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AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata

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dc.contributor.authorLiang, Xiaoen
dc.contributor.authorAkers, Kyleen
dc.contributor.authorKeenum, Ishi M.en
dc.contributor.authorWind, Lauren L.en
dc.contributor.authorGupta, Surajen
dc.contributor.authorChen, Chaoqien
dc.contributor.authorAldaihani, Reemen
dc.contributor.authorPruden, Amyen
dc.contributor.authorZhang, Liqingen
dc.contributor.authorKnowlton, Katharine F.en
dc.contributor.authorXia, Kangen
dc.contributor.authorHeath, Lenwood S.en
dc.contributor.departmentComputer Scienceen
dc.contributor.departmentCivil and Environmental Engineeringen
dc.contributor.departmentBiological Systems Engineeringen
dc.contributor.departmentDairy Scienceen
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2021-03-15T11:57:40Zen
dc.date.available2021-03-15T11:57:40Zen
dc.date.issued2021-03-10en
dc.date.updated2021-03-14T04:12:35Zen
dc.description.abstractBackground Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of antibiotic resistance. However, the ability to compare the distribution and prevalence of antibiotic resistance genes (ARGs) across multiple studies and environments is currently impossible without a complete re-analysis of published datasets. This challenge must be addressed for metagenomics to realize its potential for helping guide effective policy and practice measures relevant to agricultural ecosystems, for example, identifying critical control points for mitigating the spread of antibiotic resistance. Results Here we introduce AgroSeek, a centralized web-based system that provides computational tools for analysis and comparison of metagenomic data sets tailored specifically to researchers and other users in the agricultural sector interested in tracking and mitigating the spread of ARGs. AgroSeek draws from rich, user-provided metagenomic data and metadata to facilitate analysis, comparison, and prediction in a user-friendly fashion. Further, AgroSeek draws from publicly-contributed data sets to provide a point of comparison and context for data analysis. To incorporate metadata into our analysis and comparison procedures, we provide flexible metadata templates, including user-customized metadata attributes to facilitate data sharing, while maintaining the metadata in a comparable fashion for the broader user community and to support large-scale comparative and predictive analysis. Conclusion AgroSeek provides an easy-to-use tool for environmental metagenomic analysis and comparison, based on both gene annotations and associated metadata, with this initial demonstration focusing on control of antibiotic resistance in agricultural ecosystems. Agroseek creates a space for metagenomic data sharing and collaboration to assist policy makers, stakeholders, and the public in decision-making. AgroSeek is publicly-available at https://agroseek.cs.vt.edu/ .en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationBMC Bioinformatics. 2021 Mar 10;22(1):117en
dc.identifier.doihttps://doi.org/10.1186/s12859-021-04035-5en
dc.identifier.urihttp://hdl.handle.net/10919/102720en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderThe Author(s)en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleAgroSeek: a system for computational analysis of environmental metagenomic data and associated metadataen
dc.title.serialBMC Bioinformaticsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

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Journal Articles, BioMed Central and SpringerOpen
Destination Area: Data and Decisions (D&D)
Scholarly Works, Biological Systems Engineering
Scholarly Works, Civil and Environmental Engineering
Scholarly Works, Computer Science
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