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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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| Published in: | Cell 2021-06, Vol.184 (13), p.3376-3393.e17 |
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| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| cites | cdi_FETCH-LOGICAL-c826t-9d47f0a0f447eb89741e1af95613b6d3379d90ac8b3fd99cb4b7685e5693b8133 |
| container_end_page | 3393.e17 |
| container_issue | 13 |
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| container_title | Cell |
| container_volume | 184 |
| creator | 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. |
| description | 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. |
| doi_str_mv | 10.1016/j.cell.2021.05.002 |
| format | article |
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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.</creator><creatorcontrib>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. ; The International MetaSUB Consortium ; International MetaSUB Consortium ; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States) ; Sveriges lantbruksuniversitet</creatorcontrib><description>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.</description><identifier>ISSN: 0092-8674</identifier><identifier>ISSN: 1097-4172</identifier><identifier>EISSN: 1097-4172</identifier><identifier>DOI: 10.1016/j.cell.2021.05.002</identifier><identifier>PMID: 34043940</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>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</subject><ispartof>Cell, 2021-06, Vol.184 (13), p.3376-3393.e17</ispartof><rights>2021 The Author(s)</rights><rights>Copyright © 2021 The Author(s). Published by Elsevier Inc. 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Kou</creatorcontrib><creatorcontrib>Thomas, Andrew M.</creatorcontrib><creatorcontrib>Togashi, Takumi</creatorcontrib><creatorcontrib>Vacant, Sophie</creatorcontrib><creatorcontrib>Vann, Laura E.</creatorcontrib><creatorcontrib>Wang, Cindy</creatorcontrib><creatorcontrib>Wong, Yan Ling</creatorcontrib><creatorcontrib>Yeh, George C.</creatorcontrib><creatorcontrib>The International MetaSUB Consortium</creatorcontrib><creatorcontrib>International MetaSUB Consortium</creatorcontrib><creatorcontrib>Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)</creatorcontrib><creatorcontrib>Sveriges lantbruksuniversitet</creatorcontrib><title>A global metagenomic map of urban microbiomes and antimicrobial resistance</title><title>Cell</title><addtitle>Cell</addtitle><description>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.</description><subject>AMR</subject><subject>antimicrobial resistance</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>BGC</subject><subject>Biodiversity</subject><subject>Biodiversity and Ecology</subject><subject>Bioinformatics and Systems Biology</subject><subject>Bioinformatik och systembiologi</subject><subject>Biologi</subject><subject>Biological Sciences</subject><subject>built Environment</subject><subject>Databases, Genetic</subject><subject>de novo assembly</subject><subject>Drug Resistance, Bacterial - genetics</subject><subject>Environmental Sciences</subject><subject>global health</subject><subject>Humans</subject><subject>Life Sciences</subject><subject>Medicin och hälsovetenskap</subject><subject>metagenome</subject><subject>Metagenomics</subject><subject>Microbiology</subject><subject>Microbiology and Parasitology</subject><subject>microbiome</subject><subject>Microbiota - genetics</subject><subject>Mikrobiologi</subject><subject>Natural Sciences</subject><subject>Naturvetenskap</subject><subject>NGS</subject><subject>shotgun sequencing</subject><subject>Urban Population</subject><issn>0092-8674</issn><issn>1097-4172</issn><issn>1097-4172</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><recordid>eNp9kl2L1DAUhoso7rj6B7yQ4p3g1Hw2CYgwrK6rDHij3h6SNJ3J2DZD0hnx35va2cUVxotD4OR9zkfyFsVzjCqMcP1mV1nXdRVBBFeIVwiRB8UCIyWWDAvysFggpMhS1oJdFE9S2iGEJOf8cXFBGWJUMbQoPq_KTReM7srejXrjhtB7W_Z6X4a2PESjhzInYjA-9C6VemhyjP6Uy1h0yadRD9Y9LR61ukvu2em8LL5df_h6dbNcf_n46Wq1XlpJ6nGpGiZapFHLmHBGKsGww7pVvMbU1A2lQjUKaSsNbRulrGFG1JI7XitqJKb0sqjmuumn2x8M7KPvdfwFQXtI3cHoOB2QHGBMEZEZUGeBfQwNnPI__BR_QCbyA0vFMrs-y3aHfQ4DczNBEbNSqQxzBkwKBYq0FoRgjtJ8Rdg0yuuz5d777ysIcQPpAFjVWPAsfzfLs7Z3jXXDGHV3f4F7N4PfwiYcQRIqmZr6vZwLhDTmzawfnd3aMAzOjoDzawqhsujVLNr-U_tmtYYphyjlIu93xFlLZm3-_5Sia-8AjGByJexgciVMrgTEIbsyQy_-XuMOubVhFrydBS775uhdnEZ12VONj9OkTfD_q_8b-rbzgQ</recordid><startdate>20210624</startdate><enddate>20210624</enddate><creator>Danko, David</creator><creator>Neches, Russell Y.