RT Journal Article
SR Electronic
T1 Genomes from Bacteria Associated with the Canine Oral Cavity: a Test Case for Automated Genome-Based Taxonomic Assignment
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 577163
DO 10.1101/577163
A1 David A. Coil
A1 Guillaume Jospin
A1 Aaron E. Darling
A1 Corrin Wallis
A1 Ian J. Davis
A1 Stephen Harris
A1 Jonathan A. Eisen
A1 Lucy J. Holcombe
A1 Ciaran O’Flynn
YR 2019
UL http://biorxiv.org/content/early/2019/03/14/577163.abstract
AB 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 was less subjective, and required far less labor. The primary differences in the remaining taxonomic assignments related to proposed taxonomy changes by the GTDB team.