Has the use of molecular methods for the characterization of the human oral microbiome changed our understanding of the role of bacteria in the pathogenesis of periodontal disease?

The oral microbiome of children in health and disease-a literature review

The oral microbiome is a complex community of microorganisms residing in the oral cavity interacting with each other and with the host in a state of equilibrium. Disruptions in this balance can result in both oral and systemic conditions. Historically, studying the oral microbiome faced limitations due to culture-dependent techniques that could not capture the complexity and diversity of the microbial community. The emergence of advanced genomic technologies and the ease of sample collection from the oral cavity has revolutionized the understanding of the oral microbiome, providing valuable insights into the bacterial community in both health and disease. This review explores the oral microbiome in children, discussing its formation and dynamics in both states of health and disease, its role in various conditions such as dental caries, periodontal disease, oral cancer, cleft lip and palate, and explores its connection to several systemic consequences.

Impact of cell lysis treatment before saliva metagenomic DNA extraction on the oral microbiome and the associated resistome

OBJECTIVES

The human oral microbiome, a complex ecosystem linked to oral and systemic health, harbors a diverse array of microbial populations, including antimicrobial resistance genes (ARGs). As a critical component of the One Health approach to tackle antibiotic resistance, comprehending the oral resistome's composition and diversity is imperative. The objective of this study was to investigate the impact of chemical cell lysis treatment using MetaPolyzyme on the detectability of the oral microbiome, resistome, and DNA quality and quantity.

MATERIALS AND METHODS

Saliva samples were collected from five healthy individuals, and each of the samples was subjected to DNA extraction with and without the treatment with MetaPolyzyme. Through metagenomic sequencing, we analyzed, assessed, and compared the microbial composition, resistome, and DNA characteristics between both groups of extracted DNA.

RESULTS

Our study revealed that MetaPolyzyme treatment led to significant shifts in the detectability of microbial composition, favoring Gram-positive bacteria, notably Streptococcus, over Gram-negative counterparts. Moreover, the MetaPolyzyme treatment also resulted in a distinct change in ARG distribution. This shift was characterized by an elevated proportion of ARGs linked to fluoroquinolones and efflux pumps, coupled with a reduction in the prevalence of tetracycline and β-lactam resistance genes when compared with the nontreated group. Alpha diversity analysis demonstrated altered species and ARG distribution without affecting overall diversity, while beta diversity analysis confirmed significant differences in the taxonomical composition and oral resistome between treated and nontreated groups.

CONCLUSIONS

These findings underscore the critical role of cell lysis treatment in optimizing oral metagenomic studies and enhance our understanding of the oral resistome's dynamics in the context of antimicrobial resistance.

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.

Metronidazole-loaded polydopamine nanomedicine with antioxidant and antibacterial bioactivity for periodontitis

Aim: This study focused on treating periodontitis with bacterial infection and local over accumulation of reactive oxygen species. Materials & methods: Polydopamine nanoparticles (PDA NPs) were exploited as efficient carriers for encapsulated metronidazole (MNZ). The therapeutic efficacy and biocompatibility of PDA@MNZ NPs were investigated through both in vitro and in vivo studies. Results: The nanodrug PDA@MNZ NPs were successfully fabricated, with well-defined physicochemical characteristics. In vitro, the PDA@MNZ NPs effectively eliminated intracellular reactive oxygen species and inhibited the growth of Porphyromonas gingivalis. Moreover, the PDA@MNZ NPs exhibited synergistic therapy for periodontitisin in vivo. Conclusion: PDA@MNZ NPs were confirmed with exceptional antimicrobial and antioxidant functions, offering a promising avenue for synergistic therapy in periodontitis.

Association between periodontitis and disc structural failures in patients with cervical degenerative disorders

OBJECTIVE

Recent studies have shown that the mouth-gut-disc axis may play a key role in the process of disc structural failures (including intervertebral disc degeneration (IDD) and endplate change) in the cervical spine and neck pain. However, the potential mechanisms underlying the mouth-gut-disc axis remain elusive. Therefore, we explored whether periodontal disease is associated with disc structural failures in patients with cervical degeneration disorders and clinical outcomes.

METHODS

Adults (aged > 18 years) who met open surgery criteria for cervical spine were enrolled in this prospective cohort study. Participants were allocated into two groups based on periodontal examinations before surgery: no/mild periodontitis group and moderate/severe periodontitis group. Data were evaluated using an independent t test and Pearson's correlation analysis.

RESULTS

A total of 108 patients were enrolled, including 68 patients in the no/mild periodontitis group and 40 patients in the moderate/severe periodontitis group. The number of common causes of missing teeth (P = 0.005), plaque index (PLI) (P = 0.003), bleeding index (BI) (P = 0.000), and probing depth (PD) (P = 0.000) significantly differed between the two groups. The incidence rate of endplate change (P = 0.005) was higher in the moderate/severe periodontitis group than in the no/mild periodontitis group. A moderate negative association was found between the neck disability index (NDI) score and periodontal parameters (PLI: r = - 0.337, P = 0.013; BI: r = - 0.426, P = 0.001; PD: r = - 0.346, r = - 0.010).

CONCLUSIONS

This is the first study to provide evidence that severe periodontitis is associated with a higher occurrence rate of disc structural failures and poor clinical outcomes in patients with cervical degenerative disorders.

Metagenomic Analysis to Uncover the Subgingival and Atherosclerotic Plaque Microbiota in Patients with Coronary Artery Disease

The role of periodontal pathogens in the initiation and progression of atherosclerosis has been extensively researched, yet a precise causal mechanism has not been established. The subgingival microbiota may be a source of dissemination and may contribute to the development of atherosclerosis; hence this study attempted to characterize and compare the subgingival and atherosclerotic plaques. Plaque samples were subjected to 16S rRNA-based metagenomics to study microbiota associated with subgingival and atherosclerotic plaques collected from patients with coronary artery disease. The PCoA analysis showed that the microbiomes of subgingival plaques were highly scattered and showed a diverse microbial composition, unlike the atherosclerotic plaques that did not show evident variability in the microbial composition and formed a close distinct group. The abundance of various genera in the subgingival plaques revealed Fusobacterium (11%), Acinetobacter (13%), Veillonella (9%), and Prevotella (11%) among the top ten genera. The atherosclerotic plaques contained Acinetobacter (39%), Chryseobacterium (9%), Rhizobium (5%), and Staphylococcus (4%). All the patients examined in this study had either generalized or localized periodontitis with varying degrees of severity. The community microbiota analysis revealed that 22 bacterial genera were shared between two different plaques, with Acinetobacter being dominant. Based on the Human Oral Microbiome Database, 55% of the shared microbiota in this study have been listed as periodontal microbiota, with some of them found in increased proportions in patients with periodontitis suggesting the translocation of bacteria from the periodontal pockets into the circulation. This study provides valuable insights into the possible relationship between periodontal pathogens and atherosclerotic cardiovascular disease.

Graphical Abstract

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.

Association between periodontitis and disc structural failure in older adults with lumbar degenerative disorders: A prospective cohort study

BACKGROUND

Bacterial microbiome as a putative trigger of inflammation might indicate the cascade of mouth-gut-disc axis for causing intervertebral disc (IVD) structural failures (such as IVD degeneration and endplate change) processed. However, direct evidence for the mouth-gut-disc axis still unclear. Therefore, it is interesting to explore periodontal inflammation related to IVD structural failures and clinical outcomes.

METHODS

This prospective cohort study enrolled older adults (aged ≥ 75 years) who scheduled to undergo elective open lumbar spine surgery. Demographic, radiological, clinical, and periodontal parameters were recorded. Independent samples t-test and Pearson's correlation analysis were calculated.

