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Global Subway Metagenomics Study Reveals Cities' Microbial Fingerprints

NEW YORK – A study of the microbes living in 60 cities around the world has led to the discovery of thousands of novel viruses and hundreds of new bacterial species, as well as unique microbial fingerprints for each locale.

"Every city has its own 'molecular echo' of the microbes that define it," Christopher Mason, a genomics researcher at Weill Cornell Medicine and principal investigator of the Metagenomics and Metadesign of Subways and Urban Biomes, or MetaSUB, consortium, said in a statement. "If you gave me your shoe, I could tell you with about 90 percent accuracy the city in the world from which you came."

Studying these unique urban microbiomes has led to the discovery of 10,928 viruses and 748 bacteria that are not present in any reference databases, according to a new paper published this week by the consortium in Cell. Also present in the data is evidence of more than 80,000 new CRISPR arrays as well as evidence of regional antimicrobial resistance markers.

The researchers analyzed 4,728 samples from cities on six continents collected from 2015 to 2017. While each city was unique, the researchers found a core set of 31 species that were found in 97 percent of samples. The researchers identified 4,246 known species of microorganisms, but also found that any subsequent sampling is likely to find species that have never been seen before.

This project began in 2013, when Mason's lab started collecting and analyzing microbial samples in the New York subway system. In 2016, MetaSUB announced a goal of sequencing samples from 45 cities, including Rio de Janeiro, which hosted the Olympics that year. The project expanded to include air, water, and sewage samples.

Each sample was sequenced with 5 million to 7 million 125 bp paired-end reads on Illumina HiSeq X Ten instruments at the Hudson Alpha Genome center. Much of the bioinformatics analysis and genome assembly was done at the Extreme Science and Engineering Discovery Environment supercomputer in Pittsburgh.

Beyond the new species and CRISPR arrays, the results indicate the presence of new antibiotics and small molecules annotated from biosynthetic gene clusters, or BGCs, that have promise in drug development.

"One of the next steps is to synthesize and validate some of these molecules and predicted BGCs, and then see what they do medically or therapeutically," Mason said in a statement. "People often think a rainforest is a bounty of biodiversity and new molecules for therapies, but the same is true of a subway railing or bench."