104. Unseen Worlds: Exploring Environmental Microbiomes and Their Secrets of Human and Climate Impact with Dr. Elizabeth Henaff

[00:00:02] Erum: Elizabeth Henef, we're so excited to have you on the Grab Everything podcast. Welcome.

[00:00:10] Elizabeth: Glad to be here.

[00:00:13] Erum: have you on the podcast, because we have been running into each other at a variety of events from the Biodesign Challenge to SinBioBeta and other events that's been happening around Brooklyn.

[00:00:25] Erum: And Luckily, finally had a chance to have lunch. , a veteran of the podcast, ginger dozer. She's a two time veteran. So she was on the podcast twice. She joined us and we had such amazing conversations. And I was like, I wish I had my recorder to capture what Elizabeth is saying, because you. Talk about some of those fascinating work that you've done with your students at NYU.

[00:00:48] Erum: So thanks again for being here. I really appreciate it. so let's kick off the conversation because want to talk to you because what we've been really interested is in environmental microbiomes and your work centers around environmental microbiomes, especially in the urban and built environments to kick it off, what sparked your interest and exploring microbial life within human design spaces?

[00:01:15] Elizabeth: the first time that I heard about environmental microbiomes was when I was a freshly minted PhD and I was starting my postdoc at Weill Cornell Medicine in Chris Mason's lab. and his lab was doing a bunch of environmental microbiome work, particularly in transportation systems. so I had done my PhD work in bioinformatics, the way of knowing that I had honed during that time of understanding biological organisms was through their DNA sequences.

[00:01:45] Elizabeth: and I spent a lot of time thinking about plants and then I joined the Mason lab and everybody was thinking about microbes. and I was like, wow, we can use these tools of DNA sequencing to understand this, invisible living component of our environment. , and it was just fascinating to me because it's so counterintuitive the built environment or our city environment that feels very much built for human beings and occupied by human beings, also hosts a really.

[00:02:10] Elizabeth: Diverse and vibrant, ecosystem, but that we just can't see, but with this amazing technology of DNA sequencing, we can access that information.

[00:02:18] Erum: Wow,

[00:02:19] Karl: So just like our bodies, and the different biomes on the planet have their own microbiome, so does this built environment? does it just happen naturally? is it because humans, occupy these spaces that that microbiome develops? where does it come from?

[00:02:34] Elizabeth: That's a really good question. and the answer is going to be different depending on what aspect of the built environment you're looking at. So if you're looking at indoor spaces, most of the microbiome of indoor spaces corresponds to things that we as human inhabitants have brought into those indoor spaces.

[00:02:49] Elizabeth: So the microbes that you're going to find indoors are mostly Human microbiome related, a small portion. If you have, say, indoor plants, you might have plant or soil related microorganisms in those indoor spaces, but most of them are human related, same thing for transportation systems. so the Mason lab, and actually the global consortium, the meta sub consortium has been studying transportation systems for almost a decade now.

[00:03:15] Elizabeth: and we see the same thing with transportation systems. So it's mostly human related. but other aspects of the built environment often reflects what that built environment. Was before it was, geo engineered. So, if we look at a waterway, for example, we're going to find organisms that are related to a marine environment, or related to soil environments for more terrestrial landscapes.

[00:03:41] Erum: I'm sure pets and dogs influence it because, when I was talking to ginger, she was telling me she had gone to a built environment workshop and they were talking about how having a dog contributes to a beneficial microbiome. Can you talk a little bit about what a beneficial microbiome is?

[00:03:57] Erum: what would that look like? and to Piggyback off that, how do architectural and urban design choices influence microbiomes that flourish in cities? So both how are they beneficial? And how do our architects and urban designers even think about microbiomes?

[00:04:12] Elizabeth: The short answer to that second question is usually not, but I think more so now, a beneficial microbiome is perhaps tricky to be prescriptive about. So I couldn't give you list of species and be like, you need species ABC for that to be beneficial. but what's kind of emerging out of, a broad body of literature is that.

[00:04:31] Elizabeth: Human health and well being is really tightly related to our relationship with our microbiome. and what is generally beneficial for that is a diverse microbiome. so we can't necessarily, determine specific species that would be best for everybody, for the good reason that Health looks different for different people. but in general, being exposed to a diverse microbiome is what's going to be beneficial. those are usually hard to encounter in urban environments because urban environments, apply. Pretty strong selection pressures against diverse microbiomes.

[00:05:09] Elizabeth: and also the sources of microbiomes that would usually, we would usually find in, say a rural environment, what are just aren't present in urban environments. microbiomes associated to soil systems or to plant ecosystems as well.

[00:05:24] Karl: But can you I don't know, I'll say game your home environment, and I'll say game meaning, can you, manipulate it in a way that it's going to be more beneficial, say by either adding plants or adding, a cat to it?

[00:05:38] Elizabeth: Yeah, I'll quote the great Jack Gilbert on this one saying that the best thing that you can do for your indoor microbiome is to open your windows and have pets,

[00:05:47] Erum: nice.