RESULTS

A total of 141 patients with lumbar degenerative disorders (56 males and 85 females; age 79.73 ± 3.34 years) were divided into edentulous group (19 patients), No/Mild group (84 patients), and Moderate/Severe group (38 patients). The incidence rates of IVD degeneration in each lumbar segmental level based on Pfirrmann grade and endplate change in the fourth and fifth lumbar vertebrae, and Visual Analogue Scale (VAS) low back pain (LBP) and leg pain of patients at preoperative in dentate group was significantly higher compared with edentulous group, especially the comparisons between Moderate/Severe and edentulous groups. There were no significant differences in the range of motion, lumbar lordosis, pelvic incidence, pelvic tilt, sacral slope, and disc height between dentate and edentulous groups. There was a positive association between plaque index (PLI) and pain scores (VAS LBP: r = 0.215, P = 0.030 and VAS leg pain: r = 0.309, P = 0.005), but no significant difference in Oswestry disability index (ODI) score.

CONCLUSION

Results show that the severity of periodontitis is associated with higher incidence rates of IVD degeneration and endplate change and clinical outcomes in older adults with lumbar degenerative disorders. Furthermore, the discovery of these relationships unveils a novel mechanism through which the alterations in oral microbiome composition potentially promote IVD degeneration and pain.

Periodontal microbiology and microbial etiology of periodontal diseases: Historical concepts and contemporary perspectives

This narrative review summarizes the collective knowledge on periodontal microbiology, through a historical timeline that highlights the European contribution in the global field. The etiological concepts on periodontal disease culminate to the ecological plaque hypothesis and its dysbiosis-centered interpretation. Reference is made to anerobic microbiology and to the discovery of select periodontal pathogens and their virulence factors, as well as to biofilms. The evolution of contemporary molecular methods and high-throughput platforms is highlighted in appreciating the breadth and depth of the periodontal microbiome. Finally clinical microbiology is brought into perspective with the contribution of different microbial species in periodontal diagnosis, the combination of microbial and host biomarkers for this purpose, and the use of antimicrobials in the treatment of the disease.

Bacterial decontamination of toothbrushes by immersion in a mouthwash containing 0.05% chlorhexidine and 0.05% cetylpyridinium chloride: A randomized controlled trial

OBJECTIVE

Toothbrushes are colonized by microorganisms, implying a risk of infection. That risk can be reduced by decreasing the microbial contamination of the filaments. Therefore, this study aimed to determine the antiseptic efficacy of a 0.05% chlorhexidine + 0.05% cetylpyridinium chloride mouthwash on toothbrushes.

METHODS

A total of twelve toothbrushes used three times/day for 14 days by orally and systemically healthy people were randomly split into two groups, and their heads were immersed for 2 h in PBS (control) or Perio·Aid Active Control (treatment). The microorganisms were recovered, and their number was calculated by culture, quantitative PCR, and viability PCR. Statistical differences were first assessed with a two-way mixed ANOVA and subsequently with Student's t-test.

RESULTS

The results showed no statistical differences in the total number of cells for the treatment (mean ± CI95% of 7.27 ± 1.09 log₁₀ bacteria/ml) and the control (7.62 ± 0.64 log₁₀ bacteria/ml) groups, but a significantly lower number of live cells in the treatment group (4.58 ± 0.61 log₁₀ viable bacteria/ml and 2.15 ± 1.42 log₁₀ cfu/ml) than in the control group (6.49 ± 1.39 log₁₀ viable bacteria/ml and 5.04 ± 0.93 log₁₀ cfu/ml).

CONCLUSIONS

Based on our findings, sanitization of toothbrushes with this mouthwash reduces the number of live microorganisms adhered to the filaments. Such decrease of the bacterial load could include bacteria from the oral cavity, from the environment, and from nearby toothbrushes since the quantification was not limited to any bacterial taxon.

Inverse PCR-based detection reveal novel mobile genetic elements and their associated genes in the human oral metagenome

The human oral cavity is one of the hotspots harboring multiple mobile genetic elements (MGEs), which are segments of DNA that can move either within bacterial genomes or between bacterial cells that can facilitate the spreading of genetic materials, including antimicrobial resistance genes. It is, therefore, important to investigate genes associated with the MGEs as they have a high probability of dissemination within the bacterial population under selective pressure from human activities. As one-third of oral bacteria are not yet culturable in the laboratory condition, therefore, in this work, it is aimed to detect and identify the genetic contexts of MGEs in the oral cavity through an inverse PCR (IPCR)-based approach on the oral metagenomic. The human oral metagenome was extracted from saliva samples collected from healthy individuals in Tromsø, Norway. The extracted DNA was partially digested with the HindIII restriction enzyme and self-circularized by ligation. DNA primers targeting each MGE were designed to amplify outwards from the MGEs and used for the IPCR on the circularized DNA products. The IPCR amplicons were cloned into a pCR-XL-2-TOP vector, screened, and sequenced. Out of 40 IPCR amplicons, we confirmed and verified the genetic contexts of 11 samples amplified with primers targeting integron gene cassettes (GCs), IS431 composite transposons, and Tn916 conjugative transposons (tet(M) and xis-int). Novel integron GCs, MGEs, and variants of Tn916 conjugative transposons were identified, which is the first report using the IPCR technique to detect the genetic contexts of MGEs in the oral metagenomic DNA.

Impact of Oral Microbiome in Periodontal Health and Periodontitis: A Critical Review on Prevention and Treatment

The skin, oral cavity, digestive and reproductive tracts of the human body harbor symbiotic and commensal microorganisms living harmoniously with the host. The oral cavity houses one of the most heterogeneous microbial communities found in the human organism, ranking second in terms of species diversity and complexity only to the gastrointestinal microbiota and including bacteria, archaea, fungi, and viruses. The accumulation of microbial plaque in the oral cavity may lead, in susceptible individuals, to a complex host-mediated inflammatory and immune response representing the primary etiological factor of periodontal damage that occurs in periodontitis. Periodontal disease is a chronic inflammatory condition affecting about 20-50% of people worldwide and manifesting clinically through the detection of gingival inflammation, clinical attachment loss (CAL), radiographic assessed resorption of alveolar bone, periodontal pockets, gingival bleeding upon probing, teeth mobility and their potential loss in advanced stages. This review will evaluate the changes characterizing the oral microbiota in healthy periodontal tissues and those affected by periodontal disease through the evidence present in the literature. An important focus will be placed on the immediate and future impact of these changes on the modulation of the dysbiotic oral microbiome and clinical management of periodontal disease.

Effects of Long-Term Enclosed Environment on Human Health Based on the Analysis of Salivary Microbiota and Cytokines

The long-term exposure to enclosed environments may lead to chronic stress in crewmembers and affect their physical and mental state. Salivary microbiome and biomarkers of immune function are increasingly used in human health research. The "Lunar Palace 365" project, which was a 370-day, multicrew, enclosed experiment carried out in a ground-based bioregenerative life support system platform named Lunar Palace 1 (LP1). We investigated the temporal dynamics of the salivary microbiota and cytokines in the third phase of the "Lunar Palace 365" experiment, including 1 month before entering LP1 and 1 month after leaving Lp1. Results reveal no regular temporal change pattern in these parameters (highly abundant phyla and genera) during the experiment. Although the crewmembers' oral microbiota temporally changed, it recovered quickly after the study subjects left the enclosed environment. The levels of IL-6, IL-10, and TNF-α in crewmembers' saliva decreased after leaving the normal environment for the enclosed environment, indicating that their oral inflammatory response level was reduced. There were significant individual differences in crewmembers' salivary microbiota, however, the shared living space reduced these differences. Moreover, air microbiota might have also played a significant role in reducing the individual differences. In summary, the enclosed environment did not result in persistent changes in human salivary microbiota and oral immunity. This study provides some insights for studying the effect of enclosed controlled environments on human immunity and microbiome. IMPORTANCE Long-term exposure to space environments may influence the human microbiome, the human immune system, and the intricate balance between the two, causing impaired immunity and increased disease susceptibility. It was previously believed that the main potential factors of long-term spaceflight on human health were microgravity and radiation. However, the effects of long-term enclosed environments on human health were unclear. Bioregenerative life support systems (BLSS) is a good experimental model for studying the effects of enclosed environments on human systemic microbiota and immune disorders. We monitored the microbiota and cytokines in the saliva of crewmembers before they entered BLSS, during their stay in BLSS, and after leaving BLSS. The results indicated long-term closed environment will not cause persistent changes in human salivary microbiota and immunity.

