September 19, 2021

From New York to Tokyo, an atlas of subway microbes

It there are germs and viruses in public transport: this is not surprising, even less since the outbreak of Covid-19 in our lives. What is more is that each city has its own microbial footprint, a signature that is specific to it, as revealed by a study published on May 26 in the scientific journal Cell. The mixture of microorganisms is therefore not the same in Paris, Tokyo, London, Sydney or Rio de Janeiro.

“Give me your shoe and, if I sequence it, I could probably tell you where in the world you are from”, assure the New York Times Christopher E. Mason, the geneticist who led this large-scale research. With this study, which mobilized 900 researchers and volunteers, scientists are now able to identify where a sample comes from with an accuracy of 88%.

If you take the subway in New York, for example, there is a good chance that the cocktail of microorganisms found under your sole is rich in “Checking Carnobacterium “, A lactic acid-producing bacterium very tolerant to low temperatures, notes the journal Science. More generally, the composition of the microbial profiles of transport in cities in North America and Europe differs from those in East Asia, while urban transport closer to the equator is more diverse. microbial than those far from it. Geography, climate or even way of life… Researchers now want to understand what are the factors that give each city its specific “signature”.

“New forms of life”

To arrive at these first findings, researchers from the international consortium MetaSUB (Metagenomics and Metadesign of Subways and Urban Biomes) carried out samples in public transport in nearly sixty cities and on six continents for two years, from 2015 to 2017. Nearly 4,800 samples were collected with swabs rubbed on turnstiles, at ticket machines, on the benches of metro stations, or even on the bars of metro cars. And for cities that do not have an underground network, samples were taken from buses and trains.

Diving deep into the bowels of urban centers, the team of scientists found “An expanse and a treasure of new forms of life”, says Christopher E. Mason, founder of the MetaSUB consortium. “The balustrades and benches of our cities sometimes have as much or even more diversity than what you find in a tropical forest”, adds the professor of genetics, physiology and biophysics at New York University Weill Cornell Medicine.

With these thousands of swabs, the researchers managed to create an atlas of “Microbial ecosystems in urban areas”, available in « open data » : everyone can access it freely. “These data will be analyzed for decades”, rejoices Adam Roberts, microbiologist at the Liverpool School of Tropical Medicine, interviewed by Science. For Erica Hartmann, microbiologist at Northwestern University cited by the New York Times, this research is a tremendous scientific contribution: ” It’s enormous. The number of samples and the geographic diversity of the samples… It’s unprecedented. “

The results of these samples, taken between 2015 and 2017, are available in “open data”.  Here, one of the samples collected in Paris, at the Gare d'Austerlitz.

Not necessarily pathogens

But if the researchers of the international consortium were able to identify 4,246 species of microorganisms already known, their discoveries do not stop there. Nearly 11,000 viruses and 748 bacteria never referenced until now were also identified after extraction and sequencing of the DNA of each sample. A novelty that now requires further research to know their impact on our health. “The Covid-19 crisis has highlighted the need for extensive microbial surveillance”, can we read in the study, which continues:

Microbial genetic mapping of urban environments will provide tools for public health officials to assess risks, map epidemics and genetically characterize problematic species.

Decryption: Water companies start tracking variants in wastewater

The vast majority of the organisms identified present little risk to humans, however, experts say. While the function and source of many of these microbes remains unknown, that’s nothing to worry about, according to David Danko, director of bioinformatics for MetaSUB. Germs are part of our daily lives and we are in constant contact with them. “They belong to the ecosystem in which we live as humans”, he recalls again. “Most of them are not pathogens, they are probably harmless and some may in fact be beneficial”says Noah Fierer, a microbiologist at the University of Colorado at Boulder.

While waiting to learn more, the team of researchers, armed with sterile swabs and collection tubes, continue their harvest in subways around the world. They plan to expand their research into wastewater, we learn New Scientist. This work on the “urban signatures” of microorganisms must continue in order to understand how they influence our health and could, in fine, see themselves used in forensic investigations.

See Sylvestre Huet’s blog, Science2: Why and how to track down the coronavirus in wastewater