title: Clonal analysis of the microbiota of severe early childhood caries.
abstract: OBJECTIVE
  Severe early childhood caries is a microbial infection that severely compromises the dentition of young children. The aim of this study was to characterize the microbiota of severe early childhood caries.
  
  
  METHODS
  Dental plaque samples from 2- to 6-year-old children were analyzed using 16S rRNA gene cloning and sequencing, and by specific PCR amplification for Streptococcus mutans and Bifidobacteriaceae species.
  
  
  RESULTS
  Children with severe caries (n = 39) had more dental plaque and gingival inflammation than caries-free children (n = 41). Analysis of phylotypes from operational taxonomic unit analysis of 16S rRNA clonal metalibraries from severe caries and caries-free children indicated that while libraries differed significantly (p < 0.0001), there was increased diversity than detected in this clonal analysis. Using the Human Oral Microbiome Database, 139 different taxa were identified. Within the limits of this study, caries-associated taxa included Granulicatella elegans (p < 0.01) and Veillonella sp. HOT-780 (p < 0.01). The species associated with caries-free children included Capnocytophaga gingivalis (p < 0.01), Abiotrophia defectiva (p < 0.01), Lachnospiraceae sp. HOT-100 (p < 0.05), Streptococcus sanguinis (p < 0.05) and Streptococcus cristatus (p < 0.05). By specific PCR, S. mutans (p < 0.005) and Bifidobacteriaceae spp. (p < 0.0001) were significantly associated with severe caries.
  
  
  CONCLUSIONS
  Clonal analysis of 80 children identified a diverse microbiota that differed between severe caries and caries-free children, but the association of S. mutans with caries was from specific PCR analysis, not from clonal analysis, of samples.
authors.affiliation: Department of Molecular Genetics, The Forsyth Institute, Boston, MA 02115, USA.
authors.forename: E
authors.initials: E
authors.lastname: Kanasi
authors.forename: F E
authors.initials: FE
authors.lastname: Dewhirst
authors.forename: N I
authors.initials: NI
authors.lastname: Chalmers
authors.forename: R
authors.initials: R
authors.lastname: Kent
authors.forename: A
authors.initials: A
authors.lastname: Moore
authors.forename: C V
authors.initials: CV
authors.lastname: Hughes
authors.forename: N
authors.initials: N
authors.lastname: Pradhan
authors.forename: C Y
authors.initials: CY
authors.lastname: Loo
authors.forename: A C R
authors.initials: AC
authors.lastname: Tanner
mesh_terms: D058835:Abiotrophia / Q000145:classification; D039903:Actinobacteria / Q000145:classification; D001419:Bacteria / Q000145:classification*; D001644:Bifidobacterium / Q000145:classification; D002206:Capnocytophaga / Q000145:classification; D056568:Carnobacteriaceae / Q000145:classification; D002648:Child; D002675:Child, Preschool; D002999:Clone Cells; D003001:Cloning, Molecular; D003731:Dental Caries / Q000382:microbiology*; D003743:Dental Enamel / Q000382:microbiology; D003773:Dental Plaque / Q000382:microbiology; D003774:Dental Plaque Index; D003789:Dental Pulp Exposure / Q000382:microbiology; D003804:Dentin / Q000382:microbiology; D005260:Female; D005891:Gingivitis / Q000382:microbiology; D006094:Gram-Positive Bacteria / Q000145:classification; D006801:Humans; D008297:Male; D054892:Metagenome; D010512:Periodontal Index; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D013291:Streptococcus / Q000145:classification; D013295:Streptococcus mutans / Q000145:classification; D014678:Veillonella / Q000145:classification
chemical_list: D012336:RNA, Ribosomal, 16S