Comparison of the oral microbiome of patients with generalized aggressive periodontitis and periodontitis-free subjects

Bacteria of healthy periodontal tissues as candidates of probiotics: a systematic review

OBJECTIVES

The use of probiotics could promote the balance of the subgingival microbiota to contribute to periodontal health. This study aimed to identify the potential of bacteria commonly associated with healthy periodontal tissues as probiotic candidates.

MATERIAL AND METHODS

A systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines using the PubMed, Scopus, Science Direct, ProQuest, and Ovid databases as well as the combination of Medical Subject Headings (MeSH) and non-MeSH terms. Based on the selection criteria, original studies published in English and identifying the microorganisms present in the periodontium of healthy individuals and patients with periodontitis using the high-throughput 16S ribosomal gene sequencing technique were included.

RESULTS

Out of 659 articles, 12 met the criteria for this review. These articles were published from 2012 to 2020 and mainly originated from the United States, China, and Spain. Most of these studies reported adequate criteria for selecting participants, using standardized clinical criteria, and compliance with quality based on the tools used. In periodontal healthy tissue were identified species like Actinomyces viscosus, Actinomyces naeslundii, Haemophilus parainfluenzae, Rothia dentocariosa, Streptococcus sanguinis, Streptococcus mitis, Streptococcus oralis, Streptococcus gordonii, Streptococcus intermedius, and Prevotella nigrescens which have recognized strains with a capacity to inhibit periodontopathogens.

CONCLUSIONS

S. sanguinis, S. oralis, S. mitis, and S. gordonii are among the bacterial species proposed as potential probiotics because some strains can inhibit periodontopathogens and have been reported as safe for humans.

Effects of Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans on Modeling Subgingival Microbiome and Impairment of Oral Epithelial Barrier

Periodontitis is an exemplar of dysbiosis associated with the coordinated action of multiple members within the microbial consortium. The polymicrobial synergy and dysbiosis hypothesis proposes a dynamic host-microbiome balance, with certain modulators capable of disrupting eubiosis and driving shifts towards dysbiosis within the community. However, these factors remain to be explored. We established a Porphyromonas gingivalis- or Aggregatibacter actinomycetemcomitans-modified subgingival microbiome model and 16S rRNA sequencing revealed that P. gingivalis and A. actinomycetemcomitans altered the microbiome structure and composition indicated by α and β diversity metrics. P. gingivalis increased the subgingival dysbiosis index (SDI), while A. actinomycetemcomitans resulted in a lower SDI. Furthermore, P. gingivalis-stimulated microbiomes compromised epithelium function and reduced expression of tight junction proteins, whereas A. actinomycetemcomitans yielded mild effects. In conclusion, by inoculating P. gingivalis, we created dysbiotic microcosm biofilms in vitro resembling periodontitis-related subgingival microbiota, exhibiting enhanced dysbiosis and impaired epithelium integrity.

Methotrexate and Non-Surgical Periodontal Treatment Change the Oral-Gut Microbiota in Rheumatoid Arthritis: A Prospective Cohort Study

This study evaluated the changes in the composition of oral-gut microbiota in patients with rheumatoid arthritis (RA) caused by methotrexate (MTX) and non-surgical periodontal treatment (NSPT). Assessments were performed at baseline (T0), 6 months after MTX treatment (T1), and 45 days after NSPT (T2). The composition of the oral and gut microbiota was assessed by amplifying the V4 region of the 16S gene from subgingival plaques and stools. The results of the analysis of continuous variables were presented descriptively and non-parametric tests and Spearman's correlation were adopted. A total of 37 patients (27 with periodontitis) were evaluated at T0; 32 patients (24 with periodontitis) at T1; and 28 patients (17 with periodontitis) at T2. MTX tended to reduce the alpha diversity of the oral-gut microbiota, while NSPT appeared to increase the number of different species of oral microbiota. MTX and NSPT influenced beta diversity in the oral microbiota. The relative abundance of oral microbiota was directly influenced by periodontal status. MTX did not affect the periodontal condition but modified the correlations that varied from weak to moderate (p < 0.05) between clinical parameters and the microbiota. MTX and NSPT directly affected the composition and richness of the oral-gut microbiota. However, MTX did not influence periodontal parameters.

