Dataset Information

Microarray analysis of the microflora of root caries in elderly.

ABSTRACT: The present study used a new 16S rRNA-based microarray with probes for over 300 bacterial species to better define the bacterial profiles of healthy root surfaces and root caries (RC) in the elderly. Supragingival plaque was collected from 20 healthy subjects (Controls) and from healthy and carious roots and carious dentin from 21 RC subjects (Patients). Collectively, 179 bacterial species and species groups were detected. A higher bacterial diversity was observed in Controls than in Patients. Lactobacillus casei/paracasei/rhamnosus and Pseudoramibacter alactolyticus were notably associated with most RC samples. Streptococcus mutans was detected more frequently in the infected dentin than in the other samples, but the difference was not significant. Actinomyces was found more frequently in Controls. Thus, species other than Actinomyces and S. mutans may play a role as pathogens of RC. The results from this study were in general agreement with those of our previous study based on 16S rRNA gene sequencing.

SUBMITTER: Preza D

PROVIDER: S-EPMC2713778 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature

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Microarray analysis of the microflora of root caries in elderly.

Preza D D Olsen I I Willumsen T T Boches S K SK Cotton S L SL Grinde B B Paster B J BJ

European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 20081128 5

The present study used a new 16S rRNA-based microarray with probes for over 300 bacterial species to better define the bacterial profiles of healthy root surfaces and root caries (RC) in the elderly. Supragingival plaque was collected from 20 healthy subjects (Controls) and from healthy and carious roots and carious dentin from 21 RC subjects (Patients). Collectively, 179 bacterial species and species groups were detected. A higher bacterial diversity was observed in Controls than in Patients. L ...[more]

PMID: 19039610

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Project description:BackgroundThe studies of the distribution of Actinomyces spp. on carious and non-carious root surfaces have not been able to confirm the association of these bacteria with root caries, although they were extensively implicated as a prime suspect in root caries.ObjectiveThe aim of this study was to observe the gene expression of Actinomyces spp. in the microbiota of root surfaces with and without caries.DesignThe oral biofilms from exposed sound root surface (SRS; n=10) and active root caries (RC; n=30) samples were collected. The total bacterial RNA was extracted, and the mRNA was isolated. Samples with low RNA concentration were pooled, yielding a final sample size of SRS=10 and RC=9. Complementary DNA (cDNA) libraries were prepared and sequenced on an Illumina(®) HiSeq 2500 system. Sequence reads were mapped to eight Actinomyces genomes. Count data were normalized using DESeq2 to analyse differential gene expression applying the Benjamini-Hochberg correction (false discovery rate [FDR]<0.001).ResultsActinomyces spp. had similar numbers of reads (Mann-Whitney U-test; p>0.05), except for Actinomyces OT178 (p=0.001) and Actinomyces gerencseriae (p=0.004), which had higher read counts in the SRS. Genes that code for stress proteins (clp, dnaK, and groEL), enzymes of glycolysis pathways (including enolase and phosphoenolpyruvate carboxykinase), adhesion (Type-2 fimbrial and collagen-binding protein), and cell growth (EF-Tu) were highly - but not differentially (p>0.001) - expressed in both groups. Genes with the most significant upregulation in RC were those coding for hypothetical proteins and uracil DNA glycosylase (p=2.61E-17). The gene with the most significant upregulation in SRS was a peptide ABC transporter substrate-binding protein (log2FC=-6.00, FDR=2.37E-05).ConclusionThere were similar levels of Actinomyces gene expression in both sound and carious root biofilms. These bacteria can be commensal in root surface sites but may be cariogenic due to survival mechanisms that allow them to exist in acid environments and to metabolize sugars, saving energy.

Project description:With the aging of the population, dental caries in the elderly has received increasing attention. A comprehensive study of the oral microbiome is required to understand its polymicrobial etiology. The results of previous studies are limited and remain controversial. In this study, subjects 60 years and older with and without caries were recruited. Unstimulated saliva and dental plaque were collected from each subject and the bacterial 16S rDNA was amplified using PCR and sequenced by Illumina MiSeq high-throughput sequencing. A total of 92 samples were collected from 24 caries patients and 22 healthy controls. Sequences clustered into 147,531 OTUs, representing 16 phyla, 29 classes, 49 orders, 79 families, 149 genera, and 305 species. All predominant phyla, including Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, Actinobacteria, and Saccharibacteria, were largely consistent in different groups, but different relative abundances could be observed. The core microbiome was defined with 246 shared species among groups, which occupied 80.7% of all the species detected. Alpha diversity showed no significant differences in bacterial richness or diversity between caries patients and healthy controls, but distinction existed between samples collected from dental plaque and saliva. Beta diversity analysis was performed by PCoA and hierarchical clustering analysis, showing similar results that microorganisms vary between the two niches. The biomarkers of different groups were defined by LEfSe analysis to identify potential caries-related and health-related bacteria. The co-occurrence analysis of the predominant genera revealed significant interactions among oral microbiota and exhibited more complex and aggregated bacterial correlations in caries-free groups. Finally, the functional prediction of the microbiota present in oral samples was performed by PICRUSt, indicating vigorous microbial metabolism in the oral bacterial community. Our study provides thorough knowledge of the microbiological etiology of elderly individuals with caries and is expected to provide novel methods for its prevention and treatment.

Dataset Information

Microarray analysis of the microflora of root caries in elderly.

Publications

Microarray analysis of the microflora of root caries in elderly.

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