[00:05:48] Elizabeth: meaning, really, finding ways to create, porous boundaries between the indoor systems and the outdoor systems.

[00:05:55] Elizabeth: so, pets being themselves, their very own organisms with their very own microbiomes. They're going to be bringing in also the microbiomes that are associated with, their bodies. But also because, your dogs and cats are walking around outside and then coming inside and then you're petting them.

[00:06:10] Elizabeth: And so there's kind of means of transmission for those diverse microbiomes. Same thing for opening your windows. So just being able to open your window and get fresh air. seems too simple to be a technology or something,

[00:06:23] Karl: Right. Ha, ha,

[00:06:24] Elizabeth: but it is really effective and for a lot of urban buildings that is actually much more easily said than done because a lot of the buildings either buildings or high occupancy residential buildings.

[00:06:38] Elizabeth: don't really have. Forest building envelopes where you can open the windows. in my office at NYU, I can't open the window. I can touch a temperature dial to adjust the temperature and the HVAC system will adapt, but I can't open the window. so interestingly, a lot of the progress that has been made in HVAC systems with respect to energy conservation, optimizing in that direction of energy conservation, so mostly recycling air within the building envelope, is actually detrimental if your goal would be to foster a diverse indoor microbiome.

[00:07:13] Erum: Yeah, that is super interesting. I really want to dig into that. So let's put a pin in it because I also want to like, there's so much to unpack. earlier you mentioned the transportation system. So I want to just get that other way because we're going to go deep into the indoor built environment, which we spend a lot of time in.

[00:07:31] Erum: so you worked with Chris Mason the Mason lab on swabbing subways of NYC.

[00:07:37] Erum: Can you give our audience a highlight of. What that was like, and what was discovered in the subways and the microbiome of the subways.

[00:07:45] Elizabeth: Yeah, sure thing. yeah, that was a really exciting project, to be part of. so, in that particular project, the goal was to swab everyone of the 462, if I remember correctly, subway stations in New York City. So, we were specifically swabbing elements of the subway stations, not the trains themselves, because the trains move around.

[00:08:06] Elizabeth: And so you lose that geospatial aspect of those samples. Okay. there's several interesting highlights, to that paper. one of them, the main one being is that most of what we find in the subway from a microbial perspective is brought there by human beings.

[00:08:20] Elizabeth: So, microorganisms related to human skin, related to human guts, also related to the fermented foods that we eat. So that was one of the main takeaways is that the microbiome of the subway system is a function of the input of human beings. one interesting takeaway with respect to design of the built environment is that there's a higher prevalence of anti-biotic resistance in subway stations next to hospitals.

[00:08:51] Elizabeth: so we know that. Antibiotic resistance, like multi drug resistance, is a growing problem in hospital environments. So, microorganisms who have developed the capacity to be resistance to multiple different antibiotic treatments, that's an example that could, for example, inform certain aspects of design of the built environment.

[00:09:11] Elizabeth: So, maybe we need to rethink entrances and exits to hospital buildings, apply negative pressure so that air isn't escaping or, use antimicrobial materials in the apertures doorways of hospital buildings. So that was also an interesting takeaway.

[00:09:29] Elizabeth: Another takeaway, which is a little side figure in the paper is that when you collect biomass from the environment with the goal of studying microbes, you also get DNA from pretty much any other kind of species that is in that environment. those samples also yielded a bunch of human DNA.

[00:09:49] Elizabeth: Related to the human beings who, who are taking the subway and insufficient, like quantity for us to be able to sequence it in a way, to reconstruct reasonably accurately census information from the city. there was a good amount of human DNA collected in that process, interesting to be able to look at, the multi species assemblage, which is the subway, through this lens of DNA but it also gives you a little bit of pause with respect to privacy concerns. human beings are shedding DNA all the time in pretty much any kind of environment that we're at.

[00:10:25] Elizabeth: And with the right kind of technologies, you can collect that DNA and draw conclusions from who has been where. think we're not really talking at the moment of, genetic privacy in public places. we talk about photographic privacy in public places, but I feel like this is a conversation that's going to come up very quickly.

[00:10:44] Karl: it's been a while since I've gone back and looked at that study, but I seem to remember that there were like some very unusual organisms that were found. and I wonder if you remember, from a microbial point of view or a fungal point of view, what those might've been number one and number two, since you were collecting all this DNA, did you find any non human organisms, rat DNA?

[00:11:04] Karl: Dog dna cat dna was any of that present crocodile dna the legendary crocodiles of the new york city subway system

[00:11:12] Elizabeth: I'll answer second question first. so the analysis that we do with these DNA sequences are targeted towards a particular hypothesis. So these are similarity based analysis. So you have your kind of mixed bag of unknown of DNA sequences from unknown sources. And, computationally, you take those unknown DNA sequences and then you compare them to sequences in databases.

[00:11:37] Elizabeth: and the computational approaches that you're going to use, you select ahead of time of which database, which databases are going to interrogate. there's a particular analysis that you run interrogate microbial databases. There's another analysis that you're going to run to interrogate human sequence databases.