Bacteriome analysis of Aggregatibacter actinomycetemcomitans-JP2 genotype-associated Grade C periodontitis in Moroccan adolescents

Background

Grade C (previously aggressive) periodontitis (GCP) in adolescents is prevalent in certain parts of Africa where it is associated with JP2 genotype, a highly virulent strain of Aggregatibacter actinomycetemcomitans. The aim of this study was to characterize the subgingival bacteriome in Moroccan subjects with GCP positive to A. actinomycetemcomitans JP2 genotype.

Methods

Subgingival plaque samples were collected from shallow and deep pockets of 8 subjects with GCP (17.2 ± 1.5 years) and from gingival sulci of 13 controls with no periodontitis (14.6 ± 1.1 years). Identification and genotyping of A. actinomycetemcomitans was performed using PCR analysis of the ltx operon, while bacteriome profiling was done by 16S rRNA gene sequencing (V1-V3 region). Groups were compared in terms of microbial diversity, abundances, and dysbiosis.

Results

The shallow and deep pocket sites from GCP cases had a significantly altered microbial composition compared to controls. Species associated with health included Haemophilus parainfluenzae, Lautropia mirabilis, Streptococcus spp., Gemella spp., and Rothia spp. While known periodontal pathogens, including Porphyromonas gingivalis, Tannerella forsythia, Treponema spp. and Fretibacterium spp., were significantly enriched in GCP, non-conventional taxa, including Pseudomonas oral taxon C61 and Enterobacter cloacae were more abundant and showed stronger association with the disease. Less significant differences in abundances of individual taxa were observed between shallow and deep pockets. Overall dysbiosis measured in terms of Subgingival Microbial Dysbiosis Index (SMDI) differentiated between GCP and no-periodontitis with 95% accuracy.

Conclusions

The results suggest that several periodontal pathogens involved in the adult-type periodontitis also play a role in JP2 genotype-associated GCP. The potential role of non-conventional taxa in the pathogenesis of GCP warrants further investigation.

Impact of waterpipe smoking on the salivary microbiome

Background

While oral mirobial dysbiosis due to tobacco smoking has been studied thoroughly, there is limited data on the effect of waterpipe smoking on the oral microbiome. This study aims to compare the salivary microbiome between waterpipe smokers and non-smokers.

Materials and methods

Unstimulated saliva samples were collected from 60 participants, 30 smokers and 30 non-smokers in Kuala Lumpur and Klang Valley, Malaysia. DNA extraction was performed using the Qiagen DNA mini kit, and the 16S rRNA bacterial gene was amplified and sequenced using the Illumina MiSeq platform. Sequencing reads were processed using DADA2, and the alpha and beta diversity of the bacterial community was assessed. Significantly differentiated taxa were identified using LEfSe analysis, while differentially expressed pathways were identified using MaAsLin2.

Results

A significant compositional change (beta diversity) was detected between the two groups (PERMANOVA P < 0.05). Specifically, the levels of phylum Firmicutes and genus Streptococcus were elevated in smokers, whereas phylum Proteobacteria and genus Haemophilus were depleted compared to non-smokers. At the species level, Streptococcus oralis, Streptococcus salivarius, and Streptococcus gingivalis were enriched in smokers. We observed significant differences in the abundance of thirty-seven microbial metabolic pathways between waterpipe smokers and non-smokers. The microbial pathways enriched in smokers were those implicated in polymer degradation and amino acid metabolism.

Conclusion

The taxonomic and metabolic profile of the salivary microbiome in waterpipe smokers compared to healthy controls exhibited a paradigm shift, thus, implying an alteration in the homeostatic balance of the oral cavity posing unique challenges for oral health.

