfaces.

If we think about a biofilm, you’re thinking about the plaque on your teeth, you’re thinking about the really colorful ponds in Yellowstone. Those are biofilms. You’re thinking about the slime on rocks, and yet they were finding these on paper, on clipboards, on ink pens, and it was interesting to see that same morphology. Something that looks basically like a biofilm, but on something that is dry.

Miranda: Is learning how those biofilms work to be able to better break them down? Is that the…

Andrew Jones: I wouldn’t say break them down. I’d say live with them. That’s, I guess, another fascinating direction the research has started to take. I think there was a really cool paper in 2017 that started talking about a way to defeat this antimicrobial resistance crisis is to kind of scale back on antimicrobials. So not taking antibiotic to kill off bacteria. We don’t necessarily need to kill them off, because once we kill them, then you start doing the natural selection thing, which starts leading to things that are resistant. So, if instead, you could figure out a way to decrease their virulence, right?

So instead of worrying about how well, or instead of worrying about just their existence in our body, because we have bacteria on our skin, we have bacteria in our gut that we’re totally fine with. Why is it a problem? It’s a problem because it starts shifting things over to a dysbiosis. It starts dominating the other species. And so, if we could figure out a way of just saying you know what, what if we were to add this other thing, this other element to it to make it kind of go back to its normal contained happy state.

Miranda: What kind of dysbiosis can happen in water treatment and delivery?

Andrew Jones: That is an interesting question that might even be at the forefront of Premier, the center we talk about earlier. Looking and trying to figure out, ok, we know what dysbiosis looks like in a human—that’s a decent chunk of what my lab studies, dysbiosis in a human being. But dysbiosis in a building or a water treatment plant, that’s kind of an open question that we’re trying to probe a lot more, both in my lab and in the NSF PremiEr center at large.  How could we make sure to modify—or, COULD we even engineer that community to be the community of bacteria that we want. The community that will do no harm, or do the least harm. Right now, we don’t know even if we can engineer that community, or how that community arises in the first place. There’s a lot of study that needs to go on to figure out how that community popped up there, and how it’s so stable.

Right now, there’s not been a lot of waterborne illnesses that were aware of that are publicized, so our water treatment system is working really well right now. But could we do better? Could we do better through engineering tools or engineering practices so that we can live with a little more low-cost solutions to drinking water treatment, and also protect our most vulnerable populations, because for the most part even though those bacteria are probably benign for most people, there may be populations that are somewhat immunocompromised, that may not be able to deal with that level of bacteria in their drinking water, and right now they’re probably having to pay out of pocket to get water that meets the standard to protect their health. Could we potentially design a system that would help them as well?

My vision for the future, both the future of my lab but also the future of society, is one my lab is really positioned as a lab that develops tools for this water smart grid concept that we are proposing—kind of latching on to. And what that means for people on a day-to-day basis is just a lot more trust in your water and a lot more knowledge about your water. Right now, water quality, water information, is literally all buried. It’s all underground. You get a water report once a year. You may not even know that you get a water quality report, mandated by law, mandated by the Clean Water Act. You’re supposed to get this report from your water utility that says what’s in your water. Once a year. It’s really hard to care about what’s coming up from underground that you don’t see every day. It’s hard to care about things you don’t see. But with a water smart grid I hope that people are going to be able to see water and see their water quality better, and be able to trust it. And if they don’t trust it, to be able to act, with information, to improve their water quality system just like we can do with roads.

Miranda: What would you expect living with a more accessible, more equitable water system to look like, for a normal person?

Andrew: For a consumer, you would turn on your tap and water would flow like normal. You wouldn’t notice what’s going on underground—the same as right now. Except you would have a display, and that display would tell you things that might make you trust your water better. It might say, “You’re using this much water. Your neighbors are using this much water. You have this much water left in whatever reservoir you’re drawing from,” whether that’s a community basin or city reservoir, or your county or town reservoir. So, you’d be drawing and say, “Okay, I’m subtracting this much from these sources.” You might be able to click a screen that shows more information: projected out, with our current rainfall levels and snowfall levels, you’ll have enough to last, in this storage tank, for the next year or two years. It might show an alarm that says, “Hey, are you using this water or just letting it run?” It will tell you things about the quality of your water. The pressure of your water. Being able to see, yes, your water pressure is fine, there’s no leaks in the system. It could also say, before you turn on the tap, “Hey, you’ve been using water throughout the day…” An app on your phone, maybe, would say, “You’re using water,” but there’s no faucet running in my house right now. I haven’t turned on anything. And that can point you to a leak– that can say, “You should probably go fix this.”

We have that technology right now, the leak detection. It’s the rest of it, the… “Your water is free from arsenic, it’s free from lead, it’s free from bacteria.” Or maybe there is bacteria in your water and you might want to do something about that. You turn on your tap and you might get more information than you can deal with. But hopefully the display, as we design and iterate, would get to where we could display information that is relevant at the time of use.

Miranda: …See how much water the Joneses are using on their grass this time of year…

Andrew: Right! And see how that might impact the rest of the system.

So, if we’re trying to push these technologies out, we have to consider policy solutions and think about how policies worked in the past to improve overall health. One lovely example is that the catalytic converter was originally put out in the late 1970s, early 1980s. That was through government mandate and it immediately improved air quality for everyone. Then car companies realized, we can get more efficient engines, longer lasting… so they decided to do it themselves later on. Market forces later improved the implementation of that technology.

So, I try to blend in a little bit of policy work with the engineering work that I do, to make sure that when I develop these new technologies, they will actually get out there and help people get access to these tools to improve either their building’s health or their neighborhood’s health, or the broader community’s health.  

So that’s how the policy piece is still in my research. There’s technology and there’s policy, and how do those two things meet and interact?

Miranda: Keep your eyes on Andrew Jones and his lab here at Duke. There’s sure to be many, many interesting things coming from it in the future.

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