Maturation of the Oral Microbiome in Caries-Free Toddlers: A Longitudinal Study

D. Kahharova, B. W. Brandt, M. J. Buijs, M. Peters, R. Jackson, G. Eckert, B. Katz, M. A. Keels, S. M. Levy, M. Fontana, E. Zaura

Research output: Contribution to journalArticle

1 Scopus citations


Understanding the development of the oral microbiota in healthy children is of great importance to oral and general health. However, limited data exist on a healthy maturation of the oral microbial ecosystem in children. Moreover, the data are biased by mislabeling “caries-free” populations. Therefore, we aimed to characterize the healthy salivary and dental plaque microbiome in young children. Caries-free (ICDAS [International Caries Detection and Assessment System] score 0) children (n = 119) and their primary caregivers were followed from 1 until 4 y of child age. Salivary and dental plaque samples were collected from the children at 3 time points (T1, ~1 y old; T2, ~2.5 y old; and T3, ~4 y old). Only saliva samples were collected from the caregivers. Bacterial V4 16S ribosomal DNA amplicons were sequenced using Illumina MiSeq. The reads were denoised and mapped to the zero-radius operational taxonomic units (zOTUs). Taxonomy was assigned using HOMD. The microbial profiles of children showed significant differences (P = 0.0001) over time. Various taxa increased, including Fusobacterium, Actinomyces, and Corynebacterium, while others showed significant decreases (e.g., Alloprevotella and Capnocytophaga) in their relative abundances over time. Microbial diversity and child-caregiver similarity increased most between 1 and 2.5 y of age while still not reaching the complexity of the caregivers at 4 y of age. The microbiome at 1 y of age differed the most from those at later time points. A single zOTU (Streptococcus) was present in all samples (n = 925) of the study. A large variation in the proportion of shared zOTUs was observed within an individual child over time (2% to 42% of zOTUs in saliva; 2.5% to 38% in dental plaque). These findings indicate that the oral ecosystem of caries-free toddlers is highly heterogeneous and dynamic with substantial changes in microbial composition over time and only few taxa persisting across the 3 y of the study. The salivary microbiome of 4-y-old children is still distinct from that of their caregivers.

Original languageEnglish (US)
Pages (from-to)159-167
Number of pages9
JournalJournal of dental research
Issue number2
StatePublished - Feb 1 2020


  • 16S rRNA gene amplicon sequencing
  • caregiver
  • caries-free children
  • fungal qPCR
  • plaque
  • saliva

ASJC Scopus subject areas

  • Dentistry(all)

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    Kahharova, D., Brandt, B. W., Buijs, M. J., Peters, M., Jackson, R., Eckert, G., Katz, B., Keels, M. A., Levy, S. M., Fontana, M., & Zaura, E. (2020). Maturation of the Oral Microbiome in Caries-Free Toddlers: A Longitudinal Study. Journal of dental research, 99(2), 159-167.