AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata
Abstract Background 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 an...
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| Format: | Article |
| Language: | English |
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BMC
2021-03-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-021-04035-5 |
| _version_ | 1818574551980703744 |
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| author | Xiao Liang Kyle Akers Ishi Keenum Lauren Wind Suraj Gupta Chaoqi Chen Reem Aldaihani Amy Pruden Liqing Zhang Katharine F. Knowlton Kang Xia Lenwood S. Heath |
| author_facet | Xiao Liang Kyle Akers Ishi Keenum Lauren Wind Suraj Gupta Chaoqi Chen Reem Aldaihani Amy Pruden Liqing Zhang Katharine F. Knowlton Kang Xia Lenwood S. Heath |
| author_sort | Xiao Liang |
| collection | DOAJ |
| description | Abstract Background 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/ . |
| first_indexed | 2024-12-15T00:28:04Z |
| format | Article |
| id | doaj.art-b329ab4cf26a4b66818574e526ee6a93 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-15T00:28:04Z |
| publishDate | 2021-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-b329ab4cf26a4b66818574e526ee6a932022-12-21T22:42:07ZengBMCBMC Bioinformatics1471-21052021-03-0122111410.1186/s12859-021-04035-5AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadataXiao Liang0Kyle Akers1Ishi Keenum2Lauren Wind3Suraj Gupta4Chaoqi Chen5Reem Aldaihani6Amy Pruden7Liqing Zhang8Katharine F. Knowlton9Kang Xia10Lenwood S. Heath11Department of Computer Science, Virginia Polytechnic Institute and State UniversityInterdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State UniversityDepartment of Civil and Environmental Engineering, Virginia Polytechnic Institute and State UniversityDepartment of Biological Systems Engineering, Virginia Polytechnic Institute and State UniversityInterdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State UniversitySchool of Resource and Environmental Science, Wuhan UniversityDepartment of Computer Science, Virginia Polytechnic Institute and State UniversityDepartment of Civil and Environmental Engineering, Virginia Polytechnic Institute and State UniversityDepartment of Computer Science, Virginia Polytechnic Institute and State UniversityDepartment of Dairy Science, Virginia Polytechnic Institute and State UniversitySchool of Plant and Environmental Science, Virginia Polytechnic Institute and State UniversityDepartment of Computer Science, Virginia Polytechnic Institute and State UniversityAbstract Background 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/ .https://doi.org/10.1186/s12859-021-04035-5MetagenomicsMetadataWeb serverData scienceAntibiotic resistance |
| spellingShingle | Xiao Liang Kyle Akers Ishi Keenum Lauren Wind Suraj Gupta Chaoqi Chen Reem Aldaihani Amy Pruden Liqing Zhang Katharine F. Knowlton Kang Xia Lenwood S. Heath AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata BMC Bioinformatics Metagenomics Metadata Web server Data science Antibiotic resistance |
| title | AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata |
| title_full | AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata |
| title_fullStr | AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata |
| title_full_unstemmed | AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata |
| title_short | AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata |
| title_sort | agroseek a system for computational analysis of environmental metagenomic data and associated metadata |
| topic | Metagenomics Metadata Web server Data science Antibiotic resistance |
| url | https://doi.org/10.1186/s12859-021-04035-5 |
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