Role of the Filifactor alocis Hypothetical Protein FA519 in Oxidative Stress Resistance

In the periodontal pocket, there is a direct correlation between environmental conditions, the dynamic oral microbial flora, and disease. The relative abundance of several newly recognized microbial species in the oral microenvironment has raised questions on their impact on disease development. One such organism, Filifactor alocis, is significant to the pathogenic biofilm structure. Moreover, its pathogenic characteristics are highlighted by its ability to survive in the oxidative-stress microenvironment of the periodontal pocket and alter the microbial community dynamics. There is a gap in our understanding of its mechanism(s) of oxidative stress resistance and impact on pathogenicity. Several proteins, including HMPRFF0389-00519 (FA519), were observed in high abundance in F. alocis during coinfection of epithelial cells with Porphyromonas gingivalis W83. Bioinformatics analysis shows that FA519 contains a "Cys-X-X-Cys zinc ribbon domain" which could be involved in DNA binding and oxidative stress resistance. We have characterized FA519 to elucidate its roles in the oxidative stress resistance and virulence of F. alocis. Compared to the wild-type strain, the F. alocis isogenic gene deletion mutant, FLL1013 (ΔFA519::ermF), showed significantly reduced sensitivity to hydrogen peroxide and nitric oxide-induced stress. The ability to form biofilm and adhere to and invade gingival epithelial cells was also reduced in the isogenic mutant. The recombinant FA519 protein was shown to protect DNA from Fenton-mediated damage with an intrinsic ability to reduce hydrogen peroxide and disulfide bonds. Collectively, these results suggest that FA519 is involved in oxidative stress resistance and can modulate important virulence attributes in F. alocis. IMPORTANCE Filifactor alocis is an emerging member of the periodontal community and is now proposed to be a diagnostic indicator of periodontal disease. However, due to the lack of genetic tools available to study this organism, not much is known about its virulence attributes. The mechanism(s) of oxidative stress resistance in F. alocis is unknown. Therefore, identifying the adaptive mechanisms utilized by F. alocis to survive in the oxidative stress environment of the periodontal pocket would lead to understanding its virulence regulation, which could help develop novel therapeutic treatments to combat the effects of periodontal disease. This study is focused on the characterization of FA519, a hypothetical protein in F. alocis, as a multifunctional protein that plays an important role in the reactive oxygen species-detoxification pathway. Collectively, our results suggest that FA519 is involved in oxidative stress resistance and can modulate important virulence attributes in F. alocis.

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.

The Varied Proportion of Filifactor alocis in Periodontal Health and Disease in the South Indian Subpopulation

BACKGROUND AND AIM

The periodontal microbiome being complex, this study was aimed to detect and quantify the prevalence of Filifactor alocis in various stages of periodontitis and to evaluate its prospect as a diagnostic marker for periodontal disease.

SETTINGS AND DESIGN

Sixty subjects were selected (20 healthy controls, 20 with chronic periodontitis, and 20 with aggressive periodontitis) for the study.

MATERIALS AND METHODS

Clinical parameters probing depth and the level of clinical attachment was recorded, subgingival plaque samples were collected. The F. alocis 16srDNA was cloned, sequenced, and used as the standard for real-time quantification of bacterial load using SYBR green chemistry.

STATISTICAL ANALYSIS

Clinical, microbiological, and quantitative polymerase chain reaction (PCR) data were analyzed using ANOVA and Pearson's coefficient correlation.

RESULTS

(a) Real-time PCR analysis showed the highest average F. alocis count in chronic periodontitis subjects (32,409.85), which was followed by count in healthy controls (3046.15) and the least count in aggressive periodontitis subjects (939.84). The bacterial count was statistically significant at P = 0.005. (b) An intra-group comparison reveals that there was a statistically significant increase in the bacterial count with age and mean probing pocket depth at P = 0.0005.

CONCLUSION

F. alocis population in aggressive periodontitis was lower compared to chronic periodontitis and healthy controls. The F. alocis population surge in healthy controls may be due to geographical variations and the ethnicity of the subjects. A higher population of F. alocis in chronic periodontitis proves its high pathogenic potential to invade the host tissues to aid in further periodontal destruction.

Short-term improvement of clinical parameters and microbial diversity in periodontitis patients following Indocyanine green-based antimicrobial photodynamic therapy: A randomized single-blind split-mouth cohort

BACKGROUND

Indocyanine green-mediated photodynamic therapy is effective against chronic periodontitis. Here, we evaluated the efficiency of indocyanine green-based adjunctive antimicrobial photodynamic therapy in non-surgical treatment of chronic periodontitis patients.

METHODS

Fifty-six periodontally involved teeth of 20 patients were treated with "scaling and root planing" (control group) or "scaling and root planing with indocyanine green-based (perio-green, 0.1 mg/ml) antimicrobial photodynamic therapy" (test group) using a split-mouth design. We performed clinical assessment of probing depth, gingival recession, clinical attachment loss, and other indices, while plaque samples were collected for microbiome analysis.

RESULTS

At baseline, periodontal depth and clinical attachment loss were significantly higher in the test group (p < 0.05), and at 1-month post-treatment, we observed a significant favorable reduction of both periodontal depth and clinical attachment loss in test and control sites, with lower means maintained at 3 months (p = 0.01 and p = 0.000, respectively). Additionally, analysis of variance showed significant improvements in periodontal depth and clinical attachment loss in the indocyanine green-antimicrobial photodynamic therapy group (p = 0.001), although not for clinical attachment loss in controls (p = 0.102). Moreover, a significant reduction was observed in test sites for bleeding on probing and residual pocket post-therapy (p = 0.04 and p = 0.0001 respectively). Furthermore, microbiome analysis identified Porphyromonons gingivalis, Treponema, and Tannerella in all samples with favorable changes in test sites (p = 0.07).

CONCLUSION

We observed a significant reduction in periodontal clinical parameters (periodontal depth and clinical attachment loss) in chronic periodontitis patients treated with antimicrobial photodynamic therapy as an adjunctive procedure to conventional scaling and root planing. This improvement was associated with periodontal pathogen reduction and increase in the healthy subgingival microbiome.

