World Workshop on Oral Medicine VII: Targeting the microbiome for oral medicine specialists—Part 1. A methodological guide

Effects of Sequential Antimicrobial Phases on Root Canal Microbiome Dynamics in Two-Visit Treatment of Primary Apical Periodontitis: A Longitudinal Experimental Study

BACKGROUND

Effective management of primary apical periodontitis depends on understanding the dynamic interactions within the root canal microbiome. This study aimed to investigate the effect of sequential antimicrobial phases on the root canal microbiome during a two-visit treatment approach, with a focus on calcium hydroxide medication.

METHODS

Samples were collected from three teeth across four treatment phases: initial infection (S1), after chemomechanical preparation (S2), after intracanal medication (S3), and after a final flush (S4). DNA was extracted, and the V3-V4 regions of the 16S rRNA gene were sequenced using Illumina MiSeq. Sequencing data were analyzed with QIIME 2, and differentially abundant taxa were identified using linear discriminant analysis effect size (LEfSe).

RESULTS

While microbial community composition did not differ significantly between phases, the Firmicutes/Bacteroidetes ratio decreased after the antimicrobial stages. LEfSe analysis revealed higher abundances of Lactobacillales, Arthrobacter, and Veillonella in the untreated (CMP) group. Bifidobacterium longum was relatively more abundant in the intracanal medication (ICM) phase, and Dorea formicigenerans was more abundant in the final-flush (FF) phase.

CONCLUSIONS

Although calcium hydroxide treatment did not induce statistically significant changes in overall root canal microbial composition, trends such as a reduction in the Firmicutes/Bacteroidetes ratio and a relative increase in Bifidobacterium longum numbers suggest potential ecological shifts. The observed relative increase in Bifidobacterium longum numbers may represent a hypothesis-driven observation reflecting indirect ecological effects rather than direct pH modulation. While visual patterns (e.g., PCA clustering) were observed, they lacked statistical support. Further studies with larger sample sizes are needed to validate these observations and assess the potential role of beneficial bacteria in root canal treatments.

Oral microbiota: Taxonomic composition and functional profile in caries-free and in caries-affected individuals - A systematic review

OBJECTIVE

To compare the oral microbiota among caries-free (CF) with caries-affected (CA) individuals, both at taxonomic and at functional levels.

DESIGN

This systematic review was conducted following PRISMA guidelines. A structured search was carried out in MEDLINE/PUBMED, Web of Science, EMBASE, LILACS, SciELO, Scopus and Google Scholar databases up to September, 2023. Observational studies, without any restriction on date of publication and using next-generation targeted or untargeted sequencing methods for identification of microbial communities were included. Qualitative synthesis was performed from all included studies.

RESULTS

54 studies were included (43 cross-sectional; 11 cohort) comprising more than 3486 participants (at least 1666 CF and 1820 CA) whose saliva and/or dental plaque were used as clinical samples. Methodological quality was graded as "fair" for most of the studies. The abundance of 87 bacterial and 44 fungal genera were statistically different among CF and CA individuals. Atopobium spp., Capnocytophaga spp., Lactobacillus spp., Prevotella spp., Scardovia spp., Selenomonas spp. among others were frequently reported as being more abundant in CA individuals. Several functional patterns, such as lipids, carbohydrate, starch, sucrose, amino sugar metabolisms, among others, were identified as being specifically related to CF or to CA conditions.

CONCLUSION

In spite of the variability among the included studies and of the predominance of qualitative synthesis, groups of microorganisms as well as specific functional profiles coded by the assessed microbiota are differently abundant among caries-affected and caries-free individuals. These results need to be interpreted with caution considering the limitations inherent to each assessed primary study.

Clinical Investigation of Bacteriome in Primary Endodontic Infections With Apical Periodontitis Using High-Throughput Sequencing Analysis

INTRODUCTION

This study characterized the bacteriome in primary endodontic infection (PEI) with apical periodontitis (AP), identified core and rare bacteriome species and community diversity metrics, and analyzed the relationship between the bacteriome composition, diversity and features, and patient variables.

METHODS

Twenty-seven patients with PEI and AP were sampled. The DNA was extracted and quantified using quantitative polymerase chain reaction. Raw V3-V4 amplicon sequencing data were processed with the DADA2 pipeline to generate amplicon sequence variants, and taxonomic assignment of the amplicon sequence variants up to the species level was done against the Human Oral Microbiome Database. Core bacteriome and differential abundance analyses were performed using ANCOM. Alpha diversity was determined using Chao1, Shannon, and Simpson indexes. LeFse analysis was used to identify abundant taxa. Sparse Estimation of Correlations among Microbiomes analysis estimated linear and nonlinear relationships among bacteria.

