Teams of researchers and volunteers were distributed across the transit systems of 60 cities, collecting thousands of samples from 2015 to 2017. They wiped a variety of surfaces including turnstiles, railings, ticket offices, and benches in transit stations and subways. (In some cities without subway systems, teams focused on the bus or train system.)
Scientists' underground sampling expeditions often attracted attention. Some commuters got so curious that they joined the volunteer swab corps, while others insisted they absolutely didn't want to know what was alive on the metro poles. Passengers have occasionally misunderstood what the researchers were doing with their tiny swabs. "One man said thank you very much for cleaning the subway," said Dr. Mason.
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 "aerial microbiome" published 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 geographical diversity of the samples – that is unprecedented."
The team then extracted and sequenced the DNA from each sample to identify the species it contained. In total, they found 4,246 known species of microorganisms in all surface samples. Two-thirds of these were bacteria, while the rest was a mix of fungi, viruses, and other types of microbes.
But that was just the beginning: they also found 10,928 viruses and 748 types of bacteria that had never been documented. "We could see that these were real – they are microorganisms – but they are nowhere in a database." said Daniela Bezdan, the former managing director of MetaSUB, who is now a research assistant at the University Hospital Tübingen in Germany.
The vast majority of these organisms are likely to pose little risk to humans, experts said. Almost all of the new viruses they have found are likely bacteriophages, or viruses that infect bacteria, said Dr. Danko. In addition, genetic sequencing cannot distinguish between dead and living organisms, and no environment is sterile. In fact, our bodies rely on a rich and dynamic community of microbes to function properly.