Filifactor alocis: Recent Insights and Advances

Filifactor alocis, a fastidious Gram-positive obligate anaerobic bacterium, is a newly appreciated member of the periodontal community that is now proposed to be a diagnostic indicator of periodontal disease. Its pathogenic characteristics are highlighted by its ability to survive in the oxidative stress-rich environment of the periodontal pocket and to significantly alter the microbial community dynamics by forming biofilms and interacting with several oral bacteria. Here, we describe the current understanding of F. alocis virulence attributes, such as its comparative resistance to oxidative stress, production of unique proteases and collagenases that can cause structural damage to host cells, and dysregulation of the immune system, which enable this bacterium to colonize, survive, and outcompete other traditional pathogens in the inflammatory environment of the periodontal pocket. Furthermore, we explore the recent advancements and future directions for F. alocis research, including the potential mechanisms for oxidative stress resistance and our evolving understanding of the interactions and mechanisms of bacterial survival inside neutrophils. We also discuss the current genetic tools and challenges involved in manipulating the F. alocis genome for the functional characterization of the putative virulence genes. Collectively, this information will expedite F. alocis research and should lead to the identification of prime targets for the development of novel therapeutics to aid in the control and prevention of periodontal disease.

A pilot study of red complex and three genera subgingival microbiome in periodontitis subjects with and without diabetes, evaluated by MinION platform

Background: Subgingival niche is one biofilm habitat containing rich microbiota, which plays an active role in maintaining the health of periodontal tissue and determining host response. As such, a study of changing subgingival biofilms is important for understanding the effect of a systemic condition. In this study, we compared the occurrence of six bacteria cohabiting in the subgingival area of periodontitis subjects, with (DP, n = 8) and without (NDP, n = 4) diabetes.

Methods: The six genus and species of targeted bacteria were confirmed by 16S rRNA amplicon sequencing on MinION nanopore platform. Descriptive statistic was used to describe the obtained data.

Results: We found that the six genus and species of targeted bacteria were detected but in different quantities in either group's periodontal pocket. Our data showed that Tannerella forsythia was the most abundant species in subgingival biofilms of the DP group of the red complex bacteria. In contrast, Aggregatibacter sp., which belongs to the phylum of proteobacteria, was present at a relatively lower level. In contrast, Fusobacterium sp., which belongs to orange complex bacteria, showed relative similarities in subgingival biofilms of both groups tested, while Veillonella sp., were abundant in the DP groups. 

Conclusions: Our data show that the diversity of classic periodontopathogens increased in the subgingival niche of periodontitis subjects with diabetes. It is the first study in Indonesia to apply MinION-based, full-length 16S rRNA amplicon sequencing in periodontitis patients with and without diabetes.

Functional Metagenomic Screening for Antimicrobial Resistance in the Oral Microbiome

A large proportion of bacteria, from a multitude of environments, are not yet able to be grown in the laboratory, and therefore microbiological and molecular biological investigations of these bacteria are challenging. A way to circumvent this challenge is to analyze the metagenome, the entire collection of DNA molecules that can be isolated from a particular environment or sample. This collection of DNA molecules can be sequenced and assembled to determine what is present and infer functional potential, or used as a PCR template to detect known target DNA and potentially unknown regions of DNA nearby those targets; however assigning functions to new or conserved hypothetical, functionally cryptic, genes is difficult. Functional metagenomics allows researchers to determine which genes are responsible for selectable phenotypes, such as resistance to antimicrobials and metabolic capabilities, without the prerequisite needs to grow the bacteria containing those genes or to already know which genes are of interest. It is estimated that a third of the resident species of the human oral cavity is not yet cultivable and, together with the ease of sample acquisition, makes this metagenome particularly suited to functional metagenomic studies. Here we describe the methodology related to the collection of saliva samples, extraction of metagenomic DNA, construction of metagenomic libraries, as well as the description of functional assays that have previously led to the identification of new genes conferring antimicrobial resistance.

Inhibition of yes-associated protein dephosphorylation prevents aggravated periodontitis with occlusal trauma

BACKGROUND

Occlusal trauma can aggravate periodontitis, but the mechanism remains unclear. Yes-associated protein (YAP), a mechanical stressor protein, may play an important role in this process.

METHODS

Western blot and quantitative real-time polymerase chain reaction (qRT-PCR) were applied to detect the expression of YAP and inflammatory factors in patients with periodontitis accompanied with or without occlusal trauma. Through local administration of Porphyromonas gingivalis and composite resin bonding on maxillary molars in mice, we established periodontitis and occlusal trauma models. Treatment with or without XAV939, to inhibit YAP activation, was performed in these models. Micro-computed tomography, immunofluorescence (IF), and qRT-PCR were used to explore the YAP pathway in periodontitis with occlusal trauma. Cyclic stress and lipopolysaccharide (LPS) stimuli were applied to the L929 mouse fibroblast cell line with or without XAV939. Western blot, IF, and qRT-PCR were used to verify the in vivo results.

RESULTS

Activated dephosphorylated YAP and increased expression of inflammatory factors were observed in patients with periodontitis accompanied with occlusal trauma. In the mouse model of periodontitis with occlusal trauma, YAP transferred into the nucleus, resulting in Jun N-terminal kinases (JNK) related pro-inflammatory pathway up-regulation. L929 cell cyclic stress and LPS stimulation results confirmed the in vivo results. Application of XAV939 inhibited YAP protein dephosphorylation and reduced JNK pro-inflammatory pathway factor expression in vivo and in vitro.

CONCLUSIONS

Occlusal trauma can activate YAP nuclear transfer, resulting in the up-regulation of the JNK pro-inflammatory pathway. This can be inhibited by the XAV939 YAP inhibitor.

Biosensor and Lab-on-a-chip Biomarker-identifying Technologies for Oral and Periodontal Diseases

Periodontitis is a complex multifactorial disease that can lead to destruction of tooth supporting tissues and subsequent tooth loss. The most recent global burden of disease studies highlight that severe periodontitis is one of the most prevalent chronic inflammatory conditions affecting humans. Periodontitis risk is attributed to genetics, host-microbiome and environmental factors. Empirical diagnostic and prognostic systems have yet to be validated in the field of periodontics. Early diagnosis and intervention prevents periodontitis progression in most patients. Increased susceptibility and suboptimal control of modifiable risk factors can result in poor response to therapy, and relapse. The chronic immune-inflammatory response to microbial biofilms at the tooth or dental implant surface is associated with systemic conditions such as cardiovascular disease, diabetes or gastrointestinal diseases. Oral fluid-based biomarkers have demonstrated easy accessibility and potential as diagnostics for oral and systemic diseases, including the identification of SARS-CoV-2 in saliva. Advances in biotechnology have led to innovations in lab-on-a-chip and biosensors to interface with oral-based biomarker assessment. This review highlights new developments in oral biomarker discovery and their validation for clinical application to advance precision oral medicine through improved diagnosis, prognosis and patient stratification. Their potential to improve clinical outcomes of periodontitis and associated chronic conditions will benefit the dental and overall public health.

Bacteria associated with periodontal disease are also increased in health

Background

The objective of this cross-sectional clinical study was to analyze the differences in the microbiome in gingival sulci of adult patients in the presence or absence of chronic periodontitis.

Material and Methods

Patients with or without periodontal disease were included in this cross-sectional study. Subgingival biofilm samples were collected and analyzed by 16S massive pyrosequencing. Functional analyses were also performed.

Results

A total of 15 phyla, 154 genera and 351 species were detected globally. Differences between disease and non-disease samples were observed in all taxonomical levels which suggest functional profile changes in the community. It was found that the main species associated with non-disease samples were reduced in disease but not completely suppressed. Analysis of the functional potential of the biofilms revealed a significantly higher activity related to endocytosis and phosphatidylinositol signaling in the disease group but lower cell adhesion molecules.

Conclusions

Specific differences between health and disease suggest functional profile changes in the community, although bacteria associated with periodontal disease are also increased in health. Transcriptome studies should be conducted to confirm and deepen metabolic dysfunctions.

