Genomes From Bacteria Associated with the Canine Oral Cavity: a Test Case for Automated Genome-Based Taxonomic Assignment

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.