Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment

Abstract

Periodontal disease affects the majority of adults worldwide and has been linked to numerous systemic diseases. Despite decades of research, the reasons for the substantial differences among periodontitis patients in disease incidence, progressivity, and response to treatment remain poorly understood. While deep sequencing of oral bacterial communities has greatly expanded our comprehension of the microbial diversity of periodontal disease and identified associations with healthy and disease states, predicting treatment outcomes remains elusive. Our results suggest that combining multiple omics approaches enhances the ability to differentiate among disease states and determine differential effects of treatment, particularly with the addition of metabolomic information. Furthermore, multi-omics analysis of biofilm community instability indicated that these approaches provide new tools for investigating the ecological dynamics underlying the progressive periodontal disease process.

Discovery of a Novel Periodontal Disease-Associated Bacterium

“…The association of CBP and the periodontal pocket milieu was further explored by analyzing the presence of CBP in sequence libraries obtained from subjects with different levels of severe PD (detailed information on how PD was diagnosed and how samples were collected can be found in a previous study by Califf and colleagues [22]). The mean relative abundance of CBP was greater in deeper pockets (Kruskal-Wallis, p = 0.07; Fig.…”

“…The latter correlation was not significant, which is likely due to the high within group variability (a common feature of human microbiome sequence data). In addition, by comparing sequence libraries from PD-patients who were subjected to a 0.25% sodium hypochlorite (diluted bleach) treatment, and whose conditions either improved or worsened after treatment [22], a positive trend was observed, showing a higher abundance of CBP in samples before treatment, and in samples that worsened after treatment (Kruskal-Wallis, p = 0.65; Fig. 4d, p = 0.47; Fig.…”

“…Information on molecular and clinical methods and study population can be found in a previous study by Califf and colleagues [22]. Participants were recruited as part of a study investigating the effectiveness of dilute sodium hypochlorite on periodontitis.…”

“…Participants were recruited as part of a study investigating the effectiveness of dilute sodium hypochlorite on periodontitis. Each participant received a comprehensive clinical examination, and was randomly assigned to a control or treatment group [22, 23]. No scaling was performed before or during the treatment.…”

“…Stacked bar plot representing the relative abundance (%) of CBP, P. gingivalis , and F. nucleatum from a combined total of 272 metagenomes generated from different body sites, including gut ( n = 18), skin ( n = 14), saliva ( n = 6), sub- ( n = 16), and supragingival plaque ( n = 160) from the HMP datasets; healthy individuals ( n = 5) and individuals diagnosed with periodontitis ( n = 7) from HOMD datasets [19]; oral disease class A ( n = 10), disease class B ( n = 4), and disease class C ( n = 10) from USC dataset [22]; oral pocket disease state ranging from normal ( n = 3), moderate (n = 10), and severe ( n = 9) from the American Indian/Alaskan Native dataset [21]…”