title: Functional expression of dental plaque microbiota.
abstract: Dental caries remains a significant public health problem and is considered pandemic worldwide. The prediction of dental caries based on profiling of microbial species involved in disease and equally important, the identification of species conferring dental health has proven more difficult than anticipated due to high interpersonal and geographical variability of dental plaque microbiota. We have used RNA-Seq to perform global gene expression analysis of dental plaque microbiota derived from 19 twin pairs that were either concordant (caries-active or caries-free) or discordant for dental caries. The transcription profiling allowed us to define a functional core microbiota consisting of nearly 60 species. Similarities in gene expression patterns allowed a preliminary assessment of the relative contribution of human genetics, environmental factors and caries phenotype on the microbiota's transcriptome. Correlation analysis of transcription allowed the identification of numerous functional networks, suggesting that inter-personal environmental variables may co-select for groups of genera and species. Analysis of functional role categories allowed the identification of dominant functions expressed by dental plaque biofilm communities, that highlight the biochemical priorities of dental plaque microbes to metabolize diverse sugars and cope with the acid and oxidative stress resulting from sugar fermentation. The wealth of data generated by deep sequencing of expressed transcripts enables a greatly expanded perspective concerning the functional expression of dental plaque microbiota.
authors.affiliation: Infectious Diseases, J. Craig Venter Institute Rockville, MD, USA.
authors.forename: Scott N
authors.initials: SN
authors.lastname: Peterson
authors.affiliation: Department of Molecular and Experimental Medicine at the Scripps Research Institute La Jolla, CA, USA.
authors.forename: Tobias
authors.initials: T
authors.lastname: Meissner
authors.affiliation: Department of Molecular and Experimental Medicine at the Scripps Research Institute La Jolla, CA, USA.
authors.forename: Andrew I
authors.initials: AI
authors.lastname: Su
authors.affiliation: Infectious Diseases, J. Craig Venter Institute Rockville, MD, USA.
authors.forename: Erik
authors.initials: E
authors.lastname: Snesrud
authors.affiliation: Infectious Diseases, J. Craig Venter Institute Rockville, MD, USA.
authors.forename: Ana C
authors.initials: AC
authors.lastname: Ong
authors.affiliation: The Scripps Translational Science Institute and Scripps Health La Jolla, CA, USA.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Schork
authors.affiliation: Department of Cariology and Comprehensive Care, College of Dentistry, New York University New York, NY, USA.
authors.forename: Walter A
authors.initials: WA
authors.lastname: Bretz
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001419:Bacteria / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D018441:Biofilms; D002648:Child; D002675:Child, Preschool; D016000:Cluster Analysis; D003731:Dental Caries / Q000209:etiology / Q000473:pathology; D003773:Dental Plaque / Q000209:etiology / Q000382:microbiology*; D024881:Drug Resistance, Bacterial; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D059647:Gene-Environment Interaction; D020022:Genetic Predisposition to Disease; D006801:Humans; D054892:Metagenome; D064307:Microbiota; D018384:Oxidative Stress; D010641:Phenotype; D014158:Transcription, Genetic
chemical_list: D000900:Anti-Bacterial Agents
keywords: biofilm; caries; dental plaque; oral microbiota; transcriptome