The oral metagenome in health and disease

Abstract

The oral cavity of humans is inhabited by hundreds of bacterial species and some of them have a key role in the development of oral diseases, mainly dental caries and periodontitis. We describe for the first time the metagenome of the human oral cavity under health and diseased conditions, with a focus on supragingival dental plaque and cavities. Direct pyrosequencing of eight samples with different oral-health status produced 1 Gbp of sequence without the biases imposed by PCR or cloning. These data show that cavities are not dominated by Streptococcus mutans (the species originally identified as the ethiological agent of dental caries) but are in fact a complex community formed by tens of bacterial species, in agreement with the view that caries is a polymicrobial disease. The analysis of the reads indicated that the oral cavity is functionally a different environment from the gut, with many functional categories enriched in one of the two environments and depleted in the other. Individuals who had never suffered from dental caries showed an overrepresentation of several functional categories, like genes for antimicrobial peptides and quorum sensing. In addition, they did not have mutans streptococci but displayed high recruitment of other species. Several isolates belonging to these dominant bacteria in healthy individuals were cultured and shown to inhibit the growth of cariogenic bacteria, suggesting the use of these commensal bacterial strains as probiotics to promote oral health and prevent dental caries.

Acid-resistant genes of oral plaque microbiome from the functional metagenomics

“…The two acid-resistant genes obtained in this study were aligned with sequences from two common cariogenic genera, Actinomyces and Haemophilus [30], which represent two of seven dominant cariogenic phyla (Actinobacteria and Proteobacteria) [31]. Bioinformatics analysis found that the ORF in pSL-2–41 encodes two domains (the malic and Malic_M domains) that form the N-terminal region of the malate dehydrogenase protein, but the acid-resistance assay indicated that this fragment is sufficient to allow E. coli to survive in this hostile environment.…”

Functional profiles of coronal and dentin caries in children

“…Previous studies have shown differences in microbial gene expression based on sample site within the oral cavity [13] between health and periodontitis [14] and dental caries [15,16]. Microbial gene expression activity in dentin can differ markedly from that in enamel and closer to the tooth surface [16].…”

Cariogenic microflora and pH in superficial and deep layers of occlusal carious lesions - A metagenomic analysis

“…Atopobium has been reported to be present in varying stages of the disease including early colonization of dental tissues. [2,[22][23][24] Actinomyces is an acidogenic bacteria with 8.3% of total population from phylum Actinobacteria. Similar study have shown that microflora of clinically sound enamel surfaces contains mainly non-mutans Streptococci and Actinomyces, in which acidification is mild and infrequent.…”