A novel method for sampling subgingival microbiome: a comparative metatranscriptomic study

The subgingival microbiome has been implicated in oral and systemic diseases such as periodontitis and Alzheimer's disease. However, subgingival sampling is challenging. We developed a novel method of sampling the subgingival microbiome by rotationally swabbing the supragingival area, named subgingival-P (for proxy) samples. We sampled and metatranscriptomically analyzed subgingival and subgingival-P samples of three different teeth in 20 individuals. The subgingival-P samples were comparable to the subgingival samples in the relative abundances of microorganisms and microbial gene expression levels. Our data demonstrate that the novel method of collecting and analyzing the subgingival-P samples can act as a proxy for the subgingiva, paving the way for large and diverse studies investigating the role of the subgingival microbiome in health and disease.

Subgingival Use of Air-Polishing Powders: Status of Knowledge: A Systematic Review

Effective subgingival biofilm removal is crucial for achieving positive and stable outcomes in periodontal therapy, forming an indispensable part of any periodontal treatment approach. The development of air-polishing tools has emerged as a promising alternative to hand and ultrasonic scalers for dental biofilm removal. The objective of this systematic review was to assess existing literature regarding the subgingival use of various types of air-polishing powders, as an effective method of subgingival biofilm control. For this, 55 articles on this subjected were sourced from searched databases and subjected to an evaluation process of their contained information, which was subsequently structured and compiled into this manuscript. The existing literature acknowledges that good subgingival biofilm control is essential for the success of periodontal therapy, including through subgingival air-polishing, as an adjunctive procedure. This approach has the potential to enhance patient comfort during and after subgingival mechanical plaque removal, thereby mitigating damage to periodontal structures. Consequently, it may lead to improved healing capabilities within the periodontal tissues and the formation of a more stable reparative gingival junctional epithelium.

Relationship between Deep Marginal Elevation and Periodontal Parameters: A Systematic Review

Background and Objectives: This review focuses on reviewing studies from the literature regarding the effects of deep margin elevation on the surrounding periodontium. Materials and Methods: A review of the literature was carried out using the following online databases: Embase, The Cochrane Library, MEDLINE-PubMed and Google Scholar. Our search was limited to articles from 2010 to 2023. The search terms consisted of keywords and MeSH terms, which were 'deep margin elevation', 'coronal margin relocation', 'periodontium' and 'periodontal tissues'. The literature was searched thoroughly by two reviewers. Initially, the titles of the articles were extracted. After removing irrelevant and duplicate articles, abstracts were assessed for relevant articles. Finally, the reviewers analyzed full-text articles. Results: A total of twelve articles, including one randomized clinical trial, three systematic reviews, two prospective cohort, three case series, one a clinical study, one pilot study and one a retrospective study, were selected and analyzed. Conclusions: The review suggests potential benefits of Deep Margin Elevation (DME) over surgical crown lengthening due to reduced invasiveness, yet conclusive effects on periodontal tissue remain unclear, warranting further studies on clinical parameters and inflammatory biomarkers.

Comparative 16S rRNA gene sequencing study of subgingival microbiota of healthy subjects and patients with periodontitis from four different countries

AIM

To investigate the differences between the subgingival microbiota of healthy subjects (HS) and periodontitis patients (PP) from four different countries through a metagenomic approach.

MATERIALS AND METHODS

Subgingival samples were obtained from subjects from four different countries. Microbial composition was analysed through high-throughput sequencing of the V3-V4 region of the 16S rRNA gene. The country of origin, diagnosis and clinical and demographic variables of the subjects were used to analyse the microbial profiles.

RESULTS

In total, 506 subgingival samples were analysed: 196 from HS and 310 from patients with periodontitis. Differences in richness, diversity and microbial composition were observed when comparing samples pertaining to different countries of origin and different subject diagnoses. Clinical variables, such as bleeding on probing, did not significantly affect the bacterial composition of the samples. A highly conserved core of microbiota associated with periodontitis was detected, while the microbiota associated with periodontally HS was much more diverse.

