A global metagenomic map of urban microbiomes and antimicrobial resistance

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, an...

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Bibliographic Details
Published in:Cell 2021-06, Vol.184 (13), p.3376-3393.e17
Main Authors: Danko, David, Neches, Russell Y., Nikolayeva, Olga, Chatziefthimiou, Aspassia D., Crawford, Robert W., Elhaik, Eran, Jang, Soojin, Kelly, Frank J., Kyrpides, Nikos C., Nagarajan, Niranjan, Semmler, Torsten, Suzuki, Haruo, Ugalde, Juan A., Vayndorf, Elena M., Adel, Ait-hamlat, Araujo, Luiza F., Bello, Carla, Bernardes, Juliana, Bitard-Feildel, Tristan, Bolzli, Kevin, Carbone, Alessandra, Castro, Sofia, Cedillo, Jonathan, Chavan, Akash Keluth, Chen, Xiaoqing, Cheung, Daisy, Chiu, Shirley, Dequeker, Chloé, Devi, Monika, Dezem, Felipe S., Dotsenko, Valeriia, Du, Steven, Faiz, Iqra, Fleiss, Aubin, Flores, Denisse, Forero, Juan Carlos, Francis, Aaishah, García, Catalina, Giang, Dao Phuong, Greselle, Charlotte, Haehr, Wolfgang, Hess-Homeier, David, Humphries, Elizabeth, Islam, Sharah, de Souza Gomes Kehdy, Fernanda, Khavari, Mahshid, Kim, Hyung Jun, KoLoMonaco, Giuseppe, Kobko-Litskevitch, Nadezhda, Kozhar, Michael, Kubota, Nanami, Kuklin, Andrii, Lafontaine, Ingrid, de Lamotte, Gerardo, Livia, Mayra Arauco, Loubens, Manon, Manoir, Dimitri, Meydan, Cem, Mignotte, Mathilde, Moitra, Karobi, Molinet, Jennifer, Molomjamts, Orgil-Erdene, Moreno, Mario, Munia, Muntaha, Nakagawa, Mayuko, Nazario, Bryan, Noushmehr, Houtan, O’Hara, Niamh B., Ordioni, Nils, Osuolale, Israel O., Osuolale, Oluwatosin M., Pineda, Lisbeth, Pompa-Hogan, Brianna, Portilla, María Gabriela, Qing, Tao, Ratnanandan, Prashanthi, Read, Timothy D., Robertiello, Alessandro, Rodríguez, Paula, Rosario, Anyelic, Roth, Sandra, Saito, Yoshitaka, Sato, Seisuke, Sato, Ryo, Sayara, Nowshin, Shaaban, Heba, Shari, Aliyah, Silva, Jordana M., Souza, Camila, Sprinsky, Nicolas, Suganuma, Kiyoshi, Sullivan, Jill, Takahashi, Kou, Thomas, Andrew M., Togashi, Takumi, Vacant, Sophie, Vann, Laura E., Wang, Cindy, Wong, Yan Ling, Yeh, George C.
Format: Article
Language:English
Subjects:
AMR
antimicrobial resistance
BASIC BIOLOGICAL SCIENCES
BGC
Biodiversity
Biodiversity and Ecology
Bioinformatics and Systems Biology
Bioinformatik och systembiologi
Biologi
Biological Sciences
built Environment
Databases, Genetic
de novo assembly
Drug Resistance, Bacterial - genetics
Environmental Sciences
global health
Humans
Life Sciences
Medicin och hälsovetenskap
metagenome
Metagenomics
Microbiology
Microbiology and Parasitology
microbiome
Microbiota - genetics
Mikrobiologi
Natural Sciences
Naturvetenskap
NGS
shotgun sequencing
Urban Population
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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. [Display omitted] •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 This systematic, worldwide catalog of urban microbiomes represents a metagenomic atlas important for understanding the ecology, virulence, and antibiotic resistance of city-specific microbial communities.
ISSN:0092-8674
1097-4172
1097-4172
DOI:10.1016/j.cell.2021.05.002