</creator><creator>Nikolayeva, 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global metagenomic map of urban microbiomes and antimicrobial resistance</title><author>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.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c826t-9d47f0a0f447eb89741e1af95613b6d3379d90ac8b3fd99cb4b7685e5693b8133</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>AMR</topic><topic>antimicrobial resistance</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>BGC</topic><topic>Biodiversity</topic><topic>Biodiversity and Ecology</topic><topic>Bioinformatics and Systems Biology</topic><topic>Bioinformatik och systembiologi</topic><topic>Biologi</topic><topic>Biological Sciences</topic><topic>built Environment</topic><topic>Databases, Genetic</topic><topic>de novo assembly</topic><topic>Drug Resistance, Bacterial - genetics</topic><topic>Environmental Sciences</topic><topic>global health</topic><topic>Humans</topic><topic>Life Sciences</topic><topic>Medicin och hälsovetenskap</topic><topic>metagenome</topic><topic>Metagenomics</topic><topic>Microbiology</topic><topic>Microbiology and Parasitology</topic><topic>microbiome</topic><topic>Microbiota - genetics</topic><topic>Mikrobiologi</topic><topic>Natural Sciences</topic><topic>Naturvetenskap</topic><topic>NGS</topic><topic>shotgun sequencing</topic><topic>Urban Population</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Danko, David</creatorcontrib><creatorcontrib>Neches, Russell Y.</creatorcontrib><creatorcontrib>Nikolayeva, Olga</creatorcontrib><creatorcontrib>Chatziefthimiou, Aspassia D.</creatorcontrib><creatorcontrib>Crawford, Robert W.</creatorcontrib><creatorcontrib>Elhaik, Eran</creatorcontrib><creatorcontrib>Jang, Soojin</creatorcontrib><creatorcontrib>Kelly, Frank J.</creatorcontrib><creatorcontrib>Kyrpides, Nikos C.</creatorcontrib><creatorcontrib>Nagarajan, Niranjan</creatorcontrib><creatorcontrib>Semmler, 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M.</creatorcontrib><creatorcontrib>Pineda, Lisbeth</creatorcontrib><creatorcontrib>Pompa-Hogan, Brianna</creatorcontrib><creatorcontrib>Portilla, María Gabriela</creatorcontrib><creatorcontrib>Qing, Tao</creatorcontrib><creatorcontrib>Ratnanandan, Prashanthi</creatorcontrib><creatorcontrib>Read, Timothy D.</creatorcontrib><creatorcontrib>Robertiello, Alessandro</creatorcontrib><creatorcontrib>Rodríguez, Paula</creatorcontrib><creatorcontrib>Rosario, Anyelic</creatorcontrib><creatorcontrib>Roth, Sandra</creatorcontrib><creatorcontrib>Saito, Yoshitaka</creatorcontrib><creatorcontrib>Sato, Seisuke</creatorcontrib><creatorcontrib>Sato, Ryo</creatorcontrib><creatorcontrib>Sayara, Nowshin</creatorcontrib><creatorcontrib>Shaaban, Heba</creatorcontrib><creatorcontrib>Shari, Aliyah</creatorcontrib><creatorcontrib>Silva, Jordana M.</creatorcontrib><creatorcontrib>Souza, Camila</creatorcontrib><creatorcontrib>Sprinsky, Nicolas</creatorcontrib><creatorcontrib>Suganuma, Kiyoshi</creatorcontrib><creatorcontrib>Sullivan, Jill</creatorcontrib><creatorcontrib>Takahashi, Kou</creatorcontrib><creatorcontrib>Thomas, Andrew M.</creatorcontrib><creatorcontrib>Togashi, Takumi</creatorcontrib><creatorcontrib>Vacant, Sophie</creatorcontrib><creatorcontrib>Vann, Laura E.</creatorcontrib><creatorcontrib>Wang, Cindy</creatorcontrib><creatorcontrib>Wong, Yan Ling</creatorcontrib><creatorcontrib>Yeh, George C.