title: The effects of family, dentition, and dental caries on the salivary microbiome.
abstract: Family members share genes, environment, and microbial communities. If there is a strong effect of family on the salivary microbiota, controlling for family will enhance identification of microbial communities associated with cariogenesis. The present study was designed to assess the similarity of the salivary microbiome among families and the association between the salivary microbiome and dental decay taking age into account.
  
  
  
  We selected families (n = 49) participating in the cohort study of oral health conducted by the Center for Oral Health Research in Appalachia. All families where at least two children and at least one parent gave a saliva sample (n = 173) were included. Saliva samples were collected at least 1 hour after eating or drinking. After DNA extraction, the V6 region of the 16s rRNA gene was sequenced. Paired ends were joined using fast length adjustment of short reads, sequences were demultiplexed and filtered using Quantitative Insights Into Microbial Ecology 1.9.0, and taxonomy was assigned using the Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) classifier and sequences aligned with the CORE database using PyNAST.
  
  
  
  The salivary microbiome changed with age and was more similar within families than between families. There was no difference in the diversity of the salivary microbiome by dental decay. After taking into account age and family, signals of dental decay were weak in the saliva, whether examined at the phyla, genus, or operational taxonomic level.
  
  
  
  The salivary microbiome does not appear to be a good indicator of dental caries.
authors.affiliation: Department of Epidemiology, University of Michigan, Ann Arbor. Electronic address: bfoxman@umich.edu.
authors.forename: Betsy
authors.initials: B
authors.lastname: Foxman
authors.affiliation: Department of Epidemiology, University of Michigan, Ann Arbor.
authors.forename: Ting
authors.initials: T
authors.lastname: Luo
authors.affiliation: Department of Epidemiology, University of Michigan, Ann Arbor.
authors.forename: Usha
authors.initials: U
authors.lastname: Srinivasan
authors.affiliation: Department of Epidemiology, University of Michigan, Ann Arbor.
authors.forename: Kirtana
authors.initials: K
authors.lastname: Ramadugu
authors.affiliation: Department of Biology, University of Northern Iowa.
authors.forename: Ai
authors.initials: A
authors.lastname: Wen
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor.
authors.forename: Deborah
authors.initials: D
authors.lastname: Goldberg
authors.affiliation: Departments of Statistics and Biostatistics, University of Michigan, Ann Arbor.
authors.forename: Kerby
authors.initials: K
authors.lastname: Shedden
authors.affiliation: Department of Periodontics, West Virginia University, Morgantown; Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA.
authors.forename: Richard
authors.initials: R
authors.lastname: Crout
authors.affiliation: Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA; Department of Psychology, West Virginia University, Morgantown.
authors.forename: Daniel W
authors.initials: DW
authors.lastname: McNeil
authors.affiliation: Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA.
authors.forename: Robert
authors.initials: R
authors.lastname: Weyant
authors.affiliation: Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA.
authors.forename: Mary L
authors.initials: ML
authors.lastname: Marazita
mesh_terms: D000293:Adolescent; D000328:Adult; D000375:Aging / Q000502:physiology; D001061:Appalachian Region / Q000453:epidemiology; D002648:Child; D002675:Child, Preschool; D015331:Cohort Studies; D003731:Dental Caries / Q000453:epidemiology* / Q000235:genetics; D003817:Dentition; D005190:Family; D005260:Female; D020022:Genetic Predisposition to Disease / Q000453:epidemiology; D006801:Humans; D008297:Male; D064307:Microbiota / Q000235:genetics* / Q000502:physiology; D008875:Middle Aged; D009909:Oral Health; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012307:Risk Factors; D012463:Saliva / Q000382:microbiology; D012469:Salivary Glands / Q000382:microbiology*; D012494:Sampling Studies; D013048:Specimen Handling
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: Dental caries; Family; Salivary microbiome