16S rRNA gene-based metagenomic analysis identifies a novel bacterial co-prevalence pattern in dental caries

Abstract

Objective:To identify the prevalence of acidogenic and nonacidogenic bacteria in patients with polycaries lesions, and to ascertain caries specific bacterial prevalence in relation to noncaries controls.Materials and Methods:Total genomic DNA extracted from saliva of three adults and four children from the same family were subjected to 16S rRNA gene sequencing analysis on a next generation sequencer, the PGS-Ion Torrent. Those bacterial genera with read counts > 1000 were considered as significant in each of the subject and used to associate the occurrence with caries.Results and Conclusion:Sequencing analysis indicated a higher prevalence of Streptococcus, Rothia, Granulicatella, Gemella, Actinomyces, Selenomonas, Haemophilus and Veillonella in the caries group relative to controls. While higher prevalence of Streptococcus, Rothia and Granulicatella were observed in all caries samples, the prevalence of others was observable in 29–57% of samples. Interestingly, Rothia and Selenomonas, which are known to occur within anaerobic environments of dentinal caries and subgingival plaque biofilms, were seen in the saliva of these caries patients. Taken together, the study has identified for the first time a unique co-prevalence pattern of bacteria in caries patients that may be explored as distinct caries specific bacterial signature to predict cariogenesis in high-risk primary and mixed dentition age groups.

Host Genetic Control of the Oral Microbiome in Health and Disease

“…Moreover, the realization that there remain wild-type protective taxa that may be lost with time and environmental influences, offers clues for developing potential prevention or treatment strategies based on microbial agents. These data are also consistent with complex ecological interactions and metabolic crosstalk among multiple strains underlying dental caries_(Gross et al ., 2012; Jagathrakshakan et al ., 2015; Marsh, 2003). The microbial ecology of dental caries may be highly individualized, rather than defined by health and disease ecotypes or single-microbe etiology across populations.…”

Options and Limitations in Clinical Investigation of Bacterial Biofilms

“…This combinatorial approach does not require genetic sequences, thus worthily replacing microarrays. RNA-seq analyses revealed the proportion of the dormant cell subpopulation within the bacterial biomass of S. epidermidis and the coexistence of unknown bacterial species in oral cavity pathogenesis (183)(184)(185)(186). The heterogeneous, noncrystalline, and insoluble biofilm extracellular matrix is a rather perplexing assembly.…”

Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children

“…Typically, studies using NGS to characterize microbial communities target one or more regions of the16S rRNA gene, which due to their hypervariability serve as good markers of bacterial taxa in samples. This approach has recently been used in a series of studies to explore microbiomes of dental caries [12][13][14][15], providing better insight into the diversity of the microbial community associated with dental caries. And despite methodological differences among these studies in terms of sampling (saliva vs. supragingival plaque vs. carious dentine), hypervariable regions selected for sequencing and the bioinformatic analysis pipeline used, a number of taxa consistently showed association with dental caries, including, S. mutans, Lactobacillus spp., Propionibacterium spp., Veillonella spp., and Atopobium spp.…”