The City Of Tomorrow Is A Petri Dish–By Design

Our cities are covered in microbes. An increasing number of architects, urbanists, and scientists say we should be designing for them.

The City Of Tomorrow Is A Petri Dish–By Design

Seven thousandths of an inch. That’s how much Tyvek fabric separates researcher Elizabeth Hénaff from the toxic river beneath her feet.


If her boat should tip and her hazmat suit should tear, she’d be exposed to any number of pathogens floating around her. For 100 years, factories dumped indiscriminately into the Gowanus Canal. Coal. Heavy metals. And to add insult to injury, Brooklyn’s sewage still frequently spills into the canal, too. The water is so dirty that it actually bubbles, stinking of bacteria found in the human gut and waste. Microbiologists have discovered gonorrhea, typhoid, and cholera floating in its murk, even though, technically, oxygen levels in the water are supposed to be below thresholds for supporting life.

By 2022, this should all be cleaned up, with $506 million spent on this EPA Superfund site, dredging the Gowanus for contaminants before sealing the worst pollutants behind cement so that real estate developers can build towering apartments along the canal’s shore.

But before that happens, Hénaff, alongside landscape architects Matthew Seibert and Ian Quate, wants to sample the most viscous and vile bits the Gowanus has to offer–so she reaches a 15-foot PVC pipe down into the depths to take a sample of tar sludge floating just above the river floor.

Later, as I’m squinting at this gross charcoal water in a glass jar, I try to see what Hénaff sees with her microbiologist eyes. Because inside this toxic sludge lives its own cure. Here, highly specialized, extremophilic microbes, existing nowhere else on earth, have evolved to not only survive the specific stew in the Gowanus Canal, but to thrive on its poisons, metabolizing the compounds like an all-you-can-eat buffet. And with a little bit of coaxing, she thinks these bacteria could be harnessed to clean up the mess.

“The bacteria are already cleaning the canal, just not at an acceptable time frame for us humans,” says Hénaff. “It would take thousands of years. And developers would like to build luxury condos there in two.”

Sampling the Gowanus. Photo: Dave Rife

The Hidden Universes In Our Cities

Hénaff is but one of many researchers on the cutting edge of a new field of research known as the urban micobiome. Much like scientists are beginning to realize that the bacteria in our gut and skin plays a major role in our health, so too are architects recognizing that every railing and bit of concrete in a city is actually teeming with invisible life–life that could be similarly intrinsic to our well-being. The problem is that we’ve designed our man-made environments to minimize them.

“There’s momentum around this idea that nature got it right. Until 100 years ago, we were living in buildings that were designed to be heating systems, cooling systems, fresh air systems, lighting systems–the buildings themselves were designed through their architecture to provide these human needs,” says Kevin Van Den Wymelenberg, associate professor at the University of Oregon. “With the industrial revolution, development of the fluorescent light bulb, the reliable electric grid, mechanical cooling, everything changed.” Buildings got taller, darker, and sealed us inside with recycled air.

The way we design buildings and even plan cities may soon change back. Instead of sterilizing our spaces, we may nurture this city symbiosis for our own sake.

“I think it’s exceptionally exciting,” says Christopher Mason, associate professor of physiology and biophysics at Weill Cornell Medical College. “Think about what Columbus was doing in the 1400s. Half the world was unknown and we had to explore it. In this case, the unknown world is under our fingertips.”

Mason isn’t speaking in hyperbole. With a trillion estimated species of bacteria, fungi, and viruses on the planet, we can roughly identify only about half of what we see when swabbing the seat of a N.Y.C. subway car–something Mason’s lab has actually done in its research.


“There’s a molecular echo, a trace of where you are, what you’ve been doing, and even what you’ve been eating. We’ve even found chickpea and cucumber DNA, which I guess was a falafel someone left behind,” says Mason. The problem is, to identify this echo, scientists need to analyze found DNA. And if its genome hasn’t been sequenced already–like humans have been–it comes up as what’s lovingly dubbed as DNA dark matter.

“It’s this huge source of data we throw away because there’s no comparison,” says Regina Flores. “Like dark matter, we know it’s there, but not what it is, or how it contributes to the environment.”

Holobiont Urbanism microbiome map

Flores collaborates in a different lab than Mason and Hénaff, but is working in similar thought space. At MIT Media Lab, she and the team used a clever tact to sample the microbiomes of various N.Y.C. neighborhoods: beehives. Rather than sending undergrads with swabs around the boroughs of New York City, they realized that bees never travel more than 1.5 miles from their own hive–and they don’t like to travel over large bodies of water. This means that beehives can actually serve as an automated dumping ground of DNA found around a neighborhood–as long as you account for their inherent bias toward flowers and food.

The project, called Holobiont Urbanism, is the first major attempt of a genetic map of a city. It’s as much an art project as scientific research, an early proof-of-concept provocation to prove out the very idea that neighborhoods do have unique microbial thumbprints.

But project lead Kevin Slavin is okay with that. “What I’m trying to do is just build a worldview in which we understand that cities have these other couple billion residents, and that they’re not pathogens,” he says. “They’re not things we need to be afraid of. They’re actually nature with a far less sexy photo shoot.”

Holobiont Urbanism beehive mechanism

Designing For The Tiny Residents We Can’t See

Yet while scientists can’t identify everything they sample, and every expert I interviewed made it clear that we haven’t yet fully proven that our environmental microbiomes are tied to human health, that’s doing nothing to derail a rapidly forming consensus that we can–and must–design both buildings and cities to have a molecular thumbprint more similar to that found in nature.

