Abstract
SummaryWe 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.
Highlights
The high-density urban environment has historically been home to only a fraction of all people, with the majority living in rural areas or small villages
We collected 4,728 samples from the mass transit systems of 60 cities around the world (Table 1; Table S1). These samples were collected from at least three common surfaces in each mass transit system, with additional optional surfaces collected in each city, and all were subjected to shotgun metagenomic sequencing (125 3 125 PE reads, see STAR Methods)
We use the microbiome of mass transit systems as a proxy for the urban microbiome as a whole and present our key findings here
Summary
The high-density urban environment has historically been home to only a fraction of all people, with the majority living in rural areas or small villages. In the last two decades, the situation has reversed; 55% of the world’s population lives in urban areas (Ritchie and Roser, 2020; United Nations, 2018). Since the introduction of germ theory and John Snow’s work on. 3376 Cell 184, 3376–3393, June 24, 2021 a 2021 The Author(s).
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