Key words:Pyrosequencing, 16S rRNA, oral microbiome, periodontitis, functional potential.

How Periodontal Disease and Presence of Nitric Oxide Reducing Oral Bacteria Can Affect Blood Pressure

Nitric oxide (NO), a small gaseous and multifunctional signaling molecule, is involved in the maintenance of metabolic and cardiovascular homeostasis. It is endogenously produced in the vascular endothelium by specific enzymes known as NO synthases (NOSs). Subsequently, NO is readily oxidized to nitrite and nitrate. Nitrite is also derived from exogenous inorganic nitrate (NO₃) contained in meat, vegetables, and drinking water, resulting in greater plasma NO₂ concentration and major reduction in systemic blood pressure (BP). The recycling process of nitrate and nitrite to NO (nitrate-nitrite-NO pathway), known as the enterosalivary cycle of nitrate, is dependent upon oral commensal nitrate-reducing bacteria of the dorsal tongue. Veillonella, Actinomyces, Haemophilus, and Neisseria are the most copious among the nitrate-reducing bacteria. The use of chlorhexidine mouthwashes and tongue cleaning can mitigate the bacterial nitrate-related BP lowering effects. Imbalances in the oral reducing microbiota have been associated with a decrease of NO, promoting endothelial dysfunction, and increased cardiovascular risk. Although there is a relationship between periodontitis and hypertension (HT), the correlation between nitrate-reducing bacteria and HT has been poorly studied. Restoring the oral flora and NO activity by probiotics may be considered a potential therapeutic strategy to treat HT.

CSN: unsupervised approach for inferring biological networks based on the genome alone

BACKGROUND

Most organisms cannot be cultivated, as they live in unique ecological conditions that cannot be mimicked in the lab. Understanding the functionality of those organisms' genes and their interactions by performing large-scale measurements of transcription levels, protein-protein interactions or metabolism, is extremely difficult and, in some cases, impossible. Thus, efficient algorithms for deciphering genome functionality based only on the genomic sequences with no other experimental measurements are needed.

RESULTS

In this study, we describe a novel algorithm that infers gene networks that we name Common Substring Network (CSN). The algorithm enables inferring novel regulatory relations among genes based only on the genomic sequence of a given organism and partial homolog/ortholog-based functional annotation. It can specifically infer the functional annotation of genes with unknown homology. This approach is based on the assumption that related genes, not necessarily homologs, tend to share sub-sequences, which may be related to common regulatory mechanisms, similar functionality of encoded proteins, common evolutionary history, and more. We demonstrate that CSNs, which are based on S. cerevisiae and E. coli genomes, have properties similar to 'traditional' biological networks inferred from experiments. Highly expressed genes tend to have higher degree nodes in the CSN, genes with similar protein functionality tend to be closer, and the CSN graph exhibits a power-law degree distribution. Also, we show how the CSN can be used for predicting gene interactions and functions.

CONCLUSIONS

The reported results suggest that 'silent' code inside the transcript can help to predict central features of biological networks and gene function. This approach can help researchers to understand the genome of novel microorganisms, analyze metagenomic data, and can help to decipher new gene functions.

AVAILABILITY

Our MATLAB implementation of CSN is available at https://www.cs.tau.ac.il/~tamirtul/CSN-Autogen.

Study on oral hygiene by nanobubbles from high-density nozzle

An experiment was performed on oral bacteria removal using the design variables, which included the three-segment rotor speed of the testing device and three types of stainless steel meshes (with different layers). The overall hygienic results showed an effect of up to 95% bacteria removal, and some combinations had 100% hygienic effect. The study proposed that the use of nanobubble generated by a high-density stainless-steel mesh-manufactured nozzle removes dental bacteria. In addition, the device could also be used for auxiliary oral hygiene to decrease the frequency of future medical visits due to periodontal diseases or to enable the device to assist patients with severe periodontal disease more conveniently for oral hygiene.

Rapid Multiplex Real-Time PCR Method for the Detection and Quantification of Selected Cariogenic and Periodontal Bacteria

Dental caries and periodontal diseases are associated with a shift from symbiotic microbiota to dysbiosis. The aim of our study was to develop a rapid, sensitive, and economical method for the identification and quantification of selected cariogenic and periodontal oral bacteria. Original protocols were designed for three real-time multiplex PCR assays to detect and quantify the ratio of 10 bacterial species associated with dental caries (“cariogenic” complex) or periodontal diseases (red complex, orange complex, and Aggregatibacter actinomycetemcomitans). A total number of 60 samples from 30 children aged 2–6 years with severe early childhood caries and gingivitis were tested. In multiplex assays, the quantification of total bacterial (TB) content for cariogenic bacteria and red complex to eliminate differences in quantities caused by specimen collection was included. The mean counts for the TB load and that of ten evaluated specimens corresponded to previously published results. We found a significant difference between the microbial compositions obtained from the area of control and the affected teeth (p < 0.05). Based on this comprehensive microbiological examination, the risk of dental caries or periodontal inflammation may be determined. The test could also be used as a tool for behavioral intervention and thus prevention of the above-mentioned diseases.

Traumatic occlusion aggravates bone loss during periodontitis and activates Hippo-YAP pathway

AIM

This study aimed at exploring changes in YAP expression and their effect on periodontitis (PD) combined with traumatic occlusion (TO).

MATERIALS AND METHODS

BALB/cJ mice were used to establish a PD model by local administration of Porphyromonas gingivalis (P.g, ATCC 33277) and a TO model by occlusal elevation (OE) using composite resin bonding on the bilateral maxillary molar. The mouse fibroblast cell line (L929) and pre-osteoblast cell line (MC3T3-E1) were subjected to cyclic tensile/compressive stress and inflammatory stimuli (lipopolysaccharide from Escherichia coli) to verify in vivo results.

RESULTS

Severe bone resorption was observed by microCT scanning in OE with P.g group, when compared to OE only and P.g only groups. Mechanical stress caused by OE activated the Hippo-YAP pathway in periodontal tissues and upregulated the expression of JNK/AP-1. OE with P.g further promoted the expression of YAP and JNK/AP1, leading to the upregulation of the JNK/AP-1 related inflammatory cytokines TNF-α and IL6. Similar results were obtained when osteoblasts were subjected to mechanical stress in vitro.

CONCLUSIONS

Our study demonstrated that periodontitis with TO caused severe inflammation-induced bone resorption. Activation of YAP and upregulation of JNK/AP-1 induced by TO potentially aggravated the symptoms of PD.

Significance of oral health in adult patients with congenital heart disease

Due to improved diagnosis and treatment life expectancy of patients with congenital heart disease is steadily increasing resulting in a growing portion of adult patients. When entering, adulthood patients commonly show a shift in their specific needs for medical care. Since the treatment is mostly not curative many patients have life-long cardiovascular anomalies, among others, entailing high risk for the development of infective endocarditis. Several oral diseases, i.e., caries, apical periodontitis and periodontitis show a very high overall prevalence. These entities are primarily initiated by bacterial infections. Hence, they cause an inherent risk for bacteremia and subsequently for infective endocarditis in patients with congenital heart disease during professional dental care and various daily activities. Conversely congenital heart disease seems to be inevitably associated with considerable impairment of oral health resulting in a tight interrelation between both entities. Different preventive strategies are available to address the elevated risk for infective endocarditis due to oral diseases in patients with congenital heart disease during professional dental care and routine daily activities. This review delineates the current evidence regarding the issue of oral health in adult patients with congenital heart disease.

