February 23, 2015

Mapping the Microbes in New York City’s Subway System

At a Glance

  • Researchers created a detailed map of bacterial diversity throughout New York City.
  • The findings serve as a baseline that could aid surveillance of disease, bioterrorism threats, and health management in city environments.  
People holding onto handles on subway. The researchers created a city-scale molecular profile of DNA collected from New York City’s subway system and other public areas.FeelPic/iStock/Thinkstock

The human body is host to trillions of microbes that include bacteria, fungi, and viruses. They influence our health and disease and are, in turn, influenced by the environment. At the same time, the environment itself—everything that surrounds us—hosts an extensive assortment of bacteria, which we’re exposed to every day.


To learn more about environmental microbes and the DNA that surrounds us, a team of researchers led by Dr. Christopher E. Mason at Weill Cornell Medical College tracked and characterized the genetic material of microorganisms in New York City, particularly in its subway system. Used by 1.7 billion people a year, it’s the largest mass-transit system in the world.

The scientists used sterile swabs to collect 1,457 samples across 468 subway stations, covering 24 lines in 5 boroughs. The team sampled turnstiles, wooden and metal benches, stairway handrails, trashcans, emergency exits, and card kiosks. On trains, they sampled doors, poles, handrails, and seats. They also sampled railway stations and public parks in the city. They developed a mobile app to map the exact location and time of each sample.

The team extracted DNA from each sample, sequenced it, then classified and characterized it, using several existing databases. The study was funded in part by NIH’s National Institute of General Medical Sciences (NIGMS). Results appeared online on February 5, 2015, in Cell Systems.

The researchers found that almost half of the DNA analyzed (48%) did not match any known organism, hinting at how many species remain to be identified. They determined that 47% of the DNA came from bacteria, 0.03% came from viruses, and the rest from fungi and other organisms.

Bacterial signatures could reveal a station’s history. Marine-associated bacteria were found in the closed station that was flooded during Hurricane Sandy. The Bronx stations showed the greatest bacterial diversity, while Staten Island had the lowest diversity. By comparing their data with data from the 2010 U.S. Census, the researchers found that the predicted ancestry of human DNA left on subway surfaces echoed the U.S. Census demographic data. The team also found shifts in microbes during the course of the day after collecting samples from Penn Station every hour during a weekday.

The group detected some DNA fragments associated with known pathogens, including bubonic plague and anthrax, but didn’t find strong evidence that those organisms were present. The researchers also detected bacteria that are resistant to standard antibiotics.

“Our data show evidence that most bacteria in these densely populated, highly trafficked transit areas are neutral to human health, and much of it is commonly found on the skin or in the gastrointestinal tract,” Mason says. “These bacteria may even be helpful, since they can out-compete any dangerous bacteria.”

The team has created “PathoMap,” an interactive heatmap of their data. “We can now monitor for changes and potential threats to this balanced microbial ecosystem,” Mason says.

—by Carol Torgan, Ph.D.

Editor’s Note: The authors published an Erratum on July 29, 2015 with corrections to the paper. This page was updated accordingly on August 5, 2015.

References: Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics Cell Systems, 2015 DOI: 10.1016/j.cels.2015.01.001. Erratum DOI: http://dx.doi.org/10.1016/j.cels.2015.07.006

Funding: NIH’s National Institute of General Medical Sciences (NIGMS) and National Center for Advancing Translational Sciences (NCATS); Pinkerton Foundation; Vallee Foundation; New York University; and Indiegogo for crowdfunding and crowdsourcing support.