Microbial profiles at baseline and not the use of antibiotics determine the clinical outcome of the treatment of chronic periodontitis

Antibiotic resistance in the microbiota of periodontitis patients: an update of current findings

Systemic antibiotics are an effective adjunct in the treatment of periodontitis, but their judicious use is necessary as antimicrobial resistance is a growing global concern. This review aims to explore the current understanding and insight related to antibiotic resistance in the subgingival microbiota of periodontitis patients. A search of MEDLINE (PubMed) was carried out from 1 January 2012 to 25 November 2021 for studies related to antibiotic resistance in periodontitis patients. Of the 90 articles identified, 12 studies were selected for inclusion. A significant incidence of antibiotic resistant isolates was reported for Porphyromonas gingivalis, Prevotella intermedia, Prevotella denticola, Prevotella melaninogenica, Fusobacterium nucleatum, Tanerella forsythia, Aggretibacter actinomycetemcomitans, Streptococcus constellatus, Streptococcus intermedius, and Parvimonas micra, but resistance to specific antibiotics did not reach above 10% of isolates in most studies except for amoxicillin resistance in Aggretibacter actinomycetemcomitans. The highest frequency of resistance across all bacterial species was for amoxicillin, clindamycin, and metronidazole. However, resistance patterns were widely variable across geographical locations, and the high heterogeneity between antibiotic-resistant isolates across studies precludes any clinical recommendations from this study. Although antibiotic resistance has yet to reach critical levels in periodontitis patients, an emphasis on antibiotic stewardship interventions such as point-of-care diagnostics and education for key stakeholders is needed to curb a growing problem.

Flavonoid extract from propolis alleviates periodontitis by boosting periodontium regeneration and inflammation resolution via regulating TLR4/MyD88/NF-κB and RANK/NF-κB pathway

ETHNOPHARMACOLOGICAL RELEVANCE

In traditional Chinese medicine, propolis has been used for treating oral diseases for centuries, widely. Flavonoid extract is the main active ingredient in propolis, which has attracted extensive attention in recent years.

AIM OF THE STUDY

The objective and novelty of the current study aims to identify the mechanism of total flavonoid extract of propolis (TFP) for the treatment of periodontitis, and evaluate the therapeutic effect of TFP-loaded liquid crystal hydrogel (TFP-LLC) in rats with periodontitis.

METHODS

In this study, we used lipopolysaccharide-stimulated periodontal ligament stem cells (PDLSCs) to construct in vitro inflammation model, and investigated the anti-inflammatory effect of TFP by expression levels of inflammatory factors. Osteogenic differentiation was assessed using alkaline phosphatase activity and alizarin red staining. Meanwhile, the expression of toll like receptor 4 (TLR4), myeloid differentiation primary response 88 (MyD88), nuclear factor-kappa B (NF-κB), receptor activator of NF-κB (RANK) etc, were quantitated to investigate the therapeutic mechanism of TFP. Finally, we constructed TFP-LLC using a self-emulsification method and administered it to rats with periodontitis via periodontal pocket injection to evaluate the therapeutic effects. The therapeutic index, microcomputed tomography (Micro-CT), H&E staining, TRAP staining, and Masson staining were used for this evaluation.

RESULTS

TFP reduced the expression of TLR4, MyD88, NF-κB and inflammatory factor in lipopolysaccharide-stimulated PDLSCs. Meanwhile, TFP simultaneously regulating alkaline phosphatase, RANK, runt-associated transcription factor-2 and matrix metalloproteinase production to accelerate osteogenic differentiation and collagen secretion. In addition, TFP-LLC can stably anchor to the periodontal lesion site and sustainably release TFP. After four weeks of treatment with TFP-LLC, we observed a decrease in the levels of NF-κB and interleukin-1β (IL-1β) in the periodontal tissues of rats, as well as a significant reduction in inflammation in HE staining. Similarly, Micro CT results showed that TFP-LLC could significantly inhibit alveolar bone resorption, increase bone mineral density (BMD) and reduce trabecular bone space (Tb.Sp) in rats with periodontitis.

CONCLUSION

Collectively, we have firstly verified the therapeutic effects and mechanisms of TFP in PDLSCs for periodontitis treatment. Our results indicate that TFP perform anti-inflammatory and tissue repair activities through TLR4/MyD88/NF-κB and RANK/NF-κB pathways in PDLSCs. Meanwhile, for the first time, we employed LLC delivery system to load TFP for periodontitis treatment. The results showed that TFP-LLC could be effectively retained in the periodontal pocket and exerted a crucial role in inflammation resolution and periodontal tissue regeneration.

Personalized antibiotic selection in periodontal treatment improves clinical and microbiological outputs

Introduction

Periodontitis is a biofilm-mediated disease that is usually treated by non-surgical biofilm elimination with or without antibiotics. Antibiotic treatment in periodontal patients is typically selected empirically or using qPCR or DNA hybridization methods. These approaches are directed towards establishing the levels of different periodontal pathogens in periodontal pockets to infer the antibiotic treatment. However, current methods are costly and do not consider the antibiotic susceptibility of the whole subgingival biofilm.

Methods

In the current manuscript, we have developed a method to culture subgingival samples ex vivo in a fast, label-free impedance-based system where biofilm growth is monitored in real-time under exposure to different antibiotics, producing results in 4 hours. To test its efficacy, we performed a double-blind, randomized clinical trial where patients were treated with an antibiotic either selected by the hybridization method (n=32) or by the one with the best effect in the ex vivo growth system (n=32).

Results

Antibiotic selection was different in over 80% of the cases. Clinical parameters such as periodontal pocket depth, attachment level, and bleeding upon probing improved in both groups. However, dental plaque was significantly reduced only in the group where antibiotics were selected according to the ex vivo growth. In addition, 16S rRNA sequencing showed a larger reduction in periodontal pathogens and a larger increase in health-associated bacteria in the ex vivo growth group.

Discussion

The results of clinical and microbiological parameters, together with the reduced cost and low analysis time, support the use of the impedance system for improved individualized antibiotic selection.

Microbial biomarkers as a predictor of periodontal treatment response: A systematic review

To evaluate the prognostic accuracy of microbial biomarkers and their associations with the response to active periodontal treatment (APT) and supportive periodontal therapy (SPT). Microbial dysbiosis plays a crucial role in the disease processes of periodontitis. Biomarkers based on microbial composition may offer additional prognostic value, supplementing the limitations of current clinical parameters. While these microbial biomarkers have been clinically evaluated, there is a lack of consensus regarding their prognostic accuracy. A structured search strategy was applied to MEDLINE (PubMed), Cochrane Library, and Embase on 1/11/2022 to identify relevant publications. Prospective clinical studies involving either APT or SPT, with at least 3-month follow-up were included. There were no restrictions on the type of microbial compositional analysis. 1918 unique records were retrieved, and 13 studies (comprising 943 adult patients) were included. Heterogeneity of the studies precluded a meta-analysis, and none of the included studies had performed the sequence analysis of the periodontal microbiome. Seven and six studies reported on response to APT and SPT, respectively. The prognostic accuracy of the microbial biomarkers for APT and SPT was examined in only two and four studies, respectively. Microbial biomarkers had limited predictive accuracy for APT and inconsistent associations for different species across studies. For SPT, elevated abundance of periodontal pathogens at the start of SPT was predictive of subsequent periodontal progression. Similarly, persistent high pathogen loads were consistently associated with progressive periodontitis, defined as an increased pocket probing depth or clinical attachment loss. While there was insufficient evidence to support the clinical use of microbial biomarkers as prognostic tools for active periodontal treatment outcomes, biomarkers that quantify periodontal pathogen loads may offer prognostic value for predicting progressive periodontitis in the subsequent supportive periodontal therapy phase. Additional research will be required to translate information regarding subgingival biofilm composition and phenotype into clinically relevant prognostic tools.

