Oral microbiome of deep and shallow dental pockets in chronic periodontitis - PubMed (original) (raw)

Multicenter Study

Oral microbiome of deep and shallow dental pockets in chronic periodontitis

Xiuchun Ge et al. PLoS One. 2013.

Abstract

We examined the subgingival bacterial biodiversity in untreated chronic periodontitis patients by sequencing 16S rRNA genes. The primary purpose of the study was to compare the oral microbiome in deep (diseased) and shallow (healthy) sites. A secondary purpose was to evaluate the influences of smoking, race and dental caries on this relationship. A total of 88 subjects from two clinics were recruited. Paired subgingival plaque samples were taken from each subject, one from a probing site depth >5 mm (deep site) and the other from a probing site depth ≤3mm (shallow site). A universal primer set was designed to amplify the V4-V6 region for oral microbial 16S rRNA sequences. Differences in genera and species attributable to deep and shallow sites were determined by statistical analysis using a two-part model and false discovery rate. Fifty-one of 170 genera and 200 of 746 species were found significantly different in abundances between shallow and deep sites. Besides previously identified periodontal disease-associated bacterial species, additional species were found markedly changed in diseased sites. Cluster analysis revealed that the microbiome difference between deep and shallow sites was influenced by patient-level effects such as clinic location, race and smoking. The differences between clinic locations may be influenced by racial distribution, in that all of the African Americans subjects were seen at the same clinic. Our results suggested that there were influences from the microbiome for caries and periodontal disease and these influences are independent.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Shannon diversity index of genus- (A) and species-level (B) OTUs in the deep and shallow sites.

*, p-value<0.05; **, p-value<0.01.

Figure 2

Figure 2. Genus-level OTUs with >1.0% of abundance in at least one patient in deep and/or shallow sites.

Colors reflect the abundance of OTUs from high (red) to low (black); gray, OTU missing.

Figure 3

Figure 3. Genus-level OTUs significantly different between shallow and deep pockets.

Of 170 genera, 51 showed a statistically significant difference in abundance (%) between shallow and deep sites. Data were statistically analyzed by the two-part model and false discovery rate (FDR). The FDR q-value of 51 genera was <0.05 which represents significant difference between shallow and deep samples. Inserted figure, phylum-level OTUs significantly different between shallow and deep sites; **, p-value <0.01; ***, p-value <0.001.

Figure 4

Figure 4. Clustering analysis of log2 ratio of deep abundance to the shallow at genus level using Hierarchical Trees (HCL).

The data were obtained using log2 ratio (deep abundance/shallow abundance). Both deep and shallow abundance had 0.00001 added due to the many zeros in the samples. The genera present in fewer than 10% of samples were excluded. The genera were clustered into two groups (I and II) and 88 patients were grouped into two types (A and B), each of which contains 2 subtypes (A1 and A2, B1 and B2).

Figure 5

Figure 5. The species associated with dental caries.

The abundances of species-level OTUs were statistically analyzed in 3 levels of dental caries in deep and shallow sites, respectively. The species with a significant difference (α = 0.05) in 3 levels of dental caries were shown. HD_shallow, high decay and shallow site; MD_shallow, moderate decay and shallow site; ND_shallow, non-decay and shallow site; HD_deep, high decay and deep site; MD_ deep, moderate decay and deep site; ND_ deep, non-decay in deep site.

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