CONCLUSIONS

Periodontal diagnosis of the subjects was the main variable explaining the composition of the microbiota in the subgingival niche. Nevertheless, the country of origin also had a significant impact on the microbiota and is therefore an important factor to consider when describing subgingival bacterial communities.

Utilization of a periodontal endoscope in nonsurgical periodontal therapy: A randomized, split-mouth clinical trial

BACKGROUND

The removal of subgingival calculus to obtain gingival health is an integral part of nonsurgical periodontal therapy. The periodontal endoscope is used by some clinicians to help enhance access to effectively remove subgingival calculus; however, longer-term studies on this subject are still lacking. The purpose of this randomized, controlled clinical trial was to compare the clinical outcomes of scaling and root planing (SRP) using a periodontal endoscope versus conventional SRP using loupes for up to 12 months, utilizing a split-mouth design.

METHODS

Twenty-five patients were recruited who exhibited generalized stage II or stage III periodontitis. SRP was rendered by the same experienced hygienist using either a periodontal endoscope or conventional SRP using loupes, following random assignment of the left and right halves of the mouth. All periodontal evaluations were done by the same periodontal resident at baseline, and at 1, 3, 6, and 12 months after therapy.

RESULTS

Single-rooted teeth interproximal sites displayed a significantly lower percentage of improved sites (P < 0.05) than multirooted teeth for probing depth and clinical attachment level (CAL). Maxillary multirooted interproximal sites favored the use of the periodontal endoscope at the 3- and 6-month time periods (P = 0.017 and 0.019, respectively) in terms of the percentage of sites with improved CAL. Mandibular multirooted interproximal sites showed more sites with improved CAL using conventional SRP than with the periodontal endoscope (P < 0.05).

CONCLUSION

Overall, the use of a periodontal endoscope was more beneficial in multirooted sites compared to single-rooted sites, specifically in maxillary multirooted sites.

Whole Genome Sequencing and Phenotypic Analysis of Antibiotic Resistance in Filifactor alocis Isolates

There is scarce knowledge regarding the antimicrobial resistance profile of F. alocis. Therefore, the objective of this research was to assess antimicrobial resistance in recently obtained F. alocis clinical isolates and to identify the presence of antimicrobial resistance genes. Isolates were obtained from patients with periodontal or peri-implant diseases and confirmed by sequencing their 16S rRNA gene. Confirmed isolates had their genome sequenced by whole genome sequencing and their phenotypical resistance to nine antibiotics (amoxicillin clavulanate, amoxicillin, azithromycin, clindamycin, ciprofloxacin, doxycycline, minocycline, metronidazole, and tetracycline) tested by E-test strips. Antimicrobial resistance genes were detected in six of the eight isolates analyzed, of which five carried tet(32) and one erm(B). Overall, susceptibility to the nine antibiotics tested was high except for azithromycin in the isolate that carried erm(B). Moreover, susceptibility to tetracycline, doxycycline, and minocycline was lower in those isolates that carried tet(32). The genetic surroundings of the detected genes suggested their inclusion in mobile genetic elements that might be transferrable to other bacteria. These findings suggest that, despite showing high susceptibility to several antibiotics, F. alocis might obtain new antimicrobial resistance traits due to its acceptance of mobile genetic elements with antibiotic resistance genes in their genome.

Antimicrobial Impact of Different Air-Polishing Powders in a Subgingival Biofilm Model

Subgingival air-polishing devices (SAPD) can reduce bacterial biofilms and thus support periodontal healing. The authors of this study evaluated the effectiveness of the glycine-based and trehalose-based air-polishing powders in removing pathogenic bacteria in a subgingival biofilm model. We treated 56 subgingival pockets in porcine jaws with SAPD. Subgingival air polishing was performed in three groups of 13 pockets each: I, glycine-based powder; II, trehalose-based powder; and III, water alone. Another group (IV) served as untreated controls. Prior to air polishing, inoculated titanium bars were inserted into the pockets containing periopathogenic bacteria such as Porphyromonas gingivalis and Tannerella forsythia. Remaining bacteria were evaluated using real-time PCR. The numbers of remaining bacteria depended on the treatment procedure, with the lowest number of total bacteria in group I (median: 1.96 × 10⁶ CFU; min: 1.46 × 10⁵; max: 9.30 × 10⁶). Both polishing powders in groups I and II (median: 1.36 × 10⁷ CFU; min: 5.22 × 10⁵; max: 7.50 × 10⁷) showed a statistically significantly lower total bacterial load in comparison to both group IV (median: 2.02 × 10⁸ CFU; min: 5.14 × 10⁷; max: 4.51 × 10⁸; p < 0.05) and group III (median: 4.58 × 10⁷ CFU; min: 2.00 × 10⁶; max: 3.06 × 10⁸; p < 0.05). Both subgingival air-polishing powders investigated can reduce periopathogenic bacteria and thus support antimicrobial therapy approaches in periodontal treatment regimens.