Rookery through rehabilitation: Microbial community assembly in newborn harbour seals after maternal separation

Microbial community assembly remains largely unexplored in marine mammals, despite its potential importance for conservation and management. Here, neonatal microbiota assembly was studied in harbour seals (Phoca vitulina richardii) at a rehabilitation facility soon after maternal separation, through weaning, to the time of release back to their native environment. We found that the gingival and rectal communities of rehabilitated harbour seals were distinct from the microbiotas of formula and pool water, and became increasingly diverse and dissimilar over time, ultimately resembling the gingival and rectal communities of local wild harbour seals. Harbour seal microbiota assembly was compared to that of human infants, revealing the rapid emergence of host specificity and evidence of phylosymbiosis even though these harbour seals had been raised by humans. Early life prophylactic antibiotics were associated with changes in the composition of the harbour seal gingival and rectal communities and surprisingly, with transient increases in alpha diversity, perhaps because of microbiota sharing during close cohabitation with other harbour seals. Antibiotic-associated effects dissipated over time. These results suggest that while early life maternal contact may provide seeding for microbial assembly, co-housing of conspecifics during rehabilitation may help neonatal mammals achieve a healthy host-specific microbiota with features of resilience.

Long-term changes in the subgingival microbiota in patients with stage III-IV periodontitis treated by mechanical therapy and adjunctive systemic antibiotics: A secondary analysis of a randomized controlled trial

AIM

To explore whether adjunctive antibiotics can relevantly influence long-term microbiota changes in stage III-IV periodontitis patients.

MATERIALS AND METHODS

This is a secondary analysis of a randomized clinical trial on periodontal therapy with adjunctive 500 mg amoxicillin and 400 mg metronidazole or placebo thrice daily for 7 days. Subgingival plaque samples were taken before and 2, 8, 14 and 26 months after mechanical therapy. The V4-hypervariable region of the 16S rRNA gene was sequenced with Illumina MiSeq 250 base pair paired-end reads. Changes at the ribosomal sequence variant (RSV) level, diversity and subgingival-microbial dysbiosis index (SMDI) were explored with a negative binomial regression model and non-parametric tests.

RESULTS

Overall, 50.2% of all raw reads summed up to 72 RSVs (3.0%) that were generated from 163 stage III-IV periodontitis patients. Of those, 16 RSVs, including Porphyromonas gingivalis, Tannerella forsythia and Aggregatibacter actinomycetemcomitans, changed significantly over 26 months because of adjunctive systemic antibiotics. SMDI decreased significantly more in the antibiotic group at all timepoints, whereas the 2-month differences in alpha and beta diversity between groups were not significant at 8 and 14 months, respectively.

CONCLUSIONS

Mechanical periodontal therapy with adjunctive antibiotics induced a relevant and long-term sustainable change towards an oral microbiome more associated with oral health.

Influence of periodontal surgery on the subgingival microbiome-A systematic review and meta-analysis

OBJECTIVE

The objective of this systematic review and meta-analysis was to evaluate the effect of periodontal surgery on the subgingival microbiome.

BACKGROUND

Periodontitis is a chronic inflammation of the tooth supporting tissues caused by the dysbiosis of the subgingival biofilm. It is managed through different non-surgical and surgical treatment modalities. Recent EFP S3 guidelines recommended performing periodontal surgery as part of Step 3 periodontitis treatment after Step 1 and Step 2 periodontal therapy, with the aim to achieve pocket closure of persisting sites. Changes in the sub-gingival microbiome may explain the treatment outcomes observed at different time points. Various microbiological detection techniques for disease-associated pathogens have been evolved over time and have been described in the literature. However, the impact of different types of periodontal surgery on the subgingival microbiome remains unclear.

METHODS

A systematic literature search was conducted in Medline, Embase, LILACS and Cochrane Library supplemented by manual search (23DEC2019, updated 21APR2022).

RESULTS

From an initial search of 3046 studies, 28 were included according to our specific inclusion criteria. Seven microbiological detection techniques were used to analyse disease-associated species in subgingival plaque samples: optical microscope, culture, polymerase chain reaction (PCR), checkerboard, enzymatic reactions, immunofluorescence and 16S gene sequencing. The included studies exhibited differences in various aspects of their methodologies such as subgingival plaque sample collection or treatment modalities. Clinical data showed a significant decrease in probing pocket depths (PPD) and clinical attachment loss (CAL) after periodontal surgery. Microbiological findings were overall heterogeneous. Meta-analysis was performed on a sub-cohort of studies all using checkerboard as a microbiological detection technique. Random effect models for Treponema denticola (T. denticola), Porphyromonas gingivalis (P. gingivalis) and Tannerella forsythia (T. forsythia) did not show a significant effect on mean counts 3 months after periodontal surgery. Notably, Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans) showed a significant increase 3 months after periodontal surgery. 16S gene sequencing was used in one included study and reported a decrease in disease-associated species with an increase in health-associated species after periodontal surgery at 3 and 6 months.

CONCLUSION

This systematic review has shown that the effect of periodontal surgery on the changes in subgingival microbiome is heterogeneous and may not always be associated with a decrease in disease-associated species. The variability could be attributed to the microbiological techniques employed for the analysis. Therefore, there is a need for well-designed and adequately powered studies to understand how periodontal surgery influences the subgingival microbiome and how the individual's microbiome affects treatment outcomes after periodontal surgery.

A review on Impact of dietary interventions, drugs, and traditional herbal supplements on the gut microbiome

The gut microbiome is the community of healthy, and infectious organisms in the gut and its interaction in the host gut intestine (GI) environment. The balance of microbial richness with beneficial microbes is very important to perform healthy body functions like digesting food, controlling metabolism, and precise immune function. Alternately, this microbial dysbiosis occurs due to changes in the physiochemical condition, substrate avidity, and drugs. Moreover, various categories of diet such as "plant-based", "animal-based", "western", "mediterranean", and various drugs (antibiotic and common drugs) also contribute to maintaining microbial flora inside the gut. The imbalance (dysbiosis) in the microbiota of the GI tract can cause several disorders (such as diabetes, obesity, cancer, inflammation, and so on). Recently, the major interest is to use prebiotic, probiotic, postbiotic, and herbal supplements to balance such microbial community in the GI tract. But, there has still a large gap in understanding the microbiome function, and its relation to the host diet, drugs, and herbal supplements to maintain the healthy life of the host. So, the present review is about the updates on the microbiome concerns related to diet, drug, and herbal supplements, and also gives research evidence to improve our daily habits regarding diet, drugs, and herbal supplements. Because our regular dietary plan and traditional herbal supplements can improve our health by balancing the bacteria in our gut.