Additively manufactured Ti-29Nb-21Zr shows improved oxide polarization resistance versus Ti-6Al-4V in inflammatory simulating solution

Retrieval studies in the past two decades show severe corrosion of titanium and its alloys in orthopedic implants. This damage is promoted by mechanically assisted crevice corrosion (MACC), particularly within modular titanium-titanium junctions. During MACC, titanium interfaces may be subject to negative potentials and reactive oxygen species (ROS), generated from cathodic activation and/or inflammation. Additive manufacturing (AM) may be able to produce new, corrosion-resistant titanium alloys and admixtures that are less susceptible to these adverse electrochemical events. In this study, we characterize the impedance and corrosion properties of three new AM titanium materials, including Ti-6Al-4V with added 1% nano-yttria stabilized ZrO2 , admixed Ti-29Nb-21Zr, and pre-alloyed Ti-29Nb-21Zr. We aim to elucidate how these materials perform when subjected to high ROS solutions. We include conventionally and additively manufactured Ti-6Al-4V in our study as comparison groups. A 0.1 M H2 O2 phosphate-buffered saline (PBS) solution, simulating inflammatory conditions, significantly increased biomaterial OCP (-0.14 V vs. Ag/AgCl) compared to PBS only (-0.38 V, p = .000). During anodic polarization, Ti-6Al-4V passive current density more than doubled from 1.28 × 10-7 to 3.81 × 10-7  A/cm2 when exposed to 0.1 M H2 O2 . In contrast, Ti-29Nb-21Zr passive current density remained relatively unchanged, slightly increasing from 7.49 × 10-8 in PBS to 9.31 × 10-8 in 0.1 M H2 O2 . Ti-29Nb-21Zr oxide polarization resistance (Rp ) was not affected by 0.1 M H2 O2 , maintaining a high value (1.09 × 106 vs. 1.89 × 106  Ω cm2 ), while Ti-6Al-4V in 0.1 M H2 O2 solution had significantly diminished Rp (4.38 × 106 in PBS vs. 7.24 × 104  Ω cm2 in H2 O2 ). These results indicate that Ti-29Nb-21Zr has improved corrosion resistance in ROS containing solutions when compared with Ti-6Al-4V based biomaterials.

Parents with periodontitis drive the early acquisition of dysbiotic microbiomes in their offspring

AIM

To evaluate the microbial colonization in different dentition phases on individuals from 0 to 18 years of age belonging to families with a history of periodontitis compared to descendants of periodontally healthy parents.

MATERIALS AND METHODS

The offspring of subjects with periodontitis ('Perio' group) and the offspring of periodontally healthy subjects ('Healthy' group), matched for gender and age, were included in this cross-sectional study and divided according to the dentition phase: pre-dentate, primary, mixed and permanent. The patients were clinically assessed, and their saliva was collected. DNA was extracted, and V1-V3 and V4-V5 regions of the 16S rRNA gene were sequenced.

RESULTS

Fifty children of parents with periodontitis and 50 from healthy parents were included in the study and divided according to the dentition phase: pre-dentate (n = 5/group), primary dentition (n = 15/group), mixed dentition (n = 15/group) and permanent dentition (n = 15/group) in each group. The microbiome composition was different between dentitions for both groups. Children of the Perio group presented a microbial diversity different from that of the Healthy group in mixed and permanent dentitions. The more intense shift in the community occurred between primary and mixed dentition in the Perio group, while the transition between mixed and permanent dentition was the period with greater changes in the microbiome for the Healthy group. Furthermore, a pathogen-rich environment-higher prevalence and abundance of periodontitis-associated species such as Prevotella spp., Selenomonas spp., Leptotrichia spp., Filifactor alocis, Prevotella intermedia, Treponema denticola and Tannerella forsythia- was observed in the Perio group.

CONCLUSIONS

The parents' periodontal status significantly affects the microbiome composition of their offspring from an early age. The mixed dentition was the phase associated with establishing a dysbiotic and pathogen-rich microbiome in descendants of parents with periodontitis.

Differential analysis of culturable and unculturable subgingival target microorganisms according to the stages of periodontitis

OBJECTIVES

Culturable and unculturable microorganisms have been associated with periodontitis. Their differential proportions and composition have not been evaluated by their severity and complexity defined by stages in the 2018 AAP-EEP classification.

METHODS

One hundred eighty subgingival biofilm samples were collected in Spain and Colombia from subjects categorized as health/gingivitis: periodontitis stages I/II periodontitis stages III/IV. Target culturable microorganisms (Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Tannerella forsythia, Treponema denticola, and Eubacterium nodatum) and target unculturable microorganisms (Filifactor alocis, Eubacterium saphenum, Eubacterium brachy, Desulfobulbus oralis) were evaluated by quantitative PCR analysis. In addition, their differences and association with periodontal status were analyzed by ANCOVA and logistic regression models once adjusted to age, current smoking, and country.

