ArticlePeerJ2018
Taxonomic annotation errors incorrectly assign the family Pseudoalteromonadaceae to the order Vibrionales in Greengenes: implications for microbial community assessments.
Article in PeerJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed, 36 citations in OpenAlex.
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- Missing microbial eukaryotes and misleading meta-omic conclusions.Nature communications · 2024Article
- Possibly pathogenic bacteria in aerosols and foams as a result of aeration remediation in a polluted urban waterway.Folia microbiologica · 2024Article
- Modeling the limits of detection for antimicrobial resistance genes in agri-food samples: a comparative analysis of bioinformatics tools.BMC microbiology · 2024Article
- Challenges and insights in the exploration of the low abundance human ocular surface microbiome.Frontiers in cellular and infection microbiology · 2023Article
- Microbiota of the Rearing Water ofMicrobiology spectrum · 2022Article
- Influence of 16S rRNA reference databases in amplicon-based environmental microbiome research.Biotechnology letters · 2022Article
- RESCRIPt: Reproducible sequence taxonomy reference database management.PLoS computational biology · 2021Article
- Cydrasil 3, a curated 16S rRNA gene reference package and web app for cyanobacterial phylogenetic placement.Scientific data · 2021Article
- Benchmarking the MinION: Evaluating long reads for microbial profiling.Scientific reports · 2020Article
- Long-Term Temperature Stress in the Coral Model Aiptasia Supports the "Anna Karenina Principle" for Bacterial Microbiomes.Frontiers in microbiology · 2019Article
- Microbiome shifts with onset and progression of Sea Star Wasting Disease revealed through time course sampling.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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
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Registered trials
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