Global Genetic Cartography of Urban Metagenomes andAnti-Microbial Resistance
By
David C Danko,
Daniela Bezdan,
Ebrahim Afshinnekoo,
Sofia Ahsanuddin,
Chandrima Bhattacharya,
Daniel J Butler,
Kern Rei Chng,
Daisy Donnellan,
Jochen Hecht,
Katelyn Jackson,
Katerina Kuchin,
Mikhail Karasikov,
Abigail Lyons,
Lauren Mak,
Dmitry Meleshko,
Harun Mustafa,
Beth Mutai,
Russell Y Neches,
Amanda Ng,
Olga Nikolayeva,
Tatyana Nikolayeva,
Eileen Png,
Krista Ryon,
Jorge L Sanchez,
Heba Shaaban,
Maria A Sierra,
Dominique Thomas,
Ben Young,
Josue Alicea,
Malay Bhattacharyya,
Ran Blekhman,
Eduardo Castro-Nallar,
Ana M Canas,
Aspassia D Chatziefthimiou,
Robert W Crawford,
Christelle Desnues,
Francesca De Filippis,
Emmanuel Dias-Neto,
Marius Dybwad,
Eran Elhaik,
Danilo Ercolini,
Alina Frolova,
Alexandra B Graf,
David C Green,
Iman Hajirasouliha,
Mark Hernandez,
Gregorio Iraola,
Soojin Jang,
Andre Kahles,
Kaymisha Knights,
Nikos C Kyrpides,
Pawel P Labaj,
Patrick K. H. Lee,
Marcus H Y Leung,
Gabriella Mason-Buck,
Ken McGrath,
Cem Meydan,
Emmanuel F Mongodin,
Niranjan Nagarajan,
Marina Nieto-Caballero,
Houtan Noushmehr,
Manuela Oliveira,
Stephan Ossowski,
Olayinka O Osuolale,
David Paez-Espino,
Nicolas Rascovan,
Hugues Richard,
Gunnar Ratsch,
Lynn M. Schriml,
Leming Shi,
Teliu Shi,
Le Huu Song,
Haruo Suzuki,
Denise Syndercombe Court,
Scott Tighe,
Klas I Udekwu,
Juan A. Ugalde,
Brandon Valentine,
Dimitar I Vassilev,
Elena Vayndorf,
Maria M. Zambrano,
Jifeng Zhu,
Sibo Zhu,
Christopher Mason
Posted 05 Aug 2019
bioRxiv DOI: 10.1101/724526
We have created a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities across 3 years. This is the first systematic, worldwide study cataloging the urban microbial ecosystem. We identify taxonomically-defined microorganisms collected across three years. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics AMR markers, and novel genetic elements, including 10,928 viral, 1,302 bacteria, and 2 archaea novel species. We identify 4,4204 species of urban microorganisms and a consistent "core" of 31 species found in nearly all samples that is largely distinct from any human commensal microbiome. Profiles of AMR genes show geographic variation in type and density. Together, these results constitute a high-resolution, global metagenomic atlas, which enables the discovery of new genetic components, highlights potential forensic applications, and provides an essential first draft of the global AMR burden of the world's cities.
Download data
- Downloaded 4,300 times
- Download rankings, all-time:
- Site-wide: 2,166
- In microbiology: 159
- Year to date:
- Site-wide: 4,075
- Since beginning of last month:
- Site-wide: 2,526
Altmetric data
Downloads over time
Distribution of downloads per paper, site-wide
PanLingua
News
- 27 Nov 2020: The website and API now include results pulled from medRxiv as well as bioRxiv.
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!