Antibiotic-Therapy-Induced Gut Dysbiosis Affecting Gut Microbiota-Brain Axis and Cognition: Restoration by Intake of Probiotics and Synbiotics

Antibiotic therapy through short-term or repeated long-term prescriptions can have several damaging effects on the normal microbiota of the gastrointestinal tract. Changes in microbiota could be multiple including decreased diversity of species in gut microbiota, changed metabolic activity, and the occurrence of antibiotic-resistant strains. Antibiotic-induced gut dysbiosis in turn can induce antibiotic-associated diarrhoea and recurrent infections caused by Clostridioides difficile. There is also evidence that the use of different chemical classes of antibiotics for the treatment of a variety of ailments can lead to several health issues including gastrointestinal, immunologic, and neurocognitive conditions. This review discusses gut dysbiosis, its symptoms and one important cause, which is antibiotic therapy for the induction of gut dysbiosis. Since the maintenance of good gut health is important for the well-being and functioning of physiological and cognitive activities through the normal gut-microbiota-brain relationship, the condition of dysbiosis is not desirable. Specific therapies are prescribed by medical practitioners for the cure of a variety of ailments, and, if the prescription of antibiotics becomes unavoidable, there is a possibility of the onset of gut dysbiosis as the side or after effects. Therefore, the restoration of imbalanced gut microbiota to its balanced condition becomes necessary. A healthy relationship between gut microbiota and the brain can be achieved with the introduction of probiotic strains into the gut in a practical and consumer-friendly way, such as consumption of food and beverages prepared with the use of characterised probiotic species, fermented foods as the potential biotics, or synbiotic supplements.

Effect of Periodontal Interventions on Characteristics of the Periodontal Microbial Profile: A Systematic Review and Meta-Analysis

Our systematic review aimed to evaluate the effect of periodontal interventions on the diversity and composition of periodontal microbiota assessed by high throughput sequencing (HTS) metagenomics analysis. An electronic search was conducted from database inception to November 2021. All clinical trials that evaluated the effect of periodontal interventions on the gingival microbiota through HTS were selected. The measures of alpha diversity, richness, Shannon diversity index, and the Chao1 index, were used as the primary outcome, whereas relative abundances of bacterial genera were considered as the secondary outcome. Overall, 24 studies were eligible for the systematic review, of which 13 studies were included in the meta-analysis. Periodontal intervention for the test group decreased Shannon diversity, richness, and Chao1 index (alpha diversity), as observed from baseline to post-treatment. The most common genera that increased after periodontal therapy were Rothia, Actinomyces, Streptococcus, Veillonella, and Hemophilus, whilst Porphyromonas, Tannerella, Fusobacterium, and Treponema decreased after periodontal therapy. Periodontal interventions may decrease the bacterial diversity and richness and alter the composition of oral microbiota in the short term. Periodontal microbiota signatures could potentially be used for the assessment of periodontal disease development, progression, and success of the intervention.

Microbiome profiles of non-responding and responding paired periodontitis sites within the same participants following non-surgical treatment

Aim

Periodontitis is a site-specific, chronic disease treated by non-surgical debridement of subgingival plaque. We aimed to determine the microbiome of sites that did not respond to this treatment (NR) compared with paired good responding (GR) sites before and after treatment.

Materials and methods

In a longitudinal cohort study, clinical parameters of disease and biological samples were taken prior to and 3 months after treatment. Twelve NR sites from six participants were paired with GR sites within the same participant. Subgingival plaque samples were subjected to bacterial community analysis using 16S rRNA gene sequencing.

Results

There were no significant differences in clinical parameters and microbial communities at baseline between GR and NR sites. Bacterial communities in deep pockets were dominated by a small number of species, notably Porphyromonas gingivalis and Treponema denticola. In NR sites three months after treatment there was no significant change in bacterial composition whilst there was a collapse in the abundance of pathobionts in GR sites.

Conclusion

NR sites were not identifiable prior to treatment by clinical or microbiological parameters. Treatment failed to disrupt pathogenic bacterial community in NR sites. Targeted suppression of particular species should be considered to initiate community collapse and aid disease resolution.

SMDI: An Index for Measuring Subgingival Microbial Dysbiosis

An intuitive, clinically relevant index of microbial dysbiosis as a summary statistic of subgingival microbiome profiles is needed. Here, we describe a subgingival microbial dysbiosis index (SMDI) based on machine learning analysis of published periodontitis/health 16S microbiome data. The raw sequencing data, split into training and test sets, were quality filtered, taxonomically assigned to the species level, and centered log-ratio transformed. The training data set was subject to random forest analysis to identify discriminating species (DS) between periodontitis and health. DS lists, compiled by various "Gini" importance score cutoffs, were used to compute the SMDI for samples in the training and test data sets as the mean centered log-ratio abundance of periodontitis-associated species subtracted by that of health-associated ones. Diagnostic accuracy was assessed with receiver operating characteristic analysis. An SMDI based on 49 DS provided the highest accuracy with areas under the curve of 0.96 and 0.92 in the training and test data sets, respectively, and ranged from -6 (most normobiotic) to 5 (most dysbiotic) with a value around zero discriminating most of the periodontitis and healthy samples. The top periodontitis-associated DS were Treponema denticola, Mogibacterium timidum, Fretibacterium spp., and Tannerella forsythia, while Actinomyces naeslundii and Streptococcus sanguinis were the top health-associated DS. The index was highly reproducible by hypervariable region. Applying the index to additional test data sets in which nitrate had been used to modulate the microbiome demonstrated that nitrate has dysbiosis-lowering properties in vitro and in vivo. Finally, 3 genera (Treponema, Fretibacterium, and Actinomyces) were identified that could be used for calculation of a simplified SMDI with comparable accuracy. In conclusion, we have developed a nonbiased, reproducible, and easy-to-interpret index that can be used to identify patients/sites at risk of periodontitis, to assess the microbial response to treatment, and, importantly, as a quantitative tool in microbiome modulation studies.

Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics

Humans have a long-standing coexistence with microorganisms. In particular, the microbial community that populates the human gastrointestinal tract has emerged as a critical player in governing human health and disease. DNA and RNA sequencing techniques that map taxonomical composition and genomic potential of the gut community have become invaluable for microbiome research. However, deriving a biochemical understanding of how activities of the gut microbiome shape host development and physiology requires an expanded experimental design that goes beyond these approaches. In this review, we explore advances in high-throughput techniques based on liquid chromatography-mass spectrometry. These omics methods for the identification of proteins and metabolites have enabled direct characterisation of gut microbiome functions and the crosstalk with the host. We discuss current metaproteomics and metabolomics workflows for producing functional profiles, the existing methodological challenges and limitations, and recent studies utilising these techniques with a special focus on early life gut microbiome.

The effect of adjunctive systemic antibiotics on microbial populations compared to scaling and root planing alone for the treatment of periodontitis: A pilot randomized clinical trial

AIM

To investigate the microbial shift after periodontitis being treated by scaling and root planing (SRP) with or without adjunctive antibiotics, and to assess the relationship between oral microbiota and systemic factors.

METHODS

A 6-month pilot randomized controlled trial recruited 14 subjects with severe periodontitis, divided into test group and control group to receive full-mouth SRP with or without amoxicillin (500mg) and metronidazole (200mg) (t.i.d. 7d). Clinical examination, collection of subgingival plaque and saliva, and blood tests were performed at baseline pre-treatment, three months, and six months post-treatment. The V3V4 region of 16S DNA was sequenced; taxonomic assignment was based on the Human Oral Microbiome Database.

