A global metagenomic map of urban microbiomes and antimicrobial resistance

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Danko, DavidWeill Cornell Medicine (author)

A global metagenomic map of urban microbiomes and antimicrobial resistance

Article/chapterEnglish2021

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Elsevier BV,2021
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LIBRIS-ID:oai:DiVA.org:su-196175
https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-196175URI
https://doi.org/10.1016/j.cell.2021.05.002DOI
http://kipublications.ki.se/Default.aspx?queryparsed=id:147016894URI
https://lup.lub.lu.se/record/7304c899-1454-4879-92fc-774e334c8248URI
https://res.slu.se/id/publ/113028URI

Supplementary language notes

Language:English
Summary in:English

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SwePubSwePub

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Subject category:ref swepub-contenttype
Subject category:art swepub-publicationtype

Notes

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.

Subject headings and genre

NATURVETENSKAP Biologi hsv//swe
NATURAL SCIENCES Biological Sciences hsv//eng
NATURVETENSKAP Biologi Mikrobiologi hsv//swe
NATURAL SCIENCES Biological Sciences Microbiology hsv//eng
NATURVETENSKAP Biologi Bioinformatik och systembiologi hsv//swe
NATURAL SCIENCES Biological Sciences Bioinformatics and Systems Biology hsv//eng

Added entries (persons, corporate bodies, meetings, titles ...)

Bezdan, DanielaUniversity Hospital of Tubingen (author)
Elhaik, EranLund University,Lunds universitet,Molekylär cellbiologi,Biologiska institutionen,Naturvetenskapliga fakulteten,Bioinformatik,Forskargrupper vid Lunds universitet,Molecular Cell Biology,Department of Biology,Faculty of Science,Bioinformatics,Lund University Research Groups,Weill Cornell Medicine(Swepub:lu)er2374el (author)
Ahsanuddin, SofiaIcahn School of Medicine at Mount Sinai (author)
Bhattacharya, Chandrima (author)
Butler, Daniel J.Weill Cornell Medicine Feil Family Brain & Mind Research Institute (author)
Chng, Kern ReiA*Star, Genome Institute of Singapore (GIS) (author)
Donnellan, DaisyWeill Cornell Medicine (author)
Hecht, JochenBarcelona Institute of Science and Technology (author)
Jackson, KatelynWeill Cornell Medicine (author)
Kuchin, KaterinaWeill Cornell Medicine (author)
Karasikov, MikhailChildren's University Hospital, Zurich (author)
Lyons, AbigailWeill Cornell Medicine (author)
Mak, LaurenWeill Cornell Medicine (author)
Meleshko, DmitryWeill Cornell Medicine (author)
Mustafa, HarunChildren's University Hospital, Zurich (author)
Mutai, BethKenya Medical Research Institute - Kisumu (author)
Neches, Russell Y.Joint Genome Institute (JGI) (author)
Ng, AmandaA*Star, Genome Institute of Singapore (GIS) (author)
Nikolayeva, OlgaIndependent Researcher (author)
Nikolayeva, TatyanaIndependent Researcher (author)
Png, EileenA*Star, Genome Institute of Singapore (GIS) (author)
Ryon, Krista A.Weill Cornell Medicine (author)
Sanchez, Jorge L.Weill Cornell Medicine (author)
Shaaban, HebaWeill Cornell Medicine (author)
Sierra, Maria A.Weill Cornell Medicine (author)
Thomas, DominiqueWeill Cornell Medicine (author)
Young, BenWeill Cornell Medicine (author)
Abudayyeh, Omar O.Massachusetts Institute of Technology (author)
Alicea, JosueWeill Cornell Medicine (author)
Bhattacharyya, MalayIndian Statistical Institute, Kolkata (author)
Blekhman, RanUniversity of Minnesota (author)
Castro-Nallar, EduardoAndrés Bello National University (author)
Cañas, Ana M.Weill Cornell Medicine (author)
Chatziefthimiou, Aspassia D. (author)
Crawford, Robert W.California State University (author)
De Filippis, FrancescaUniversity of Naples Federico II (author)
Deng, YoupingUniversity of Hawai'i at Hilo (author)
Desnues, ChristelleMediterranean Institute of Oceanography, Marseille (author)
Dias-Neto, EmmanuelA. C. Camargo Cancer Center (author)
Dybwad, MariusNorwegian Defence Research Establishment (author)
Elhaik, Eran (author)
Ercolini, DaniloUniversity of Naples Federico II (author)
Frolova, AlinaKyiv Academic University (author)
Gankin, DennisMassachusetts Institute of Technology (author)
Gootenberg, Jonathan S.Massachusetts Institute of Technology (author)
Graf, Alexandra B.University of Vienna (author)
Green, David C.King's College London (author)
Hajirasouliha, ImanWeill Cornell Medicine (author)
Hastings, Jaden J. A. (author)
Hernandez, Mark (author)
Iraola, Gregorio (author)
Jang, Soojin (author)
Kahles, Andre (author)
Kelly, Frank J. (author)
Knights, Kaymisha (author)
Kyrpides, Nikos C. (author)
Łabaj, Paweł P. (author)
Lee, Patrick K. H. (author)
Leung, Marcus H. Y. (author)
Ljungdahl, Per O.Stockholms universitet,Institutionen för molekylär biovetenskap, Wenner-Grens institut(Swepub:su)pelju (author)
Mason-Buck, Gabriella (author)
McGrath, Ken (author)
Meydan, Cem (author)
Mongodin, Emmanuel F. (author)
Moraes, Milton Ozorio (author)
Nagarajan, Niranjan (author)
Nieto-Caballero, Marina (author)
Noushmehr, Houtan (author)
Oliveira, Manuela (author)
Ossowski, Stephan (author)
Osuolale, Olayinka O. (author)
Özcan, Orhan (author)
Paez-Espino, David (author)
Rascovan, Nicolás (author)
Richard, Hugues (author)
Rätsch, Gunnar (author)
Schriml, Lynn M. (author)
Semmler, Torsten (author)
Sezerman, Osman U. (author)
Shi, Leming (author)
Shi, Tieliu (author)
Siam, Rania (author)
Song, Le Huu (author)
Suzuki, Haruo (author)
Court, Denise Syndercombe (author)
Tighe, Scott W. (author)
Tong, Xinzhao (author)
Udekwu, KlasSveriges lantbruksuniversitet,Stockholms universitet,Institutionen för molekylär biovetenskap, Wenner-Grens institut,Swedish University of Agricultural Sciences, Sweden,Institutionen för vatten och miljö,Department of Aquatic Sciences and Assessment,Stockholm University(Swepub:su)kudek (author)
Ugalde, Juan A. (author)
Valentine, Brandon (author)
Vassilev, Dimitar (author)
Vayndorf, Elena M. (author)
Velavan, Thirumalaisamy P. (author)
Wu, JunEast China Normal University (author)
Zambrano, Maria M. (author)
Zhu, Jifeng (author)
Zhu, Sibo (author)
Mason, Christopher E. (author)
Weill Cornell MedicineUniversity Hospital of Tubingen (creator_code:org_t)
Sveriges lantbruksuniversitet

