Large study of urban microbiomes finds each city has own ‘molecular echo’
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A large global study of urban microbiomes found that each city has its own “molecular echo.”
Researchers completed the largest ever metagenomic study of city microbiomes by analyzing samples collected on public transit in 60 cities around the world.
Source: Adobe Stock.
The study, which was published in Cell, included thousands of bacteria, viruses and archaea that were not in reference databases.
“Every city has its own ‘molecular echo’ of the microbes that define it,” Christopher MasonPhD, a professor of physiology and biophysics at Weill Cornell Medicine and the director of the WorldQuant Initiative for Quantitative Prediction, said in a press release. “If you gave me your shoe, I could tell you with about 90% accuracy the city in the world from which you came.”
Mason and colleagues examined 4,728 samples from public transit air in cities on six continents. Using this data, they created an “atlas” featuring the geospatial profiles of microbial strains, characteristics, antimicrobial resistance markers and genetic elements of 10,928 viruses, 1,302 bacteria, two archaea and 838,532 CRISPR arrays that were not previously included in reference databases.
In an accompanying study, Mason and colleagues analyzed antimicrobial resistance markers from Denver, Hong Kong, London, New York City, Oslo and Stockholm.
They found 468 species-level taxa, 96.5% of which were bacteria. Viruses accounted for 3.21%, fungi accounted for 0.19% and archaea accounted for 0.043%.
Mason and colleagues said that because their results showed that the resistome of public transit air was most similar with soil and human skin, the public transit air microbiome and resistome are mainly sourced from commuters and the outdoors.
“Additional public transit factors (eg, occupancy and ridership, temperature, humidity) should be included in correlative analyses to extend our understanding of how different environmental attributes shape the public transit air microbiome,” the authors wrote. “Longitudinal and seasonal investigations of public transit environments, when integrated with clinical and agricultural microbial community and antibiotics usage data, can broaden our understanding of the roles of time, climate, urbanization rate, ethnicity, population density and antibiotic use may play shaping the public transit air microbiome and resistome at local, regional and global scales.”
“One of the next steps is to synthesize and validate some of these molecules and predicted [biosynthetic gene clusters], and then see what they do medically or therapeutically,” Mason said. “People often think a rainforest is a bounty of biodiversity and new molecules for therapies, but the same is true of a subway railing or bench."
References:
Danko D, et al. Cell. 2021;doi:10.1016/j.cell.2021.05.002.
Leung MHY, et al. Microbiome. 2021;doi:10.1186/s40168-021-01044-7.
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