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

Autor: Peter A. Noble, M. Colby Hunter, Alex E. Pozhitkov
Rok vydání: 2016
Předmět:
0301 basic medicine
Male
Microbiological Techniques
Oral Health
Bioinformatics
0302 clinical medicine
Abundance (ecology)
RNA
Ribosomal
16S
False positive paradox
False Negative Reactions
Oligonucleotide Array Sequence Analysis
Genetics
0303 health sciences
Microbiota
High-Throughput Nucleotide Sequencing
Nucleic Acid Hybridization
Middle Aged
3. Good health
Molecular Diagnostic Techniques
Calibration
Gene Targeting
Female
DNA Probes
Sequence Analysis
Microbiology (medical)
Adult
DNA
Bacterial
Washington
Dental Plaque
Biology
Dental Caries
Microbiology
03 medical and health sciences
medicine
Humans
False Positive Reactions
Periodontitis
Molecular Biology
Gene
030304 developmental biology
Edentulism
Mouth
Bacteria
Base Sequence
030206 dentistry
Sequence Analysis
DNA
Red complex
medicine.disease
16S ribosomal RNA
030104 developmental biology
Pyrosequencing
Dysbiosis
Zdroj: Journal of microbiological methods. 131
ISSN: 1872-8359
Popis: 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.
Databáze: OpenAIRE
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