Seth Commichaux1,2,3, Nidhi Shah1,4, Jay Ghurye1,4, Alexander Stoppel1, Jessica A Goodheart5, Guillermo G Luque6, Michael P Cummings1, Mihai Pop1,4. 1. Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA. 2. Biological Science Graduate Program, University of Maryland, College Park, MD, USA. 3. Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, USA. 4. Department of Computer Science, University of Maryland, College Park, MD, USA. 5. Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92037, USA. 6. Department of Microbiome Science, Max Planck Institute for Developmental Biology, Germany.
Abstract
MOTIVATION: Microbial gene catalogs are data structures that organize genes found in microbial communities, providing a reference for standardized analysis of the microbes across samples and studies. Although gene catalogs are commonly used, they have not been critically evaluated for their effectiveness as a basis for metagenomic analyses. RESULTS: As a case study, we investigate one such catalog, the Integrated Gene Catalog (IGC), however our observations apply broadly to most gene catalogs constructed to date. We focus on both the approach used to construct this catalog and, on its effectiveness, when used as a reference for microbiome studies. Our results highlight important limitations of the approach used to construct the IGC and call into question the broad usefulness of gene catalogs more generally. We also recommend best practices for the construction and use of gene catalogs in microbiome studies and highlight opportunities for future research. AVAILABILITY: All supporting scripts for our analyses can be found on GitHub: https://github.com/SethCommichaux/IGC.git. The supporting data can be downloaded from: https://obj.umiacs.umd.edu/igc-analysis/IGC_analysis_data.tar.gz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Microbial gene catalogs are data structures that organize genes found in microbial communities, providing a reference for standardized analysis of the microbes across samples and studies. Although gene catalogs are commonly used, they have not been critically evaluated for their effectiveness as a basis for metagenomic analyses. RESULTS:As a case study, we investigate one such catalog, the Integrated Gene Catalog (IGC), however our observations apply broadly to most gene catalogs constructed to date. We focus on both the approach used to construct this catalog and, on its effectiveness, when used as a reference for microbiome studies. Our results highlight important limitations of the approach used to construct the IGC and call into question the broad usefulness of gene catalogs more generally. We also recommend best practices for the construction and use of gene catalogs in microbiome studies and highlight opportunities for future research. AVAILABILITY: All supporting scripts for our analyses can be found on GitHub: https://github.com/SethCommichaux/IGC.git. The supporting data can be downloaded from: https://obj.umiacs.umd.edu/igc-analysis/IGC_analysis_data.tar.gz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.