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Thousands of Unknown Microbes Found in Subways Around the World

A team of more than 900 scientists and volunteers swabbed the surfaces of 60 public transit systems

Passengers ride the New York City subway on May 24, 2021. (Tayfun Coskun/Anadolu Agency via Getty Images)
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Research published this week in the journal Cell catalogues the microbial makeup of 60 public transportation systems around the globe.

Between 2015 and 2017, more than 900 scientists and volunteers on six continents swabbed the benches, railings, turnstiles and ticket kiosks of subway and bus stops, Emily Anthes reports for the New York Times. The effort resulted in the discovery of the “core urban microbiome,” or 31 species of bacteria common to 97 percent of the samples gathered in the study. The research also revealed the presence of almost 11,000 viruses and over 700 bacteria species that have not yet been identified.

The study is “fantastic,” says Liverpool School of Tropical Medicine microbiologist Adam Roberts, who was not involved in the research, to Cathleen O’Grady at Science magazine. “They’ve done an amazing job bringing this all together. I think this data will be analyzed for decades to come.”

Because the study covers dozens of cities instead of just one, it presents an opportunity to answer new questions, Roberts tells Science. The research team was led by Christopher Mason, whose 2015 study on the microbes of the New York subway system sparked other researchers’ interest. The team grew as passersby seeing the scientists meticulously swabbing surfaces in the subway volunteered to help, reports the New York Times.

By swabbing surfaces, the researchers gathered DNA from the microbes that had lived and died there. Surfaces were swabbed for long enough to gather the DNA, but not so long that the researchers and commuting crowds became too uncomfortable. Three minutes of swabbing per surface was “the perfect balance between DNA yield and social discomfort,” Mason tells Science.

The samples yielded 4,246 known species of microbes. Two-thirds were bacteria, while the other third was a mix of fungi, viruses and other microbes. Thirty-one bacteria species were present in nearly every city, earning them the title of the core urban microbiome. About half of those 31 bacteria species are common on the human body, especially on the skin. Other species are commonly found in dirt, water or dust.

Each city had a different microbial makeup. That means that the researchers could predict with 88 percent accuracy which city a random sample came from. Further research could establish recognizable urban fingerprints for use in forensics, Mason tells Science.

But the research also found 748 bacteria and 10,928 viruses that haven’t yet been identified.

“We could see these were real—they’re microorganisms—but they’re not anywhere in any database,” says University Hospital Tübingen biologist Daniela Bezdan, former executive director of MetaSUB, the research consortium that ran the study, to the New York Times.

The mystery microbes are not a cause for concern, the researchers say. Most of the viruses are probably bacteriophages, which infect bacteria, not humans. The sample collection technique that they used also can’t differentiate between microbes that are living and dead—when bacteria, viruses and fungi die on the subway surfaces, their DNA is left behind.

The research could open new methods for monitoring public health or new candidates for antibiotics.

“The amount of microbial diversity is just incomprehensibly vast,” says Northwestern University microbiologist Erica Hartmann, who was not involved in the study, to the New York Times. “There’s so much out there that we just don’t really understand, and there could be all kinds of nifty biotechnologies and all kinds of fun chemistries that we’re not aware of yet.”

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