The Canine Oral Microbiome

Determining the bacterial composition of the canine oral microbiome is of interest for two primary reasons. First, while the human oral microbiome has been well studied using molecular techniques, the oral microbiomes of other mammals have not been studied in equal depth using culture independent methods. This study allows a comparison of the number of bacterial taxa, based on 16S rRNA-gene sequence comparison, shared between humans and dogs, two divergent mammalian species. Second, canine oral bacteria are of interest to veterinary and human medical communities for understanding their roles in health and infectious diseases. The bacteria involved are mostly unnamed and not linked by 16S rRNA-gene sequence identity to a taxonomic scheme. This manuscript describes the analysis of 5,958 16S rRNA-gene sequences from 65 clone libraries. Full length 16S rRNA reference sequences have been obtained for 353 canine bacterial taxa, which were placed in 14 bacterial phyla, 23 classes, 37 orders, 66 families, and 148 genera. Eighty percent of the taxa are currently unnamed. The bacterial taxa identified in dogs are markedly different from those of humans with only 16.4% of oral taxa are shared between dogs and humans based on a 98.5% 16S rRNA sequence similarity cutoff. This indicates that there is a large divergence in the bacteria comprising the oral microbiomes of divergent mammalian species. The historic practice of identifying animal associated bacteria based on phenotypic similarities to human bacteria is generally invalid. This report describes the diversity of the canine oral microbiome and provides a provisional 16S rRNA based taxonomic scheme for naming and identifying unnamed canine bacterial taxa

Consensus neighbor-joining tree for phyla Proteobacteria and Spirochaetes.

<p>Labeling and methods used are as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036067#pone-0036067-g001" target="_blank">Fig. 1</a>. The Greek letters mark the respective Proteobacteria classes.</p

Consensus neighbor-joining tree for canine oral tax in phyla Actinobacteria, Firmicutes and Tenericutes.

<p>The name of each taxon is followed by Canine Oral Taxon number, reference clone designation, GenBank accession number, and the number of clones out of 5958 that were identified as this taxon. Taxa marked with a filled circle are also found in the human oral cavity. Taxa for which there were 30 or more clones are shown in bold. The tree was constructed with MEGA 4 using the Jukes and Cantor correction neighbor-joining distance matrix. Comparisons with missing data were eliminated pairwise. The numbers to the left of the branches indicate the percent of time the clade was recovered out of 1,000 bootstrap resamplings. Only bootstrap percentages greater than 50 are shown. Roman numerals following a genus name indicate Collins' <i>Clostridia</i> cluster numbers <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036067#pone.0036067-Collins1" target="_blank">[17]</a> The scale bar shows 5% sequence divergence. The encircled numbers mark clades discussed in the text.</p

Consensus neighbor-joining tree for class <i>Clostridia</i>, families <i>Peptostrepto-coccaceae</i> and <i>Lachnospiraceae</i>.

<p>Labeling and methods used are as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036067#pone-0036067-g001" target="_blank">Fig. 1</a>.</p

Bacterial phyla identified in canine subgingival plaque.

a<p>Clones from libraries made using 9–27F (F24) and 1525–1541R (Y36) primers.</p>b<p>Clones from libraries made using expanded coverage 9–27F (F24/AE35) and 1492–1509R (C72) primers.</p>c<p>Clones from libraries made using “Spirochaetes-selective" F24/M98 primer pair.</p>d<p>Clones from libraries made using “Bacteroidetes-selective" F24/F01 primer pair.</p

Consensus neighbor-joining tree for phyla Bacteroidetes, Fusobacteria, Chlorobi, Chloroflexi, Synergistetes and candidate divisions TM7, SR1, GN02 and WPS-2.

<p>Labeling and methods used are as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036067#pone-0036067-g001" target="_blank">Fig. 1</a>.</p