• Wed. Jun 23rd, 2021

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Cities like London and Tokyo have their own unique microbiomes

Tokyo

The skyline of Tokyo, Japan

Sara Winter/Alamy

Each city has its own distinct microbiome, according to a vast survey of microbes in 60 urban areas worldwide that also discovered 11,000 new viruses and bacteria.

Christopher Mason at Cornell University in New York and his team asked colleagues around the world to collect swabs from urban transport systems, such as subways, between 2015 and 2017. In all, 4728 samples were collected from cities including London, New York, Rio de Janeiro and Tokyo. Some 58 per cent of the cities were in east Asia and Europe.

The nylon swabs, which were placed into a tube containing a DNA and RNA preservative agent, were then genetically analysed to see what kinds of bacteria and viruses existed on the surfaces. “I ride the subway every day to the lab, so I wanted to know what I was grabbing under my hands,” says Mason.

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From there, each city was assigned an endemicity score – the number of microbial species endemic to a specific area that can define the unique fingerprint of each city.

The larger the city, the more complex and diverse microbial life. And in any city, regardless of size, every kilometre of distance between two samples was associated with, on average, a 0.056 per cent difference in microbes sampled.

“We could probably tell with about 90 per cent accuracy where someone was from, and this data gets better when we do more sampling,” says Mason.

This suggests that the microbiomes could have applications in forensic investigations, perhaps to establish whether an individual visited a particular city in the recent past.

Mason and his team discovered 10,928 new viruses and 748 new bacteria that didn’t exist in any reference databases. “I was surprised at how many there were,” he says. “I think it’s a wonderful affirmation of how much left we have to discover about the world.”

The team plans to expand sampling from surfaces to waste water, and intends to analyse samples from the upcoming Tokyo Olympics – if they go ahead. The hope is to integrate the findings into public health databases to track new viruses.

Journal reference: Cell, DOI: 10.1016/j.cell.2021.05.002

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