Oral Microbiome and Gingival Transcriptome Profiles of Ligature-Induced Periodontitis

Abstract

This investigation evaluated the relationship of the oral microbiome and gingival transcriptome in health and periodontitis in nonhuman primates ( Macaca mulatta). Subgingival plaque samples and gingival biopsies were collected from healthy sites and at sites undergoing ligature-induced periodontitis. Microbial samples were analyzed with 16S amplicon sequencing to identify bacterial profiles in young (3 to 7 y) and adult (12 to 23 y) animals. The gingival transcriptome was determined with a microarray analysis and focused on the expression level of 452 genes that are associated with the development of inflammation and innate and adaptive immune responses. Of the 396 total operational taxonomic units (OTUs) identified across the samples, 81.8% were detected in the young group and 99.5% in the adult group. Nevertheless, 58 of the OTUs composed 88% of the signal in adults, and 49 OTUs covered 91% of the OTU readouts in the young group. Correlation analyses between the microbiome members and specific gingival genes showed a high number of significant bacteria-gene correlations in the young healthy tissues, which decreased by 75% in diseased tissues. In contrast, these correlations increased by 2.5-fold in diseased versus healthy tissues of adult animals. Complexes of bacteria were delineated that related to specific sets of immune genes, differing in health and disease and in the young versus adult animals. The correlated gene profiles demonstrated selected pathway overrepresentation related to particular bacterial complexes. These results provide novel insights into microbiome changes with disease and the relationship of these changes to specific gene profiles and likely biologic activities occurring in healthy and diseased gingival tissues in this human-like periodontitis model.

Oral Microbiome and Gingival Tissue Apoptosis and Autophagy Transcriptomics

“…Beyond the clear differences in the host gingival response, changes in the oral microbiome also occur during ligatureinduced periodontitis, in many ways similar to the differences that have been reported with human disease (43,53). This study identified unique features of the microbiome in disease that significantly correlated with these changes in the gingival transcriptome.…”

Proteome and Microbiome Mapping of Human Gingival Tissue in Health and Disease

“…Different proteome and microbiome studies have been performed to understand periodontal diseases, yet few have focused on gingival tissues. Earlier studies indicated that the microbial content of the periodontal pocket in non-human primates or human determines the gene expression patterns in the gingival tissues (Papapanou et al, 2009 ; Ebersole et al, 2020 ). In the present study, we successfully applied a contemporary PCT-assisted workflow to dissect the gingival proteome and microbiome of both diseased and healthy sites from patients with periodontitis.…”

Oral microbiome interactions with gingival gene expression patterns for apoptosis, autophagy and hypoxia pathways in progressing periodontitis

“…First, the ligatures in primates do elicit both soft and hard tissue changes related to periodontal lesions, albeit, generally the animals do not lose substantial bone architecture in this experimental model that does occur in naturally occurring disease. Second, while the ligature clearly increases the accumulation of bacteria and does provide some mechanical disruption to the tissues that differs somewhat from human disease, the oral microbiome in the nonhuman primates shows extensive overlap in changes observed with naturally occurring 57 and ligature‐induced disease 56,109 . Additionally, we have shown that gingival gene expression profiles documenting local host response features for a number of pathways are comparable in naturally occurring and ligature‐induced disease models 47,110 .…”

“…Finally, epidemiologic data support various demographic modifiers (e.g., age, sex) of periodontitis expression in humans, as well as the identification of substantial individual variation in risk for more extensive and severe disease. While the ligature model does not necessarily reflect this individual feature of human periodontitis, we have shown that the magnitude of ligature‐induced disease in the nonhuman primates is altered by age 56 and sex, 111 as well as recent data demonstrating matriline (e.g., genetic, familial) susceptibility age of onset and extent of disease 112,113 . Thus, the evidence suggests that this model should be able to provide some insights into the earliest phases of disease initiation and progression that would be difficult to obtain in a human disease model.…”

“…Bacterial samples were obtained by a curette and analysed using a MiSeq instrument 52,53 for the total composition of the microbiome from each sample 54–56 . Sequences were clustered into phylotypes based on their sequence similarity, and these binned phylotypes were assigned to their respective taxonomic classification using the Human Oral Microbiome Database (HOMD V13; http://www.homd.org/index.php?name=seqDownload%26file%26type=R).…”