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A global metagenomic map of urban microbiomes and antimicrobial resistance

Danko, David ; Bezdan, Daniela ; Afshin, Evan E ; Ahsanuddin, Sofia ; Bhattacharya, Chandrima ; Butler, Daniel J ; Chng, Kern Rei ; Donnellan, Daisy ; Hecht, Jochen and Jackson, Katelyn , et al. (2021) In Cell 184(13). p.17-3393
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... (More)

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.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Cell
volume
184
issue
13
pages
17 - 3393
publisher
Cell Press
external identifiers
  • scopus:85106902108
  • pmid:34043940
ISSN
1097-4172
DOI
10.1016/j.cell.2021.05.002
language
English
LU publication?
yes
id
7304c899-1454-4879-92fc-774e334c8248
date added to LUP
2021-09-20 13:04:58
date last changed
2025-03-25 01:47:07
@article{7304c899-1454-4879-92fc-774e334c8248,
  abstract     = {{<p>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.</p>}},
  author       = {{Danko, David and Bezdan, Daniela and Afshin, Evan E and Ahsanuddin, Sofia and Bhattacharya, Chandrima and Butler, Daniel J and Chng, Kern Rei and Donnellan, Daisy and Hecht, Jochen and Jackson, Katelyn and Kuchin, Katerina and Karasikov, Mikhail and Lyons, Abigail and Mak, Lauren and Meleshko, Dmitry and Mustafa, Harun and Mutai, Beth and Neches, Russell Y and Ng, Amanda and Nikolayeva, Olga and Nikolayeva, Tatyana and Png, Eileen and Ryon, Krista A and Sanchez, Jorge L and Shaaban, Heba and Sierra, Maria A and Thomas, Dominique and Young, Ben and Abudayyeh, Omar O and Alicea, Josue and Bhattacharyya, Malay and Blekhman, Ran and Castro-Nallar, Eduardo and Cañas, Ana M and Chatziefthimiou, Aspassia D and Crawford, Robert W and De Filippis, Francesca and Deng, Youping and Desnues, Christelle and Dias-Neto, Emmanuel and Dybwad, Marius and Elhaik, Eran and Ercolini, Danilo and Frolova, Alina and Gankin, Dennis and Gootenberg, Jonathan S and Graf, Alexandra B and Green, David C and Hajirasouliha, Iman and Wu, Jun and Mason, Christopher E}},
  issn         = {{1097-4172}},
  language     = {{eng}},
  month        = {{06}},
  number       = {{13}},
  pages        = {{17--3393}},
  publisher    = {{Cell Press}},
  series       = {{Cell}},
  title        = {{A global metagenomic map of urban microbiomes and antimicrobial resistance}},
  url          = {{http://dx.doi.org/10.1016/j.cell.2021.05.002}},
  doi          = {{10.1016/j.cell.2021.05.002}},
  volume       = {{184}},
  year         = {{2021}},
}