RESULTS

P. gingivalis was significantly associated with periodontitis stages I/II, OR 2.44 (CI 95% 1.08-5.47) and stages III/V, OR 6.43 (CI 95% 2.43-16.9). T forsythia, OR 7.53 (CI 95% 2.07-27.4); D. oralis, OR 5.99 (CI 95% 2.71-13.23); F. alocis, OR 10.9 (CI 95% 4.56-23.2); E. brachy, 3.57 (CI 95% 1.40-9.11); and E. saphenum, 4.85 (CI 95% 1.99-11.7) were significantly associated only with stages III/IV periodontitis. P. gingivalis evidenced significant differences with the increase in the severity of the periodontal lesion: 2.97 colony forming unit (CFU)/μL (CI 95% 2.32-3.54) health/gingivitis, and 4.66 CFU/μL (CI 95% 4.03-5.30) and 5.90 CFU/μL (CI 95% 5.20-6.48) in stages I/II and III/IV respectively (p < 0.0001). Unculturable microorganisms only evidenced differences in concentration in stages III/IV compared with health-gingivitis (p ≤ 0.001).

CONCLUSION

Culturable and unculturable are strongly associated with stages III/IV periodontitis. Classic culturable microorganisms are more sensitive to differentiate between stages of periodontitis in the quantitative analysis.

CLINICAL RELEVANCE

Future interventional studies of periodontal disease should include Filifactor alocis, Eubacterium saphenum, Eubacterium brachy, and Desulfobulbus oralis as possible markers of therapy response and as indicators of progressive disease.

Tobacco smoke exacerbates Filifactor alocis pathogenicity

AIM

Filifactor alocis has recently emerged as a periodontal pathobiont that appears to thrive in the oral cavity of smokers. We hypothesized that identification of smoke-responsive F. alocis genes would provide insight into adaptive strategies and that cigarette smoke would enhance F. alocis pathogenesis in vivo.

MATERIALS AND METHODS

F. alocis was grown in vitro and cigarette smoke extract-responsive genes determined by RNAseq. Mice were exposed, or not, to mainstream 1R6F research cigarette smoke and infected with F. alocis, or not, in an acute ligature model of periodontitis. Key clinical, infectious, and immune data were collected.

RESULTS

In culture, F. alocis growth was unaffected by smoke conditioning and only a small number of genes were specifically regulated by smoke exposure. Reduced murine mass, differences in F. alocis-cognizant antibody production, and altered immune profiles as well as altered alveolar bone loss were all attributable to smoke exposure and/or F. alocis infection in vivo.

CONCLUSIONS

F. alocis is well-adapted to tobacco-rich conditions and its pathogenesis is enhanced by tobacco smoke exposure. A smoke-exposed ligature model of periodontitis shows promise as a tool with which to further unravel mechanisms underlying tobacco-enhanced, bacteria-induced disease.

Prevalence of Periodontal Pathogens in Slovak Patients with Periodontitis and Their Possible Aspect of Transmission from Companion Animals to Humans

Oral health and diseases are greatly influenced by oral bacteria. During dysbiosis, bacterial composition changes, which can lead to periodontitis. Periodontitis in humans is associated with periodontal pathogens such as Treponema denticola, Porphyromonas gingivalis, Tannerella forsythia and Aggregatibacter actinomycetemcomitans. Animal-to-human transmission of some of these pathogens has also been reported. The aim of this study was to evaluate the prevalence of periodontal pathogens in Slovak patients and to assess the possible risk of transmission of these pathogens from animals to their owners. The presence of periodontal pathogens in dental plaque was monitored by PCR. Amplified products were analysed using Sanger sequencing. T. forsythia isolates were assessed for the susceptibility to different antibiotics using the disk diffusion method. In humans, T. denticola, P. gingivalis, T. forsythia and A. actinomycetemcomitans were present in 69.23%, 69.23%, 100% and 84.62%, respectively. Most isolates of T. forsythia were susceptible to amoxicillin-clavulanic acid, clindamycin and moxifloxacin, but they were resistant to metronidazole. The transmission of T. forsythia from animals to their owners was not proven based on sequence analysing. On the other hand, transmission of Porphyromonas gulae was confirmed, but the risk of its involvement in the pathogenesis of periodontitis in humans must be further investigated.