[00:11:55] Elizabeth: and as far as I know, and we didn't publish this aspect of it, but I don't think this was even done, as preliminary analyses. I don't think that we ran it against any other databases besides human and microbial. surely we would be finding dogs and rats and avian, surely.

[00:12:16] Elizabeth: I don't know if the pigeon genome is sequenced or not.

[00:12:19] Elizabeth: The funny thing though about that particular approach is that, we don't have, reference sequence like genome sequences for all organisms, ever when you start taking these environmental DNA and comparing it to your database of known sequences, you'll often get hits that are not quite.

[00:12:39] Elizabeth: Accurate. DNA that might be coming from, say, a plant that does not have a reference genome in the database is going to be reported as matching the closest thing that does exist in that database. so, for example, an agricultural plant. which are highly represented in our databases.

[00:12:59] Elizabeth: So when you start asking really broad questions like that, you can actually get biased results because the databases that we have to compare to are themselves biased because just because they're incomplete.

[00:13:13] Erum: Mm hmm. Yeah. I mean, so to follow up on that, for the information or the DNA that was gathered, is it continuously being interrogated against databases that are being updated? Is there someone still continuing to work on this?

[00:13:25] Elizabeth: Oh, that's a good question. , there's more publications that have come out of the medicine consortium, looking at this from a global perspective. 1 of the follow up publications to this study was looking at the prevalence of antimicrobial resistance genes across the globe.

[00:13:41] Elizabeth: So, drawing antimicrobial resistance profiles of different cities across the globe. in that sense, you can reanalyze that data. you have new algorithms or new hypotheses, you can go back to that data and reanalyze that. , with that in mind,

[00:13:56] Erum:

[00:13:56] Elizabeth: to go back to that other question, that you had with respect to interesting species, that were discovered, there was another result from that paper. that was really interesting, and that sparked a research direction that I've been following in my lab is that there was 1 subway station, the South 3 subway station that had been flooded during Hurricane Sandy, which had occurred a few years before that study, but not too long before that study was in 2000.

[00:14:21] Elizabeth: and so the subway station that had been flooded maintained this trace of marine related microorganisms. So, even though the floodwaters had long ago receded and, the subway was back in action an active again, there was this microbial echo of the history of that had happened, in that particular environment.

[00:14:44] Elizabeth: so that's something that really captured my imagination at the time, and has stayed with me of this idea that, Microbial species adapt very quickly to their environment, and the signal of that adaptation can persist over time. And so in a certain sense, being able to sample these microbial populations and see, who they are, but also what they're doing, what kind of functions encode.

[00:15:08] Elizabeth: Oftentimes gives you read into the history of that particular site. Sometimes it's the history of human intervention. If you see, these microbes have adapted to say, anthropogenic contaminants or something like that, or it can be a history related to, climate events like flooding.

[00:15:26] Karl: this is so super interesting talking about that study, but you've been studying environmental microbiomes and do you feel That knowledge has shifted our understanding of biodiversity in cities.

[00:15:37] Karl: you just mentioned, a subway station that flooded, that has remnants of the ocean microbiome in it. how does that change our understanding of cities? And do you think cities or global structures actually get it right when it comes to microbial diversity?

[00:15:51] Elizabeth: I think usually not because we don't have microbes in mind. When we're designing the built environment. I think that, if living organisms are taking non human or more than human living organisms are taken into account, thinking of macroscopic organisms.

[00:16:06] Elizabeth: So, usually thinking about green spaces and urban environments, and I think microbes are rarely taken into account except for. Pathogen surveillance and eradication, so the idea of designing the built environment with probiotic concerns in mind, I think, has not quite latched on to the public imagination, though, I think that, we're certainly making progress.

[00:16:29] Elizabeth: In that direction, I think 1 of the hurdles is the fact that these are organisms that we can't see. So we can't really. Build a relationship with them. and measuring them is actually pretty difficult. being able to get accurate metrics of a microbiome in the environment is quite difficult.

[00:16:46] Elizabeth: And I think that that's 1 of the necessary conditions to be able to build that into a design pipeline is to be able to get accurate metrics. to draw an analogy, we designed spaces with a bunch of different environmental metrics in mind, we designed for optimal temperature for human comfort and CO2 concentrations in indoor environments and, light quality as well.

[00:17:13] Elizabeth: these are all environmental factors that we have easy. Metrics for, we're able to have sensors that take continuous readings. We can model things, like the thermodynamics or air flow in an environment. So, those are all factors that we can, measure and model.

[00:17:32] Elizabeth: Accurately and so therefore we can design for them and microbes. We can't measure accurately. It's actually quite difficult. it's hard to model for them. so therefore it's hard to design for them.

