Going beyond testing wastewater! Meet the urban microbiome!
"In the subway: Researchers have taken to swabbing and “mapping” the biome of urban transit systems, hospitals, sewage canals, and other public places—creating an atlas of microorganisms found in mass transit systems around the world."
From the highlights and abstract:
"Highlights
• Cities possess a consistent “core” set of non-human microbes
• Urban microbiomes echo important features of cities and city-life
• Antimicrobial resistance genes are widespread in cities
• Cities contain many novel bacterial and viral species
Summary
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities."
A global metagenomic map of urban microbiomes and antimicrobial resistance (open access)
Graphical abstract
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