</creatorcontrib><creatorcontrib>The International MetaSUB Consortium</creatorcontrib><creatorcontrib>International MetaSUB Consortium</creatorcontrib><creatorcontrib>Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)</creatorcontrib><creatorcontrib>Sveriges lantbruksuniversitet</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><collection>OSTI.GOV - Hybrid</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><collection>SWEPUB Stockholms universitet full text</collection><collection>SwePub</collection><collection>SwePub Articles</collection><collection>SWEPUB Freely available online</collection><collection>SWEPUB Stockholms universitet</collection><collection>SwePub Articles full text</collection><collection>SWEPUB Lunds universitet full text</collection><collection>SWEPUB Lunds universitet</collection><jtitle>Cell</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Danko, David</au><au>Neches, Russell Y.</au><au>Nikolayeva, Olga</au><au>Chatziefthimiou, Aspassia D.</au><au>Crawford, Robert W.</au><au>Elhaik, Eran</au><au>Jang, Soojin</au><au>Kelly, Frank J.</au><au>Kyrpides, Nikos C.</au><au>Nagarajan, Niranjan</au><au>Semmler, Torsten</au><au>Suzuki, Haruo</au><au>Ugalde, Juan A.</au><au>Vayndorf, Elena M.</au><au>Adel, Ait-hamlat</au><au>Araujo, Luiza F.</au><au>Bello, Carla</au><au>Bernardes, Juliana</au><au>Bitard-Feildel, Tristan</au><au>Bolzli, Kevin</au><au>Carbone, Alessandra</au><au>Castro, Sofia</au><au>Cedillo, Jonathan</au><au>Chavan, Akash Keluth</au><au>Chen, Xiaoqing</au><au>Cheung, Daisy</au><au>Chiu, Shirley</au><au>Dequeker, Chloé</au><au>Devi, Monika</au><au>Dezem, Felipe S.</au><au>Dotsenko, Valeriia</au><au>Du, Steven</au><au>Faiz, Iqra</au><au>Fleiss, Aubin</au><au>Flores, Denisse</au><au>Forero, Juan Carlos</au><au>Francis, Aaishah</au><au>García, Catalina</au><au>Giang, Dao Phuong</au><au>Greselle, Charlotte</au><au>Haehr, Wolfgang</au><au>Hess-Homeier, David</au><au>Humphries, Elizabeth</au><au>Islam, Sharah</au><au>de Souza Gomes Kehdy, Fernanda</au><au>Khavari, Mahshid</au><au>Kim, Hyung Jun</au><au>KoLoMonaco, Giuseppe</au><au>Kobko-Litskevitch, Nadezhda</au><au>Kozhar, Michael</au><au>Kubota, Nanami</au><au>Kuklin, Andrii</au><au>Lafontaine, Ingrid</au><au>de Lamotte, Gerardo</au><au>Livia, Mayra Arauco</au><au>Loubens, Manon</au><au>Manoir, Dimitri</au><au>Meydan, Cem</au><au>Mignotte, Mathilde</au><au>Moitra, Karobi</au><au>Molinet, Jennifer</au><au>Molomjamts, Orgil-Erdene</au><au>Moreno, Mario</au><au>Munia, Muntaha</au><au>Nakagawa, Mayuko</au><au>Nazario, Bryan</au><au>Noushmehr, Houtan</au><au>O’Hara, Niamh B.</au><au>Ordioni, Nils</au><au>Osuolale, Israel O.</au><au>Osuolale, Oluwatosin M.</au><au>Pineda, Lisbeth</au><au>Pompa-Hogan, Brianna</au><au>Portilla, María Gabriela</au><au>Qing, Tao</au><au>Ratnanandan, Prashanthi</au><au>Read, Timothy D.</au><au>Robertiello, Alessandro</au><au>Rodríguez, Paula</au><au>Rosario, Anyelic</au><au>Roth, Sandra</au><au>Saito, Yoshitaka</au><au>Sato, Seisuke</au><au>Sato, Ryo</au><au>Sayara, Nowshin</au><au>Shaaban, Heba</au><au>Shari, Aliyah</au><au>Silva, Jordana M.</au><au>Souza, Camila</au><au>Sprinsky, Nicolas</au><au>Suganuma, Kiyoshi</au><au>Sullivan, Jill</au><au>Takahashi, Kou</au><au>Thomas, Andrew M.</au><au>Togashi, Takumi</au><au>Vacant, Sophie</au><au>Vann, Laura E.</au><au>Wang, Cindy</au><au>Wong, Yan Ling</au><au>Yeh, George C.</au><aucorp>The International MetaSUB Consortium</aucorp><aucorp>International MetaSUB Consortium</aucorp><aucorp>Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)</aucorp><aucorp>Sveriges lantbruksuniversitet</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A global metagenomic map of urban microbiomes and antimicrobial resistance</atitle><jtitle>Cell</jtitle><addtitle>Cell</addtitle><date>2021-06-24</date><risdate>2021</risdate><volume>184</volume><issue>13</issue><spage>3376</spage><epage>3393.e17</epage><pages>3376-3393.e17</pages><issn>0092-8674</issn><issn>1097-4172</issn><eissn>1097-4172</eissn><notes>AC02-05CH11231</notes><notes>USDOE Office of Science (SC)</notes><notes>These authors contributed equally</notes><notes>Lead contact</notes><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.
