Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment

David A. CoilID, Guillaume Jospin, Aaron E. Darling, Corrin Wallis, Ian J. Davis, Stephen Harris, Jonathan A Eisen, Lucy J. Holcombe, Ciaran O'Flynn

Research output: Contribution to journalArticle

Abstract

Taxonomy for bacterial isolates is commonly assigned via sequence analysis. However, the most common sequence-based approaches (e.g. 16S rRNA gene-based phylogeny or whole genome comparisons) are still labor intensive and subjective to varying degrees. Here we present a set of 33 bacterial genomes, isolated from the canine oral cavity. Taxonomy of these isolates was first assigned by PCR amplification of the 16S rRNA gene, Sanger sequencing, and taxonomy assignment using BLAST. After genome sequencing, taxonomy was revisited through a manual process using a combination of average nucleotide identity (ANI), concatenated marker gene phylogenies, and 16S rRNA gene phylogenies. This taxonomy was then compared to the automated taxonomic assignment given by the recently proposed Genome Taxonomy Database (GTDB). We found the results of all three methods to be similar (25 out of the 33 had matching genera), but the GTDB approach required fewer subjective decisions, and required far less labor. The primary differences in the non-identical taxonomic assignments involved cases where GTDB has proposed taxonomic revisions.

Original languageEnglish (US)
Article numbere0214354
JournalPloS one
Volume14
Issue number6
DOIs
StatePublished - Jun 1 2019

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Mouth
Canidae
Taxonomies
mouth
Bacteria
Genes
Genome
taxonomy
genome
dogs
bacteria
Phylogeny
rRNA Genes
testing
ribosomal RNA
Databases
phylogeny
labor
Bacterial Genomes
genes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

CoilID, D. A., Jospin, G., Darling, A. E., Wallis, C., Davis, I. J., Harris, S., ... O'Flynn, C. (2019). Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment. PloS one, 14(6), [e0214354]. https://doi.org/10.1371/journal.pone.0214354

Genomes from bacteria associated with the canine oral cavity : A test case for automated genome-based taxonomic assignment. / CoilID, David A.; Jospin, Guillaume; Darling, Aaron E.; Wallis, Corrin; Davis, Ian J.; Harris, Stephen; Eisen, Jonathan A; Holcombe, Lucy J.; O'Flynn, Ciaran.

In: PloS one, Vol. 14, No. 6, e0214354, 01.06.2019.

Research output: Contribution to journalArticle

CoilID, DA, Jospin, G, Darling, AE, Wallis, C, Davis, IJ, Harris, S, Eisen, JA, Holcombe, LJ & O'Flynn, C 2019, 'Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment', PloS one, vol. 14, no. 6, e0214354. https://doi.org/10.1371/journal.pone.0214354
CoilID, David A. ; Jospin, Guillaume ; Darling, Aaron E. ; Wallis, Corrin ; Davis, Ian J. ; Harris, Stephen ; Eisen, Jonathan A ; Holcombe, Lucy J. ; O'Flynn, Ciaran. / Genomes from bacteria associated with the canine oral cavity : A test case for automated genome-based taxonomic assignment. In: PloS one. 2019 ; Vol. 14, No. 6.
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