RESULTS

The periodontal condition significantly improved in both groups; the test group showed a greater improvement in plaque index, probing depth, and bleeding index than the control group. The test group demonstrated significantly lower microbial richness and diversity, and less abundant Porphyromonas than the control group in at three months for both subgingival microbiome and salivary microbiome. However, the microbial differences narrowed within six months. The subgingival and salivary microbiota shifted synergistically. Glucose was positively related to subgingival Porphyromonas; mean platelet volume was positively related to subgingival Leptotrichia.

CONCLUSIONS

Systemic administration of amoxicillin and metronidazole along with SRP had an advantage over SRP alone in clinical improvement and infection control in both the subgingival region and saliva three months post-treatment. Microbial advantage nearly disappeared at six months; however, the clinical advantage lasted longer. The use of antibiotics also has potential benefits for systemic inflammation and glucose. This article is protected by copyright. All rights reserved.

Steady-State Pre-rRNA Analysis to Investigate the Functional Microbiome

The gut microbiome is recognized as a critical regulator of human diseases. Constituents of the microbiota and their individual activities can affect a broad range of disease states related to autoimmunity, cancer, infection, metabolism, mental health, and toxicant exposure. A substantial number of microbiome species are not culturable, limiting their study in vitro. Sequencing methods have allowed quantification of the composition of the microbiome, but methods to characterize the physiological status of bacterial species remain limited. Ribosomal RNA precursors (pre-rRNAs) are species-specific intermediates in bacterial ribosomal synthesis, and their levels are highly responsive to environmental changes. Immediately before and during active growth, pre-rRNA levels are high, whereas in non-dividing cells, copy numbers are orders of magnitude lower. These dynamics are conserved in all bacterial species and occur exclusively in viable cells, allowing the specific characterization of living and functional bacteria in their native states. Pre-rRNA analysis has been shown to yield valuable real-time information on the physiology of individual bacterial species within complex samples, beyond what traditional qPCR and sequencing methods can offer. Herein, we describe a PCR-based protocol to interrogate and quantify the in situ growth status of bacterial species of interest within a complex microbiome. We also describe an in vitro protocol to characterize the pre-rRNA/growth relationship for a given bacterial species to provide greater context for values obtained from natural samples. Improved understanding of microbial physiological responses to exposures could reveal novel toxicological mechanisms, biomarkers, and potential treatments. © 2021 Wiley Periodicals LLC. Basic Protocol: Targeted steady-state pre-rRNA analysis Support Protocol: Characterization of pre-rRNA/growth relationship © 2021 by John Wiley & Sons, Inc.

Submucosal microbiome of peri-implant sites: A cross-sectional study

AIM

To study the peri-implant submucosal microbiome in relation to implant disease status, dentition status, smoking habit, gender, implant location, implant system, time of functional loading, probing pocket depth (PPD), and presence of bleeding on probing.

MATERIALS AND METHODS

Biofilm samples were collected from the deepest peri-implant site of 41 patients with paper points, and analysed using 16S rRNA gene pyrosequencing.

RESULTS

We observed differences in microbial profiles by PPD, implant disease status, and dentition status. Microbiota in deep pockets included higher proportions of the genera Fusobacterium, Prevotella, and Anaeroglobus compared with shallow pockets that harboured more Rothia, Neisseria, Haemophilus, and Streptococcus. Peri-implantitis (PI) sites were dominated by Fusobacterium and Treponema compared with healthy implants and peri-implant mucositis, which were mostly colonized by Rothia and Streptococcus. Partially edentulous (PE) individuals presented more Fusobacterium, Prevotella, and Rothia, whereas fully edentulous individuals presented more Veillonella and Streptococcus.

CONCLUSIONS

PPD, implant disease status, and dentition status may affect the submucosal ecology leading to variation in composition of the microbiome. Deep pockets, PI, and PE individuals were dominated by Gram-negative anaerobic taxa.

Structure and Function of Oral Microbial Community in Periodontitis Based on Integrated Data

Objective

Microorganisms play a key role in the initiation and progression of periodontal disease. Research studies have focused on seeking specific microorganisms for diagnosing and monitoring the outcome of periodontitis treatment. Large samples may help to discover novel potential biomarkers and capture the common characteristics among different periodontitis patients. This study examines how to screen and merge high-quality periodontitis-related sequence datasets from several similar projects to analyze and mine the potential information comprehensively.

Methods

In all, 943 subgingival samples from nine publications were included based on predetermined screening criteria. A uniform pipeline (QIIME2) was applied to clean the raw sequence datasets and merge them together. Microbial structure, biomarkers, and correlation network were explored between periodontitis and healthy individuals. The microbiota patterns at different periodontal pocket depths were described. Additionally, potential microbial functions and metabolic pathways were predicted using PICRUSt to assess the differences between health and periodontitis.

Results

The subgingival microbial communities and functions in subjects with periodontitis were significantly different from those in healthy subjects. Treponema, TG5, Desulfobulbus, Catonella, Bacteroides, Aggregatibacter, Peptostreptococcus, and Eikenella were periodontitis biomarkers, while Veillonella, Corynebacterium, Neisseria, Rothia, Paludibacter, Capnocytophaga, and Kingella were signature of healthy periodontium. With the variation of pocket depth from shallow to deep pocket, the proportion of Spirochaetes, Bacteroidetes, TM7, and Fusobacteria increased, whereas that of Proteobacteria and Actinobacteria decreased. Synergistic relationships were observed among different pathobionts and negative relationships were noted between periodontal pathobionts and healthy microbiota.

Conclusion

This study shows significant differences in the oral microbial community and potential metabolic pathways between the periodontitis and healthy groups. Our integrated analysis provides potential biomarkers and directions for in-depth research. Moreover, a new method for integrating similar sequence data is shown here that can be applied to other microbial-related areas.

A scoping review of longitudinal airway microbiota studies

INTRODUCTION

The role of the microbiota in inflammatory airway diseases is unclear. Antimicrobial therapies have predominantly been guided by culture results. However, molecular sequencing has shown that the airway microbiota is much more complex and accurate modeling requires longitudinal analysis.

AREAS COVERED

A Preferred Reporting Items for Systematic Reviews and Meta-Analyses scoping review was performed by searching Medline, Scopus, and Web of Science databases for all longitudinal airway microbiota studies that utilized molecular techniques. 38 studies with 1,993 participants were included in this review. Healthy microbial communities were more diverse, individualized and stable over time. Acute infections resulted in changes in the microbiota that were detected earlier and more sensitively by molecular sequencing than culture. Distinct microbiota profiles have been demonstrated in chronic obstructive pulmonary disease patients associated with exacerbation frequency and severity.

EXPERT OPINION

Longitudinal studies provide essential data on the stability of the microbiota over time and valuable information about the dynamic interactions between host, disease and microbes. We believe that molecular sequencing will be increasingly incorporated into research and clinical practice in the future. These advances can lead to improved diagnosis, enhanced prescribing guidance and reduce unnecessary antibiotic usage.