Mapping of a Subgingival Dual-Species Biofilm Model Using Confocal Raman Microscopy

Techniques for continuously monitoring the formation of subgingival biofilm, in relation to the determination of species and their accumulation over time in gingivitis and periodontitis, are limited. In recent years, advancements in the field of optical spectroscopic techniques have provided an alternative for analyzing three-dimensional microbiological structures, replacing the traditional destructive or biofilm staining techniques. In this work, we have demonstrated that the use of confocal Raman spectroscopy coupled with multivariate analysis provides an approach to spatially differentiate bacteria in an in vitro model simulating a subgingival dual-species biofilm. The present study establishes a workflow to evaluate and differentiate bacterial species in a dual-species in vitro biofilm model, using confocal Raman microscopy (CRM). Biofilm models of Actinomyces denticolens and Streptococcus oralis were cultured using the “Zürich in vitro model” and were analyzed using CRM. Cluster analysis was used to spatially differentiate and map the biofilm model over a specified area. To confirm the clustering of species in the cultured biofilm, confocal laser scanning microscopy (CLSM) was coupled with fluorescent in vitro hybridization (FISH). Additionally, dense bacteria interface area (DBIA) samples, as an imitation of the clusters in a biofilm, were used to test the developed multivariate differentiation model. This confirmed model was successfully used to differentiate species in a dual-species biofilm and is comparable to morphology. The results show that the developed workflow was able to identify main clusters of bacteria based on spectral “fingerprint region” information from CRM. Using this workflow, we have demonstrated that CRM can spatially analyze two-species in vitro biofilms, therefore providing an alternative technique to map oral multi-species biofilm models.

Manipulation of Saliva-Derived Microcosm Biofilms To Resemble Dysbiotic Subgingival Microbiota

In line with the new paradigm of the etiology of periodontitis, an inflammatory disorder initiated by dysbiotic subgingival microbiota, novel therapeutic strategies have been proposed targeting reversing dysbiosis and restoring host-compatible microbiota rather than eliminating the biofilms unselectively. Thus, appropriate laboratory models are required to evaluate the efficacy of potential microbiome modulators.

Periodontitis is a highly prevalent oral inflammatory disease triggered by dysbiotic subgingival microbiota. For the development of microbiome modulators that can reverse the dysbiotic state and reestablish a health-associated microbiota, a high-throughput in vitro multispecies biofilm model is needed. Our aim is to establish a model that resembles a dysbiotic subgingival microbial biofilm by incorporating the major periodontal pathogen Porphyromonas gingivalis into microcosm biofilms cultured from pooled saliva of healthy volunteers. The biofilms were grown for 3, 7, and 10 days and analyzed for their microbial composition by 16S rRNA gene amplicon sequencing as well as measurement of dipeptidyl peptidase IV (DPP4) activity and butyric acid production. The addition of P. gingivalis increased its abundance in saliva-derived microcosm biofilms from 2.7% on day 3 to >50% on day 10, which significantly reduced the Shannon diversity but did not affect the total number of operational taxonomic units (OTUs). The P. gingivalis-enriched biofilms displayed altered microbial composition as revealed by principal-component analysis and reduced interactions among microbial species. Moreover, these biofilms exhibited enhanced DPP4 activity and butyric acid production. In conclusion, by adding P. gingivalis to saliva-derived microcosm biofilms, we established an in vitro pathogen-enriched dysbiotic microbiota which resembles periodontitis-associated subgingival microbiota in terms of increased P. gingivalis abundance and higher DPP4 activity and butyric acid production. This model may allow for investigating factors that accelerate or hinder a microbial shift from symbiosis to dysbiosis and for developing microbiome modulation strategies.

