Metagenomic analysis of the canine oral cavity as revealed by high-throughput pyrosequencing of the 16S rRNA gene

Efficient characterization of the canine oral microbiome is critical for understanding the role of oral bacteria in health and for providing insight into early diagnosis and treatment strategies against periodontal disease. To date, characterization has been limited to cloning-based sequencing and conventional culture-based studies, which generally underestimate community diversity as a result of inherent biases in their methodologies. Pyrosequencing, a cloning- and culture-independent sequencing approach, eliminates these elements of bias from the analysis and enables extensive sequencing of microbial populations. In this report, pyrosequencing of the 16S rRNA gene was used to examine oral samples from six healthy dogs in an effort to determine community membership, diversity, and zoonotic implications. Pyrosequencing revealed a mean (SD) of 226 (59) operational taxonomic units (OTUs, 97% similarity), representing 181 genera from 13 bacterial phyla. The phyla Bacteroidetes (60.2%), Proteobacteria (20.8%), Firmicutes (11.4%), Fusobacteria (4.7%), and Spirochaetes (1.7%) predominated. The most commonly identified genera were Porphyromonas (39.2% of sequences), Fusobacterium (4.5%), Capnocytophaga (3.8%), Derxia (3.7%), Moraxella (3.3%), and Bergeyella (2.7%). Fifty-six OTUs, corresponding to 38 unique genus-level identifications, were present in all samples, which supports the concept of a stable core microbiome existing between healthy dogs. Potentially zoonotic and periodontal bacteria were detected in all dogs, and highlights the zoonotic and disease potential of the oral microflora. Results suggest that the canine oral cavity harbors a rich and diverse bacterial community, and exceeds estimates by previous culture- and cloning-based studies.