Microbial Signatures of Oral Dysbiosis, Periodontitis and Edentulism Revealed by Gene Meter Methodology

Abstract

Conceptual models suggest 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=25 nt). 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 (R2>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.

Tracing the dynamics of gene transcripts after organismal death

“…In contrast to previous studies, the abundances of mRNA transcripts from the entire D. rerio body, and the brains and livers of M. musculus were assessed through postmortem time. The mRNA transcripts were measured using the 'Gene Meter' approach that precisely reports transcript abundances based on a calibration curve for each microarray probe [6][7][8][9].…”

Gene expression in the twilight of death

“…To facilitate sample comparisons, these approaches require the data to be normalized, which introduce biases that can significantly affect interpretation of the data [21,22]. To avoid these biases, we developed and used the "Gene Meter" approach, which precisely determines the transcript abundances of specific genes in biological samples and minimizes noise in the microarray signal [23][24][25][26]. The reason this approach is precise is because the behavior of every microarray probe is determined by calibration À which is analogous to calibrating a pH meter with buffers.…”

Datasets used to discover the microbial signatures of oral dysbiosis, periodontitis and edentulism in humans

“…That study sequenced amplified 16S rRNA genes obtained from extracting DNA from microbial samples obtained from patients with one of the following conditions: caries, edentulism, periodontitis or health. Another study [1] has analyzed the same amplified rRNA genes using Gene Meter methodology. The Gene Meter methodology was originally described in Refs.…”