RESULTS

Of 27, 24 root canal samples were analyzed, and 3 root canal sampling were filtered out with a low read count. The bacterial phyla with top mean relative abundance were Bacteroidetes, Firmicutes, Synergistetes, Fusobacteria, and Actinobacteria. A total of 113 genera and 215 species were identified. The samples were gathered into 3 clusters. LefSe analysis identified differences in abundant taxa between distinct age, gender, symptomatology, and lesion size groups. Sparse Estimation of Correlations among Microbiomes distance analysis indicated Slackia exigua as the node with the highest degree.

CONCLUSIONS

The bacteriome in PEI with AP among the patients in this study was complex and displayed high microbial heterogeneity. Moreover, age, gender, symptomatology, and lesion size were associated with differences in bacteriome features in PEI with AP.

Therapeutic Strategies and Genetic Implications for Periodontal Disease Management: A Systematic Review

The objective of this review is to identify the microbiological alterations caused by various therapy modalities by critically analyzing the current findings. We limited our search to English-language papers published between 1 January 2004 and 7 May 2024 in PubMed, Scopus, and Web of Science that were relevant to our topic. In the search approach, the Boolean keywords "microbio*" AND "periodontitis" were used. A total of 5152 papers were obtained from the databases Web of Science (2205), PubMed (1793), and Scopus (1154). This resulted in 3266 articles after eliminating duplicates (1886), and 1411 entries were eliminated after their titles and abstracts were examined. The qualitative analysis of the 22 final articles is included in this study. Research on periodontal disease shows that periodontitis alters the oral microbiome and increases antibiotic resistance. Treatments like scaling and root planing (SRP), especially when combined with minocycline, improve clinical outcomes by reducing harmful bacteria. Comprehensive mechanical debridement with antibiotics, probiotics, EMD with bone grafts, and other adjunctive therapies enhances periodontal health. Personalized treatment strategies and advanced microbial analyses are crucial for effective periodontal management and antibiotic resistance control.

Microbial diagnostics in periodontal diseases

Microbial analytical methods have been instrumental in elucidating the complex microbial etiology of periodontal diseases, by shaping our understanding of subgingival community dynamics. Certain pathobionts can orchestrate the establishment of dysbiotic communities that can subvert the host immune system, triggering inflammation and tissue destruction. Yet, diagnosis and management of periodontal conditions still rely on clinical and radiographic examinations, overlooking the well-established microbial etiology. This review summarizes the chronological emergence of periodontal etiological models and the co-evolution with technological advances in microbial detection. We additionally review the microbial analytical approaches currently accessible to clinicians, highlighting their value in broadening the periodontal assessment. The epidemiological importance of obtaining culture-based antimicrobial susceptibility profiles of periodontal taxa for antibiotic resistance surveillance is also underscored, together with clinically relevant analytical approaches to guide antibiotherapy choices, when necessary. Furthermore, the importance of 16S-based community and shotgun metagenomic profiling is discussed in outlining dysbiotic microbial signatures. Because dysbiosis precedes periodontal damage, biomarker identification offers early diagnostic possibilities to forestall disease relapses during maintenance. Altogether, this review highlights the underutilized potential of clinical microbiology in periodontology, spotlighting the clinical areas most conductive to its diagnostic implementation for enhancing prevention, treatment predictability, and addressing global antibiotic resistance.

Mechanisms and Potential Clinical Implications of Oral Microbiome in Oral Squamous Cell Carcinoma

Microorganisms in the oral cavity are abundant in the human body. At present, more than 700 species of oral microorganisms have been identified. Recently, a lot of literature has indicated that the oral microbiota plays an important role in the occurrence, development, and prognosis of oral squamous cell carcinoma (OSCC) through various mechanisms. And researchers are now trying to utilize oral microbiota in cancer diagnosis and treatment. However, few articles systematically summarize the effects of oral microbes in the diagnosis, treatment, and disease outcomes of oral cancer. Herein, we made a summary of the microbial changes at cancerous sites and placed more emphasis on the mechanisms by which the oral microbiome promotes cancerization. Moreover, we aimed to find out the clinical value of the oral microbiome in OSCC.

