Microbial signatures of oral dysbiosis, periodontitis and edentulism revealed by Gene Meter methodology

Abstract

Conceptual models suggest that certain microorganisms (e.g., the "red" complex) are indicative of a specific disease state (e.g., periodontitis); however, recent studies have questioned the validity of these models. Here, the abundances of 500+ microbial species were determined in 16 patients with clinical signs of one of the following oral conditions: periodontitis, established caries, edentulism, and oral health. Our goal was to determine if the abundances of certain microorganisms reflect dysbiosis or a specific clinical condition that could be used as a 'signature' for dental research. Microbial abundances were determined by the analysis of 138,718 calibrated probes using Gene Meter methodology. Each 16S rRNA gene was targeted by an average of 194 unique probes (n=25nt). The calibration involved diluting pooled gene target samples, hybridizing each dilution to a DNA microarray, and fitting the probe intensities to adsorption models. The fit of the model to the experimental data was used to assess individual and aggregate probe behavior; good fits (R>0.90) were retained for back-calculating microbial abundances from patient samples. The abundance of a gene was determined from the median of all calibrated individual probes or from the calibrated abundance of all aggregated probes. With the exception of genes with low abundances (<2 arbitrary units), the abundances determined by the different calibrations were highly correlated (r~1.0). Seventeen genera were classified as 'signatures of dysbiosis' because they had significantly higher abundances in patients with periodontitis and edentulism when contrasted with health. Similarly, 13 genera were classified as 'signatures of periodontitis', and 14 genera were classified as 'signatures of edentulism'. The signatures could be used, individually or in combination, to assess the clinical status of a patient (e.g., evaluating treatments such as antibiotic therapies). Comparisons of the same patient samples revealed high false negatives (45%) for next-generation-sequencing results and low false positives (7%) for Gene Meter results.

Reassessing the Role of Entamoeba gingivalis in Periodontitis

“…Contrariwise, periodontitis, as a biofilm disease (Schaudinn et al, 2009 ), may result from the integration of various causative parameters. Bacteria are among these parameters and the composition of the microbial communities accurately correlates with clinical outcome (Feres et al, 2016 ; Hunter et al, 2016 ). Indeed, some species can be efficiently used as markers for diagnosis (Meuric et al, 2017 ), re-opening ways for considerations about the use of bacterial identification–though in a multi-variate fashion–for epidemiology or treatment follow-up.…”

High-throughput method to test antimicrobial gels against a multispecies oral biofilm

“…They were especially effective in reducing S. gordonii and T. denticola in the biofilm. S. gordonii along with 16 other genera, has been previously classified under ‘signatures of dysbiosis’ due to its predominance in patients with periodontitis and edentulism (Hunter et al , 2016). Also, its role in co-aggregation and metabolic interactions with other periodontal pathogens is well-known (Hajishengallis and Lamont, 2016; Sakanaka et al , 2015).…”

Initial stage of the biofilm formation on the NiTi and Ti6Al4V surface by the sulphur-oxidizing bacteria and sulphate-reducing bacteria

“…It is recognized to be associated with human infections [ 26 , 36 , 45 – 47 ], and are able to survive within oral epithelial cells as well as to modulate the epithelial immune response, leading to initiation and progression of periodontal diseases [ 25 ]. Bacteria of the Thiobacillus genus that belong to the SOB group were only sometimes detected in the human oral cavity [ 21 , 48 , 49 ]. However, it already has been shown that many bacterial genera have been identified by DNA sequencing, but they were not detected using the microarray probes which did not target the 16S rRNA genes specific for the bacteria [ 49 ].…”

“…Bacteria of the Thiobacillus genus that belong to the SOB group were only sometimes detected in the human oral cavity [ 21 , 48 , 49 ]. However, it already has been shown that many bacterial genera have been identified by DNA sequencing, but they were not detected using the microarray probes which did not target the 16S rRNA genes specific for the bacteria [ 49 ].…”