Microbiomes Associated with Pre- and Post-treatment Periodontitis and Periodontal Health

Objectives: It was hypothesized that oral microbiota may be distinct among subjects of different periodontal status. The objective is to identify features of subgingival and salivary microbiomes in periodontally healthy subjects, and in subjects with chronic periodontitis before and after nonsurgical periodontal therapy.
Methods: 238 microbial samples from 6 groups (A-F) were analyzed, including (A) subgingival plaque (N=42) and (B) saliva (N=18) from healthy subjects/healthy sites, (C) subgingival plaque (N=96) and (D) saliva (N=45) from diseased subjects/diseased sites/pre-treatment, and (E) subgingival plaque (N=19) and (F) saliva (N=18) from diseased subjects following treatment (diseased subjects/diseased sites/post-treatment). The v4 region of the 16S rDNA genes in sample DNA was PCR-amplified and sequenced on an Illumina platform. A subset of the samples from Group A (N=19), Group C (N=24) and Group E (N=16) were subjected to functional genomic analysis via HuMiChip functional gene microarray. Community analysis was performed with STAMP, R, vegan and MetagenomeSeq, and our in-house analysis pipeline.
Results: 1979 operational taxonomic units (OTUs) were defined across 238 samples based on 16S rDNA analysis. Twelve OTUs were overabundant in Group A, with 9 of the 12 taxa increased an average of 39% after treatment. Twenty-eight taxa were overabundant in Group C; the levels of these taxa were reduced by an average of 42% after treatment. Six taxa were overabundant in Group D. Four distinct clusters of subgingival samples were identified based on HuMiChip functional gene profiles. Clusters 1 & 2 composed primarily of diseased samples, and Clusters 3 & 4 composed primarily of healthy samples. Cluster 2 includes a majority (11 of 16) of Group E samples.
Conclusions: Microbiota were distinct in subgingival sites in subjects without periodontitis and subjects with periodontitis before and after initial periodontal therapy.