Q&A: Mapping the Urban Microbiome

Q&As

It’s a question that’s plagued every New York commuter: “Why is this subway pole sticky?” Weill Cornell Medical College Assistant Professor of Genetics Chris Mason, who recently spoke at February’s SciCafe may soon have a very detailed answer.


 Mason and colleagues have been going out on “swabventures” to public spaces like subway station, collecting genetic samples all over the city to learn what microbes call the city home, and in what proportion. Eventually, researchers hope to be able to track local levels of microbes—including those that can cause disease. In this Q&A, Mason elaborates on the project, called PathoMap

What is the urban microbiome, and what are you aiming to do with PathoMap?

What we’re trying to create with Pathomap is a baseline description of the pathogens and species that are present in the environment. For the first time ever, we’ve got a molecular view of an entire city. 

Why is this view important?

We’re vastly outnumbered by microbes in our own body, and in the built environment of buildings and subways systems as well. Now that we have this baseline DNA map, it lets us see if there are any perturbations that could be dangerous. We can also use it to look at other cities and do similar work in places with higher temperatures or more humidity and explore how those factors affect microbial populations.

What methods and tools are you using?

The protocol we developed uses GPS, a mobile app, and old-fashioned cotton swabs. Our volunteers go on what we call swabventures, taking samples from different places throughout New York City. 

Travelers passing through a subway turnstile at Penn Station Flickr/John St. John

Travelers passing through a subway turnstile at Penn Station

Flickr/John St. John


Is there any special techniques for collecting in public spaces?

Personally, I look at my phone while I’m swabbing, for example, a turnstile. But people have all sorts of techniques. Some of our volunteers make very direct eye contact with other people while they’re swabbing. Others go the opposite way—they avoid eye contact at all costs and just look like they’re wandering around the subway station, which is of course, not an uncommon look for people riding the subway.

Do people ask what you’re doing?

Sometimes, but it’s actually pretty rare. In gathering our 4,000 samples, we only had one volunteer get stopped and questioned. We had another volunteer who was swabbing a handrail outside a building when someone came up to her and thanked her for cleaning up the city. So the reactions can really vary.

How did you become interested in this field?

The field of microbiome study has been blowing up in the last few years, and I was reading a lot of papers on the topic when I was putting my daughter in daycare for the first time. I dropped her off and was watching her and other kids put toys in their mouths and pass those toys around, and it occurred to me that this was their first real exposure to the microbiomes of other people. Then it occurred to me to swab her mouth before and after I dropped her at daycare, because the results would certainly be different. 

Chris Mason discusses the macrobiome with a packed house at SciCafe. © AMNH/M. Shanley

Chris Mason discusses the macrobiome with a packed house at SciCafe.

© AMNH/M. Shanley


And did you?

I didn’t, because I didn’t want to be a creepy dad. But that idea never left my head. Every time you touch the surface of a subway pole and its warm, or wet, or sticky, that’s evidence of another microbial environment. Once the idea was in my head, it didn’t take long to get very interested in the microbiome of the built environment and how it impacts us. It’s an unexplored country.

What’s next for mapping the microbial environment of cities?

In the long term, this is the first step toward building smarter cities. People with allergies already have pollen alerts that can help them take precautions. One day in the future, we could be able to use maps like this one—but much more advanced, of course—to warn people when and where pathogen populations are spiking around them.

We also want to get more people involved in this mapping, so we’re launching a crowdfunding and crowdsourcing aspect to our future work. People will be able to buy swab kits to use at their homes or sponsor kits to be sent to schools. That money will help fund our work, and people will send us the swabs, which will allow us to expand the scope of it as well.

Tags: SciCafe, Q&A