‘Next-Generation’ Perspectives: A Classical Cohort’s Subgingival Microbiome and Periodontal Disease

Abstract

Objectives: To analyze via next-generation sequencing and microbiome-based clustering, how periodontal disease experience over 4 decades linked with subgingival plaque composition in a historical, well-studied Sri-Lankan tea worker cohort. Methods: Subgingival plaque was collected from 23 subjects with over 40-years clinical periodontal data and analyzed by Illumina MISeq sequencing of 16S rRNA gene (V3-V4) amplicons. Sequence data were processed using QIIME and assigned taxonomy with Greengenes (version13.8) database at 97% sequence similarity. 'Enterotype' like clustering was based on normalized OTU abundances, using Jensen-Shannon distances and Partitioning Around Meloids (PAM) algorithms in R. Clusters were compared using similarity percentages breakdown (SIMPER) at all taxonomic levels. Subjects were categorized into 'severe' or 'moderate' periodontal disease experience categories based on their long-term clinical data. Frequency weighted Chi Square tests were done to assess distribution of each periodontal disease category among the microbiome-based clusters. Results: High taxonomic diversity and richness of the subgingival microbiome was evident in this tropical and rural living cohort. From a total of 58,729 sequences, 3654 OTUs were identified. The oral distributions of several taxa, particularly within the class Clostridia, appear to be unique to this cohort. Clustering based on the microbiome data was most robust at 2; partitioning the subjects into two enterotype-like groups. Severe periodontal disease sufferers were significantly overrepresented in a cluster enriched with multiple Proteobacteria, Chlamydiae, Flavobacteriia, Bacilli and Treponema phylotypes. This cluster was also marked by lower abundances of total Firmicutes, Coriobacteria, Bifidobacteriales and, several phylotypes of the order Clostridiales not very commonly described within oral niches. Conclusions: High coverage,'next-generation' profiling and pattern-analysis revealed subgingival microbiome configuration could be linked to long-term periodontal disease experience in a historical Sri Lankan cohort having a highly diverse microbiota. These patterns may be suggestive of both the nature of microbial dysbiosis related to periodontal disease and beneficial or protective taxa within this unique cohort.