A global metagenomic map of urban microbiomes and antimicrobial resistance

The International MetaSUB Consortium

Research output: Contribution to journalArticlepeer-review

13 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)3376-3393.e17
JournalCell
Volume184
Issue number13
DOIs
Publication statusPublished - 2021 Jun 24

Keywords

  • AMR
  • BGC
  • NGS
  • antimicrobial resistance
  • built Environment
  • de novo assembly
  • global health
  • metagenome
  • microbiome
  • shotgun sequencing

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

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