Newly identified pathogens in periodontitis: evidence from an association and an elimination study

We assessed the level of evidence for the presence of new periodontal pathogens by (i) comparing the occurrence of non-classical periodontal taxa between healthy vs. periodontitis patients (Association study); (ii) assessing the modifications in the prevalence and levels of these species after treatments (Elimination study). In the Association study, we compared the prevalence and levels of 39 novel bacterial species between periodontally healthy and periodontitis patients. In the Elimination study, we analyzed samples from periodontitis patients assigned to receive scaling and root planing alone or with metronidazole+ amoxicillin TID/ 14 days. Levels of 79 bacterial species (39 novel and 40 classic) were assessed at baseline, 3 and 12 months post-therapy. All samples were analyzed using Checkerboard DNA-DNA hybridization. Out of the 39 novel species evaluated, eight were categorized as having strong and four as having moderate association with periodontitis. Our findings suggest strong evidence supporting Lancefieldella rimae, Cronobacter sakazakii, Pluralibacter gergoviae, Enterococcus faecalis, Eubacterium limosum, Filifactor alocis, Haemophilus influenzae, and Staphylococcus warneri, and moderate evidence supporting Escherichia coli, Fusobacterium necrophorum, Spiroplasma ixodetis, and Staphylococcus aureus as periodontal pathogens. These findings contribute to a better understanding of the etiology of periodontitis and may guide future diagnostic and interventional studies.

Systemic Antibiotics and Chlorhexidine Associated with Periodontal Therapy: Microbiological Effect on Intraoral Surfaces and Saliva

The effect of systemic antibiotics on the microbial profile of extracrevicular sites after periodontal treatment is currently the subject of research. This study evaluated the microbiological effects on different oral cavity sites of scaling and root planing (SRP) combined with antimicrobial chemical control in the treatment of periodontitis. Sixty subjects were randomly assigned to receive SRP alone or combined with metronidazole (MTZ) + amoxicillin (AMX) for 14 days, with or without chlorhexidine mouth rinse (CHX) for 60 days. Microbiological samples were evaluated by checkerboard DNA-DNA hybridization until 180 days post therapy. The adjunctive use of antibiotics plus CHX significantly reduced the mean proportions of red complex species from subgingival biofilm and saliva (p < 0.05). Furthermore, the analysis of all intraoral niches showed a significantly lower mean proportion of the red complex species in the same group. In conclusion, the concomitant use of antimicrobial chemical control (systemic and local) demonstrated a beneficial effect on the composition of the oral microbiota.

The oral microbiome of treated and untreated chronic HCV infection: A preliminary study

OBJECTIVES

Chronic hepatitis C virus (HCV) infection is a debilitating disease that is lately treated using direct-acting antivirals (DAAs). Changes in the oral microbiome were detected in other liver diseases; however, oral microbiome was never investigated in patients having chronic HCV infection, whether pre- or post-treatment.

MATERIALS AND METHODS

This case-control preliminary study enrolled three equal groups: Group (I): untreated HCV patients; group (II): HCV patients who achieved viral clearance after DAA administration; and group (III): healthy controls. For each participant, a buccal swab was harvested and its 16S rRNA was sequenced.

RESULTS

The oral microbiome of chronic HCV patients had a significantly distinct bacterial community compared to healthy controls, characterized by high diversity and abundance of certain pathogenic species. These changes resemble that of oral lichen planus patients. After treatment by DAAs, the oral microbiome shifted to a community with partial similarity to both the diseased and the healthy ones.

CONCLUSIONS

Chronic HCV is associated with dysbiotic oral microbiome having abundant pathogenic bacteria. With HCV clearance by DAAs, the oral microbiome shifts to approach the healthy composition.

Metataxonomic and metaproteomic profiling of the oral microbiome in oral lichen planus - a pilot study

Background

A growing body of evidence demonstrates a different bacterial composition in the oral cavity of patients with oral lichen planus (OLP).

Patients and methods

Buccal swab samples were collected from affected and non-affected sites of six patients with reticular OLP and the healthy oral mucosa of six control subjects. 16S rRNA gene MiSeq sequencing and mass spectrometry-based proteomics were utilised to identify the metataxonomic and metaproteomic profiles of the oral microbiome in both groups.