Multi-omics analysis reveals the host–microbe interactions in aged rhesus macaques

Aging is a complex multifactorial process that greatly affects animal health. Multi-omics analysis is widely applied in evolutionary biology and biomedical research. However, whether multi-omics can provide sufficient information to reveal comprehensive changes in aged non-human primates remains unclear. Here, we explored changes in host–microbe interactions with aging in Chinese rhesus macaques (Macaca mulatta lasiota, CRs) using multi-omics analysis. Results showed marked changes in the oral and gut microbiomes between young and aged CRs, including significantly reduced probiotic abundance and increased pathogenic bacterial abundance in aged CRs. Notably, the abundance of Lactobacillus, which can metabolize tryptophan to produce aryl hydrocarbon receptor (AhR) ligands, was decreased in aged CRs. Consistently, metabolomics detected a decrease in the plasma levels of AhR ligands. In addition, free fatty acid, acyl carnitine, heparin, 2-(4-hydroxyphenyl) propionic acid, and docosahexaenoic acid ethyl ester levels were increased in aged CRs, which may contribute to abnormal fatty acid metabolism and cardiovascular disease. Transcriptome analysis identified changes in the expression of genes associated with tryptophan metabolism and inflammation. In conclusion, many potential links among different omics were found, suggesting that aged CRs face multiple metabolic problems, immunological disorders, and oral and gut diseases. We determined that tryptophan metabolism is critical for the physiological health of aged CRs. Our findings demonstrate the value of multi-omics analyses in revealing host–microbe interactions in non-human primates and suggest that similar approaches could be applied in evolutionary and ecological research of other species.

Validity of a combination of periodontal pathogens and salivary biomarkers as predictors of periodontitis

OBJECTIVE

Chronic periodontitis is caused by multiple risk factors. To predict chronic periodontitis in older people, we evaluated the association between a combination of major periodontal pathogens and salivary biomarkers and the presence of periodontitis.

METHODS

Stimulated saliva samples were collected to analyze the prevalence of Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, and Prevotella intermedia, as well as four biomarkers: interleukin (IL)-1β, IL-6, tumor necrosis factor-α (TNF-α), and prostaglandin E2 (PGE2). A total of 201 Japanese patients were recruited. Oral examinations ware performed to determine chronic periodontitis as measured by Community Periodontal Index. The sociodemographic and behavioral characteristics were also obtained, and the parameters were adjusted as potential confounders to employ statistical models.

RESULTS

The odds ratio (OR) for the presence of P. gingivalis and the third tertile level of IL-1β as compared with the absence of P. gingivalis and the lowest tertile of IL-1β was highest in individuals with periodontitis (OR = 13.98; 95% confidence interval [CI] 3.87-50.52) with the best level (0.79) of area under the curve (AUC) based on the receiver operating characteristic curve. The OR for the presence of P. gingivalis and the third tertile of PGE2 was 7.76 (CI 1.89-31.91) with an AUC of 0.78. The coexistence of more than two periodontal bacteria and the third tertile of PGE2 was also strongly associated with chronic periodontitis (OR = 9.23, 95% CI 2.38-35.79) with an AUC of 0.76.

CONCLUSIONS

The combined information of the presence of P. gingivalis in stimulated saliva, and higher levels of salivary IL-1β may play a vital role in the detection and prediction of chronic periodontitis in older adults.

Campylobacter Species of the Oral Microbiota as Prognostic Factor for Cardiovascular Outcome after Coronary Artery Bypass Grafting Surgery

Background: The oral microbiota has been implicated in a variety of systemic diseases, including cardiovascular (CV) disease. The main objective of this study (DRKS-ID: DRKS00015776) was to evaluate the prognostic importance of the oral microbiota for further CV events in patients undergoing coronary artery bypass grafting surgery (3-year follow-up). Methods: In this longitudinal cohort study, 102 CV patients were enrolled, of whom 95 completed the 3-year follow-up. The CV outcome was assessed using the major adverse cardiac and cerebrovascular events criteria. To evaluate subgingival colonization, 16S rRNA genes were amplified, targeting the V3/V4 region (Illumina MiSeq). Results: Regarding the specific number of operational taxonomic units (OTUs), no significant differences in CV outcome were determined (alpha diversity, Shannon index). In linear discriminant analyses and t-tests, the disease-specific differences in the beta diversity of the microbiota composition were evaluated. It was evident that bacteria species of the genus Campylobacter were significantly more prevalent in patients with a secondary CV event (p = 0.015). This hierarchical order also includes Campylobacter rectus, which is considered to be of comprehensive importance in both periodontal and CV diseases. Conclusions: Here, we proved that subgingival occurrence of Campylobacter species has prognostic relevance for cardiovascular outcomes in CV patients undergoing coronary artery bypass grafting.