[00:17:45] Erum: Yeah, yeah, To us, to our entrepreneurs, it seems like there's a lot of opportunity to make for microbiomes and microbes, right? It sounds like On the analysis side, the measurement side, like you're mentioning, and then, how we build our environments in a way where beneficial microbes and microbiomes are introduced? And we've been teasing it in the podcast, but I know this is an exploration that we've been going down. talking about what microbiomes. Exists in the built environment, but many built environments have been sterilized. I talked about hospitals earlier, and we quote unquote clean them, meaning that just kill a lot of microbes with cleaning solution.

[00:18:22] Erum: So. What do you think, or know through your studies, are the implications of such sterile environments on human health and the microbiome that we naturally interact with, versus the microbiomes we naturally interact with being outdoors?

[00:18:36] Elizabeth: Mm. yeah, we certainly take a scorched earth approach to microbiome in our environment.

[00:18:41] Karl: Yeah.

[00:18:42] Erum: Why?

[00:18:45] Elizabeth: you know, I think there's a lot of interesting cultural factors to that, and I trace it to the post-war Kooning effect. post World War II, there was a cultural shift towards, isolation of the home environment with respect to the public environment, which came along with promoting, nuclear family and, this isolation of home environment versus community and the idea of, the home being the castle.

[00:19:14] Elizabeth: There's a lot of interesting, cultural artifacts that you can find also in the world of advertising, with respect to cleaning products, which results from. So there was a lot of chemical industry development during the war with respect to cleaning products.

[00:19:28] Elizabeth: To, producing chemicals for warfare. And once that was over, the industry had to kind of repurpose these chemicals, that they were able to mass produce. so a lot of those turned industrial chemicals into cleaning products. you can see this boom in the advertisement for cleaning and disinfection products.

[00:19:46] Elizabeth: After the war, so there's, cultural aspects of that, a lot of advertisements of white, clean, sparkling kitchens, with a thin white woman presiding over it.

[00:20:00] Erum: Yes,

[00:20:01] Elizabeth: So a lot to unpack there about why sterile and clean, like cleanliness is associated with Positive qualities. that's probably a whole other philosophical discussion for a whole nother hour.

[00:20:17] Elizabeth: But there's a lot of literature that shows that lack of exposure to diverse microbial populations leads to negative. Health outcomes, particularly increasing the prevalence of non-communicable diseases, autoimmune disorders, for example, being one of them.

[00:20:36] Elizabeth: and there's a lot of common practices that lead to that. so most of the studies had been correlation based, so not necessarily establishing causation, but there's a few really elegant papers that have been published within the last, I'd say, 5 or 10 years that show positive causal effects of.

[00:20:56] Elizabeth: Interventions so biodiversity interventions actually having positive health outcomes. 1 example of that was published. I believe the study was performed in northern Europe. So the biodiversity intervention that they did was changing the ground substrate of a playground from that weird squishy asphalt stuff to wood chips, and wood chips being a, bio receptive material.

[00:21:26] Elizabeth: there was a measurable difference in the, diversity of the microbiome in that. Playground and then measurable differences in positive health outcomes for the Children, the cohort of Children who were playing in that playground. It's really amazing.

[00:21:40] Karl: wild. Yeah.

[00:21:43] Karl: So, tell us about your lab. You do projects that are, this intersection of scientific inquiry in design. So it's a very interdisciplinary, multidisciplinary approach, to help, explore and solve problems around microbiome and human spaces. Can you talk about that?

[00:21:59] Karl: what are you guys working on?

[00:22:01] Elizabeth: Yeah, sure. we're working on a bunch of cool stuff. in general, we have a portfolio of projects that really use New York City as a living laboratory to start to understand that relationship between a biotic aspects of the built environment. So, like, non living factors of the built environment, and then the microbiomes that inhabit.

[00:22:21] Elizabeth: so for example, we have a project. We've been, studying the microbiome of the Gowanus Canal for a long time now. That idea started in the Mason lab that has just been one of my all time favorite projects so we're looking at, the Guana Canal, which is a Superfund site, an EPA Superfund site, highly contaminated, with anthropogenic contamination.

[00:22:44] Elizabeth: so the microbiome that inhabits. That contaminated sediment has adapted, to that particular cocktail of contaminants and is able to degrade some of those toxic compounds. it's really interesting from a biotech perspective because that's a complex community of microbes that is able to degrade this.

[00:23:04] Elizabeth: cocktail of contaminants. and it is something that we would never be able to engineer in the lab. So we can engineer like a microbe to do a thing, but engineering like a community of microorganisms that lives and play nice all with each other. And that also collectively encode these complex biodegradation.

[00:23:23] Elizabeth: Functions is something that we wouldn't be able to make from scratch. so it's interesting from a biotech perspective, but also with respect to this microbial memory perspective. So, we can look at the list of Metabolic pathways that correspond to degradation of different contaminants, and then you can look at the historical data of the factories that have been operate in operation around the site.

[00:23:46] Elizabeth: And so you can see a correlation between all of these, but also you can see microbial metabolisms corresponding to contaminants that are not present in the human records. the microbial records are in a certain way more accurate than human kept records, which kind of makes sense because, the legal dumping isn't going to be reported.