Consumer Safety Considerations of Skin and Oral Microbiome Perturbation

Microbiomes associated with human skin and the oral cavity are uniquely exposed to personal care regimes. Changes in the composition and activities of the microbial communities in these environments can be utilized to promote consumer health benefits, for example, by reducing the numbers, composition, or activities of microbes implicated in conditions such as acne, axillary odor, dandruff, and oral diseases. It is, however, important to ensure that innovative approaches for microbiome manipulation do not unsafely disrupt the microbiome or compromise health, and where major changes in the composition or activities of the microbiome may occur, these require evaluation to ensure that critical biological functions are unaffected. This article is based on a 2-day workshop held at SEAC Unilever, Sharnbrook, United Kingdom, involving 31 specialists in microbial risk assessment, skin and oral microbiome research, microbial ecology, bioinformatics, mathematical modeling, and immunology. The first day focused on understanding the potential implications of skin and oral microbiome perturbation, while approaches to characterize those perturbations were discussed during the second day. This article discusses the factors that the panel recommends be considered for personal care products that target the microbiomes of the skin and the oral cavity.

Importance of Virulence Factors for the Persistence of Oral Bacteria in the Inflamed Gingival Crevice and in the Pathogenesis of Periodontal Disease

Periodontitis is a chronic inflammation that develops due to a destructive tissue response to prolonged inflammation and a disturbed homeostasis (dysbiosis) in the interplay between the microorganisms of the dental biofilm and the host. The infectious nature of the microbes associated with periodontitis is unclear, as is the role of specific bacterial species and virulence factors that interfere with the host defense and tissue repair. This review highlights the impact of classical virulence factors, such as exotoxins, endotoxins, fimbriae and capsule, but also aims to emphasize the often-neglected cascade of metabolic products (e.g., those generated by anaerobic and proteolytic metabolism) that are produced by the bacterial phenotypes that survive and thrive in deep, inflamed periodontal pockets. This metabolic activity of the microbes aggravates the inflammatory response from a low-grade physiologic (homeostatic) inflammation (i.e., gingivitis) into more destructive or tissue remodeling processes in periodontitis. That bacteria associated with periodontitis are linked with a number of systemic diseases of importance in clinical medicine is highlighted and exemplified with rheumatoid arthritis, The unclear significance of a number of potential "virulence factors" that contribute to the pathogenicity of specific bacterial species in the complex biofilm-host interaction clinically is discussed in this review.

The subgingival microbial community of feline periodontitis and gingivostomatitis: characterization and comparison between diseased and healthy cats

Periodontitis is a common and important health problem in domestic cats. The subgingival microbiota of cats diagnosed with chronic periodontitis (CP), aggressive periodontitis (AP), and feline chronic gingivostomatitis (FCGS) are not well characterized. Thus, the aim of the present study was to characterize and compare the periodontal microbiota of periodontally healthy cats versus cats diagnosed with CP, AP, and FCGS by using next-generation sequencing. In total, 44 domestic cats were enrolled, and 139 subgingival samples were subjected to 16S rRNA gene sequencing to investigate the microbiota composition of each periodontal group evaluated. Our results identified several key genera previously described in periodontal disease (e.g. Treponema and Filifactor) and in the oral microbiota (e.g. Moraxella and Capnocytophaga) of healthy cats. Phylogenetic beta diversity analysis showed that the microbiota of periodontally healthy cats were distinguishable from diseased cats. Even though most of the genera known to be associated with periodontal disease were also identified in healthy cats, they were present at significantly lower relative abundance. Remarkably, alpha diversity was found to be higher in the disease groups compared to healthy animals. These results suggest a pathological mechanism involving opportunistic behavior. Our findings corroborate those in the current literature regarding the complexity of the subgingival microbiota of the domestic cat and reveal both differences and similarities among periodontally healthy and diseased cats.

[Oral microbiological diversity in patients with salivary adenoid cystic carcinoma]

OBJECTIVE

The aim of this study was to identify the differences in microbial diversity and community in patients with salivary adenoid cystic carcinoma (SACC).

METHODS

Saliva was collected from 13 patients with SACC confirmed by histopathological diagnosis and 10 healthy control subjects. Total metagenomic DNA was extracted. The DNA amplicons of the V3-V4 hypervariable regions of the 16S rRNA gene were generated and subjected to high-throughput sequencing. Microbial diversity and community structure were analyzed with Mothur software.

RESULTS

A total of 16 genera of dominant bacteria in the SACC group were found, including Streptococcus (36.68%), Neisseria (8.55%), Prevotella_7 (7.53%), and Veillonella (6.37%), whereas 15 dominant bacteria in the control group were found, including Streptococcus (18.41%), Neisseria (18.20%), Prevotella_7 (8.89%), Porphyromonas (6.20%), Fusobacterium (5.86%) and Veillonella (5.82%). The statistically different phyla between the two groups were Firmicutes, Proteobacteria and Fusobacterium (P<0.05). The statistically different genera between the two groups were Streptococcus, Neisseria and Porphyromonas (P<0.05), and Capnocytophaga was only detected in patients with SACC.

CONCLUSIONS

Significant differences were observed in the oral microorganisms between the two groups.

Putative Periodontal Pathogens, Filifactor Alocis and Peptoanaerobacter Stomatis, Induce Differential Cytokine and Chemokine Production by Human Neutrophils

Periodontitis is a highly prevalent infectious disease that affects ~ 50% of the adults in the USA alone. Two Gram-positive anaerobic oral bacteria, Filifactor alocis and Peptoanaerobacterstomatis, have emerged as important periodontal pathogens. Neutrophils are a major component of the innate host response in the gingival tissue, and the contribution of neutrophil-derived cytokines and chemokines plays a central role in disease progression. The pattern of cytokines and chemokines released by human neutrophils upon stimulation with newly appreciated periodontal bacteria compared to the keystone oral pathogen Porphyromonas gingivalis was investigated. Our results showed that both F. alocis and P. stomatis triggered TLR2/6 activation. F. alocis induced significant changes in gene expression of cytokines and chemokines in human neutrophils compared to unstimulated cells. However, except for IL-1ra, neutrophils released lower levels of cytokines and chemokines in response to F. alocis compared to P. stomatis. Furthermore, bacteria-free conditioned supernatant collected from neutrophils challenged with P. stomatis, but not from P. gingivalis or F. alocis, was chemotactic towards both neutrophils and monocytes. Elucidating stimuli-specific modulation of human neutrophil effector functions in the context of dysbiotic microbial community constituents provides valuable information for understanding the pathogenesis of periodontal diseases.

Periodontitis and the microbiome: a systematic review and meta-analysis

INTRODUCTION

The association between the oral microbiome and periodontal diseases is still unclear. We performed a systematic review and meta-analysis to quantify the association between the specific pathogens and periodontitis.

EVIDENCE ACQUISITION

A computerized medical search was performed using MEDLINE and SCOPUS database between 1950 and May 2017 to identify all case-control studies that evaluated the association between specific pathogens and periodontitis. The pooled Odds Ratio with relative 95% confidence interval (95% CI) was calculated and plotted in the forest plot.

EVIDENCE SYNTHESIS

Eleven RCTs involving 2111 patients were included. The retrieved case-control studies evaluated the presence or absence of different targeted pathogens. Among the microrganisms evaluated Porphyromonas gengivalis (OR [95% CI] 2.93 [0.98,8.87]; P<0.0001) and Streptococcus mutans (OR [95% CI] 1.77 [0.89-3.54]; P=0.03) were found to be risk factors for the development of periodontitis, while Aggregatibacter actinomycetemcomitans (OR [95% CI] 0.52 [0.33-0.83]) played a protective role for periodontitis.

CONCLUSIONS

It seems that changes in the taxonomic composition of the microbiome rather than single targeted pathogens is the key determinant of periodontitis.

