Open Access Highly Accessed Research article

Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health

Wim Crielaard1, Egija Zaura1, Annemarie A Schuller2, Susan M Huse3, Roy C Montijn4 and Bart JF Keijser4*

Author Affiliations

1 Department of Experimental Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Free University Amsterdam, Gustav Mahlerlaan 3004, 1081 LA Amsterdam, the Netherlands

2 TNO Quality of Life, PO box 2215, 2301 CE Leiden, the Netherlands

3 Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, USA

4 TNO Quality of Life, Business Unit Food and Biotechnology Innovations, Microbial Genomics Group, Utrechtseweg 48, 3704 HE Zeist, the Netherlands

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BMC Medical Genomics 2011, 4:22  doi:10.1186/1755-8794-4-22

Published: 4 March 2011



An understanding of the relation of commensal microbiota to health is essential in preventing disease. Here we studied the oral microbial composition of children (N = 74, aged 3 - 18 years) in natural transition from their deciduous to a permanent dentition and related the microbial profiles to their oral health status. The microbial composition of saliva was assessed by barcoded pyrosequencing of the V5-V6 hypervariable regions of the 16 S rRNA, as well as by using phylogenetic microarrays.


Pyrosequencing reads (126174 reads, 1045 unique sequences) represented 8 phyla and 113 higher taxa in saliva samples. Four phyla - Firmicutes, Bacteriodetes, Proteobacteria and Actinobacteria - predominated in all groups. The deciduous dentition harboured a higher proportion of Proteobacteria (Gammaproteobacteria, Moraxellaceae) than Bacteroidetes, while in all other groups Bacteroidetes were at least as abundant as Proteobacteria. Bacteroidetes (mainly genus Prevotella), Veillonellaceae family, Spirochaetes and candidate division TM7 increased with increasing age, reflecting maturation of the microbiome driven by biological changes with age.

Microarray analysis enabled further analysis of the individual salivary microbiota. Of 350 microarray probes, 156 gave a positive signal with, on average, 77 (range 48-93) probes per individual sample.

A caries-free oral status significantly associated with the higher signal of the probes targeting Porphyromonas catoniae and Neisseria flavescens.


The potential role of P. catoniae and N. flavescens as oral health markers should be assessed in large-scale clinical studies. The combination of both, open-ended and targeted molecular approaches provides us with information that will increase our understanding of the interplay between the human host and its microbiome.