The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation

Abstract

The goals of this study were to better understand the ecology of oral subgingival communities in health and periodontitis and elucidate the relationship between inflammation and the subgingival microbiome. Accordingly, we used 454-pyrosequencing of 16S rRNA gene libraries and quantitative PCR to characterize the subgingival microbiome of 22 subjects with chronic periodontitis. Each subject was sampled at two sites with similar periodontal destruction but differing in the presence of bleeding, a clinical indicator of increased inflammation. Communities in periodontitis were also compared with those from 10 healthy individuals. In periodontitis, presence of bleeding was not associated with different a-diversity or with a distinct microbiome, however, bleeding sites showed higher total bacterial load. In contrast, communities in health and periodontitis largely differed, with higher diversity and biomass in periodontitis. Shifts in community structure from health to periodontitis resembled ecological succession, with emergence of newly dominant taxa in periodontitis without replacement of primary health-associated species. That is, periodontitis communities had higher proportions of Spirochetes, Synergistetes, Firmicutes and Chloroflexi, among other taxa, while the proportions of Actinobacteria, particularly Actinomyces, were higher in health. Total Actinomyces load, however, remained constant from health to periodontitis. Moreover, an association existed between biomass and community structure in periodontitis, with the proportion of specific taxa correlating with bacterial load. Our study provides a global-scale framework for the ecological events in subgingival communities that underline the development of periodontitis. The association, in periodontitis, between inflammation, community biomass and community structure and their role in disease progression warrant further investigation.

Dysbiosis and Alterations in Predicted Functions of the Subgingival Microbiome in Chronic Periodontitis

“…Raw sequencing reads were obtained from three other studies: the HMP (42), Griffen et al (30), and Abusleme et al (31). The reads were downloaded from the HMP DACC website and the Sequence Read Archive (SRA) (SRA accession number SRP009299 for data reported by Griffen et al and SRA accession number SRP012422 for data reported by Abusleme et al).…”

“…Recently, culture-independent molecular methods targeting small-subunit rRNA sequences (16S rRNA) in combination with high-throughput DNA sequencing have emerged as a popular approach to profile microbial flora from diverse sites of the human body. By amplification and deep sequencing of 16S rRNA gene segments, this approach has provided an unprecedented view of human-associated microbial communities and has uncovered novel or previously unrecognized microbes associated with health and disease (16,(28)(29)(30)(31). The Human Microbiome Project (HMP) data set is currently the largest reference data set (143 individuals) for the subgingival microbiome (32).…”

“…Several groups have since used the 16S rRNA and metagenomic approaches to survey subgingival microbiota from subjects recruited in the community (30,33). These "community" data sets have demonstrated a difference between periodontitis-associated and health-associated microbiota in both the overall microbial community structure (30,31) and the predicted functional capabilities (34,35). A number of bacterial taxa and genes were found to be differentially abundant between health and disease.…”

“…We used 16S rRNA deep sequencing to analyze subgingival microbiota from 25 subjects with chronic periodontal disease and 25 periodontally healthy controls and compared our data set with previously reported data sets from the HMP, Griffen et al (30), and Abusleme et al (31). In addition, we used PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) (36), a bioinformatics tool designed to predict metagenome functional content from marker gene surveys and full genomes, to predict functional compositions of subgingival metagenomes in healthy and diseased individuals.…”

Treponema denticola enolase contributes to the production of antibodies against ENO1 but not to the progression of periodontitis

“…Periodontitis is caused by dysbiosis of the subgingival biofilm that accompanies increases in the amounts of periodontal pathogens such as Porphyromonas gingivalis, Treponema denticola , and Tannerella forsythia [1]. Accumulating evidence supports an association between periodontitis and rheumatoid arthritis (RA).…”