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.
Highlights
Another example of the importance of accurate pathogen identification from nextgeneration sequencing data is the ability to detect Salmonella from fresh produce
To demonstrate how the problem of confirming the presence of specific taxa in metagenomic samples can be addressed, we created Platypus Conquistador, a BSDlicensed Python package based on BLAST (4) and SortMeRNA (5)
Platypus Conquistador confirms the presence or absence of a taxon of interest within shotgun metagenomic datasets by relying on two reference sequence databases: an inclusion database, which includes the sequences of interest (e.g., Salmonella), and an exclusion database, which includes any known sequence background
Summary
A. Gonzalez,a Y. Vázquez-Baeza,b J. B. Pettengill,c A. Ottesen,c D. McDonald,d R. Knighta,b Department of Pediatrics, University of California San Diego, San Diego, California, USAa; Department of Computer Science and Engineering, University of California San Diego, San Diego, California, USAb; Food and Drug Administration, Center for Food Safety and Applied Nutrition (CFSAN), College Park, Maryland, USAc; Institute for Systems Biology, Seattle, Washington, USAd
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