Metagenomic Study Finds that Cities Have Unique Microbial Signatures

A metagenomic study of urban microbiomes, spanning both the air and the surfaces of 60 cities, was published in Cell yesterday. The international project, which sequenced and analyzed samples collected from public transit systems and hospitals in cities around the world, features comprehensive analysis and annotation for all the microbial species identified—including thousands of viruses and bacteria and two archaea not found in reference databases.

"Every city has its own 'molecular echo' of the microbes that define it," says senior author Christopher Mason, a professor at Weill Cornell Medicine (WCM). "If you gave me your shoe, I could tell you with about 90% accuracy the city in the world from which you came."

The findings, which are based on 4,728 samples from cities on six continents taken over the course of three years, characterize regional antimicrobial resistance markers, and represent the first systematic worldwide catalog of the urban microbial ecosystem. In addition to distinct microbial signatures in various cities, the analysis revealed a core set of 31 species that were found in 97% of samples across the sampled urban areas. The researchers identified 4,246 known species of urban microorganisms, but they also found that any subsequent sampling will still likely continue to find species that have never been seen before, which highlights the raw potential for discoveries related to microbial diversity and biological functions awaiting in urban environments.

This project began in 2013, when Mason started collecting and analyzing microbial samples in the New York City subway system. After he published his first findings, he was contacted by researchers from all over the world who wanted to do similar studies in their own cities. He developed a protocol for collecting the samples and posted an instructional video on YouTube. The samples were collected with DNA- and RNA-free swabs and sent to a lab at WCM for analysis, along with positive and negative controls. Much of the analysis and assemblage of sequences was done on an Extreme Science and Engineering Discovery Environment (XSEDE) supercomputer in Pittsburgh, which led to the discovery of 10,928 viruses and 748 bacteria that are not present in any reference databases.