The New Era of Salivaomics in Dentistry: Frontiers and Facts in the Early Diagnosis and Prevention of Oral Diseases and Cancer

Nowadays, with the development of new and highly sensitive, blood is not the only medium of choice for the diagnosis of several diseases and pathological conditions. Saliva is now considered a safe and non-invasive sample to study oral and systemic diseases, showing great diagnostic potential. According to several recent studies, saliva has emerged as an emerging biofluid for the early diagnosis of several diseases, indicated as a mirror of oral and systemic health and a valuable source of clinically relevant information. Indeed, several studies have observed that saliva is useful for detecting and diagnosing malignant tumours, human immunodeficiency virus, heart disease, and autoimmune diseases. The growing realisation that saliva is an inexhaustible source of information has led to the coining of the term ‘Salivaomics’, which includes five “omics” in connection with the main constituents of saliva: genome and epigenome, transcriptomics, metabolomics, lipidomics, proteomics and microbiota. All those may be changed by disease state, so they offer significant advantages in the early diagnosis and prognosis of oral diseases. The aim of the present review isto update and highlight the new frontiers of salivaomics in diagnosing and managing oral disorders, such as periodontitis, premalignant disorders, and oral squamous cell carcinoma (OSCC).

Simultaneous presence of Mycoplasma salivarium and Tannerella forsythia in the implant sulcus after lateral augmentation with autogenous root grafts is associated with increased sulcus probing depth

Objective

To characterize a potential pathogenic role of Mycoplasma salivarium and bacterial co-detection patterns on different implant augmentation types.

Material and methods

36 patients were non-randomly assigned to autogenous lateral alveolar ridge augmentation with either cortical autogenous bone blocks, or healthy autogenous tooth roots or non-preservable teeth. Mucosal inflammation was assessed by probing pocket depth (PD) at all sampling sites and by bleeding on probing (BOP) in a subset of sampling sites, and standardized biofilm samples were obtained from the submucosal peri-implant sulcus and sulcus of a contralateral tooth at two times (t1 after implant placement; t2 after six months). Seven bacterial species were quantified using Taqman PCR.

Results

Mucosal inflammation did not differ between augmentation groups, but peri-implant sulci showed increased abundance of M. salivarium after augmentation with autogenous tooth roots lasting for at least six months (t1 p = 0.05, t2 p = 0.011). In M. salivarium-positive samples, Tannerella forsythia was correlated with PD (R = 0.25, p = 0.035) This correlation was not observed in M. salivarium-negative samples. Compared to all other samples, PD was deeper in co-detection (i.e., simultaneous M. salivarium and T. forsythia) positive samples (p = 0.022). No association of single or co-detection of bacteria with BOP was observed.

Conclusion

Presence of M. salivarium in peri-implant sulci varies with augmentation method and is associated with increased PD but not BOP. A potential causal role of M. salivarium in inflammation through a mechanism involving co-presence of T. forsythia requires further study.

The role of oral microbiome in periodontitis under diabetes mellitus

Periodontitis is among most common human inflammatory diseases and characterized by destruction of tooth-supporting tissues that will eventually lead to tooth loss. Diabetes mellitus (DM) is a group of metabolic disorders characterized by chronic hyperglycemia which results from defects in insulin secretion and/or insulin resistance. Numerous studies have provided evidence for the inter-relationship between DM and periodontitis that has been considered as the sixth most frequent complication of DM. However, the mechanisms are not fully understood yet. The impact of DM on periodontitis through hyperglycemia and inflammatory pathways is well described, but the effects of DM on oral microbiota remain controversial according to previous studies. Recent studies using next-generation sequencing technology indicate that DM can alter the biodiversity and composition of oral microbiome especially subgingival microbiome. This may be another mechanism by which DM risks or aggravates periodontitis. Thus, to understand the role of oral microbiome in periodontitis of diabetics and the mechanism of shifts of oral microbiome under DM would be valuable for making specific therapeutic regimens for treating periodontitis patients with DM or preventing diabetic patients from periodontitis. This article reviews the role of oral microbiome in periodontal health (symbiosis) and disease (dysbiosis), highlights the oral microbial shifts under DM and summarizes the mechanism of the shifts.

