Cities have their own distinct microbial fingerprints

Populated street in New York City.

Chris Mason’s daughter used to touch surfaces on the New York City subway when she was a baby, and he was fascinated by it. Then she licked a pole one day. Mason, a geneticist at Weill Cornell Medicine, believes there was a clear microbial interaction. “I was desperate to find out what had happened.”

So he started swabbing the subway, sampling the microbial world that coexists with people in our transit systems. After his 2015 study revealed a wealth of previously unknown species in New York City, other researchers contacted him to contribute. Now, Mason and dozens of collaborators have released their study of subways, buses, elevated trains, and trams in 60 cities worldwide, from Baltimore to Bogotá, Colombia, to Seoul, South Korea. They identified thousands of new viruses and bacteria, and found that each city has a unique microbial “fingerprint.”

According to Adam Roberts, a microbiologist at the Liverpool School of Tropical Medicine who was not involved in the research, the discovery is “wonderful.” Although smaller studies have looked at individual cities or transport systems, the new research is at a significantly larger scale than anything before it, allowing it to investigate new problems, he says. “They’ve done an incredible job putting it all together. This data, I believe, will be studied for decades.”

Mason and his partners had to discover how to collect samples regularly before they could create a worldwide snapshot of transit microbiomes around the world. They settled on swabbing benches, turnstiles, and ticket kiosks. All are found in transport systems around the world. “It’s the perfect compromise between DNA yield and social discomfort,” Mason says. Scientists swabbed surfaces for 3 minutes, which was long enough to extract enough DNA but not so long that it became uncomfortable for the researchers and spectators.

The researchers studied the DNA in the lab. They discovered that roughly 45 percent of the samples didn’t belong to any recognized species: Nearly 11,000 viruses and 1302 bacteria were discovered for the first time.

The researchers also discovered that 31 species were present in 97 percent of the samples, forming a “core” urban microbiome. A total of 1145 species were found in more than 70% of the samples. In comparison to surfaces like windows, samples taken from surfaces that people contact, such as railings, were more likely to have bacteria associated with human skin. Bacteria commonly found in soil, water, air, and dust were also included in the mix.

However, the researchers discovered certain species that were less common. These provided each city its own microbiome, which let the researchers estimate which city random samples came from with 88 percent accuracy, according to a paper published today in Cell. They discovered a lot of Carnobacterium inhibens, a lactic acid-producing bacteria that is resistant to low temperatures, in New York City, for example. Unique urban fingerprints like this, Mason believes, could be beneficial for forensics with more research.

According to Noah Fierer, a microbiologist at the University of Colorado, Boulder, who was not involved in the research, the study’s greatest significance lies in its accessible data, which is available at metagraph.ethz.ch. Other researchers will be able to investigate new questions as a result of this. Fierer explains that “different cities have diverse microbiological communities.” “It’s not unexpected at all. For me, the question is, “Why?”

Although some people are concerned about the bacteria that lurk in our cities, the findings show that they are rather safe, according to Mason. Antimicrobial resistance genes, for example, were found in considerably lower concentrations in transit samples than in human gut or hospital samples, he claims.

Mason, on the other hand, sees public transport systems as a source of untapped and spectacular biodiversity. As an opportunity for “awe and excitement.” He believes that newly discovered species might be used in drug development, and that large-scale mapping and monitoring of urban microbiomes might be beneficial to public health by allowing researchers to recognize emerging infections early.

Monitoring urban microbiomes would have been a “weird” and extremely expensive idea until recently, Mason claims. People can now see how valuable it could be: Mason believes that if researchers had been looking for RNA in samples throughout the world, they might have seen the pandemic coronavirus arise. “What if we had been looking all along?”

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