Every week we talk about the human microbiome that makes up each and every one of us, but what about the environmental microbiome, particularly in urban areas? Cities are just like people (kind of), and they have a microbiome too! A very cool study published yesterday in Cell Systems describes New York City's microbiome. A large team of scientists, led by a group at Weill Cornell Medical College investigated the DNA profile of the city’s public transit system, several public spaces, and the Gowanus Canal.

They collected samples from every open NYC subway station (466 of them), the Staten Island Railway, 12 locations along the Gowanus Canal in Brooklyn, four public parks, as well as the South Ferry Station that was closed at the time of sampling due to flooding from Hurricane Sandy. At the subway stations, they sampled inside the trains, kiosks, benches, turnstiles, garbage cans, and railings. The results were fascinating.

Almost half of all the reads could not be matched to any known organism. They found that South Ferry Station, the only station in NYC that was completely submerged in Hurricane Sandy, represented a marine environment. They discovered that some known pathogenic bacteria, such as Yersinia pestis, the cause of the bubonic plague, and Bacillus anthracis, anthrax, were present in a few subway stations.

Not surprisingly, the scientists found that the most common bacteria in these locations were those that are abundant on humans' skin. This makes sense as thousands of people pass through each one of the subway stations every day. In addition, stations with the greatest levels of traffic on a daily basis, like Grand Central and Times Square, had the greatest diversity of bacteria.

What about all these unknown organisms that couldn’t be identified? These exemplify the huge amount of life right in front of us that has yet to be characterized. What about all the pathogenic bacteria and antibiotic resistant bacteria like MRSA that were identified? Should we be worried that these? The authors state that the subways generally contain safe surfaces for the following reasons. First, they note that it is impossible to tell if the sequenced organisms are dead or alive. Second, even more importantly, these bacteria help make up a dynamic and shared urban infrastructure, and they may even help maintain its equilibrium. Finally, the bacteria that were connected to the plague, anthrax, and other diseases were found in very small traces, not enough to colonize our bodies. (Did you know that people in the United States, almost exclusively on the West Coast, are still getting the bubonic plague today?)

It will be very interesting to see what comes from this study. I, for one, would like to know what the South Ferry Station microbiome looks like now compared to when the scientists initially sampled, because the sampling was performed when it was still closed due to Hurricane Sandy. Now that it is back up and running with thousands of people passing through it every day, how has the ecosystem of the station changed?.

The authors suggest that a study like this could help facilitate forensic investigations. For example, the bottom of one’s shoe could represent where that person traveled over the past day or week. They also suggest that faster, or maybe even real-time analysis, of the microbiome of the city’s transit system could be used to protect the city from bioterrorism and other public health threats like our recent scare with Ebola.

If you want to see what bacteria were found at your favorite station, The Wall Street Journal put together a very easy-to-use interactive map. Check it out here.