Big Data Project Provides First Genetic Profile of City Transit System

February 6, 2015 in News

Researchers have created the first big-data genetic profile of the New York City subway system by collecting, identifying and mapping the micro-organisms found through the system, the Wall Street Journal reports.

The researchers on Thursday published the results of their 18-month long project, called PathoMap, in the journal Cell Systems.


According to the Journal, projects across the U.S. aim to combine microbiology, genomics and population genetics to identify the micro-organisms inhabiting buildings and confined locations in cities. Researchers hope that by documenting the micro-organisms they will be able to better track disease outbreaks and combat antibiotic resistance.

Project Details

For the project, Christopher Mason, a geneticist at Weill Cornell Medical College, and a team of researchers collected DNA from various surfaces throughout the transit system’s 466 open locations, including:

  • Benches;
  • Railings; and
  • Ticket kiosks.

The researchers sequenced the more than 10 billion sections of biochemical code they collected and sorted them using a supercomputer. The researchers then compared the results with genetic databases of:

  • Known bacteria;
  • Viruses; and
  • Other life-forms.


Overall, the researchers identified 15,152 different life forms, almost half of which belonged to bacteria. According to researchers, germs found at various locations could cause:

  • Antibiotic-resistant infections;
  • Bubonic plague;
  • Meningitis; and
  • Other conditions.

The researchers noted that most of the bacteria would not cause harm and were present in such low levels that they would not threaten public health (Lee Hotz, Wall Street Journal, 2/5).

The researchers also noted that about half of the DNA they found did not match any known life forms (Harris, New York Times, 2/5). In addition, some of the DNA comparisons could be inaccurate because relatively few organisms have had their entire genome sequenced, according to the researchers. In some instances, computers could have matched partial DNA from certain life forms to the nearest known species available (Wall Street Journal, 2/5).

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