Microbiome city maps

Have you ever wondered which city is the most microbially diverse in the world? It is a strange, if interesting, question. How would one go about finding out? Given that millions of people are in transit every day and interact with many surfaces, it seems reasonable to assume that a good location to kick off such a study would be in transportation systems.

A group of researchers led by Christopher Mason at Weill Cornell Medical College have chosen transportation hubs as locations for their study of microbe populations in urban environments.

For 3 years, the Metagenomics and Metadesign of Subways and Urban Biomes (MetaSUB) International Consortium—which Mason founded in 2015—collected more than 4,700 samples from subways, trams, and buses in 60 cities around the world to gain a better understanding of their microbial diversity.

In a prior study, Mason had concentrated his research efforts in New York City and built a metagenomic map that geographically categorized the variety of microorganisms in the city. At that time, Mason cited forensic applications, health management, and long-term disease surveillance in New York City as potential future uses of the map and its supporting data. But that study and others like it were limited because they only studied a small number of cities on a handful of occasions.

Together, consortium members were able to cast a wider net. To create a global atlas of the microbiome, MetaSUB researchers collected and aggregated DNA data from thousands of samplesfrom 60 cities around the world, from Auckland, New Zealand to Zurich.

So what does the atlas tell us? What the researchers discovered is fascinating. First, about 45% of the DNA sequences of the samples collected did not match any known species—meaning that close to 11,000 viruses and more than 1,300 bacteria detected were new to science.

Second, there is a “consistent urban microbiome core . . . which is supplemented by geographic variation . . . and microbial signatures based on the specific attributes of a city,” Mason and his collaborators write in a preprint, which hasn’t been peer-reviewed (bioRxiv 2020, DOI: 10.1101/724526). Each city has its own unique fingerprint.

To translate this into numbers, it means that 97% of the samples share a set of 31 species—a “core” urban microbiome. Seventy percent of samples shared a further 1,145 species—a group made up of bacteria commonly found in skin, soil, water, and dust. But the researchers also detected species that gave each location its own genetic profile. The samples are geographically specific, and researchers can predict with 88% accuracy which city they came from by using the cities’ fingerprint.

In addition to providing this new city-specific source-tracking application, the data collected can help us understand how antimicrobial resistance is transmitted in urban environments. The researchers analyzed the patterns of antimicrobial-resistant (AMR) genes and found that “there was uneven distribution of AMR genes across cities and that fewer antimicrobial-resistant genes were identified in samples from Oceania and the Middle East,” which may suggest different levels of antibiotic use across the different regions. The researchers were also able to quantify how the microbial diversity of the samples is affected by climate and latitude: samples show greater diversity near the equator and “are estimated to lose 6.9672 species for each degree of latitude away from the equator.”

The next time you wander around your city enjoying the sights and what surrounds you at the macrolevel, you can now learn more about what’s around you at the microlevel—provided your city is one of the 60 included in the study. Discover your city’s microbiome at metasub.org/map/.

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