ArticlePloS one2019
Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Metagenomics reveals seasonal changes of intestinal microbes in Eospalax rothschildi.BMC microbiology · 2025Article
- Non-cyanobacterial diazotrophs support the survival of marine microalgae in nitrogen-depleted environment.Genome biology · 2025Article
- Article
- Prevotella diversity, niches and interactions with the human host.Nature reviews. Microbiology · 2021Review
- GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.Bioinformatics (Oxford, England) · 2019Article
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9 authors.
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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.
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