Dataset Information

Oral Microbiome Shifts From Caries-Free to Caries-Affected Status in 3-Year-Old Chinese Children: A Longitudinal Study.

ABSTRACT: As one of the most prevalent human infectious diseases, dental caries results from dysbiosis of the oral microbiota driven by multiple factors. However, most of caries studies were cross-sectional and mainly focused on the differences in the oral microbiota between caries-free (CF) and caries-affected (CA) populations, while little is known about the dynamic shift in microbial composition, and particularly the change in species association pattern during disease transition. Here, we reported a longitudinal study of a 12-month follow-up of a cohort of 3-year-old children. Oral examinations and supragingival plaque collections were carried out at the beginning and every subsequent 6 months, for a total of three time points. All the children were CF at enrollment. Children who developed caries at 6-month follow-up but had not received any dental treatment until the end of the study were incorporated into the CA group. Children who remained CF at the end of the study were incorporated into the CF group. Using Illumina Miseq Sequencing of the 16S rRNA gene, we monitored the shift of supragingival microbiome during caries initiation and progression in children who developed caries over the 12-month study period. Intriguingly, principle coordinates analyses revealed two major shifting patterns in microbial structures during caries initiation and progression in CA group, but not in CF group. Dynamic co-occurring OTU network study showed that compared to CF group, there was significant increase in both number and intensity of correlations between microbial taxa, as well as the formation of tight clusters of specific bacteria in CA group. Furthermore, there were enhanced correlations, positive ones between CA-enriched taxa, and negative ones between CF-enriched and CA-enriched species within CA group. Our data suggested coordinated microbial interactions could be essential to caries pathogenesis. Most importantly, our study indicated that significant microbial shifts occur not only during caries development, but even in the sub-clinical state. Using supragingival microbiome profiles, we were able to construct a caries-onset prediction model with a prediction accuracy of 93.1%. Our study indicated that the microbial shifts prior to the onset of caries might potentially be used for the early diagnosis and prediction of caries.

SUBMITTER: Xu H

PROVIDER: S-EPMC6121080 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Oral Microbiome Shifts From Caries-Free to Caries-Affected Status in 3-Year-Old Chinese Children: A Longitudinal Study.

Xu He H Tian Jing J Hao Wenjing W Zhang Qian Q Zhou Qiong Q Shi Weihua W Qin Man M He Xuesong X Chen Feng F

Frontiers in microbiology 20180828

As one of the most prevalent human infectious diseases, dental caries results from dysbiosis of the oral microbiota driven by multiple factors. However, most of caries studies were cross-sectional and mainly focused on the differences in the oral microbiota between caries-free (CF) and caries-affected (CA) populations, while little is known about the dynamic shift in microbial composition, and particularly the change in species association pattern during disease transition. Here, we reported a l ...[more]

PMID: 30210479

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Project description: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.

Project description:BackgroundCaries in young children has received more and more attention. The study of the oral microbiota may help to understand the polymicrobial etiology of dental caries.ObjectivesTo investigate the diversity and structure of microbial communities in saliva samples from 5-year-old children with versus without dental caries.MethodsA total of 36 saliva samples were collected from 18 children with high caries (HB group) and from 18 children without caries (NB group). Then, 16S rDNA was amplified from bacterial samples using polymerase chain reaction, and high-throughput sequencing was performed using Illumina Novaseq platforms.ResultsSequences were clustered into operational taxonomic units (OTUs), which were distributed among 16 phyla, 26 classes, 56 orders, 93 families, 173 genera, and 218 species. Firmicutes, Bacteroides, Proteobacteria, Actinobacteria, Fusobacteria, Patescibacteria, Epsilonbacteraeota, Cyanobacteria, Acidobacteria and Spirochaetes were basically the same in different groups, but their relative abundances were different. The core microbiome was defined as the species from 218 shared microbial taxa. The alpha diversity test showed that there were no significant differences in microbial abundance and diversity between the high caries and no caries groups. The results from principal coordinate analysis (PCoA) and hierarchical clustering showed that the two groups had similar microorganisms. The biomarkers of different groups were defined by LEfSe analysis to identify potential caries-related and health-related bacteria. Co-occurrence network analysis of dominant genera showed that oral microbial communities in the no caries group were more complex and aggregated than those in the high caries group. Finally, the PICRUSt algorithm was used to predict the function of the microbial communities from saliva samples. The obtained results showed that mineral absorption was greater in the no caries group than in the high caries group. BugBase was used to determine phenotypes present in microbial community samples. The obtained results showed that Streptococcus was greater in the high caries group than in the no caries group.ConclusionFindings of this study provide a comprehensive understanding of the microbiological etiology of dental caries in 5-year-old children and are expected to provide new methods for its prevention and treatment.

Dataset Information

Oral Microbiome Shifts From Caries-Free to Caries-Affected Status in 3-Year-Old Chinese Children: A Longitudinal Study.

Publications

Oral Microbiome Shifts From Caries-Free to Caries-Affected Status in 3-Year-Old Chinese Children: A Longitudinal Study.

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