Genomes From Bacteria Associated with the Canine Oral Cavity: a Test Case for Automated Genome-Based Taxonomic Assignment
Data files
May 04, 2019 version files 15.44 MB
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Actinomyces_16S.nexml
265.40 KB
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Actinomyces_WGS.nexml
182.08 KB
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ActinomycesANI.xlsx
34.66 KB
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All_strains_16S.nexml
3.82 MB
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Atopobium_WGS.nexml
101.16 KB
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Bacillus.ANI.xlsx
13.54 KB
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Bacteroides(Prevotella)_16S.nexml
1.68 MB
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Bacteroides(Prevotella).ANI.xlsx
10.71 KB
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Campylobacter_16S_Type.nexml
33.99 KB
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Campylobacter_WGS.nexml
10.47 KB
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Campylobacter.ANI.xlsx
9.78 KB
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Clostridiales_Type.nexml
242.78 KB
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Comamonadaceae_16S.nexml
2.69 MB
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Comamonadaceae_Type.nexml
124.46 KB
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Comamonadaceae_WGS.nexml
65.36 KB
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Conchiformibius_16S.nexml
17.55 KB
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Desulfovibrio_16S.nexml
108.04 KB
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Desulfovibrio_WGS.nexml
59.70 KB
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Desulfovibrio.ANI.xlsx
10.59 KB
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Erysipelotrichaceae_16S.nexml
95.79 KB
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Erysipelotrichaceae_WGS.nexml
41.76 KB
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Fusobacterium_16S.nexml
280.85 KB
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Fusobacterium_WGS.nexml
118.04 KB
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Fusobacterium.ANI.xlsx
10.81 KB
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Leifsonia.ANI.xlsx
10.01 KB
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Leptotrichia_16S.nexml
51.68 KB
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Leptotrichia_WGS.nexml
21.08 KB
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Leptotrichia.ANI.xlsx
9.89 KB
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Leucobacter_16S.nexml
32.91 KB
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Prevotella_16S.nexml
525.29 KB
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Prevotella_WGS.nexml
211.34 KB
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Prevotella.ANI.xlsx
10.79 KB
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Propionibacteriaceae_16S.nexml
143.41 KB
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Propionibacteriaceae_WGS.nexml
72.80 KB
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Staphylococcus.ANI.xlsx
9.64 KB
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Streptococcus_16S_type.nexml
102.15 KB
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Streptococcus_WGS_OH4692.nexml
3.73 MB
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Streptococcus_WGS_OH953.nexml
198.97 KB
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Streptococcus.ANI.xlsx
19.22 KB
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Tannerella_16S.nexml
244.57 KB
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Tannerella.ANI.xlsx
9.64 KB
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 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.