TY - JOUR
T1 - A global metagenomic map of urban microbiomes and antimicrobial resistance
AU - The International MetaSUB Consortium
AU - Danko, David
AU - Bezdan, Daniela
AU - Afshin, Evan E.
AU - Ahsanuddin, Sofia
AU - Bhattacharya, Chandrima
AU - Butler, Daniel J.
AU - Chng, Kern Rei
AU - Donnellan, Daisy
AU - Hecht, Jochen
AU - Jackson, Katelyn
AU - Kuchin, Katerina
AU - Karasikov, Mikhail
AU - Lyons, Abigail
AU - Mak, Lauren
AU - Meleshko, Dmitry
AU - Mustafa, Harun
AU - Mutai, Beth
AU - Neches, Russell Y.
AU - Ng, Amanda
AU - Nikolayeva, Olga
AU - Nikolayeva, Tatyana
AU - Png, Eileen
AU - Ryon, Krista A.
AU - Sanchez, Jorge L.
AU - Shaaban, Heba
AU - Sierra, Maria A.
AU - Thomas, Dominique
AU - Young, Ben
AU - Abudayyeh, Omar O.
AU - Alicea, Josue
AU - Bhattacharyya, Malay
AU - Blekhman, Ran
AU - Castro-Nallar, Eduardo
AU - Cañas, Ana M.
AU - Chatziefthimiou, Aspassia D.
AU - Crawford, Robert W.
AU - De Filippis, Francesca
AU - Deng, Youping
AU - Desnues, Christelle
AU - Dias-Neto, Emmanuel
AU - Dybwad, Marius
AU - Elhaik, Eran
AU - Ercolini, Danilo
AU - Frolova, Alina
AU - Gankin, Dennis
AU - Gootenberg, Jonathan S.
AU - Graf, Alexandra B.
AU - Bartelli, Thais F.
AU - Kwong, Lawrence
AU - Pizzi, Melissa P.
N1 - Publisher Copyright:
© 2021 The Author(s)
PY - 2021/6/24
Y1 - 2021/6/24
N2 - 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.
AB - 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.
KW - AMR
KW - BGC
KW - NGS
KW - antimicrobial resistance
KW - built Environment
KW - de novo assembly
KW - global health
KW - metagenome
KW - microbiome
KW - shotgun sequencing
UR - http://www.scopus.com/inward/record.url?scp=85106902108&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85106902108&partnerID=8YFLogxK
U2 - 10.1016/j.cell.2021.05.002
DO - 10.1016/j.cell.2021.05.002
M3 - Article
C2 - 34043940
AN - SCOPUS:85106902108
SN - 0092-8674
VL - 184
SP - 3376-3393.e17
JO - Cell
JF - Cell
IS - 13
ER -