[00:24:06] Elizabeth: And history is always written by the victor. And, human kept records notoriously flawed. This idea of microbial memory to me is really interesting, and how it can be inscribed within their living DNA sequences, living genomes.

[00:24:21] Erum: Wow.

[00:24:22] Elizabeth: we have another project actually that Started with that Sandy subway idea with this idea of climate related events, being able to alter the microbial composition of a built environment. so with a colleague at Tandon, Andrea Silverman, we've been looking at the micro at the impact of street level flooding. On microbial populations, so floodwaters in New York, we have combined sewage systems so floodwaters are full of a bunch of different contaminants, biological contaminants from untreated sewage, but also chemical contaminants that are mobilized from the floodwaters.

[00:25:01] Elizabeth: and so we have some interesting data, preliminary data that shows that the microbiome of the sidewalk will change drastically after a flood event. And then it takes about a couple of weeks for it to move back to get back to its original configuration. So we're interested in anthropogenic change, contamination, climate change, also thinking about designing for indoor microbiomes.

[00:25:24] Elizabeth: so I have a rock star PhD student who's no longer a PhD student. She is now a doctor, Dr. Phoebe. Mankiewicz Ledens, who led this really awesome study, looking at how you can tweak design criteria for green wall infrastructure in indoor environments so that green wall infrastructure can seed indoor environments with beneficial kind of diverse microbiomes. So that's the array of projects from a technical standpoint. But I think one thing also that we're really interested in the lab is that, for any of these, Ideas that we're developing within the scientific community to ever be translated to the public. We need to overcome this, public hesitancy towards microbes in the environment.

[00:26:07] Elizabeth: most of the time, when you talk about microbes in the environment, the reaction is like, yuck.

[00:26:14] Karl: All right

[00:26:15] Elizabeth: For all sorts of good reasons, because, they make us say, also coming out of a global pandemic. We're all now, very painfully aware of the pathogenic potential of, invisible biological entities in our air streams in our environment.

[00:26:32] Elizabeth: there's a lot of work to do to. convey a public understanding of the science to be able to, accept the idea of probiotic environments of designing for microbes in our environment. and science isn't the best way to do that. reading scientific articles is, actually pretty dry.

[00:26:53] Elizabeth: If you're not really motivated to do that, so alongside the science, what I've been doing with members of my lab and then also industry professionals in artistic fields is. Producing artworks to try to break this idea to the public about what does it mean to imagine microbes in an environment?

[00:27:12] Elizabeth: how could we imagine building at a human scale, for the microscopic scale of microbes? how do we push back against these power hierarchies between us large multicellular, um, organisms and the microscopic, that's another type of output that we really focus on at the lab is, building art installations.

[00:27:33] Elizabeth: And it's really fun.

[00:27:35] Erum: Yeah. that's incredible. I am really curious. So you mentioned about the Kiwanis canal that there's microbial fingerprints of what actually was dumped in the canal. what did you discover? And is there anything surprising?

[00:27:48] Erum: well, they're bones, which I'm sure they're probably were bones and human remains. because this is Brooklyn, Hello. but what type of contaminants are these PFAS? is it effluent from certain industries that you're like, okay, yeah, and it is, These microbial consortia that came together to degrade them, what contaminants and what microbes come together, just to give us an example of what you were able to unravel from this investigation.

[00:28:15] Elizabeth: Yeah, sure. so the main source of contamination in the Gowanus canal is related to energy production, specifically coal tar. so the sediment at the bottom of the canal is Black and viscous and smells like gasoline. People call it black mayonnaise.

[00:28:32] Erum: Yeah,

[00:28:33] Elizabeth: it's heavily contaminated with Hydrocarbons and that's really the main source of contamination.

[00:28:39] Elizabeth: There's also a bunch of heavy metals and there's also P fast. and there's also, solvents, there was, a lot of tanneries and paint making industry. but most of the contaminants are related to energy production. those are the main metabolisms that we see.

[00:28:56] Erum: and just so our audience knows, the Gones Canal cuts through northern Brooklyn. it goes straight to the ocean. it is a super fun site. It's been investigated and supposedly being cleaned for at least a decade. there's also an enormous amount of construction going on around.

[00:29:12] Karl: The Gowanus Canal, something like 8, 000 units are being built because it is right in the middle of everything. So it's super interesting to talk about, remediating the canal. which has been something that supposedly has been worked on, but even despite the fact that it is not remediated, all this construction has been happening around it and really urbanizing, the canal.

[00:29:32] Elizabeth: Yeah, it's a tricky situation, and it's classic story of gentrification also, because I think it was declared a Superfund And maybe 2010 or 2013 and immediately after property values skyrocketed because once it was declared a super fund, then there is a plan and also funding for remediation and cleanup.

[00:29:54] Elizabeth: which is currently underway, the dredging is happening now. the idea is that they're dredging, as much sediment as possible. and then sealing it with an impermeable layer. and then, putting the water back. I mean, the water is there, and then calling it good.

[00:30:11] Erum: sounds a lame to me. I mean, hate that just cement something over.

