An international team of researchers says that every city has its own fingerprint — in the shape of pathogens.
The largest ever genetic study of urban microbiomes (including both surfaces and the air in 60 cities worldwide) reports that each city has its own microbial fingerprint. The project sequenced and analyzed samples from public transit systems and hospitals in cities around the world, identifying thousands of viruses, bacteria, and two archaea not found in reference databases.
Roughly 4,730 different samples, taken from cities on six continents over the course of three years were used as part of this study, the team explains. The analysis also revealed a set of 31 species that were found in 97% of the samples.
“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) and the director of the WorldQuant Initiative for Quantitative Prediction.
“If you gave me your shoe, I could tell you with about 90% accuracy the city in the world from which you came.”
This study is the first systematic, worldwide catalog of urban microbial ecosystems, according to the authors. Despite the breadth of the results here, the team is confident that any subsequent sampling of this kind will continue to find new species.
The paper draws its roots in 2013, when Mason started collecting and analyzing microbial samples in the New York City subway system. After publishing his findings, Mason was contacted by other researchers from around the world who wanted to perform similar analyses in their own cities. So he worked out a protocol that they could follow, posting it on YouTube. Samples were to be collected using DNA- and RNA-free swabs and sent to a lab at WCM for analysis along with controls. Most of the analysis part was handled by an Extreme Science and Engineering Discovery Environment (XSEDE) supercomputer in Pittsburgh.
Two years later, in 2015, Mason created the International MetaSUB (Metagenomics and Metadesign of Subways and Urban Biomes) Consortium to better handle all the data people were sending him. Samples from air, water, and sewage were now coming in from across the world in addition to those from hard surfaces.
Such genomic studies can help detect outbreaks of both known and unknown infections and can help us keep tabs on the levels of antibiotic-resistant microbes in different urban environments. It’s also a very useful tool when analyzing the evolution of microbial life.
“There are millions of species on Earth, but we have a complete, solid genome reference for only 100,000 to 200,000 at this point,” Mason says, explaining that the discovery of new species can help with the building of microbial family trees to see how different species are related to one another.
“Based on the sequence data that we’ve collected so far, we’ve already found more than 800,000 new CRISPR arrays,” he says. Additionally, the findings indicate the presence of new antibiotics and small molecules annotated from biosynthetic gene clusters (BGCs) that have promise for drug development.
These samples led to the results published in this paper: 4,246 known species of microorganisms were identified worldwide, 31 of which were present in 97% of all samples from urban areas.
“One of the next steps is to synthesize and validate some of these molecules and predicted biosynthetic gene clusters (BGCs), and then see what they do medically or therapeutically,” Mason says. “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.”
The paper “”A global metagenomic map of urban microbiomes and antimicrobial resistance” has been published in the journal Cell.