Oral Dysbiotic Communities and Their Implications in Systemic Diseases

The human body supports the growth of a wide array of microbial communities in various niches such as the oral cavity, gastro-intestinal and urogenital tracts, and on the surface of the skin. These host associated microbial communities include yet-un-cultivable bacteria and are influenced by various factors. Together, these communities of bacteria are referred to as the human microbiome. Human oral microbiome consists of both symbionts and pathobionts. Deviation from symbiosis among the bacterial community leads to “dysbiosis”, a state of community disturbance. Dysbiosis occurs due to many confounding factors that predispose a shift in the composition and relative abundance of microbial communities. Dysbiotic communities have been a major cause for many microbiome related systemic infections. Such dysbiosis is directed by certain important pathogens called the “keystone pathogens”, which can modulate community microbiome variations. One such persistent infection is oral infection, mainly periodontitis, where a wide array of causal organisms have been implied to systemic infections such as cardio vascular disease, diabetes mellitus, rheumatoid arthritis, and Alzheimer’s disease. The keystone pathogens co-occur with many yet-cultivable bacteria and their interactions lead to dysbiosis. This has been the focus of recent research. While immune evasion is one of the major modes that leads to dysbiosis, new processes and new virulence factors of bacteria have been shown to be involved in this important process that determines a disease or health state. This review focuses on such dysbiotic communities, their interactions, and their virulence factors that predispose the host to other systemic implications.

Filifactor alocis manipulates human neutrophils affecting their ability to release neutrophil extracellular traps induced by PMA

Neutrophils operate at the site of injury or inflammation in the periodontal pocket to ensure periodontal health and clearance of bacterial pathogens. Filifactor alocis is recently identified as a potential periodontal pathogen, and in this study, we assessed the formation of neutrophil extracellular traps (NETs), in response to the presence of the organism. NET formation by human neutrophils was not induced when challenged with F. alocis, independent of opsonization, viability, time, or bacterial dose. F. alocis also failed to induce NETs from TNF-α-primed neutrophils and did not induce the release of extracellular neutrophil elastase. However, significant NET induction was observed when neutrophils were challenged with Streptococcus gordonii or Peptoanaerobacter stomatis, In addition, co-infection studies revealed that the presence of F. alocis with S. gordonii or P. stomatis does not enhance or reduce NETs. Additionally, F. alocis failed to impact pre-formed NETs induced by either S. gordonii or P. stomatis. Pretreatment with F. alocis prior to stimulation with phorbol 12-myristate 13-acetate (PMA), S. gordonii, or P. stomatis revealed that the bacterium is capable of reducing only PMA but not S. gordonii or P. stomatis NET formation. These results indicate that F. alocis manipulates neutrophils, inhibiting the triggering of NET induction.

Efficacy of Miswak toothpaste and mouthwash on cariogenic bacteria

Objectives:

To evaluate the efficacy of Salvadora persica (Miswak) products on cariogenic bacteria in comparison with ordinary toothpaste.

Methods:

The study was conducted in Zakho city, Kurdistan region, Iraq during the period from October 2013 to January 2014. A randomized controlled clinical trial of 40 students randomly allocated into 4 groups. They were instructed to use Mismark toothpaste, Miswak mouthwash, and ordinary toothpaste with water or with normal saline. Salivary samples were collected at 3-time intervals: before, immediately after use, and after 2 weeks of use. The effect of each method on Streptococcus mutans and Lactobacilli was evaluated by using caries risk test.

Results:

One-way repeated measure analysis of variance (ANOVA), one-way ANOVA, and least significant difference tests were used. Miswak wash has a significant reduction effect on both bacteria immediately and after 2 weeks of use. Miswak paste has a similar effect on Lactobacilli, while Streptococcus mutans showed a significant decrease only after 2 weeks of use. Ordinary paste showed a non significant effect on both bacteria at both time intervals; while the addition of normal saline showed a significant effect on both bacteria only after 2 weeks of use.

Conclusion:

Miswak products, especially mouth wash, were more effective in reducing the growth of cariogenic bacteria than ordinary toothpaste.

Microbiome and Microbial Biofilm Profiles of Peri-Implantitis: A Systematic Review

BACKGROUND

This systematic review assesses microbiologic profiles of peri-implantitis, periodontitis, and healthy implants based on studies that evaluated microbial biofilms and entire microbiomes to establish their similarities and differences.

METHODS

The Medical Literature Analysis and Retrieval System Online via PubMed, Excerpta Medica Database, and Cochrane Central Register of Controlled Trials, were searched without language restrictions through July 30, 2016. Observational studies that evaluated microbial profiles or entire microbiomes of peri-implantitis compared with healthy implants or periodontitis were considered eligible for inclusion. A descriptive summary was created to determine quantity of data and interstudy variations.

RESULTS

Of 126 potentially eligible articles, 26 were included in this study. Twenty-one of these articles evaluated the microbiologic profile of peri-implantitis versus healthy implants or periodontitis using conventional microbiologic techniques. Five articles evaluated the entire microbiome using genomic sequencing. Teeth with periodontitis, healthy implants, or implants with peri-implantitis were colonized by periodontal microorganisms. Porphyromonas gingivalis and especially Prevotella intermedius/nigrescens were often identified at peri-implantitis sites. Peri-implantitis sites were also colonized by uncultivable asaccharolytic anaerobic Gram-positive rods and anaerobic Gram-negative rods, which were not frequently identified in teeth with periodontitis or healthy implants. Opportunistic microorganisms were not found very frequently in peri-implantitis sites.

CONCLUSIONS

Peri-implantitis represents a heterogeneous mixed infection that includes periodontopathic microorganisms, uncultivable asaccharolytic anaerobic Gram-positive rods and other uncultivable Gram-negative rods, and, rarely, opportunistic microorganisms such as enteric rods and Staphylococcus aureus. Sequencing methods that evaluate the entire microbiome improve identification of microorganisms associated with peri-implantitis.

Probiotics: A Promising Role in Dental Health

Probiotics have a role in maintaining oral health through interaction with oral microbiome, thus contributing to healthy microbial equilibrium. The nature and composition of any individual microbiome impacts the general health, being a major contributor to oral health. The emergence of drug resistance and the side effects of available antimicrobials have restricted their use in an array of prophylactic options. Indeed, some new strategies to prevent oral diseases are based on manipulating oral microbiota, which is provided by probiotics. Currently, no sufficient substantial evidence exists to support the use of probiotics to prevent, treat or manage oral cavity diseases. At present, probiotic use did not cause adverse effects or increased risks of caries or periodontal diseases. This implicates no strong evidence against treatment using probiotics. In this review, we try to explore the use of probiotics in prevention, treatment and management of some oral cavity diseases and the possibilities of developing designer probiotics for the next generation of oral and throat complimentary healthcare.

Salivary Diagnostics in Pediatrics: Applicability, Translatability, and Limitations

In the last decade, technological advances, combined with an improved appreciation of the ability of saliva to inform caregivers about both oral health and systemic disease, have led to the emergence of salivary diagnostic platforms. However, the majority of these assays have targeted diseases that more commonly affect the adult population, largely neglecting infants and children who arguably could benefit the most from non-invasive assessment tools for health monitoring. Gaining access into development, infection, and disease through comprehensive "omic" analyses of saliva could significantly improve care and enhance health access. In this review, we will highlight novel applications of salivary diagnostics in pediatrics across the "omic" spectrum, including at the genomic, transcriptomic, proteomic, microbiomic, and metabolomic level. The challenges to implementing salivary platforms into care, including the effects of age, diet, and developmental stage on salivary components, will be reviewed. Ultimately, large-scale, multicenter trials must be performed to establish normative biomarker values across the age spectrum to accurately discriminate between health and disease. Only then can salivary diagnostics truly translate into pediatric care.

