The canine oral microbiome: variation in bacterial populations across different niches

Abstract

Background: Microbiota from different niches within the canine oral cavity were profiled and compared. Supragingival plaque and stimulated saliva, were collected alongside samples from the buccal and tongue dorsum mucosa, from 14 Labrador retrievers at three timepoints within a 1 month timeframe. The V3-V4 region of the 16S rRNA gene was sequenced via Illumina MiSeq.

Results: Supragingival plaque microbiota had the highest bacterial diversity and the largest number of significant differences in individual taxa when compared to the other oral niches. Stimulated saliva exhibited the highest variability in microbial composition between dogs, yet the lowest bacterial diversity amongst all the niches. Overall, the bacteria of the buccal and tongue dorsum mucosa were most similar.

Conclusions: The bacterial community profiles indicated three discrete oral niches: soft tissue surfaces (buccal and tongue dorsum mucosa), hard tissue surface (supragingival plaque) and saliva. The ability to distinguish the niches by their microbiota signature offers the potential for microbial biomarkers to be identified in each unique niche for diagnostic use.

Keywords: Buccal; Canine; Microbiome; Oral; Plaque; Saliva; Tongue.

Fig. 1

(a) UpSet plot based on presence/absence of operational taxonomic units where presence > 0.5% average OTU abundance mapped alongside (b) principal component scores with 95% confidence regions from analysis performed on the log₁₀ proportions of operational taxonomic units identified in each of the oral niches: Buccal mucosa (yellow), supragingival plaque (green), saliva (purple) and tongue dorsum mucosa (magenta)

Fig. 2

Average phylogenetic distribution of operational taxonomic units based on sequence reads across the canine oral niches. Asterisks indicate candidate phyla. Central image: © Emily McDougall Art

Fig. 3

(a) Shannon diversity index with 95% confidence intervals (b) plotted against bacterial species indicating significant differences between the four niches within the dogs’ mouth. (b) indicates operational taxomomic units with abundance > 0.5% for at least one of the oral niches, where the size of the circles represent the proportion and the colours represent the phylum

Fig. 4

Proportions of bacterial species per sample discriminated by (a) Gram-stain status and (b) oxygen requirements. Coloured bars indicate mean proportions of OTUs with 95% confidence intervals across the canine oral niches: Buccal mucosa (yellow), supragingival plaque (green), saliva (purple) and tongue dorsum mucosa (magenta). Black bars and asterisks indicate niches with significant differences (all p < 0.001)