Microscopic subway passengers with a ticket to ride

A complete map of the microbiome of the New York City subway system? It’s possible – and all it takes is a few eager students, some swabs and a toddler. Research leader Dr Chris Mason tells us more about PathoMap…

How did you come up with the idea to create a PathoMap? The idea of PathoMap all started in 2010 when I was dropping off my daughter, Maddie, at daycare (she is in the acknowledgements of the paper!). When I came to pick her up I saw that she was exploring the world with her mouth. She would put toys in her mouth, place them down and then the next kid would come and do the same. In essence she was making out with the other kids by toy proxy. Around the same time the human microbiome project came out and I wanted to swab her mouth before and after daycare- but then I'd be that creepy guy swabbing kids. But since then I've always been curious of the microbiome of the surfaces around us. Since I take the subway everyday it was the best place to start.

Why study microbiomes? The microbiome is the ecosystem of microorganims that live on, in and around us. The metagenome is the collection of all the DNA around us, human, bacteria, other animals, and plants. Many studies have shown that there is a link between the microbiome and metagenomics and human health. But more importantly, these fields are still relatively new and developing, our study and studies like it are crucial to moving the field forward and being able to translate the data to actual applications (public health, bioterrorism surveillance, urban planning, etc.)

Tell us more about PathoMap. The study began in the summer of 2013 since I had eager students from Weill Cornell Medical College, Cornell University, and the Macaulay Honors College who were eager to get out there and swab. It started off as a proof of principle- can we even collect DNA from these surfaces? Eventually we found the best kind of swab and time interval to get enough DNA to sequence. The project began and still is primarily aimed at creating a molecular portrait of the city, a baseline of the microbiome across an entire city- notably the built environment of the mass transit system. Once a baseline is created, then we can start to look for changes or perturbations to the city's genetic ecosystem.

What did the maps you create reveal? Many things! Overall they are a great way to visualise the trends and dynamics of the microbiome of NYC's subway system. You can find that some organisms have hot spots in certain areas around the city while other organisms like Pseudomonas are prevalent throughout the entire system. The subway system is not something to fear. The majority of bacteria we have found are not associated with any disease and any organisms we have found that are potentially pathogenic, all we have to report are fragments of DNA. There is no evidence to suggest these organisms are living on these surfaces and threaten the health of New Yorkers.

What was the most unusual microbe that you found? We have found 637 species in our study, 562 of them being bacteria. It's hard to pick just one but Shewanella frigidimarina a species only found in the South Ferry station is really interesting as it is thought to be only an Antarctic species and highly associated with fish. It clearly shows that the aftermath of Superstorm Sandy is still felt in the "microbe aura" or "molecular echo" of the station.

What was your most interesting finding? There is a lot to take away from the preliminary results. New York City is the epitome of a busy, diverse, metropolis and we were excited to see our findings reflect the same with the city's microscopic residents. But the three most interesting things were (1) that nearly half (48%) of the DNA we uncovered matches no known organism. It shows that this study has just begun to scratch the surface of the microbiome and metagenome of surfaces and cities. (2) A "molecular echo" can be seen, such that the DNA present in a station can reveal its history, like marine-associated bacteria from the South Ferry station that was flooded during Hurricane Sandy.  (3) Even human DNA left behind carries a "molecular echo,' wherein the DNA from a station can match the U.S. Census data and recapitulate the same demographics.

How can we protect ourselves from germs on the subway in general? Is this different from other areas where germs lurk? Ask Jack Gilbert reported in Science last year, every place has its own microbe aura associated with it and as you move through these areas you interact with the surfaces around you and these auras mingle. More microbiome studies like the earth microbiome project (EMP), home microbiome project, hospital microbiome project, extreme microbiome project (XMP), and our international version of PathoMap (MetaSUB) will create this incredible opportunity to compare datasets and really see how surfaces and different areas compare. There is nothing to fear of the subway- I'm sure there will always be people riding with gloves, holding the rails with plastic sheets, etc. but really all you need is to exercise common hygeine practices: wash your hands, don't walk around with gaping wounds-use a bandaid, and keep your immune system healthy with a good diet and sleep. Embrace the microbiome!

Tell us about the abandoned South Ferry Station? The South Ferry Station was flooded in 2012 by Super Storm Sandy and with the help of the MTA we were able to get access to the part of the station that was closed off. Even though it was a year after Sandy its microbe aura kept the unique signature of a marine environment. It was the station with the greatest diversity, 10 species found nowhere else in the subway system. Many of these species were associated with fish, salty waters, and as you noted Antarctica. The most plausible explanation is that these bacteria were associated with the ocean and so when the Hudson River flooded the station these bacteria remained on the walls, floors, and poles of the station. It was amazing to see them present even though a year had past. For a dynamic interactive representation of the abandoned station dataset check out http://www.pathomap.org/blog/

What’s next? Our major goal is to expand PathoMap internationally through a project we're callingMetaSUB the Metagenomics of the Subway and Urban Built environment, which will be studying the microbiomes of subway systems from around the world.

To view the PathoMap go to http://www.pathomap.org/