Influence of culture conditions on porphyrin production in Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis

BACKGROUND

Increasing antibiotic resistance among pathogens has raised the demands for new treatment methods such as antimicrobial photodynamic therapy (aPDT) and phototherapy (PT). Experiments for investigating the effects of these methods are often performed in vitro, but the procedures for cultivation of microbes vary between different studies. The aim of this study has been to elucidate how the profile of endogenously produced porphyrins differs by changing the variables of bacteria culturing conditions.

METHODS

Two oral pathogens, Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis, were selected as model organisms. The contents of porphyrins and heme in the bacteria were analysed with liquid chromatography-tandem mass spectrometry when bacteria was cultivated for different lengths of time (3-9 days), upon passaging as well as when growth medium were supplemented with or without horse blood.

RESULTS

Both porphyrin and heme content in A. actinomycetemcomitans are highly affected by the age of the culture, and that the porphyrin profiles changes during cultivation. When cultivated colonies of A. actinomycetemcomitans were passaged onto a new, fresh growth medium a large change in porphyrin content occurred. Additional porphyrins were detected; uroporphyrin and 7-carboxylporphyrin, and the total porphyrin content increased up to 28 times. When P. gingivalis was grown on blood containing medium higher concentrations of protoporphyrin IX (2.5 times) and heme (5.4 times) were quantified compared to bacteria grown without blood.

CONCLUSIONS

This study demonstrate that there is a need for more standardized culturing protocols when performing aPDT and PT experiments in vitro to avoid large variations in porphyrin profiles and concentrations, the aPDT/PT target compounds, depending on the culturing conditions.

FACIN, a Double-Edged Sword of the Emerging Periodontal Pathogen Filifactor alocis: A Metabolic Enzyme Moonlighting as a Complement Inhibitor

Periodontal disease is one of the most common inflammatory infectious diseases worldwide and it is associated with other syndromes, such as cardiovascular disease or rheumatoid arthritis. Recent advances in sequencing allowed for identification of novel periodontopathogens such as Gram-positive Filifactor alocis, but its virulence mechanisms remain largely unknown. We confirmed that F. alocis is a prevalent species in periodontitis patients, and we also observed strong correlation of this bacterium with clinical parameters, highlighting its role in the pathogenesis of the disease. Further, we found that preincubation of human serum with F. alocis resulted in abolished bactericidal activity and that F. alocis was surviving readily in full blood. We demonstrated that one of the key contributors to F. alocis complement resistance is a unique protein, FACIN (F. alocis complement inhibitor), which binds to C3, resulting in suppression of all complement pathways. Interestingly, FACIN is a nonclassical cell surface protein, a cytosolic enzyme acetylornithine transaminase, for which we now identified a moonlighting function. FACIN binds to C3 alone, but more importantly it also captures activated complement factor 3 within the complex with factor B, thereby locking in the convertase in an inactive state. Because of the indispensable role of alternative pathway convertase in amplifying complement cascades, its inhibition by FACIN results in a very potent downregulation of activated complement factor 3 opsonization on the pathogen surface, accompanied by reduction of downstream C5 cleavage.

Human neutrophils and oral microbiota: a constant tug-of-war between a harmonious and a discordant coexistence

Neutrophils are a major component of the innate host response, and the outcome of the interaction between the oral microbiota and neutrophils is a key determinant of oral health status. The composition of the oral microbiome is very complex and different in health and disease. Neutrophils are constantly recruited to the oral cavity, and their protective role is highlighted in cases where their number or functional responses are impeded, resulting in different forms of periodontal disease. Periodontitis, one of the more severe and irreversible forms of periodontal disease, is a microbial-induced chronic inflammatory disease that affects the gingival tissues supporting the tooth. This chronic inflammatory disease is the result of a shift of the oral bacterial symbiotic community to a dysbiotic more complex community. Chronic inflammatory infectious diseases such as periodontitis can occur because the pathogens are able to evade or disable the innate immune system. In this review, we discuss how human neutrophils interact with both the symbiotic and the dysbiotic oral community; an understanding of which is essential to increase our knowledge of the periodontal disease process.

PCR-based detection of composite transposons and translocatable units from oral metagenomic DNA

A composite transposon is a mobile genetic element consisting of two insertion sequences (ISs) flanking a segment of cargo DNA often containing antibiotic resistance (AR) genes. Composite transposons can move as a discreet unit. There have been recently several reports on a novel mechanism of movement of an IS26-based composite transposon through the formation of a translocatable unit (TU), carrying the internal DNA segment of a composite transposon and one copy of a flanking IS. In this study, we determined the presence of composite transposons and TUs in human oral metagenomic DNA using PCR primers from common IS elements. Analysis of resulting amplicons showed four different IS1216 composite transposons and one IS257 composite transposon in our metagenomic sample. As our PCR strategy would also detect TUs, PCR was carried out to detect circular TUs predicted to originate from these composite transposons. We confirmed the presence of two novel TUs, one containing an experimentally proven antiseptic resistance gene and another containing a putative universal stress response protein (UspA) encoding gene. This is the first report of a PCR strategy to amplify the DNA segment on composite transposons and TUs in metagenomic DNA. This can be used to identify AR genes associated with a variety of mobile genetic elements from metagenomes.

Using a PCR approach, we have detected composite transposons and TUs directly from human oral metagenomic DNA.

The use of PCR/Electrospray Ionization-Time-of-Flight-Mass Spectrometry (PCR/ESI-TOF-MS) to detect bacterial and fungal colonization in healthy military service members

Background

The role of microbial colonization in disease is complex. Novel molecular tools to detect colonization offer theoretical improvements over traditional methods. We evaluated PCR/Electrospray Ionization-Time-of-Flight-Mass Spectrometry (PCR/ESI-TOF-MS) as a screening tool to study colonization of healthy military service members.

Methods

We assessed 101 healthy Soldiers using PCR/ESI-TOF-MS on nares, oropharynx, and groin specimens for the presence of gram-positive and gram-negative bacteria (GNB), fungi, and antibiotic resistance genes. A second set of swabs was processed by traditional culture, followed by identification using the BD Phoenix automated system; comparison between PCR/ESI-TOF-MS and culture was carried out only for GNB.

Results

Using PCR/ESI-TOF-MS, at least one colonizing organism was found on each individual: mean (SD) number of organisms per subject of 11.8(2.8). The mean number of organisms in the nares, groin and oropharynx was 3.8(1.3), 3.8(1.4) and 4.2(2), respectively. The most commonly detected organisms were aerobic gram-positive bacteria: primarily coagulase-negative Staphylococcus (101 subjects: 341 organisms), Streptococcus pneumoniae (54 subjects: 57 organisms), Staphylococcus aureus (58 subjects: 80 organisms) and Nocardia asteroides (45 subjects: 50 organisms). The mecA gene was found in 96 subjects. The most commonly found GNB was Haemophilus influenzae (20 subjects: 21 organisms) and the most common anaerobe was Propionibacterium acnes (59 subjects). Saccharomyces species (30 subjects) were the most common fungi detected. Only one GNB (nares E. coli) was identified in the same subject by both diagnostic systems.

Conclusion

PCR/ESI-TOF-MS detected common colonizing organisms and identified more typically-virulent bacteria in asymptomatic, healthy adults. PCR/ESI-TOF-MS appears to be a useful method for detecting bacterial and fungal organisms, but further clinical correlation and validation studies are needed.