Citizen-science based study of the oral microbiome in Cystic fibrosis and matched controls reveals major differences in diversity and abundance of bacterial and fungal species

Introduction: Cystic fibrosis (CF) is an autosomal genetic disease, associated with the production of excessively thick mucosa and with life-threatening chronic lung infections. The microbiota of the oral cavity can act as a reservoir or as a barrier for infectious microorganisms that can colonize the lungs. However, the specific composition of the oral microbiome in CF is poorly understood.Methods: In collaboration with CF associations in Spain, we collected oral rinse samples from 31 CF persons (age range 7-47) and matched controls, and then performed 16S rRNA metabarcoding and high-throughput sequencing, combined with culture and proteomics-based identification of fungi to survey the bacterial and fungal oral microbiome.Results: We found that CF is associated with less diverse oral microbiomes, which were characterized by higher prevalence of Candida albicans and differential abundances of a number of bacterial taxa that have implications in both the connection to lung infections in CF, as well as potential oral health concerns, particularly periodontitis and dental caries.Conclusion: Overall, our study provides a first global snapshot of the oral microbiome in CF. Future studies are required to establish the relationships between the composition of the oral and lung microbiomes in CF.

In Vitro Anti-Biofilm and Antibacterial Properties of Streptococcus downii sp. nov

The aim of this study was to evaluate the potential anti-biofilm and antibacterial activities of Streptococcus downii sp. nov. To test anti-biofilm properties, Streptococcus mutans, Actinomyces naeslundii, Veillonella parvula, Fusobacterium nucleatum, Porphyromonas gingivalis, and Aggregatibacter actinomycetemcomitans were grown in a biofilm model in the presence or not of S. downii sp. nov. for up to 120 h. For the potential antibacterial activity, 24 h-biofilms were exposed to S. downii sp. nov for 24 and 48 h. Biofilms structures and bacterial viability were studied by microscopy, and the effect in bacterial load by quantitative polymerase chain reaction. A generalized linear model was constructed, and results were considered as statistically significant at p < 0.05. The presence of S. downii sp. nov. during biofilm development did not affect the structure of the community, but an anti-biofilm effect against S. mutans was observed (p < 0.001, after 96 and 120 h). For antibacterial activity, after 24 h of exposure to S. downii sp. nov., counts of S. mutans (p = 0.019) and A. actinomycetemcomitans (p = 0.020) were significantly reduced in well-structured biofilms. Although moderate, anti-biofilm and antibacterial activities of S. downii sp. nov. against oral bacteria, including some periodontal pathogens, were demonstrated in an in vitro biofilm model.

Metagenomic sequencing provides new insights into the subgingival bacteriome and aetiopathology of periodontitis

"Open-ended" molecular techniques such as 16S rRNA sequencing have revealed that the oral bacteriome of subgingival plaque is more diverse than originally thought. 16S rRNA analysis has demonstrated that constituents of the overall bacterial community are qualitatively similar in health and disease, differing mainly in their relative proportions with respect to each other. Species in low abundance can also act as critical species, leading to the concept of global community dysbiosis which relates to shifts in community structure, rather than shifts in membership. Correlation analysis suggests that coordinated interactions in the community are essential for incipient dysbiosis and disease pathogenesis. The subgingival bacteriome also provides biomarkers that are useful for disease detection and management. Combined with clinical and biological parameters, these may assist clinicians in developing and implementing effective treatment strategies to restore microbial homeostasis and monitor disease. Identification of higher risk groups or poor responders to treatment using unique subgingival bacteriome signatures may also lead to early intervention.

Did Omics change periodontal therapy?

The starting point for defining effective treatment protocols is a clear understanding of the etiology and pathogenesis of a condition. In periodontal diseases, this understanding has been hindered by a number of factors, such as the difficulty in differentiating primary pathogens from nonpathogens in complex biofilm structures. The introduction of DNA sequencing technologies, including taxonomic and functional analyses, has allowed the oral microbiome to be investigated in much greater breadth and depth. This article aims to compile the results of studies, using next-generation sequencing techniques to evaluate the periodontal microbiome, in an attempt to determine how far the knowledge provided by these studies has brought us in terms of influencing the way we treat periodontitis. The taxonomic data provided, to date, by published association and elimination studies using next-generation sequencing confirm previous knowledge on the role of classic periodontal pathogens in the pathobiology of disease and include new species/genera. Conversely, species and genera already considered as host-compatible and others less explored were associated with periodontal health as their levels were elevated in healthy individuals and increased after therapy. Functional and transcriptomic analyses also demonstrated that periodontal biofilms are taxonomically diverse, functionally congruent, and highly cooperative. Very few interventional studies to date have examined the effects of treatment on the periodontal microbiome, and such studies are heterogeneous in terms of design, sample size, sampling method, treatment provided, and duration of follow-up. Hence, it is still difficult to draw meaningful conclusions from them. Thus, although OMICS knowledge has not yet changed the way we treat patients in daily practice, the information provided by these studies opens new avenues for future research in this field. As new pathogens and beneficial species become identified, future randomized clinical trials could monitor these species/genera more comprehensively. In addition, the metatranscriptomic data, although still embryonic, suggest that the interplay between the host and the oral microbiome may be our best opportunity to implement personalized periodontal treatments. Therapeutic schemes targeting particular bacterial protein products in subjects with specific genetic profiles, for example, may be the futuristic view of enhanced periodontal therapy.

Microbiome changes in young periodontitis patients treated with adjunctive metronidazole and amoxicillin

BACKGROUND

To our knowledge, to date, no studies have comprehensively assessed the changes occurring in the subgingival microbiome of young patients with periodontitis treated by means of mechanical and antibiotic therapy. Thus, this study aimed to use next-generation sequencing to evaluate the subgingival microbial composition of young patients with severe periodontitis treated with scaling and root planing and systemic metronidazole and amoxicillin.

METHODS

Subgingival samples from healthy individuals and shallow and deep sites from periodontitis patients were individually collected at baseline and 90 days post-treatment. The samples were analyzed using 16S rRNA-gene sequencing (MiSeq-Illumina) and QIIME pipeline. Differences between groups for the microbiological data were determined using principal coordinate analysis (PCoA), linear mixed models, and the PERMANOVA test.

RESULTS

One hundred samples were collected from 10 periodontitis patients and seven healthy individuals. PCoA analysis revealed significant partitioning between pre-and post-treatment samples. No major differences in the composition of the subgingival microbiota were observed between shallow and deep sites, at baseline or at 90-days post-treatment, and the microbiome of both site categories after treatment moved closer in similarity to that observed in periodontal health. Treatment significantly improved all clinical parameters and reduced the relative abundance of classical periodontal pathogens and of Fretibacterium fastidiosum, Eubacterium saphenum, Porphyromonas endodontalis, Treponema medium, Synergistetes, TM7, and Treponema spp, and increased that of Actinomyces, Rothia, Haemophilus, Corynebacterium, and Streptococci spp.

CONCLUSION

Mechanical treatment associated with metronidazole and amoxicillin promoted a beneficial change in the microbiome of young individuals with severe periodontitis.

A systematic review on bacterial community changes after periodontal therapy with and without systemic antibiotics: An analysis with a wider lens

BACKGROUND

This systematic review aimed to provide a comprehensive view on microbial community shifts after periodontal therapy with and without systemic antibiotics, conducted in randomized controlled trials (RCTs).

METHODS

Search functions in PubMed, Scopus, the Web of Knowledge, and the Cochrane Oral Health Library databases were used to locate studies published up to December 2018 that reported at least two bacteria before and after periodontal therapy. Gray literature and manual searching were done. Information about reported bacteria in those studies were extracted, and a descriptive microbial community analysis was conducted to observe trends and influencing factors on microbial dynamics. Methodological aspects were examined, including the bacterial detection method, heterogeneity of procedures, and risk of bias (RoB) of the studies.

