Our Subways Are Teeming With Microscopic Life

By Margaret Ramirez

With each swipe of his MetroCard and every ride on the New York City subway, Ebrahim Afshinnekoo envisions a trip into an underworld teeming with mysterious microorganisms and live bacteria.

Ebrahim Afshinnekoo collecting a swab of organisms from a subway map.

Ebrahim Afshinnekoo collecting a swab of organisms from a subway map.

Until recently, few researchers ventured to find out more about those microbes. But a new study released by a team of investigators at Weill Cornell Medical College has produced the first genetic profile of New York City’s subway system, uncovering a vast ecosystem of bacterial, fungal and animal species.

After collecting DNA samples from all 468 subway stations, researchers detected 15,152 types of microorganisms including traces of germs that can cause bubonic plague, anthrax and meningitis. Other samples told the life stories of the subways revealing bacteria from foods like cucumbers and cheese, house pets, plants and rats.

The pathogen mapping project, dubbed PathoMap, was led by Dr. Christopher Mason, an assistant professor at Weill Cornell Medical College and involved dozens of professors, researchers and graduate students in New York City and across the nation. Afshinnekoo, 21, a senior at Macaulay Honors College at Queens College, began working on the project as a summer intern and eventually took on a leadership role that led to his title as co-lead author of the study that was published online in the journal Cell Systems.

For Afshinnekoo, the most surprising discovery was not the trace amounts of harmless bacteria. He was more intrigued by the finding that 48 percent of the DNA collected from subway surfaces matched no known organisms.

“It’s really amazing because it just shows there is so much left out there to discover,” Afshinnekoo said. “At the end of the day, a lot of this has to do with our databases. There is not even a genome of a cockroach yet, which you would expect there would be.”

“So, this is really the beginning of a revolution in metagenomics and microbiomes.”

In the study, the research team sought to define the microbiome in New York City’s subway system, which is used by about 5.5 million riders every day. In addition to Afshinnekoo, four other CUNY students were part of the research team. Shanin Chowdhury attends Macaulay at Hunter and Sofia Ahsanuddin attends Macaulay at Brooklyn College. Sean Dhanraj and Tanzina Nawrin are enrolled at Brooklyn College.

Over the past 17 months, the team boarded subways, armed with swabs and collected DNA samples from the surfaces of 468 stations on 24 lines across five boroughs. They swabbed turnstiles, wooden and metal benches, stairway hand railings and trashcans. The team also swabbed the inside of trains, including seats, doors, windows, poles and handrails, often drawing stares from riders.

Mason said the PathoMap provides a baseline assessment that could be used for long-term, accurate disease surveillance or tracking disease outbreaks.

While news reports hyped the traces of bubonic plague and anthrax, Afshinneko said their presence isn’t substantial enough to pose a health threat.

“The subway system has been around for over a century and there has never been reported cases of outbreaks or any sort of disease,” he said. “So it’s really a testament to our immune systems and our capabilities to interact with this environment. I take the subway every day. You take the subway. We’re not getting sick. This isn’t something to be afraid of. It’s something to embrace, this whole idea of the microbiome and discovering the world beyond us.”

Afshinnekoo, who plans to attend medical school after receiving his undergraduate degree, said he hopes to find more areas where environmental science and medicine intersect in the field of public health.

For now, every subway ride reminds him of the unknown richness inside the subway’s DNA.

“It’s fascinating to me,” he said, “and it’s incredible to see this whole world that’s basically hiding right in front of our eyes.”