Teams of researchers and volunteers fanned out across the mass transit systems of 60 cities, collecting thousands of samples from 2015 to 2017. They swabbed a wide variety of surfaces, including turnstiles, railings, ticket kiosks and benches inside transit stations and subway cars. (In a handful of cities that did not have subway systems, the teams focused on the bus or train system.)

The scientists’ subterranean sampling expeditions often attracted attention. Some commuters grew so curious that they joined the volunteer swabbing corps, while others insisted that they absolutely did not want to know what was living on the subway poles. Passengers occasionally misunderstood what the researchers were doing with their tiny swabs. “One man effusively thanked us for cleaning the subway,” Dr. Mason said.

The researchers also collected air samples from the transit systems of six cities — New York, Denver, London, Oslo, Stockholm and Hong Kong — for a companion paper on the “air microbiome” that was published on Wednesday in the journal Microbiome.

“This is huge,” said Erica Hartmann, a microbiologist at Northwestern University who was not involved in the study. “The number of samples and the geographic diversity of samples — that’s unprecedented.”

Then the team extracted and sequenced the DNA from each sample to identify the species it contained. In total, across all of the surface samples, they found 4,246 known species of microorganisms. Two-thirds of these were bacteria, while the remainder were a mix of fungi, viruses and other kinds of microbes.

But that was just the beginning: They also found 10,928 viruses and 748 kinds of bacteria that had never been documented. “We could see these were real — they’re microorganisms — but they’re not anywhere in any database,” said Daniela Bezdan, the former executive director of MetaSUB who is now a research associate at the University Hospital Tübingen in Germany.

The vast majority of these organisms probably pose little risk to humans, experts said. Nearly all of the new viruses they found are likely to be bacteriophages, or viruses that infect bacteria, Dr. Danko said. Moreover, genetic sequencing cannot distinguish between organisms that are dead and those that are alive, and no environment is sterile. In fact, our bodies rely on a rich and dynamic community of microbes in order to function properly.

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