Clonal analysis of the microbiota of severe early childhood caries.
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.
Kanasi
E
E
Department of Molecular Genetics, The Forsyth Institute, Boston, MA 02115, USA.
Dewhirst
F E
FE
Chalmers
N I
NI
Kent
R
R
Moore
A
A
Hughes
C V
CV
Pradhan
N
N
Loo
C Y
CY
Tanner
A C R
AC
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
D012336:RNA, Ribosomal, 16S