The simplest approach is to adopt what are called more “bioreceptive” materials. Few people probably realize that the drywall in our houses, for instance, is treated with antimicrobial agents, or that most wood we use in architecture has been processed to resist fungus. That’s useful for preventing stains and some deterioration. But it’s also an infrastructure-scale strategy that’s contributing to a rise in disease and allergies.

At the city scale, Sandra Manso Blanco, a researcher from the University College of London, is developing a new type of concrete that could encourage microbes to move in. Formulated with a lower pH level, it’s inherently more suitable for life to grow. To her, it’s a potential play to increase the green space in cities. A more bioreceptive concrete could take environmentally friendly buildings a step beyond green roofs. As algae populate the facade, it could grow across one entire side of a building, populating like moss on a rock. It would offer easy maintenance; anything that grew would be native to the area already; and it could clean the air like a park. Visually, these green-covered buildings would create the kind of cityscape you’d see in sci-fi, in which nature finds a way.

“The thing is, we also need a change of way of thinking. If we want something more natural, we cannot have 100% control of the aesthetics,” says Blanco. “It’s really difficult. The evolution of [these] populations is something difficult to monitor and takes time. In nature it’s much more developed.”

Scientists are exploring the same idea in the interiors of buildings. Inside Jessica Green’s lab at University of Oregon, they’ve been slowly proving that minimal interventions can make major impacts on the microbiome of homes, hospitals, and offices. For the most part, we’re surrounded by the DNA of one another in these spaces, basically stewing in one another’s stuff.


Offices with windows, for instance, seem to have microbial footprints similar to what you’d find in soil. (As it happens, gardening has been found to have an antidepressive effect–potentially due to the microbes in dirt.) Meanwhile, environments with antibacterial compounds like triclosan in the air (the same stuff that’s getting banned in antibacterial soaps) have evidence of containing more antibiotic-resistant microbes.

Holobiont Urbanism beekeeping

But there’s a relatively simple fix to indoor air quality–and in fact, Green may soon be monetizing it through HVAC systems and other technologies that she’s developing in stealth with her microbiome company Phylagen. Her own lab at University of Oregon has found that “night flushing,” the green cooling solution that simply requires opening the windows and bringing in air at night, can reset indoor environments to better match outdoor ones. The next step to scaling those findings would be to embed night flushing technology more intimately into HVAC systems and building design itself.

“In classrooms, you see a shift in the indoor microbiome that goes from one that is what we’d call stagnant air, the leftover microbial soup from all the students during the day, to fresh air and microbes commonly found in plants, soils, and bodies of water,” says Green. “You can imagine a future where we design buildings that have different modes of ventilation depending on the time of day or season, where if for example, particulate matter–which can be carcinogenic–is really high outdoors during the day, you’re filtering that particulate matter out. But then at night, when your occupant density is low, and particulate matter is low, it’s letting the outdoor air in unfiltered during that time.”

It’s more than a bit ironic, however, that if the ultimate solution to having healthier indoor environments may come down to letting more of the outside in–which brings us back to the city itself as a microbe-friendly environment. In fact, another finding of Green’s lab is that the microbes in air over concrete expanses differ from the microbes over green spaces. Those green spaces create the sorts of air microbes that science suspects we should be breathing.

“I can imagine a future when urban planners understand the importance and value of green space in a way they didn’t before,” says Green, “because they’re factoring in how trees influence air quality from a microbial perspective.”


But promoting a healthy, indoor microbiome isn’t without its own environmental costs. Because the fact of the matter is, our greenest buildings, celebrated by certification programs like LEED, are incredibly well-insulated. They’re even cooled and heated by ground water rather than fresh-air options like night flushing.

“The most energy efficient building is not the healthiest [microbiome] building, because for energy efficiency, you’d turn the fresh air off and seal the building up. You wouldn’t have windows,” says Van Den Wymelenberg. “These are not habitable places. If you take energy efficiency to its logical conclusion, and these are not buildings you want to live in,” from a health or user experience perspective.

In this regard, Van Den Wymelenberg imagines that a certification process like LEED will naturally begin to adopt best practices for microbiomes–and in fact, he and Green are helping to organize the first Health and Energy Consortium in 2017 on the topic. The consortium’s goal is to “illuminate tension” between the absolute greenest technologies and the absolute healthiest ones. “We need to change the public’s belief that it’s healthier to be in a hermetically sealed environment,” he says. “[But that means] we need to think about healthier outdoor environments to have healthier indoor environments.”

In The Future, All Architecture Is Landscape Architecture

Holobiont Urbanism microbiome map

Hénaff and I sit in her workshop space, surrounded by gigantic industrial cutting and tooling machines. It’s the sort of roughneck place that will readily crush a hand or cut off a finger if you lean against the wrong table. And it’s the complete antithesis of Hénaff’s other workspace, a far more conventional chemistry lab where jars bubble and the researchers don white coats.

But Hénaff has spent the last year learning to use these machines, because it’s a necessity of her research. She believes–and in fact she’s proven–that she can not only extract microbes from the Gowanus Canal. She can seed them into the pockets of artificial coral–spongy-feeling concrete blocks that she’s learned to 3D print and mold. One day, these blocks might be used to build sprawling subaquatic structures, with each brick supporting a pier or building, all while scrubbing the water clean with organized communities of microbes. It represents a more informed version of mankind’s progress in which we can architect a natural harmony with our planet, rather than erecting more giant, sterile monuments.


“It’s really beautiful to think that even in the depths of the darkest human mistakes, nature is able to respond,” says Hénaff. Nature–and maybe human nature, too.

About the author

Mark Wilson is a senior writer at Fast Company who has written about design, technology, and culture for almost 15 years. His work has appeared at Gizmodo, Kotaku, PopMech, PopSci, Esquire, American Photo and Lucky Peach