Nonsurgical Periodontal Treatment Options and Their Impact on Subgingival Microbiota

BACKGROUND

Different periodontal treatment methods (quadrant-wise debridement, scaling and root planing (Q-SRP), full-mouth scaling (FMS), full-mouth disinfection (FMD), and FMD with adjuvant erythritol air-polishing (FMDAP)) were applied in periodontitis patients (stage III/IV). The study objective (substudy of ClinicalTrials.gov Identifier: NCT03509233) was to compare the impact of treatments on subgingival colonization.

METHODS

Forty patients were randomized to the treatment groups. Periodontal parameters and subgingival colonization were evaluated at baseline and 3 and 6 months after treatment.

RESULTS

Positive changes in clinical parameters were recorded in every treatment group during the 3-month follow-up period, but did not always continue. In three groups, specific bacteria decreased after 3 months; however, this was associated with a renewed increase after 6 months (FMS: Porphyromonas gingivalis; FMD: Eubacterium nodatum, Prevotella dentalis; and FMDAP: uncultured Prevotella sp.).

CONCLUSIONS

The benefit of all clinical treatments measured after 3 months was associated with a decrease in pathogenic bacteria in the FMS, FMD, and FMDAP groups. However, after 6 months, we observed further improvement or some stagnation in clinical outcomes accompanied by deterioration of the microbiological profile. Investigating the subgingival microbiota might help appraise successful periodontal treatment and implement individualized therapy.

Toward Personalized Oral Diagnosis: Distinct Microbiome Clusters in Periodontitis Biofilms

Periodontitis is caused by pathogenic subgingival microbial biofilm development and dysbiotic interactions between host and hosted microbes. A thorough characterization of the subgingival biofilms by deep amplicon sequencing of 121 individual periodontitis pockets of nine patients and whole metagenomic analysis of the saliva microbial community of the same subjects were carried out. Two biofilm sampling methods yielded similar microbial compositions. Taxonomic mapping of all biofilms revealed three distinct microbial clusters. Two clinical diagnostic parameters, probing pocket depth (PPD) and clinical attachment level (CAL), correlated with the cluster mapping. The dysbiotic microbiomes were less diverse than the apparently healthy ones of the same subjects. The most abundant periodontal pathogens were also present in the saliva, although in different representations. The single abundant species Tannerella forsythia was found in the diseased pockets in about 16–17-fold in excess relative to the clinically healthy sulcus, making it suitable as an indicator of periodontitis biofilms. The discrete microbial communities indicate strong selection by the host immune system and allow the design of targeted antibiotic treatment selective against the main periodontal pathogen(s) in the individual patients.

Antipsychotic-induced gastrointestinal hypomotility and the alteration in gut microbiota in patients with schizophrenia

AIM

Gut microbiota play an important role in the pathogenesis of gut hypomotility and are critical for the production of the intestinal immune system and the maintenance of the intestinal homeostasis. Patients with psychotic disorders are at a high risk of antipsychotic-induced constipation. However, the mechanisms might be more than neurotransmission properties of antipsychotics.

METHODS

We recruited a total of 45 patients with constipation according to Rome IV criteria and objective test for colonic motility and the other 45 gender- and age-matching patients without constipation and investigated their differences in composition of gut microbiota. The demographic and serum metabolic indices were collected. The subjective constipation assessment scale (CAS) and the Bristol stool classification (BSS) were also used to evaluate the degree of constipation in both groups. The fecal samples were analysed using the 16S rRNA gene sequencing.

