Microbiota of progressing caries in children

Objectives: Dental caries can progress rapidly in young children. This study compared the microbiota of caries-free (CF) children with children with caries and caries progression. Microbial diversity of samples was assayed using Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS).
Methods: Children 2-6 years-old were recruited from a community dental center directed to underserved populations. Demographics and diet history was by survey. Child caries status (dft) was measured at baseline and 6-monthly to assess caries status and new cavity formation. Bacterial samples were collected at each visit, DNA was purified and sequenced on an Illumina MiSeq with identifications from the sequence-based Probe Seq. Univariate and multivariate analyses examined associations between species/taxa and caries status.
Results: 199 children were recruited, 80% had 6 mo. and 67% had 12 mo. follow-ups. 97 children were CF (mean 4.9yr, 49% boys) and 102 had dft≥1 (mean 5.4yr, 62% boys). New lesions were detected in 41% children. Plaque samples from 94 children were analyzed. There was greater diversity (Shannon Index) in the CF children (dft=0) than dft≥1. Separation in microbial communities by principal component analysis (PCoA) was observed by dft status (0 vs >0) and new lesion development. LEfSe analysis indicated that the principal caries (dft≥1) biomarker was Actinomyces gerencseriae whereas the lead CF biomarker was Neisseria elongata. Univariate analysis selected the same taxa for positive and negative association with caries progression. Other caries-associated taxa included Gemella hemolysans, Veillonella dentocariosi, Actinomyces meyeri and Oribacterium sinus. Scardovia wiggsiae association with caries prediction was p=0.085, whereas S. mutans was not significantly associated with caries measures in these analyses.
Conclusions: Longitudinal monitoring indicated development of new carious lesions. PCoA separates bacterial communities picking out A. gerensceriae with caries progression and N. elogata as a stability marker. These findings indicate that community analyses are important in caries assessment.