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In:Cell: Elsevier BV184:13, s. 3376-33930092-86741097-4172

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By the author/editor: Danko, David; Bezdan, Daniela; Elhaik, Eran; Ahsanuddin, Sofi ...; Bhattacharya, Ch ...; Butler, Daniel J ...; show more...; Chng, Kern Rei; Donnellan, Daisy; Hecht, Jochen; Jackson, Katelyn; Kuchin, Katerina; Karasikov, Mikha ...; Lyons, Abigail; Mak, Lauren; Meleshko, Dmitry; Mustafa, Harun; Mutai, Beth; Neches, Russell ...; Ng, Amanda; Nikolayeva, Olga; Nikolayeva, Taty ...; Png, Eileen; Ryon, Krista A.; Sanchez, Jorge L ...; Shaaban, Heba; Sierra, Maria A.; Thomas, Dominiqu ...; Young, Ben; Abudayyeh, Omar ...; Alicea, Josue; Bhattacharyya, M ...; Blekhman, Ran; Castro-Nallar, E ...; Cañas, Ana M.; Chatziefthimiou, ...; Crawford, Robert ...; De Filippis, Fra ...; Deng, Youping; Desnues, Christe ...; Dias-Neto, Emman ...; Dybwad, Marius; Ercolini, Danilo; Frolova, Alina; Gankin, Dennis; Gootenberg, Jona ...; Graf, Alexandra ...; Green, David C.; Hajirasouliha, I ...; Hastings, Jaden ...; Hernandez, Mark; Iraola, Gregorio; Jang, Soojin; Kahles, Andre; Kelly, Frank J.; Knights, Kaymish ...; Kyrpides, Nikos ...; Łabaj, Paweł P.; Lee, Patrick K. ...; Leung, Marcus H. ...; Ljungdahl, Per O ...; Mason-Buck, Gabr ...; McGrath, Ken; Meydan, Cem; Mongodin, Emmanu ...; Moraes, Milton O ...; Nagarajan, Niran ...; Nieto-Caballero, ...; Noushmehr, Houta ...; Oliveira, Manuel ...; Ossowski, Stepha ...; Osuolale, Olayin ...; Özcan, Orhan; Paez-Espino, Dav ...; Rascovan, Nicolá ...; Richard, Hugues; Rätsch, Gunnar; Schriml, Lynn M.; Semmler, Torsten; Sezerman, Osman ...; Shi, Leming; Shi, Tieliu; Siam, Rania; Song, Le Huu; Suzuki, Haruo; Court, Denise Sy ...; Tighe, Scott W.; Tong, Xinzhao; Udekwu, Klas; Ugalde, Juan A.; Valentine, Brand ...; Vassilev, Dimita ...; Vayndorf, Elena ...; Velavan, Thiruma ...; Wu, Jun; Zambrano, Maria ...; Zhu, Jifeng; Zhu, Sibo; Mason, Christoph ...; show less...

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Microbiology

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Bioinformatics a ...

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