[00:30:16] Elizabeth: Yeah, yeah,

[00:30:18] Erum: did they reach out to you in your lab? since you guys have done so much research, I mean, hello, there's something to be done. I mean, here's super fun.

[00:30:25] Erum: I'm like, is there a lot of money going into this is

[00:30:27] Erum: it going

[00:30:28] Erum: to the pockets of people?

[00:30:29] Elizabeth: there is a lot of money going into it. And one interesting thing about the Superfund program is that the way that they fund these, remediations is by holding accountable companies who have acquired. The liability of the contamination. so usually that's the present day company who owns the land where the factories were that were originally sources that contamination.

[00:30:54] Elizabeth: And so the present day company is kind of so kind of has acquired. Both the assets and the liability concern related to that contamination. but the question of remediation is really tricky. I think it's really hard to have black and white ideas about it because it's very much a question of timeframe.

[00:31:12] Elizabeth: so the microbes are doing their thing and they're meeting the canal, but given the kinetics of these reactions And the, accessibility or lack of accessibility of those contaminants, it could take, hundreds or thousands of years for that to go away. Maybe never, that's why, tar pits exist naturally.

[00:31:28] Elizabeth: And even though there's microbes that are surely, consuming the hydrocarbons in those tar pits, they're still there, eons later, that time frame is hard to, reconcile with our inpatient human timeframe

[00:31:40] Elizabeth: of developers who want to sell waterfront properties, but also the real danger of exposure to families who have been living in that area for the last few decades, where, no remediation has been performed.

[00:31:55] Elizabeth: The unfortunate thing is that those families are being displaced by the process of gentrification, usually historically underserved minorities. And so the families who have been suffering from exposure from that canal are not the ones who are benefiting, from mediation efforts.

[00:32:11] Karl: you have these polluted, areas throughout urban environments. I mean, like in New York City, the other very polluted places, Newtown Creek, which is the boundary between Brooklyn and Queens. in your work and studying these things, how does it help people understand, what's going on on a biological level?

[00:32:31] Karl: maybe not even the remediation, but just so that people understand, I mean, you mentioned that there's this consortia of microbes that are playing nice with each other and are also able to degrade these, terrible chemicals that have been dumped there.

[00:32:42] Karl: But what do you do, or what can we do to help people understand what's going on biologically?

[00:32:47] Elizabeth: Yeah, I think that really is the role of artists and designers, is to be able to make that legible to the public. because I can make all of the data visualizations and graphs and plots that I want, but that's not necessarily what's going to tell a compelling story.

[00:33:03] Elizabeth: Story and compelling stories is really what we need now. and I keep coming back to this idea that one of the hurdles is the fact that these are organisms that we can't see. And so they're just hard to relate to, because we can't build an immediate relationship with them. and if anything, the relationship that we have is to the, tool or interface that we have to relate with them.

[00:33:26] Elizabeth: and just to give you an example of why I think design of collaborative tools or tools that aim towards collaboration with microbes are important, is that the most common tool that we have to interact with microbes is the swab. that's a tool that allows us. To collect biomass from a particular environment, and, then you take it to the lab and understand something about that. we're all very uncomfortably familiar with the swab now, the thing is that the swab is, it's a clinical tool that was designed for. For a clinical environment, and it doesn't give us good vibes about what we're collecting with that swab tool. An example of that is there was a lot of people who Challenged our undergrads while they were running around the subway, collecting these swab samples. and a lot of those reactions were to the tool of the swab. people were like, oh, gosh, is there an epidemic? You're monitoring for an epidemic. This was pre pandemic.

[00:34:23] Elizabeth: there was even a team. That was accused of implanting HIV in the subway and that reaction was very much to the tool because it looks scary. It belongs in a clinical setting. It makes us think of contamination and illness. but at the same time you could take a microbial sample by just grabbing a handful of dirt.

[00:34:42] Elizabeth: And if you think about that gesture, that gesture feels very different from the gesture of taking a swab, swabs, make us think of illness. And then a handful of dirt makes us think of, groundedness and connectedness with nature and has all sorts of, positive associations. I think really the role of. communicating the role of artists, the role of designers is to be able to think about, creating interfaces or means of interaction with the microbial world that carry this, positive balance and connotation, as opposed to the tools that are most frequently at our disposal, which carry this, negative connotation with respect to that interaction.

[00:35:23] Erum: Yeah, I mean, I love that. Wow. That is so powerful. what are the ways to make the invisible visible, What a great design and exercise. and there's, so many tools now on the scientific side, but how do you make them more user friendly, more understandable? so we talked about. Microbiomes in the water and soil and subways. you and I and Ginger and Carl had also talked about the microbiomes in the air. And you guys have been doing an excellent study of the Arab biome I think in Brooklyn particularly. and you guys have come up with some very ways to examine the aero biome not using swabs, but using.