RESULTS

The 30 included studies reported 130 different bacterial genera. Four different detection methods were reported: cultivation, polymerase chain reaction, DNA-DNA-checkerboard hybridization, and 16S rDNA amplicon sequencing. No general compositional change between the antibiotic and placebo groups could be found after therapy on the community level. Fifty-five bacteria were reported in two or more studies. Of those, 24 genera decreased and 13 increased more frequently after antibiotic use. Great heterogeneity between procedures and variability in RoB were found among the studies.

CONCLUSIONS

Microbial shifts occurred regardless of the use of antibiotics. Antibiotic therapy seems to induce more changes in single bacteria. The heterogeneity in methods and reporting of the included studies preclude clinical recommendations on the use or not of adjunctive antibiotics. The present results may guide further research on the topic.

Differences in the periodontal microbiome of successfully treated and persistent aggressive periodontitis

AIMS

The primary aim of this investigation was to analyse the periodontal microbiome in patients with aggressive periodontitis (AgP) following treatment.

METHODS

Sixty-six AgP patients were recalled on average 7 years after completion of active periodontal treatment and had subgingival plaque samples collected and processed for 16S rRNA gene sequencing analyses.

RESULTS

Of 66 participants, 52 showed persistent periodontal disease, while 13 participants were considered as "successfully treated AgP" (no probing pocket depths >4 mm) and 1 was fully edentulous. Genera associated with persistent generalized disease included Actinomyces, Alloprevotella, Capnocytophaga, Filifactor, Fretibacterium, Fusobacterium, Leptotrichia, Mogibacterium, Saccharibacteria [G-1], Selenomonas and Treponema. "Successfully treated" patients harboured higher proportions of Haemophilus, Rothia, and Lautropia and of Corynebacterium, Streptococcus and Peptidiphaga genera. Overall, patients with persistent generalized AgP (GAgP) revealed higher alpha diversity compared to persistent localized AgP (LAgP) and stable patients (p < .001). Beta diversity analyses revealed significant differences only between stable and persistent GAgP groups (p = .004).

CONCLUSION

Patients with persistent AgP showed a more dysbiotic subgingival biofilm than those who have been successfully treated. It remains to be established whether such differences were predisposing to disease activity or were a result of a dysbiotic change associated with disease recurrence in the presence of sub-standard supportive periodontal therapy or other patient-related factors.

Using next-generation sequencing to detect oral microbiome change following periodontal interventions: A systematic review

Objectives

This systematic review was to evaluate the change of oral microbiome based on next‐generation sequencing (NGS)‐metagenomic analysis following periodontal interventions among systematically healthy subjects.

Materials and Methods

A structured search strategy consisting of “metagenomics” and “oral diseases” was applied to PubMed, EMBASE, and Web of Science to identify effective papers. The included studies were original studies published in English, using metagenomic approach to analyze the effectiveness of periodontal intervention on oral microbiome among systematically healthy human subjects with periodontitis.

Results

A total of 12 papers were included in this review. Due to the heterogeneity of selected study, quantitative analysis was not performed. The findings as to how alpha diversity changed after interventions were not consistent across studies. Six studies illustrated clear separation of microbial composition between dental plaque samples collected before and after intervention using principal coordinates/component analysis. The most commonly detected genera before intervention were Porphyromonas, Treponema, Tannerella, and Prevotella, while Streptococcus and Actinomyces usually increased and became the dominant genera after intervention. Correlation network analysis revealed that after intervention, the topology of network was different compared to the corresponding pre‐interventional samples.

Conclusion

Existing evidence of metagenomic studies depicts a complex change in oral microbiome after periodontal intervention.

Oral biofilms exposure to chlorhexidine results in altered microbial composition and metabolic profile

Oral diseases (e.g., dental caries, periodontitis) are developed when the healthy oral microbiome is imbalanced allowing the increase of pathobiont strains. Common practice to prevent or treat such diseases is the use of antiseptics, like chlorhexidine. However, the impact of these antiseptics on the composition and metabolic activity of the oral microbiome is poorly addressed. Using two types of oral biofilms—a 14-species community (more controllable) and human tongue microbiota (more representative)—the impact of short-term chlorhexidine exposure was explored in-depth. In both models, oral biofilms treated with chlorhexidine exhibited a pattern of inactivation (>3 log units) and fast regrowth to the initial bacterial concentrations. Moreover, the chlorhexidine treatment induced profound shifts in microbiota composition and metabolic activity. In some cases, disease associated traits were increased (such as higher abundance of pathobiont strains or shift in high lactate production). Our results highlight the need for alternative treatments that selectively target the disease-associated bacteria in the biofilm without targeting the commensal microorganisms.

Metagenomic Assessment of Different Interventions for Treatment of Chronic Periodontitis: A Systematic Review and Meta-Analysis

Background:

Chronic periodontitis is attributed to oral microbial imbalance and host inflammatory reaction.

Objective:

Our review addresses the question of: Are the available interventions able to regain oral microbial balance in patients having chronic periodontitis?

Data Sources:

We performed a comprehensive systematic search of MEDLine via Pubmed, Cochrane CENTRAL, Clinicalkey, Clarivate Analytics, Springer materials, Wiley, SAGE, Elsevier, Taylor & Francis group, and Wolter Kluwer, together with hand searching and searching the grey literature.

Eligibility Criteria:

We included interventional studies testing the microbiome analysis using metagenomic techniques as an outcome to any intervention for chronic periodontitis.

Study Appraisal and Synthesis Methods:

All studies were imported in Mendeley. The risk of bias was assessed using the specific tool for each study design. The results were analysed using RevMan. All the review steps were performed in duplicates.

Results:

The search yielded 2700 records. After exclusion steps, 10 records were found eligible. We included 5 RCTs, 1 non-RCT, 3 before-and-after studies, and 1 ongoing study. The studies tested non-surgical periodontal treatment with and without antibiotic coverage, probiotics, sodium hypochlorite rinse, and different toothpaste ingredients. One RCT tested the use of enamel matrix derivatives in cases with furcation involvement.

Limitations:

The eligible available studies were small in number. Also, the risk of bias and lack of a standardized protocol impaired the ability to pool all the results.

Conclusions:

The body of the available evidence is not sufficient, and future studies are recommended to better evaluate the effect of periodontal treatments on the periodontal microbiome.

No differences in microbiome changes between anti-adhesive and antibacterial ingredients in toothpastes during periodontal therapy

Aim

This subgroup analysis of a 12‐week randomized, double‐blind, and two‐center trial aimed to evaluate whether two different toothpaste formulations can differentially modulate the dental microbiome.

Material and Methods

Forty one mild to moderate periodontitis patients used as an adjunct to periodontal treatment either a toothpaste with anti‐adhesive zinc‐substituted carbonated hydroxyapatite (HA) or with antimicrobial and anti‐adhesive amine fluoride/stannous fluoride (AmF/SnF₂) during a 12‐week period. Plaque samples from buccal/lingual, interproximal, and subgingival sites were taken at baseline, 4 weeks after oral hygiene phase, and 8 weeks after periodontal therapy. Samples were analyzed with paired‐end Illumina Miseq 16S rDNA sequencing. The differences and changes on community level (alpha and beta diversity) and on the level of single agglomerated ribosomal sequence variants (aRSV) were calculated with analysis of covariance (ANCOVA) and likelihood ratio test (LRT).

