Taxonomic annotation errors incorrectly assign the family Pseudoalteromonadaceae to the order Vibrionales in Greengenes: implications for microbial community assessments

PeerJ
Keri Ann Lydon, Erin K Lipp

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 indeed Vibrio spp. but were improperly assigned to the Pseudoalteromonadaceae family (rather than to Vibrionaceae). Use of this database is common; we identified 68 peer-reviewed papers since 2013 that likely included erroneous annotations specifically associated with Vibrionales and Pseudoalteromonadaceae, 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 are commonly encountered as conditiona...Continue Reading

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Citations

Mar 22, 2020·Scientific Reports·Robert Maximilian LeidenfrostRöbbe Wünschiers
Jan 30, 2021·The Journal of Dermatology·Virginia ValentiniAntonio Giovanni Richetta
Jul 1, 2020·Journal of Microbiological Methods·Jade A EzzedineStéphan Jacquet
Nov 9, 2021·PLoS Computational Biology·Michael S RobesonNicholas A Bokulich

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Methods Mentioned

BETA
amplicon sequencing

Software Mentioned

SeqMatch
Unipro UGENE
MUSCLE
PhyloChip
Greengenes
BLAST
SINA
SILVA
QIIME
PhyML

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