Evaluation of 16S rRNA Databases for Taxonomic Assignments Using a Mock Community
Taxonomic identification is fundamental to all microbiology studies. Particularly in metagenomics, which identifies the composition of microorganisms using thousands of sequences, its importance is even greater. Identification is inevitably affected by the choice of database. This study was conducte...
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| Format: | Article |
| Language: | English |
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BioMed Central
2018-12-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2018-16-4-e24.pdf |
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| author | Sang-Cheol Park Sungho Won |
| author_facet | Sang-Cheol Park Sungho Won |
| author_sort | Sang-Cheol Park |
| collection | DOAJ |
| description | Taxonomic identification is fundamental to all microbiology studies. Particularly in metagenomics, which identifies the composition of microorganisms using thousands of sequences, its importance is even greater. Identification is inevitably affected by the choice of database. This study was conducted to evaluate the accuracy of three widely used 16S databases—Greengenes, Silva, and EzBioCloud—and to suggest basic guidelines for selecting reference databases. Using public mock community data, each database was used to assign taxonomy and to test its accuracy. We show that EzBioCloud performs well compared with other existing databases. |
| format | Article |
| id | doaj-art-c9bfbfb8d6624116bf07e508d9054ea8 |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2018-12-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-c9bfbfb8d6624116bf07e508d9054ea82025-02-02T18:43:57ZengBioMed CentralGenomics & Informatics2234-07422018-12-0116410.5808/GI.2018.16.4.e24528Evaluation of 16S rRNA Databases for Taxonomic Assignments Using a Mock CommunitySang-Cheol Park0Sungho Won1 Institute of Health and Environment, Seoul National University, Seoul 08826, Korea Institute of Health and Environment, Seoul National University, Seoul 08826, KoreaTaxonomic identification is fundamental to all microbiology studies. Particularly in metagenomics, which identifies the composition of microorganisms using thousands of sequences, its importance is even greater. Identification is inevitably affected by the choice of database. This study was conducted to evaluate the accuracy of three widely used 16S databases—Greengenes, Silva, and EzBioCloud—and to suggest basic guidelines for selecting reference databases. Using public mock community data, each database was used to assign taxonomy and to test its accuracy. We show that EzBioCloud performs well compared with other existing databases.http://genominfo.org/upload/pdf/gi-2018-16-4-e24.pdfclassificationevaluation studiesgenetic databasesmicrobiotaRNAtechnology assessment16S ribosomal |
| spellingShingle | Sang-Cheol Park Sungho Won Evaluation of 16S rRNA Databases for Taxonomic Assignments Using a Mock Community Genomics & Informatics classification evaluation studies genetic databases microbiota RNA technology assessment 16S ribosomal |
| title | Evaluation of 16S rRNA Databases for Taxonomic Assignments Using a Mock Community |
| title_full | Evaluation of 16S rRNA Databases for Taxonomic Assignments Using a Mock Community |
| title_fullStr | Evaluation of 16S rRNA Databases for Taxonomic Assignments Using a Mock Community |
| title_full_unstemmed | Evaluation of 16S rRNA Databases for Taxonomic Assignments Using a Mock Community |
| title_short | Evaluation of 16S rRNA Databases for Taxonomic Assignments Using a Mock Community |
| title_sort | evaluation of 16s rrna databases for taxonomic assignments using a mock community |
| topic | classification evaluation studies genetic databases microbiota RNA technology assessment 16S ribosomal |
| url | http://genominfo.org/upload/pdf/gi-2018-16-4-e24.pdf |
| work_keys_str_mv | AT sangcheolpark evaluationof16srrnadatabasesfortaxonomicassignmentsusingamockcommunity AT sunghowon evaluationof16srrnadatabasesfortaxonomicassignmentsusingamockcommunity |