Snapshot of the three domains of life in the oral niche

Abstract

The human oral microbiome is a complex microbial community constantly influenced by several external factors such as diet, oral hygiene, lifestyle and antibiotic exposures, to name a few. Hence it may be expected that subjects with different geographical, socioeconomic or ethnic backgrounds will have different oral microbial community structures. Recent studies using next generation sequencing (NGS) have almost exclusively focused on the oral microbiota of individuals from North America or Europe, who have ‘good’ oral health, or common oral diseases such as periodontitis or caries. Very few studies have been done on subjects of Asian lineage. Among Chinese communities, oral diseases such as periodontitis are relatively prevalent; hence it is important to elucidate their oral microbial communities, to identify putative differences. To address this, we analyzed the subgingival plaque of subjects with periodontitis versus periodontitis-free controls using 454 pyrosequencing; targeting hypervariable regions of the 16S rRNA for Eubacteria and Archaea, and the 18S rRNA for the Eukarya. Analysis of the pyrosequencing data revealed that Actinobacteria, Bacteriodetes, Firmicutes, Fusobacteria, Proterobacteria and Spirochaetes were the common phyla recovered from both the periodontitis and periodontitis-free subjects, although in different proportions. Firmicutes was the most abundant phylum recovered from periodontitis-free subjects followed by Actinobacteria. As for the periodontitis subjects, Bacteriodetes was predominant, with the majority of sequences recovered corresponding to Porphyromonas. Furthermore, levels of the genus Treponema were also significantly higher in periodontitis subjects. Only sparse fungi sequences were recovered and Saccharomycetes was more in number among the periodontitis-free subjects. Lastly, Archaea was only evident in the periodontitis subjects and 100% of the sequences recovered were highly similar to Methanobrevibacter oralis. This study gives an overview of the diversity of the three domains of life in the oral micro-niche.