Results

Interproximal and subgingival sites harbored predominately Fusobacterium and Prevotella species associated with periodontitis, whereas buccal/lingual sites harbored mainly Streptococcus and Veillonella species associated with periodontal health. Alpha and beta diversity did not change noticeably differently between both toothpaste groups (P > 0.05, ANCOVA). Furthermore, none of the aRSVs showed a noticeably different change between the tested toothpastes during periodontal therapy (P_adj .> 0.05, LRT).

Conclusion

The use of a toothpaste containing anti‐adhesive HA did not induce statistically noticeably different changes on microbial composition compared to an antimicrobial and anti‐adhesive AmF/SnF₂ formulation.

Metabolic changes during periodontitis therapy assessed by real-time ambient mass spectrometry

It has been shown that bacteria in periodontally diseased patients can be recognized by the detection of volatile metabolites in the headspace of saliva by real-time ambient mass spectrometry. The aim of this study was to use this detection method to analyze the oral metabolome in diseased periodontitis patients before and after therapy to monitor disease evolution and healing events. Twelve patients with advanced chronic periodontal disease and 12 periodontally healthy controls served as test and control groups, respectively. Clinical data, subgingival plaque samples and saliva samples were collected at baseline (BL) and 3 months after treatment. The test group received non-surgical scaling and root planing using systemic antibiotics and the control group received one session of supragingival cleaning. Saliva samples from all subjects were analyzed with ambient mass spectrometry. Significant metabolic alterations were found in the headspace of saliva of periodontitis patients 3 months after the non-surgical periodontal treatment. Furthermore, the diseased group showed metabolic features after the treatment that were similar to the healthy control group. In addition, 29 metabolic features correlated with A. actinomycetemcomitans, 17 features correlated with P. gingivalis and one feature correlated with T. denticola. It was shown that headspace secondary electrospray ionization - mass spectrometry allows the detection of different volatile metabolites in healthy and diseased patients. It can be concluded that this rapid and minimally invasive method could have the potential to routinely diagnose and monitor periodontal diseases in the headspace of saliva samples and, eventually, in exhaled breath.

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.

Increased transferrin saturation is associated with subgingival microbiota dysbiosis and severe periodontitis in genetic haemochromatosis

Genetic haemochromatosis (GH) is responsible for iron overload. Increased transferrin saturation (TSAT) has been associated with severe periodontitis, which is a chronic inflammatory disease affecting tissues surrounding the teeth and is related to dysbiosis of the subgingival microbiota. Because iron is essential for bacterial pathogens, alterations in iron homeostasis can drive dysbiosis. To unravel the relationships between serum iron biomarkers and the subgingival microbiota, we analysed samples from 66 GH patients. The co-occurrence analysis of the microbiota showed very different patterns according to TSAT. Healthy and periopathogenic bacterial clusters were found to compete in patients with normal TSAT (≤45%). However, significant correlations were found between TSAT and the proportions of Porphyromonas and Treponema, which are two genera that contain well-known periopathogenic species. In patients with high TSAT, the bacterial clusters exhibited no mutual exclusion. Increased iron bioavailability worsened periodontitis and promoted periopathogenic bacteria, such as Treponema. The radical changes in host-bacteria relationships and bacterial co-occurrence patterns according to the TSAT level also suggested a shift in the bacterial iron supply from transferrin to NTBI when TSAT exceeded 45%. Taken together, these results indicate that iron bioavailability in biological fluids is part of the equilibrium between the host and its microbiota.

Effects of Bifidobacterium probiotic on the treatment of chronic periodontitis: A randomized clinical trial

AIM

This randomized placebo-controlled clinical trial evaluated the effect of Bifidobacterium animalis subsp. lactis (B. lactis) HN019-containing probiotic lozenges as adjuvant to scaling and root planing (SRP) in patients with generalized chronic periodontitis.

MATERIALS AND METHODS

Forty-one chronic periodontitis patients were recruited and monitored clinically, immunologically, and microbiologically at baseline (before SRP) and 30 and 90 days after SRP. All patients were randomly assigned to a Test (SRP + Probiotic, n = 20) or Control (SRP + Placebo, n = 21) group. The probiotic lozenges were used twice a day for 30 days. The data were statistically analysed.

RESULTS

The Test group presented a decrease in probing pocket depth and a clinical attachment gain significantly higher than those of the Control group at 90 days. The Test group also demonstrated significantly fewer periodontal pathogens of red and orange complexes, as well as lower proinflammatory cytokine levels when compared to the Control group. Only the Test group showed an increase in the number of B. lactis HN019 DNA copies on subgingival biofilm at 30 and 90 days.

CONCLUSION

The use of B. lactis HN019 as an adjunct to SRP promotes additional clinical, microbiological, and immunological benefits in the treatment of chronic periodontitis (NCT03408548).

Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis

Empiric antibiotics are often used in combination with mechanical debridement to treat patients suffering from periodontitis and to eliminate disease-associated pathogens. Until now, only a few next generation sequencing 16S rDNA amplicon based publications with rather small sample sizes studied the effect of those interventions on the subgingival microbiome. Therefore, we studied subgingival samples of 89 patients with chronic periodontitis (solely non-smokers) before and two months after therapy. Forty-seven patients received mechanical periodontal therapy only, whereas 42 patients additionally received oral administered amoxicillin plus metronidazole (500 and 400 mg, respectively; 3x/day for 7 days). Samples were sequenced with Illumina MiSeq 300 base pairs paired end technology (V3 and V4 hypervariable regions of the 16S rDNA). Inter-group differences before and after therapy of clinical variables (percentage of sites with pocket depth ≥ 5mm, percentage of sites with bleeding on probing) and microbiome variables (diversity, richness, evenness, and dissimilarity) were calculated, a principal coordinate analysis (PCoA) was conducted, and differential abundance of agglomerated ribosomal sequence variants (aRSVs) classified on genus level was calculated using a negative binomial regression model. We found statistically noticeable decreased richness, and increased dissimilarity in the antibiotic, but not in the placebo group after therapy. The PCoA revealed a clear compositional separation of microbiomes after therapy in the antibiotic group, which could not be seen in the group receiving mechanical therapy only. This difference was even more pronounced on aRSV level. Here, adjunctive antibiotics were able to induce a microbiome shift by statistically noticeably reducing aRSVs belonging to genera containing disease-associated species, e.g., Porphyromonas, Tannerella, Treponema, and Aggregatibacter, and by noticeably increasing genera containing health-associated species. Mechanical therapy alone did not statistically noticeably affect any disease-associated taxa. Despite the difference in microbiome modulation both therapies improved the tested clinical parameters after two months. These results cast doubt on the relevance of the elimination and/or reduction of disease-associated taxa as a main goal of periodontal therapy.

Ecological Therapeutic Opportunities for Oral Diseases

The three main oral diseases of humans, that is, caries, periodontal diseases, and oral candidiasis, are associated with microbiome shifts initiated by changes in the oral environment and/or decreased effectiveness of mucosal immune surveillance. In this review, we discuss the role that microbial-based therapies may have in the control of these conditions. Most investigations on the use of microorganisms for management of oral disease have been conducted with probiotic strains with some positive but very discrete clinical outcomes. Other strategies such as whole oral microbiome transplantation or modification of community function by enrichment with health-promoting indigenous oral strains may offer more promise, but research in this field is still in its infancy. Any microbial-based therapeutics for oral conditions, however, are likely to be only one component within a holistic preventive strategy that should also aim at modification of the environmental influences responsible for the initiation and perpetuation of microbiome shifts associated with oral dysbiosis.

