The Oral Microbiome in the Elderly With Dental Caries and Health

Abstract

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.

Keywords: aged; biodiversity; dental caries; dental plaque; high-throughput nucleotide sequencing; microbiota; saliva.

Figure 1

The phylogenetic tree of the 50 most abundant genera. Each branch represents a taxon, the length shows phylogenic distances between two taxa, and different colors represent different phyla. The bar plot on the right side shows the relative abundance of each genus in four groups.

Figure 2

The distributions of the predominant bacteria. (A) Results at the phylum level. (B) Results at the genus level. The predominant taxa (relative abundance >2% on average) are shown.

Figure 3

Wilcoxon rank-sum test bar plot on genus level. (A) Results of the CP and TP groups. (B) Results of the CS and TS groups. ^*Represents a significant difference (P < 0.05).

Figure 4

Venn diagram at the species level. Different colors represent different groups. The overlaps represent the common taxa between groups, and the non-overlapping portions represent unique taxa in each group.

Figure 5

PCoA based on Bray-Curtis distances at the OTU level at 97% identity. Each sample is represented by a dot. Circles in different colors represent different groups. PC1 explained 22.28% of the variation observed, and PC2 explained 10.83% of the variation.

Figure 6

The potential biomarkers were defined by LEfSe. (A,B) Cladogram for taxonomic representation of significant differences between caries-active and caries-free groups. The colored nodes from the inner to the outer circles represent taxa from the phylum to genus level. The significantly different taxa are signified by different colors representing the four groups. (C,D) Histogram of the LDA scores for differentially abundant features among groups. The threshold on the logarithmic LDA score for discriminative features was set to 3.0.

Figure 7

Network analysis showed interactions of 20 richest genera (|SpearmanCoef| > 0.8 and P < 0.01). (A) Bacterial interactions in dental plaque. (B) Bacterial interactions in saliva. (C) Bacterial interactions of four different groups. The size of the node is proportional to the genera abundance. Node color corresponds to phylum taxonomic classification. Edge color represents positive (red) and negative (green) correlations.

Figure 8

Function prediction by PICRUSt. (A) The compositions of COG function in the four groups. (B) The abundance of COG function in all samples.