Results

From the metataxonomic analysis, the most abundant species in the three subgroups were Streptococcus oralis and Pseudomonas aeruginosa, accounting for up to 70% of the total population. Principal Coordinates Analysis showed differential clustering of samples from the healthy and OLP groups. ANCOM-BC compositional analysis revealed multiple species (including P. aeruginosa and several species of Veillonella, Prevotella, Streptococcus and Neisseria) significantly over-represented in the control group and several (including Granulicatella elegans, Gemella haemolysans and G. parahaemolysans) in patients with OLP. The metaproteomic data were generally congruent and revealed that several Gemella haemolysans-belonging peptidases and other proteins with inflammatory and virulence potential were present in OLP lesions.

Conclusion

Our data suggest that several bacterial species are associated with OLP. Future studies with larger cohorts should be conducted to determine their role in the aetiology of OLP and evaluate their potential as disease biomarkers.

A critical analysis of research methods and experimental models to study the root canal microbiome

Endodontic microbiology deals with the study of the microbial aetiology and pathogenesis of pulpal and periradicular inflammatory diseases. Research in endodontic microbiology started almost 130 years ago and since then has mostly focussed on establishing and confirming the infectious aetiology of apical periodontitis, identifying the microbial species associated with the different types of endodontic infections and determining the efficacy of treatment procedures in eradicating or controlling infection. Diverse analytical methods have been used over the years, each one with their own advantages and limitations. In this review, the main features and applications of the most used technologies are discussed, and advice is provided to improve study designs in order to properly address the scientific questions and avoid setbacks that can compromise the results. Finally, areas of future research are described.

Patient attitude and habits regarding removable denture home hygiene and correlation with prosthesis cleanliness: A cross-sectional study of elderly Italians

STATEMENT OF PROBLEM

With the aging population, an increasing number of patients will require removable dental prostheses. Despite the recent public efforts to improve oral healthcare, knowledge of hygiene procedures for removable dental prostheses is sparse.

PURPOSE

The purpose of this cross-sectional study was to determine, through questionnaires, the level of awareness and education of home hygiene procedures among elderly Italian individuals wearing removable dental prostheses and to correlate self-reported hygiene habits and prosthesis cleanliness, as determined by a clinical examination.

MATERIAL AND METHODS

A cross-sectional study was performed by questionnaires administered by a dental hygienist to patients attending the dental clinics (prosthodontic and periodontology clinical units) at San Paolo Hospital of Milan from January 2014 to October 2015 and who volunteered to participate. The questionnaire included demographic data and oral hygiene habits. Each participant received an intraoral and prosthesis examination performed by the same dental hygienist. The cleanliness of the removable dental prosthesis was classified according to a 3-point scoring system. Categorical variables were expressed as a percentage of study participants and compared by using the χ² test, while, for the statistical correlations between continuous and categorical variables, the point-biserial correlation calculator was used (α=.05).

RESULTS

Questionnaires were collected from 161 study participants: 92 women (mean ±standard deviation age: 76 ±7.59 years; range: 65-93 years) and 69 men (mean ±standard deviation age: 74 ±6.31 years; range: 65-86 years). A total of 239 prostheses were considered. A significant correlation was found between older participants, older removable dental prostheses, and reduced prosthesis cleanliness, correlating age ranges of participants as well as of removable dental prostheses with the degrees of prosthesis cleanliness (P=.001 and P=.004, respectively). Half the study participants (n=81; 50.3%) reported prosthesis removal during the night, while the others reported sleeping with the prosthesis in place. Some study participants (n=32; 19.9%) reported that they had never received instructions about how to clean the prosthesis. Mechanical brushing with toothbrush and toothpaste was the most common cleaning method (n=47; 29.2%), while the recommended combined cleaning method based on both mechanical brushing and immersion in dental cleanser was applied by 34 (21.1%) study participants. A similar number (n=25; 15.5%) reported at least 1 episode of denture-related stomatitis.

CONCLUSIONS

In the analyzed cohort, patient attitude and habits toward home procedures for denture hygiene resulted in poor prosthesis cleanliness. Most individuals used a toothbrush and toothpaste to clean their device, although combining mechanical and chemical cleaning is typically reported to be the optimal method.

Increasing Reproducibility in Oral Microbiome Research

Evidence on the role of the oral microbiome in health and disease is changing the way we understand, diagnose, and treat ailments. Numerous studies on diseases affecting the oral cavity have revealed a large amount of data that is invaluable for the advancements in diagnosing and treating these diseases. However, the clinical translation of most of these exploratory data is stalled by variable methodology between studies and non-uniform reporting of the data.Understanding the key areas that are gateways to bias in microbiome studies is imperative to overcome this challenge faced by oral microbiome research. Bias can be multifactorial and may be introduced in a microbiome research study during the formulation of the study design, sample collection and storage, or the sample processing protocols before sequencing. This chapter summarizes the recommendations from literature to eliminate bias in the microbiome research studies and to ensure the reproducibility of the microbiome research data.