IMPORTANCE In line with the new paradigm of the etiology of periodontitis, an inflammatory disorder initiated by dysbiotic subgingival microbiota, novel therapeutic strategies have been proposed targeting reversing dysbiosis and restoring host-compatible microbiota rather than eliminating the biofilms unselectively. Thus, appropriate laboratory models are required to evaluate the efficacy of potential microbiome modulators. In the present study, we used the easily obtainable saliva as an inoculum, spiked the microcosm biofilms with the periodontal pathogen Porphyromonas gingivalis, and obtained a P. gingivalis-enriched microbiota, which resembles the in vivo pathogen-enriched subgingival microbiota in severe periodontitis. This biofilm model circumvents the difficulties encountered when using subgingival plaque as the inoculum and achieves microbiota in a dysbiotic state in a controlled and reproducible manner, which is required for high-throughput and large-scale evaluation of strategies that can potentially modulate microbial ecology.

Microbial biogeography and ecology of the mouth and implications for periodontal diseases

In humans, the composition of microbial communities differs among body sites and between habitats within a single site. Patterns of variation in the distribution of organisms across time and space are referred to as "biogeography." The human oral cavity is a critical observatory for exploring microbial biogeography because it is spatially structured, easily accessible, and its microbiota has been linked to the promotion of both health and disease. The biogeographic features of microbial communities residing in spatially distinct, but ecologically similar, environments on the human body, including the subgingival crevice, have not yet been adequately explored. The purpose of this paper is twofold. First, we seek to provide the dental community with a primer on biogeographic theory, highlighting its relevance to the study of the human oral cavity. We summarize what is known about the biogeographic variation of dental caries and periodontitis and postulate that disease occurrence reflects spatial patterning in the composition and structure of oral microbial communities. Second, we present a number of methods that investigators can use to test specific hypotheses using biogeographic theory. To anchor our discussion, we apply each method to a case study and examine the spatial variation of the human subgingival microbiota in 2 individuals. Our case study suggests that the composition of subgingival communities may conform to an anterior-to-posterior gradient within the oral cavity. The gradient appears to be structured by both deterministic and nondeterministic processes, although additional work is needed to confirm these findings. A better understanding of biogeographic patterns and processes will lead to improved efficacy of dental interventions targeting the oral microbiota.

Comparison of clinical effectiveness of single and multiple applications of 1% chlorhexidine varnish (Cervitec Plus) along with scaling and root planing in patients with chronic periodontitis

Background:

Local drug delivery is most commonly used as an adjunct to scaling and root planing (SRP) for the treatment of periodontal disease. Varied success rates have been documented for various vehicles used for intrasite delivery of active therapeutic agents. Recently, varnishes acting as a reservoir of chlorhexidine have shown potential for the management of chronic periodontitis patients. The aim of the present investigation was a comparative evaluation of the clinical effectiveness of single and multiple applications of 1% chlorhexidine and thymol varnish (Cervitec Plus) along with SRP in patients with chronic periodontitis.

Materials and Methods:

The present study included 30 patients with chronic periodontitis divided into three groups based on the number of subgingival applications of chlorhexidine varnish single application (Group A), two applications at a week's interval (Group B), and three applications with 7-day interval in between two applications (Group C). Clinical parameters, namely plaque index (PI), sulcus bleeding index, probing pocket depth (PPD), and relative attachment level (RAL) were recorded at baseline, 1 month and 3 months in all three groups to compare the clinical efficacy.

Results:

A statistically significant reduction was observed in PI, sulcus bleeding index, PPD, and RAL at 1 and 3 months in all the three groups. Greater (though statistically nonsignificant) improvements were observed in Groups B and C.