The oral microbiome - an update for oral healthcare professionals. Br Dent J. 2016;221:657-666. [PMID: 27857087 DOI: 10.1038/sj.bdj.2016.865]

For millions of years, our resident microbes have coevolved and coexisted with us in a mostly harmonious symbiotic relationship. We are not distinct entities from our microbiome, but together we form a 'superorganism' or holobiont, with the microbiome playing a significant role in our physiology and health. The mouth houses the second most diverse microbial community in the body, harbouring over 700 species of bacteria that colonise the hard surfaces of teeth and the soft tissues of the oral mucosa. Through recent advances in technology, we have started to unravel the complexities of the oral microbiome and gained new insights into its role during both health and disease. Perturbations of the oral microbiome through modern-day lifestyles can have detrimental consequences for our general and oral health. In dysbiosis, the finely-tuned equilibrium of the oral ecosystem is disrupted, allowing disease-promoting bacteria to manifest and cause conditions such as caries, gingivitis and periodontitis. For practitioners and patients alike, promoting a balanced microbiome is therefore important to effectively maintain or restore oral health. This article aims to give an update on our current knowledge of the oral microbiome in health and disease and to discuss implications for modern-day oral healthcare.

Insights into study design and statistical analyses in translational microbiome studies

Research questions in translational microbiome studies are substantially more complex than their counterparts in basic science. Robust study designs with appropriate statistical analysis frameworks are pivotal to the success of these translational studies. This review considers how study designs can account for heterogeneous phenotypes by adopting representative sampling schemes for recruiting the study population and making careful choices about the control population. Advantages and limitations of 16S profiling and whole-genome sequencing, the two primary techniques for measuring the microbiome, are discussed followed by an overview of bioinformatic processing of high-throughput sequencing data from these measurements. Practical insights into the downstream statistical analyses including data processing and integration, variable transformations, and data exploration are provided. The merits of regularization and ensemble modeling for analyzing microbiome data are discussed along with a recommendation for selecting modeling approaches based on data-driven simulations and objective evaluation. The review builds on several recent discussions of study design issues in microbiome research but with a stronger emphasis on the downstream and often-ignored aspects of statistical analyses that are crucial for bridging the gap between basic science and translation.

Signature of Microbial Dysbiosis in Periodontitis

Periodontitis is driven by disproportionate host inflammatory immune responses induced by an imbalance in the composition of oral bacteria; this instigates microbial dysbiosis, along with failed resolution of the chronic destructive inflammation. The objectives of this study were to identify microbial signatures for health and chronic periodontitis at the genus level and to propose a model of dysbiosis, including the calculation of bacterial ratios. Published sequencing data obtained from several different studies (196 subgingival samples from patients with chronic periodontitis and 422 subgingival samples from healthy subjects) were pooled and subjected to a new microbiota analysis using the same Visualization and Analysis of Microbial Population Structures (VAMPS) pipeline, to identify microbiota specific to health and disease. Microbiota were visualized using CoNet and Cytoscape. Dysbiosis ratios, defined as the percentage of genera associated with disease relative to the percentage of genera associated with health, were calculated to distinguish disease from health. Correlations between the proposed dysbiosis ratio and the periodontal pocket depth were tested with a different set of data obtained from a recent study, to confirm the relevance of the ratio as a potential indicator of dysbiosis. Beta diversity showed significant clustering of periodontitis-associated microbiota, at the genus level, according to the clinical status and independent of the methods used. Specific genera (Veillonella, Neisseria, Rothia, Corynebacterium, and Actinomyces) were highly prevalent (>95%) in health, while other genera (Eubacterium, Campylobacter, Treponema, and Tannerella) were associated with chronic periodontitis. The calculation of dysbiosis ratios based on the relative abundance of the genera found in health versus periodontitis was tested. Nonperiodontitis samples were significantly identifiable by low ratios, compared to chronic periodontitis samples. When applied to a subgingival sample set with well-defined clinical data, the method showed a strong correlation between the dysbiosis ratio, as well as a simplified ratio (Porphyromonas, Treponema, and Tannerella to Rothia and Corynebacterium), and pocket depth. Microbial analysis of chronic periodontitis can be correlated with the pocket depth through specific signatures for microbial dysbiosis.IMPORTANCE Defining microbiota typical of oral health or chronic periodontitis is difficult. The evaluation of periodontal disease is currently based on probing of the periodontal pocket. However, the status of pockets "on the mend" or sulci at risk of periodontitis cannot be addressed solely through pocket depth measurements or current microbiological tests available for practitioners. Thus, a more specific microbiological measure of dysbiosis could help in future diagnoses of periodontitis. In this work, data from different studies were pooled, to improve the accuracy of the results. However, analysis of multiple species from different studies intensified the bacterial network and complicated the search for reproducible microbial signatures. Despite the use of different methods in each study, investigation of the microbiota at the genus level showed that some genera were prevalent (up to 95% of the samples) in health or disease, allowing the calculation of bacterial ratios (i.e., dysbiosis ratios). The correlation between the proposed ratios and the periodontal pocket depth was tested, which confirmed the link between dysbiosis ratios and the severity of the disease. The results of this work are promising, but longitudinal studies will be required to improve the ratios and to define the microbial signatures of the disease, which will allow monitoring of periodontal pocket recovery and, conceivably, determination of the potential risk of periodontitis among healthy patients.

Introduction to Clinical Microbiology for the General Dentist

Clinical oral microbiology may help dental professionals identify infecting pathogenic species and evaluate their in vitro antimicrobial susceptibility. Saliva, dental plaque biofilms, mucosal smears, abscess aspirates, and soft tissue biopsies are sources of microorganisms for laboratory testing. Microbial-based treatment end points may help clinicians better identify patients in need of additional or altered dental therapies before the onset of clinical treatment failure, and help improve patient oral health outcomes. Microbiological testing appears particularly helpful in periodontal disease treatment planning. Further research and technological advances are likely to increase the availability and clinical utility of microbiological analysis in modern dental practice.

In Situ Anabolic Activity of Periodontal Pathogens Porphyromonas gingivalis and Filifactor alocis in Chronic Periodontitis

Porphyromonas gingivalis and Filifactor alocis are fastidious anaerobic bacteria strongly associated with chronic forms of periodontitis. Our understanding of the growth activities of these microorganisms in situ is very limited. Previous studies have shown that copy numbers of ribosomal-RNA precursor (pre-rRNA) of specific pathogen species relative to genomic-DNA (gDNA) of the same species (P:G ratios) are greater in actively growing bacterial cells than in resting cells. The method, so-called steady-state pre-rRNA-analysis, represents a novel culture-independent approach to study bacteria. This study employed this technique to examine the in situ growth activities of oral bacteria in periodontitis before and after non-surgical periodontal therapy. Sub-gingival paper-point samples were taken at initial and re-evaluation appointments. Pre-rRNA and gDNA levels of P. gingivalis and F. alocis were quantified and compared using reverse-transcriptase qPCR. The results indicate significantly reduced growth activity of P. gingivalis, but not F. alocis, after therapy. The P:G ratios of P. gingivalis and F. alocis were compared and a low-strength, but statistically significant inter-species correlation was detected. Our study demonstrates that steady-state pre-rRNA-analysis can be a valuable culture-independent approach to studying opportunistic bacteria in periodontitis.