Taxonomic annotation errors incorrectly assign the family Pseudoalteromonadaceae to the order Vibrionales in Greengenes: Implications for microbial community assessments
- Published
- Accepted
- Subject Areas
- Bioinformatics, Ecology, Marine Biology, Microbiology, Taxonomy
- Keywords
- Greengenes, Taxonomy, 16S rRNA gene, next-generation sequencing, microbial ecology, Alteromonadales, Vibrionales, Pseudoalteromonadaceae, Vibrionaceae, marine microbiology
- Copyright
- © 2018 Lydon et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. Taxonomic annotation errors incorrectly assign the family Pseudoalteromonadaceae to the order Vibrionales in Greengenes: Implications for microbial community assessments. PeerJ Preprints 6:e26824v1 https://doi.org/10.7287/peerj.preprints.26824v1
Abstract
Next-generation sequencing has provided powerful tools to conduct microbial ecology studies. Analysis of community composition relies on annotated databases of curated sequences to provide taxonomic assignments; however, these databases occasionally have errors with implications for downstream analyses. Systemic taxonomic errors were discovered in Greengenes database (v13_5 and 13_8) related to orders Vibrionales and Alteromonadales. These orders have family level annotations that were erroneous at least one taxonomic level, e.g., 100% of sequences assigned to the Pseudoalteromonadaceae family were placed improperly in Vibrionales (rather than Alteromonadales) and >20% of these sequences were assigned to the Pseudoalteromonadaceae family (rather than to Vibrionaceae). Use of this database is common; we identified 67 peer-reviewed papers since 2013 that likely included erroneous annotations, with 20 explicitly stating the incorrect taxonomy. Erroneous assignments using these specific versions of Greengenes can lead to incorrect conclusions, especially in marine systems where these taxa can be common.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Sequence search results in NCBI, RDP, and SILVA for all representative sequences in Greengenes 13_8 labeled within the family Pseudoalteromonadaceae
Tab 1 provides a summary of each Greengenes representative sequence and provides the taxonomic identities for search using NCBI, RDP, and SILVA. The other tabs indicate the raw data search results that are summarized in the first tab.