Inflammatory Networks Linking Oral Microbiome with Systemic Health and Disease

The dance between microbes and the immune system takes place in all biological systems, including the human body, but this interaction is especially complex in the primary gateway to the body: the oral cavity. Recent advances in technology have enabled deep sequencing and analysis of members and signals of these communities. In a healthy state, the oral microbiome is composed of commensals, and their genes and phenotypes may be selected by the immune system to survive in symbiosis. These highly regulated signals are modulated by a network of microbial and host metabolites. However, in a diseased state, host-microbial networks lead to dysbiosis and considerable burden to the host prior to systemic impact that extends beyond the oral compartment. Interestingly, we presented data demonstrating similarities between human and mice immune dysbiosis and discussed how this affects the host response to similar pathobionts. The host and microbial signatures of a number of disease states are currently being examined to identify potential correlations. How the oral microbiome interacts with inflammation and the immune system to cause disease remains an area of active research. In this review, we summarize recent advancements in understanding the role of oral microbiota in mediating inflammation and altering systemic health and disease. In line with these findings, it is possible that existing conditions may be resolved by targeting specific immune-microbial markers in a positive way.

A systematic review of the microbiota composition in various peri-implant conditions: data from 16S rRNA gene sequencing

OBJECTIVE

To systematically review the literature regarding the microbiota composition in various peri-implant conditions as analyzed by 16S rRNA gene sequencing methods.

METHODS

Electronic searches were conducted at MEDLINE/PubMed, Scopus, Embase, ScienceDirect and Web of Science databases looking for articles published up to April 2020. Observational prospective investigations were considered with systemically healthy patients and that had presented the description of the microbiota composition of peri-implantitis (PI), peri-implant mucositis (PM) and/or health implants (HI) by using 16S rRNA gene sequencing analysis were considered eligible.

RESULTS

From 1,380 titles found, 8 studies were considered for qualitative analysis. One article was excluded due to high risk of bias, remaining 7 studies for descriptive analysis. In 6 out of 7 studies the PI microbiota was reported as being in relative abundance and variety though with a different composition from those with HI. There was no consensus regarding which condition had more diversity. The main observed phyla among PI were Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria and Spirochaetes, while the genera were mainly Actinomyces, Eubacterium, Fusobacterium, Mogibacterium, Moraxella, Treponema and Porphyromonas. Comparisons between PI and PM microbiota showed conflicting results: one study suggested that PI has greater bacterial diversity; another study reported the opposite result, while another investigation found similar variety for both conditions.

CONCLUSIONS

The microbiota of peri-implant conditions have been reported as distinct, although the available literature presents discrepancies. Nonetheless, considering the findings in most studies, it can be suggested that the relative abundance of microbiota and bacterial diversity increased with the progress of peri-implant disease.

3 D nano bilayered spatially and functionally graded scaffold impregnated bromelain conjugated magnesium doped hydroxyapatite nanoparticle for periodontal regeneration

Chronic periodontal disease affect the tissues supporting around the teeth like gingival tissue, connective tissue, alveolar bone and periodontal ligaments. Hitherto, periodontal treatment was targeted to selectively repopulate the defect site with cell that has capability to regenerate lost tissue by promoting the concept of guided tissue regeneration but it requires second surgery due to non- biodegradability. The use of polymeric biodegradable nanofibrous coated scaffold that have the ability to deliver bioactives required for regeneration to occur is relatively a newer concept. The functionalization of polymeric scaffold with Bromelain and magnesium doped hydroxyapatite nanoparticle enhanced the mechanical, physico-chemical, thermal and biological properties of the scaffold by imitating the intricate extracellular matrix (ECM) architecture which provided the necessary bioactive cues that offered control over cellular functions by showing antibacterial potential, hemocompatibility and increasing the proliferation and migration rate in vitro. In addition, in ovo chicken chorioallantoic membrane assay and ex vivo aortic ring assay confirmed the efficacy of the developed scaffold by encouraging angiogenesis required for maintaining its viability after implanting onto the infected area. Further, the scaffold positively interacted with the host and actively contributed to the process of tissue regeneration in vivo in Wistar rat model.