[00:36:04] Erum: Either another object or just looking at nature in a very unique way. Can you share a little bit about the, your Arab biome project and how you guys went about it? And then one other thing I would love for you to talk about, I'm just going to say two words, red, honey,

[00:36:19] Elizabeth: Sure, it's all connected. yeah, to me, are just fascinating when I realized that, you can think of air as a fluid medium. That is also carrying biological organisms. It just totally blew my mind. I was like, oh, my gosh, they're everywhere. what we think of the void is not void. And it's actually full of living organisms.

[00:36:42] Elizabeth: Awesome. sampling the aerobiome is particularly tricky because it's not very dense. So there's the similar challenges sampling air as we have sampling water, actually, that you need to sample large volumes of it and concentrate it into a small volume to get some kind of insight from it.

[00:37:01] Elizabeth: So in the lab, we've developed a couple of different approaches to that. And with the perspective of having the approach. adapted to the scale of the thing that we want to study. So coming back to our tools being our means of interaction, and the swab being the tool that we use most frequently, a swab can sample an area of maybe 20 by 20 centimeters.

[00:37:26] Elizabeth: So we're talking about square centimeters in scale. But if we want to study, say, the microbiome of an entire neighborhood or even a city block, then that tool, the swab, it's resolution is not adapted to the size of the thing that we want to study. we've invented a couple of tools to address this question of scale in the lab, starting with large scale.

[00:37:47] Elizabeth: this was a collaboration, with Kevin Slavin when he was at the media lab and also started in the Mason lab. Where we were like, what can we do to sample, the aerobiome of an entire city block or of an entire neighborhood, and went through a bunch of ideas. And this was the time when there was that news article in the New York Times about the red honey.

[00:38:07] Elizabeth: So these honeybees that started making red honey and the beekeeper couldn't figure out why that was the case. And it turned out that they were getting, that they were, Going to forage in, Maraschino cherry factory, and then there was a health inspection about, why are there honeybees that are getting into this cherry factory in the first place?

[00:38:26] Elizabeth: And then it turned into a whole other thing where actually the cherry factory was a front for a large weed growing operation. and anyways, it was, it was a big story.

[00:38:36] Erum: Yes. Yes. I just love the fact that biology and science and you're investigating something is uncovering all of these crimes true crime is the

[00:38:45] Erum: top podcast, true crime biotech podcast. Like that's next year. We got to do that. Well, that

[00:38:51] Elizabeth: a good idea. Yeah. Um,

[00:38:54] Erum: but yeah,

[00:38:55] Elizabeth: but what came out of that whole series of news stories is that, , bees are very much reporting on what they interact with in the environment and their foraging range defines what they're able to report back to. so we observed that these honeybees were basically doing what we had been asking the, hordes of undergraduates to do for the subway study, which was, go out, interact, go out into the world, interact with, things in the city, and then always come back to the same place, which is the hive or the lab for the undergrads.

[00:39:26] Elizabeth: , that sparks this wild idea where we were like, gosh, bees are really. they're out foraging, they forage in about a 2 mile radius. This is very much an average, depends on nutrient availability and things like that. but it's, quite large radius at the scale of New York City.

[00:39:42] Elizabeth: and they always come back to this very specific place. our hypothesis is it anything about honeybees, what they produce, honey, propolis, etc. or anything about their hives that would give us a readout of the microbial environments that they're interacting with. so we did a whole pilot study, and the conclusion of that pilot study is that the debris that accumulates at the bottom of a beehive, can be queried for microbial signatures of the microbial environments that bees are interacting with as they go and forage around.

[00:40:14] Elizabeth: And so we figured that we would find plant microbes because like bees and plants and flowers, that don't make sense, but it turns out also that we were finding microbes related to all sorts of other aspects of the environments that they were traversing. So bodies of water, if there happened to be aquatic microbes, if there happened to be some kind of body of water in their foraging range, microbes related to humans, microbes related to our pets.

[00:40:37] Elizabeth: so that totally Reframed our idea of what was happening in these in the bees, environment is that this idea that even though they weren't necessarily physically contacting these different things, like, going into the pond and prospect park, or, landing on a dog or something like that.

[00:40:55] Elizabeth: they were, traversing these microbial clouds, to use a Jack Gilbert term again, as they were going on their foraging trips, and then bringing all of that information back to the beehive. that's a study, then Figured out a protocol about how to figure out these microbial signatures from a beehive and then did that globally.

[00:41:13] Elizabeth: So we had collaborated with beekeepers, here in New York, in Europe, Tokyo and Australia and published that paper just a couple of years ago.

[00:41:22] Karl: so you're saying that if we have beehives every two miles in a place like, New York City, we could really have a much better understanding of what's going on microbially than having a bunch of grad students running around swabbing every surface.

[00:41:37] Elizabeth: Yes. again, it's tuned to the scale and resolution of where bees are at. but that tiling would work quite well. And so Tokyo was the city where we had the most dense layout of hives. And so we could pretty much correlate, geographic distance with microbial distance.

[00:41:54] Elizabeth: So the further those hives away were away from each other, the more different those signatures were.

[00:41:59] Karl: It's amazing.

[00:42:00] Erum: Wow.

