Avoiding Pandemic Fears in the Subway and Conquering the Platypus

ABSTRACT Metagenomics is increasingly used not just to show patterns of microbial diversity but also as a culture-independent method to detect individual organisms of intense clinical, epidemiological, conservation, forensic, or regulatory interest. A widely reported metagenomic study of the New Yor...

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Autores principales:	A. Gonzalez, Y. Vázquez-Baeza, J. B. Pettengill, A. Ottesen, D. McDonald, R. Knight
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2016
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/abfcaa9e974342fbb81f00d0cba1faa6
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spelling	oai:doaj.org-article:abfcaa9e974342fbb81f00d0cba1faa62021-12-02T19:45:29ZAvoiding Pandemic Fears in the Subway and Conquering the Platypus10.1128/mSystems.00050-162379-5077https://doaj.org/article/abfcaa9e974342fbb81f00d0cba1faa62016-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00050-16https://doaj.org/toc/2379-5077ABSTRACT Metagenomics is increasingly used not just to show patterns of microbial diversity but also as a culture-independent method to detect individual organisms of intense clinical, epidemiological, conservation, forensic, or regulatory interest. A widely reported metagenomic study of the New York subway suggested that the pathogens Yersinia pestis and Bacillus anthracis were part of the “normal subway microbiome.” In their article in mSystems, Hsu and collaborators (mSystems 1(3):e00018-16, 2016, http://dx.doi.org/10.1128/mSystems.00018-16 ) showed that microbial communities on transit surfaces in the Boston subway system are maintained from a metapopulation of human skin commensals and environmental generalists and that reanalysis of the New York subway data with appropriate methods did not detect the pathogens. We note that commonly used software pipelines can produce results that lack prima facie validity (e.g., reporting widespread distribution of notorious endemic species such as the platypus or the presence of pathogens) but that appropriate use of inclusion and exclusion sets can avoid this issue.A. GonzalezY. Vázquez-BaezaJ. B. PettengillA. OttesenD. McDonaldR. KnightAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmSystems, Vol 1, Iss 3 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 A. Gonzalez Y. Vázquez-Baeza J. B. Pettengill A. Ottesen D. McDonald R. Knight Avoiding Pandemic Fears in the Subway and Conquering the Platypus
description	ABSTRACT Metagenomics is increasingly used not just to show patterns of microbial diversity but also as a culture-independent method to detect individual organisms of intense clinical, epidemiological, conservation, forensic, or regulatory interest. A widely reported metagenomic study of the New York subway suggested that the pathogens Yersinia pestis and Bacillus anthracis were part of the “normal subway microbiome.” In their article in mSystems, Hsu and collaborators (mSystems 1(3):e00018-16, 2016, http://dx.doi.org/10.1128/mSystems.00018-16 ) showed that microbial communities on transit surfaces in the Boston subway system are maintained from a metapopulation of human skin commensals and environmental generalists and that reanalysis of the New York subway data with appropriate methods did not detect the pathogens. We note that commonly used software pipelines can produce results that lack prima facie validity (e.g., reporting widespread distribution of notorious endemic species such as the platypus or the presence of pathogens) but that appropriate use of inclusion and exclusion sets can avoid this issue.
format	article
author	A. Gonzalez Y. Vázquez-Baeza J. B. Pettengill A. Ottesen D. McDonald R. Knight
author_facet	A. Gonzalez Y. Vázquez-Baeza J. B. Pettengill A. Ottesen D. McDonald R. Knight
author_sort	A. Gonzalez
title	Avoiding Pandemic Fears in the Subway and Conquering the Platypus
title_short	Avoiding Pandemic Fears in the Subway and Conquering the Platypus
title_full	Avoiding Pandemic Fears in the Subway and Conquering the Platypus
title_fullStr	Avoiding Pandemic Fears in the Subway and Conquering the Platypus
title_full_unstemmed	Avoiding Pandemic Fears in the Subway and Conquering the Platypus
title_sort	avoiding pandemic fears in the subway and conquering the platypus
publisher	American Society for Microbiology
publishDate	2016
url	https://doaj.org/article/abfcaa9e974342fbb81f00d0cba1faa6
work_keys_str_mv	AT agonzalez avoidingpandemicfearsinthesubwayandconqueringtheplatypus AT yvazquezbaeza avoidingpandemicfearsinthesubwayandconqueringtheplatypus AT jbpettengill avoidingpandemicfearsinthesubwayandconqueringtheplatypus AT aottesen avoidingpandemicfearsinthesubwayandconqueringtheplatypus AT dmcdonald avoidingpandemicfearsinthesubwayandconqueringtheplatypus AT rknight avoidingpandemicfearsinthesubwayandconqueringtheplatypus
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Avoiding Pandemic Fears in the Subway and Conquering the Platypus

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