Conclusion:

Within limitations of the study, it can be concluded that multiple applications of 1% chlorhexidine and thymol varnish (Cervitec Plus) have an added benefit over the single application in the treatment of chronic periodontitis.

Microcosm biofilms cultured from different oral niches in periodontitis patients

Objective: Periodontal diseases are triggered by dysbiotic microbial biofilms. Therefore, it is essential to develop appropriate biofilm models. Aim of the present study was to culture microcosm biofilms inoculated from different niches in periodontitis patients and compare their microbial composition to those inoculated from subgingival plaque. Methods: Saliva, subgingival plaque, tongue and tonsils were sampled in five periodontitis patients to serve as inocula for culturing biofilms in vitro in an active attachment model. Biofilms were grown for 14 or 28 d and analyzed for their microbial composition by 16S rDNA sequencing. Results: As classified by HOMD, all biofilms were dominated by periodontitis-associated taxa, irrespective which niche had been used for inoculation. There was a low similarity between 14 d biofilms and their respective inocula (Bray-Curtis similarity 0.26), while biofilms cultured for 14 and 28 d shared high similarity (0.69). Principal components analysis showed much stronger clustering per patient than per niche indicating that the choice of patients may be more crucial than choice of the respective niches in these patients. Conclusion: Saliva, tongue scrapings or tonsil swabs may represent sufficient alternative inocula for growing microcosm biofilms resembling periodontitis-associated microbial communities in cases when sampling subgingival plaque is not possible.

Oral Biofilm Sampling for Microbiome Analysis in Healthy Children

Oral biofilm and its molecular analysis provide a basis for investigating various dental research and clinical questions. Knowledge of biofilm composition leads to a better understanding of cariogenic and periopathogenic mechanisms. Microbial changes taking place in the oral cavity during childhood are of interest for several reasons. The evolution of the child oral microbiota and shifts in its composition need to be analyzed further to understand and possibly prevent the onset of disease. At the same time, advanced knowledge of the natural composition of oral biofilm is needed. Early stages of caries-free permanent dentition with healthy gums provide a widely unaffected subgingival habitat that can serve as an in situ baseline for studying features of oral health and disease. Analysis of children's oral biofilm during different stages in life is thus an important theme in the field. Modern molecular analysis methods can provide comprehensive information about the bacterial diversity of such biofilms. To enable microbiota data comparison, it is important to standardize each step in the procedure for molecular data generation. This procedure spans from clinical sampling, Next Generation Sequencing (NGS), bioinformatic data processing, to taxonomic interpretation. One of the most critical factors here is biofilm sampling. Sampling in children is even more challenging in particular due to limited space in subgingival areas. We thus focus on the use of paper points for subgingival sampling. This article provides a detailed protocol for oral biofilm sampling of the subgingival sulcus, the mucosa, and saliva in children.

The Landscape Ecology and Microbiota of the Human Nose, Mouth, and Throat

Landscape ecology examines the relationships between the spatial arrangement of different landforms and the processes that give rise to spatial and temporal patterns in local community structure. The spatial ecology of the microbial communities that inhabit the human body-in particular, those of the nose, mouth, and throat-deserves greater attention. Important questions include what defines the size of a population (i.e., "patch") in a given body site, what defines the boundaries of distinct patches within a single body site, and where and over what spatial scales within a body site are gradients detected. This Review looks at the landscape ecology of the upper respiratory tract and mouth and seeks greater clarity about the physiological factors-whether immunological, chemical, or physical-that govern microbial community composition and function and the ecological traits that underlie health and disease.

The expression of gingival epithelial junctions in response to subgingival biofilms

