Cities have a unique microbiome, just like your gut

Researchers swabbing subway stations for microbial life have created the first worldwide catalogue of urban microbial ecosystems, and in the process discovered thousands of bacterial and viral species completely new to science.

"Every city has its own signature," geneticist Christopher Mason told Quirks & Quarks host Bob McDonald. "If you give me a random sample from one of these cities around the world, I could tell you with about 90 percent accuracy where you came from."

Between 2015 and 2017, over 900 scientists and volunteers from 60 cities and 32 countries collected over 4,700 samples, as a part of an international effort to understand how the world's microbes differ from place to place.

"We thought we would just be classifying differences, but we didn't anticipate that we'd find all this new biology," said Mason, who led the study.

The research was published in the journal Cell.

Inspired by daughter grabbing subway poles

Mason, a professor of genomics, physiology, and biophysics at Weill Cornell Medicine, wanted to learn more about the bacteria, viruses and other microorganisms that live among humans. He was initially inspired while on his morning commute on the New York City subway system.

"I'd always been curious, just as a scientist, because I ride the subway everyday to the lab," he said.

Further inspiration struck once he became a parent.

"I watched my daughter grab subway poles and sometimes put food from the subway in her mouth... some truly gross parental moments."

After publishing the findings from his initial New York City subway swabbing study in 2015, he was contacted by dozens of researchers from around the world who wanted to do similar experiments in their own cities. As a group they formed MetaSUB (Metagenomics and Metadesign of Subways and Urban Biomes) and came up with a way to standardize the process to make the most accurate comparison possible between the cities.

"It became a really wonderful, almost family of scientists and clinicians and city planners and engineers and some artists all working together," said Mason.

Thousands of bacteria and viruses — vast majority not harmful

After collecting over 5,000 samples, the team discovered 10,928 viruses and 748 bacteria new to science. However, Mason adds that these are not potential threats to humans.

"The microbes we found, the vast majority are really just out to get each other rather than out to get us," he said.

His analysis also uncovered widespread antimicrobial resistance genes, but not enough to be of concern. 

"It's less than what you would normally find, say, in a human gut sample or like in a soil sample. So we actually think it's relatively reassuring and that seems to be represent a pretty low risk environment in terms of pathogens."

And while most cities had their own unique collection of microbes, they had many in common as well. The team found 31 non-human microbe species in 97 per cent of the samples, microbes that live and thrive in urban environments.

"These 31 species that we see almost everywhere are this kind of core urban signature," said Mason. "They're kind of hardy and resistant to radiation, resistant to even high levels of carbon dioxide. You know, sometimes they're kind of like a hardy city inhabitants that can take a licking and keep on going."

The research for this paper ended in 2017, but Mason and his team have continued the work and expect to build on it in the future in order to scan for emerging pathogens of concern.

"We have more and more data we're collecting every year, including during the COVID-19 pandemic. And we're also linking all this other data to hunt for new viruses, to hunt for new bacteria in all these additional cities, but also looking in wastewater, having this as a real time microbial tracking system," he said.

Produced and written by Amanda Buckiewicz.