Scientists Create First Global Atlas Of Urban Microorganisms

“If you gave me your shoe, I could tell you with about 90% accuracy the city in the world from which you came,” says Christopher Mason, Ph.D., a professor at Weill Cornell Medicine in New York, NY, co-author of the first global atlas of urban microorganisms.

Scientists Create First Global Atlas of Urban Microorganisms

By Romullo Baratto

The study, carried out by the international Metagenomics and Metadesign of Subways and Urban Biomes (MetaSUB) consortium, creates a map of the microbiome of some of the largest cities in the world.

Over 3 years, scientists from MetaSUB collected 4,728 metagenomic samples from mass-transit systems in 60 cities resulting in the first systematic, worldwide catalog of the urban microbial ecosystem. They discovered that each city has a unique microbial fingerprint, likely as a result of differences in climate and geography. 

Public transportation seemed an obvious choice to analyze the cities’ microbiome; with approximately 1.2 billion people using mass transit systems, such as subways and bus networks, around the world every day, it is one of the most shared spaces of the urban environment, featuring a rich and diverse world of unseen organisms.

The lab used a technique called shotgun metagenomic sequencing to identify 4,246 known species of urban microorganisms from their DNA. They also found 10,928 viruses and 1,302 bacteria that were unknown to science. In addition, there was a “core” set of 31 species that are not found in the human body but cropped up in 97% of all the samples.

According to the MetaSUB team, “continually updated, global microbial genetic atlas has the potential to aid physicians, public health departments, government officials, and scientists in tracing, diagnosing, and predicting epidemiological risks and trends.” The scientists believe that the research can help track the spread of infectious organisms in urban environments and also be a valuable resource for new antimicrobial treatments and forensic applications.

One important limitation of the current study was that it only sequenced DNA. Future projects will also sequence RNA, which is the genetic material of many important viruses, such as SARS-CoV-2, which causes COVID-19.

Public transportation has been one of the sectors most affected by the global coronavirus pandemic, having witnessed a dramatic reduction in the number of users worldwide. Given this sudden change, the consortium is now looking into the impacts of quarantine on the composition of each city’s microbiome.

Originally published at Arch daily

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