Periodontitis is an infectious inflammatory disease that destroys the tooth-supporting tissues. It is caused by the formation of subgingival biofilms on the surface of the tooth. Characteristic bacteria associated with subgingival biofilms are the Gram-negative anaerobes Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola, collectively known as the “red complex” species. Inter-epithelial junctions ensure the barrier integrity of the gingival epithelium. This may however be disrupted by the biofilm challenge. The aim of this in vitro study was to investigate the effect of subgingival biofilms on the expression of inter-epithelial junctions by gingival epithelia, and evaluate the relative role of the red complex. Multi-layered human gingival epithelial cultures were challenged with a 10-species in vitro subgingival biofilm model, or its variant without the red complex, for 3 h and 24 h. A low-density array microfluidic card platform was then used for analyzing the expression of 62 genes encoding for tight junctions, gap junctions, adherens junctions, and desmosomes. Although there was a limited effect of the biofilms on the expression of tight, adherens and gap junctions, the expression of a number of desmosomal components was affected. In particular, Desmoglein-1 displayed a limited and transient up-regulation in response to the biofilm. In contrast, Desmocollin-2, Desmoplakin and Plakoglobin were down-regulated equally by both biofilm variants, after 24 h. In conclusion, this subgingival biofilm model may down-regulate selected desmosomal junctions in the gingival epithelium, irrespective of the presence of the “red complex.” In turn, this could compromise the structural integrity of the gingival tissue, favoring bacterial invasion and chronic infection.

Microbial dynamics during conversion from supragingival to subgingival biofilms in an in vitro model

The development of dental caries and periodontal diseases result from distinct shifts in the microbiota of the tooth-associated biofilm. This in vitro study aimed to investigate changes in biofilm composition and structure, during the shift from a 'supragingival' aerobic profile to a 'subgingival' anaerobic profile. Biofilms consisting of Actinomyces oris, Candida albicans, Fusobacterium nucleatum, Streptococcus oralis, Streptococcus mutans and Veillonella dispar were aerobically grown in saliva-containing medium on hydroxyapatite disks. After 64 h, Campylobacter rectus, Prevotella intermedia and Streptococcus anginosus were further added along with human serum, while culture conditions were shifted to microaerophilic. After 96 h, Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola were finally added and the biofilm was grown anaerobically for another 64 h. At the end of each phase, biofilms were harvested for species-specific quantification and localization. Apart from C. albicans, all other species gradually increased during aerobic and microaerophilic conditions, but remained steady during anaerobic conditions. Biofilm thickness was doubled during the microaerophilic phase, but remained steady throughout the anaerobic phase. Extracellular polysaccharide presence was gradually reduced throughout the growth period. Biofilm viability was reduced during the microaerophilic conversion, but was recovered during the anaerobic phase. This in vitro study has characterized the dynamic structural shifts occurring in an oral biofilm model during the switch from aerobic to anaerobic conditions, potentially modeling the conversion of supragingival to subgingival biofilms. Within the limitations of this experimental model, the findings may provide novel insights into the ecology of oral biofilms.

Antibiotic resistance in an in vitro subgingival biofilm model

INTRODUCTION

The purpose of this study was to utilize an in vitro biofilm model of subgingival plaque to investigate resistances in subgingival biofilm communities to antibiotics commonly used as adjuncts to periodontal therapy.

METHODS

Biofilms were grown on saliva-coated hydroxyapatite supports in trypticase-soy broth for 4 h-10 days and then exposed for 48 h to either increasing twofold concentrations of tetracycline, amoxicillin, clindamycin, and erythromycin or therapeutically achievable concentrations of tetracycline, doxycycline, minocycline, amoxicillin, metronidazole, amoxicillin/clavulanate, and amoxicillin/metronidazole.

RESULTS

Concentrations necessary to inhibit bacterial strains in steady-state biofilms were up to 250 times greater than the concentrations needed to inhibit the same strains grown planktonically. In the presence of therapeutically available antibiotic concentrations, significantly higher proportions of the biofilms remained viable as the biofilms reached steady-state growth. The combinations of amoxicillin/clavulanate and amoxicillin/metronidazole were the most effective in suppressing growth. These combinations were particularly effective against biofilms up to and including 7 days of age and inhibited 90% or more of the bacteria present relative to untreated controls. As the biofilms approached steady state, these combinations were less effective with 50-60% of the bacteria retaining viability.

CONCLUSION

Most, but not all, species of subgingival bacteria are considerably more resistant in biofilms than in planktonic cultures. Resistance appeared to be age-related because biofilms demonstrated progressive antibiotic resistance as they matured with maximum resistance coinciding with the steady-state phase of biofilm growth.