A global metagenomic map of urban microbiomes and antimicrobial resistance
Danko, David
Bezdan, Daniela
Afshin E., Evan
Ahsanuddin, Sofia
Bhattacharya, Chandrima
Butler, Daniel J.
Chng, Kern Rei
Donnellan, Daisy
Hecht, Jochen
Jackson, Katelyn
Kuchin, Katerina
Karasikov, Mikhail
Lyons, Abigail
Mak, Lauren
Meleshko, Dmitry
Mustafa, Harun
Mutai, Beth
Neches, Russell Y.
Ng, Amanda
Nikolayeva, Olga
Nikolayeva, Tatyana
Png, Eileen
Ryon, Krista A.
Sanchez, Jorge L.
Shaaban, Heba
Sierra, Maria A.
Thomas, Dominique
Young, Ben
Abudayyeh, Omar O.
Alicea, Josue
Bhattacharyya, Malay
Blekhman, Ran
Castro-Nallar, Eduardo
Cañas, Ana M.
Chatziefthimiou, Aspassia D.
Crawford, Robert W.
De Filippis, Francesca
Deng, Youping
Desnues, Christelle
Dias-Neto, Emmanuel
Dybwad, Marius
Elhaik, Eran
Ercolini, Danilo
Frolova, Alina
Gankin, Dennis
Gootenberg, Jonathan S.
Graf, Alexandra B.
Green, David C.
Hajirasouliha, Iman
Hastings, Jaden J.A.
Hernandez, Mark
Iraola, Gregorio
Jang, Soojin
Kahles, Andre
Kelly, Frank J.
Knights, Kaymisha
Kyrpides, Nikos C.
Łabaj, Paweł P.
Lee, Patrick K.H.
Leung, Marcus H.Y.
Ljungdahl, Per O.
Mason-Buck, Gabriella
McGrath, Ken
Meydan, Cem
Mongodin, Emmanuel F.
Moraes, Milton Ozorio
Nagarajan, Niranjan
Nieto-Caballero, Marina
Noushmehr, Houtan
Oliveira, Manuela
Ossowski, Stephan
Osuolale, Olayinka O.
Özcan, Orhan
Paez-Espino, David
Rascovan, Nicolás
Richard, Hugues
Rätsch, Gunnar
Schriml, Lynn M.
Song, Le Huu
Suzuki, Haruo
Syndercombe Court, Denise
Tighe, Scott W.
Tong, Xinzhao
Udekwz, Klas I.
Ugalde, Juan A.
Valentine, Brandon
Vassilev, Dimitar I.
Vayndorf, Elena M.
Velavan, Thirumalaisamy P.
Wu, Jun
Zambrano, María M.
Zhu, Jifeng
Zhu, Sibo
Mason, Christopher E.
The intrnational MetaSUB Consortium
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.
