Metagenomic Analysis of Giant Panda (Ailuropoda melanoleuca) Dental Plaque Microbiome

Abstract

Objectives: Dental plaque microbiome has direct relevance to the etiology of dental diseases such as dental caries and periodontitis. However, there are very little metagenomic data available on the compositions of animal dental plaques. Making use of massively parallel DNA sequencing, the present study focused on the comprehensive characterization of healthy and diseased dental plaque microbiomes of Giant Panda (Ailuropoda melanoleuca) to provide insights to dental health. Methods : To perform comparative metagenomics analysis, dental plaque samples were collected from caries-free and gingivitis-free sites (GP-H), and from the sites with gingivitis (GP-D). Bacterial DNAs were isolated and subjected to metagenomic sequencing using the current generations of Roche 454 Titanium and Illumina GAIIx Sequencers. De novo assembly was carried out using Newbler and the assembled contigs were subjected to BLASTx search (E <0.001) using NCBI non-redundant protein sequence database (13.5 million CDS). Taxonomy classification was made using MEGAN/MG-RAST. Sequences were further cross-compared with the human oral metaogeneomics of dental plaque datasets available at the NOCA sites.

Results: Bacterial species accounted for 10.9% and 11.8% of total sequences in GP-H and GP-D, respectively. Only minor components of viruses (less than 0.02%) and archea (less than 0.003%) were present. Majority of the sequences belonged to the unclassified category, i.e. GP-H (83.4%) and GP-D (81.3%). Eukayotes sequences (5.5% and 6.8%) represented Chordata family, which derived predominately from gingival cells of the Giant Panda. The composition of dental plaque microbiome in Giant Panda was approximately 80% similar to the oral microbiome in humans. Firmucutes bacteria were fewer and proteobacteria were higher in Giant Panda oral microbiome compared to human oral microbiome (percentage of reads).

Conclusion: The present study generates for the first time the data of dental plaque microbiome in Giant Panda. The data would be valuable for future inter-species comparative studies of dental plaque biofilm.

This abstract is based on research that was funded entirely or partially by an outside source: This study was funded by HKU Research Output Prize to CJS and Modern Dental Laboratory/HKU Endowment fund to LJJ, and the HKU University Development Fund administrated by SL