[00:42:01] Elizabeth: That was a really fun project. obviously that works only during bee season, which during in our part of the world is May to September.

[00:42:12] Erum: Wow. so that's a published paper. So we can link that in the show notes. People can explore more. Yeah,

[00:42:17] Erum: that's just incredible. I just love the level of thinking and just how many leaps of thought had to happen to be able to just have the hypothesis of looking at these. it's just incredible.

[00:42:28] Elizabeth: I mean, that's what happens when you work with an interdisciplinary team and a lot of those early conversations were with artists more so than scientists

[00:42:37] Elizabeth: and Kevin and Chris and I wrote up a little behind the paper article explaining the genesis of this project. This project and its data were shown at the Venice Biennale before they were published

[00:42:48] Karl: amazing. Amazing. as we get ready to close out this conversation, we've talked a lot about the microbiome of, the built environment and, we're seeing this Trend towards, the building of our colleges, I think of the line in Saudi Arabia these, generally would be like you say, a very potentially sterile environment.

[00:43:10] Karl: But how do you think an environment like that, or as we start to, like, even, maybe climatical forces to create these bigger. Our colleges around New York City or Nevada or wherever, how should. designers of these places be thinking about that microbiome that's going to be living in there.

[00:43:25] Elizabeth: Yeah, that's a tricky one because the insight that I have, from the Gowanus Canal is that the microbiome that we find in that environment, we couldn't engineer in a lab. I think it's also the case that when we think of, a beneficial microbiome for human health, we can probably also not engineer that in the lab. So I don't think we're going to have a room spray or something that would be effective, to maintaining a diverse and stable microbial ecosystem in an indoor environment. I think we're going to have to think. Holistically about fostering diverse ecosystems in general, across all scales and trophic levels.

[00:44:10] Elizabeth: and that in that process, we're also fostering a diverse microbial environment.

[00:44:15] Karl: And it sounds actually like it can be pretty simple. It's open your windows, have a pet and have some plants around.

[00:44:22] Elizabeth: Yeah. And, have diverse ecosystems outside of your window too.

[00:44:27] Karl: Yeah.

[00:44:28] Erum: And then go out into the world more Go out into the world, go hang out in the

[00:44:33] Elizabeth: forest,

[00:44:34] Erum: yeah, go hang out in the forest listeners might be going for a run. That'd be great. But if they're listening indoors, get outside, go out there, lick a tree. I don't know what would happen, but

[00:44:45] Erum: yeah,

[00:44:45] Erum: hug a tree,

[00:44:46] Karl: Not health advice, not health advice.

[00:44:49] Erum: Oh yeah. consult your physician.

[00:44:51] Karl: Before you go licking subway, handles.

[00:44:55] Elizabeth: no, I don't advise that. But there's a reason why we feel good outdoors, I mean, biophilia is a real thing. there's a reason why, it feels really good to go for a walk in the forest. And I think that surely part of that feeling good comes from our body registering the fact that we are being exposed to these diverse microbial populations.

[00:45:17] Elizabeth: we've talked a lot about tools and how, have this, push towards developing, technologies and, modern objects to interact with these microbes. But we've also never not lived in a microbial world. our understanding of microbiology as being a recent thing that has been developed by Western biotechnology, we've known about DNA for, 75 years now, which is a very short period of time.

[00:45:40] Elizabeth: And that's 1 of the main bases of our understanding of microbes. So it feels like this is a fresh new thing that we've discovered. Only since we've had these biotechnological tools, but we've never not lived in a microbial world. And I do believe that there are ways of paying attention to our environment that surely have been lost in the society.

[00:46:03] Elizabeth: At least that I live in here in Western society. but Traditional ecological knowledge certainly has ways of interacting and mediating this microbial relationship that long predates our Western concept biotechnology and the tools that we've developed. coming back to that idea of, why does it feel good to be in the forest?

[00:46:26] Elizabeth: I think that there's, means of close observation that we could cultivate that are also ways of interacting with the invisible living component of our environment that don't necessarily need, the high tech approaches of DNA sequencing.

[00:46:41] Karl: Thanks,

[00:46:42] Erum: that's a whole nother podcast you just started. Does the indigenous approaches to, living healthy and, their understanding of microbial world or, this invisible force, I guess you can say, that was at the time that we are trying to make more visible biotechnology, but it's almost like we're starting from scratch because we've lost a lot of that wisdom, but we're getting there slowly, but surely, hopefully. but thank you so much, Elizabeth, for coming on the podcast, sharing your work, the work that you're doing at your lab, the work your students are doing and your collaborators. It's so very exciting. I know you're going to be up to more and more exciting work in biology, art, design, we'll have to bring you back on because we just scratched the surface.

[00:47:25] Erum: Whether it's sterile or it has microbes on it, we just scratched it, but we're going to go deep. but I'll see you soon again, I'm sure just being around the world of Brooklyn. and again, thank you so much for coming on.

[00:47:36] Elizabeth: sure. Thank you. My pleasure. Great talking with both of you.

[00:47:39] Karl: Thank you.