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•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.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>34043940</pmid><doi>10.1016/j.cell.2021.05.002</doi><orcidid>https://orcid.org/0000-0003-0015-8142</orcidid><orcidid>https://orcid.org/0000-0002-7706-0998</orcidid><orcidid>https://orcid.org/0000-0003-4102-2671</orcidid><orcidid>https://orcid.org/0000-0002-7398-9820</orcidid><orcidid>https://orcid.org/0000-0002-2758-0880</orcidid><orcidid>https://orcid.org/0000-0001-9642-0007</orcidid><orcidid>https://orcid.org/0000-0003-3594-0353</orcidid><orcidid>https://orcid.org/0000-0002-7089-9459</orcidid><orcidid>https://orcid.org/0000-0001-8291-7063</orcidid><orcidid>https://orcid.org/0000-0003-2098-5743</orcidid><orcidid>https://orcid.org/0000-0003-1534-3455</orcidid><orcidid>https://orcid.org/0000-0001-5728-1104</orcidid><orcidid>https://orcid.org/0000-0002-6672-1762</orcidid><orcidid>https://orcid.org/0000-0002-2423-3867</orcidid><orcidid>https://orcid.org/0000-0001-5264-8296</orcidid><orcidid>https://orcid.org/0000-0003-1341-4256</orcidid><orcidid>https://orcid.org/0000-0002-9049-2269</orcidid><orcidid>https://orcid.org/0000-0003-2397-7925</orcidid><orcidid>https://orcid.org/0000-0003-1986-5007</orcidid><orcidid>https://orcid.org/0000-0003-4544-8055</orcidid><orcidid>https://orcid.org/0000-0003-4829-0687</orcidid><orcidid>https://orcid.org/0000-0001-5251-7923</orcidid><orcidid>https://orcid.org/0000-0001-5419-5796</orcidid><orcidid>https://orcid.org/0000-0002-3886-0896</orcidid><orcidid>https://orcid.org/0000-0002-2129-5878</orcidid><orcidid>https://orcid.org/0000-0003-2402-5395</orcidid><orcidid>https://orcid.org/0000-0002-3750-6561</orcidid><orcidid>https://orcid.org/0000-0003-4051-8114</orcidid><orcidid>https://orcid.org/0000-0002-4284-3597</orcidid><orcidid>https://orcid.org/0000-0003-2864-5698</orcidid><orcidid>https://orcid.org/0000-0002-2178-0355</orcidid><orcidid>https://orcid.org/0000-0002-9565-743X</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0092-8674 |
| ispartof | Cell, 2021-06, Vol.184 (13), p.3376-3393.e17 |
| issn | 0092-8674 1097-4172 1097-4172 |
| language | eng |
| recordid | cdi_swepub_primary_oai_slubar_slu_se_113028 |
| source | BACON - Elsevier - GLOBAL_SCIENCEDIRECT-OPENACCESS |
| 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 |
| title | A global metagenomic map of urban microbiomes and antimicrobial resistance |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-09-21T09%3A48%3A43IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-pubmed_swepu&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=A%20global%20metagenomic%20map%20of%20urban%20microbiomes%20and%20antimicrobial%20resistance&rft.jtitle=Cell&rft.au=Danko,%20David&rft.aucorp=The%20International%20MetaSUB%20Consortium&rft.date=2021-06-24&rft.volume=184&rft.issue=13&rft.spage=3376&rft.epage=3393.e17&rft.pages=3376-3393.e17&rft.issn=0092-8674&rft.eissn=1097-4172&rft_id=info:doi/10.1016/j.cell.2021.05.002&rft_dat=%3Cpubmed_swepu%3E34043940%3C/pubmed_swepu%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c826t-9d47f0a0f447eb89741e1af95613b6d3379d90ac8b3fd99cb4b7685e5693b8133%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_id=info:pmid/34043940&rfr_iscdi=true |