RESULTS

The constipation group had a significantly increased alpha diversity in Observed species, Chao 1, and ACE as compared to the non-constipation group. At the phylum levels, the relative abundances of Bacteroidetes and Fusobacteria decreased significantly, while those of Firmicutes, Verrucomicrobia, and Synergistetes increased significantly in the constipation group. At the genus level, the relative abundances of Christensenella and Desulfovibrio were higher in the constipation group. The α-diversity indices of gut microbiota were correlated positively with the levels of serum total bile acid and correlated negatively with BSS scores. The BSS scores were positively correlated with the relative abundance of Bacteroidetes but negatively correlated with the relative abundance of Firmicutes. PICRUSt analysis revealed the potential metabolic pathways of lipopolysaccharide, vitamin B6, riboflavin, pyruvate, and propionate functions.

CONCLUSIONS

The alternation of the gut microbiota in schizophrenia patients with antipsychotic-induced constipation indicates antipsychotic agents might affect gastrointestinal motility via varying microbiome-related metabolites, and the specific bacteria, such as Synergistetes which might act as an anti-inflammatory factor in the healthy human gut, related to colonic transit motility seem inconsistent to the findings from previous literature in gastroenterology. However, the causal effects are still unknown. Our study provides a new possibility to understand the mechanisms of antipsychotic-induced constipation.

Patterns of subgingival microbiota in different periodontal phenotypes

OBJECTIVES

To compare the subgingival microbiota of patients with aggressive (AgP) or chronic periodontitis (CP) to healthy (H), non-periodontitis patients as well as to explore their relevant associations to different host genetic variants.

METHODS

Following clinical examination, blood and subgingival plaque sampling of 471 study participants (125 AgP, 121 CP, 225 H), subgingival community analysis was performed by next generation sequencing of the 16S rRNA. Microbial data from 266 participants (75 AgP, 95 CP, 98 H) were available for analysis. SNPs in the IL6, IL6R and FTO gene were selected for genetic marker analyses.

RESULTS

Combined periodontitis patients (AgP + CP), particularly those classified with AgP, exhibited lower alpha- and beta- diversity. Several genera (including Peptostreptococcaceae, Filifactor, Desulfobulbus, Tannerella and Lachnospiracee) and species were over-abundant in combined periodontitis vs. healthy individuals, while other genera such as Prevotella or Dialister were found to be more abundant in healthy cases. The only genus with difference in abundance between AgP and CP was Granulicatella. No associations between IL6, IL6RA and FTO genetic variants and microbial findings were detected.

CONCLUSION

This study suggests that limited microbial differences existed between AgP and CP and challenges the current notion that periodontitis is associated with increased subgingival microbial diversity compared with periodontal health.

CLINICAL SIGNIFICANCE

The findings of this study cast some doubts on the notion that the dysbiosis characteristic of periodontal disease is expressed as increased microbial diversity.

Oral Health and the Altered Colonic Mucosa-Associated Gut Microbiota

BACKGROUND

Systemic diseases have been associated with oral health and gut microbiota. We examined the association between oral health and the community composition and structure of the adherent colonic gut microbiota.

METHODS

We obtained 197 snap-frozen colonic biopsies from 62 colonoscopy-confirmed polyp-free individuals. Microbial DNA was sequenced for the 16S rRNA V4 region using the Illumina MiSeq, and the sequences were assigned to the operational taxonomic unit based on SILVA. We used a questionnaire to ascertain tooth loss, gum disease, and lifestyle factors. We compared biodiversity and relative abundance of bacterial taxa based on the amount of tooth loss and the presence of gum disease. The multivariable negative binomial regression model for panel data was used to estimate the association between the bacterial count and oral health. False discovery rate-adjusted P value (q value) < .05 indicated statistical significance.

RESULTS

More tooth loss and gum disease were associated with lower bacterial alpha diversity. The relative abundance of Faecalibacterium was lower (q values < .05) with more tooth loss. The association was significant after adjusting for age, ethnicity, obesity, smoking, alcohol use, hypertension, diabetes, and the colon segment. The relative abundance of Bacteroides was higher in those with gum disease.

CONCLUSIONS

Oral health was associated with alteration in the community composition and structure of the adherent gut bacteria in the colon. The reduced anti-inflammatory Faecalibacterium in participants with more tooth loss may indicate systemic inflammation. Future studies are warranted to confirm our findings and investigate the systemic role of Faecalibacterium.

Rumen Bacterial Community of Grazing Lactating Yaks (Poephagus grunniens) Supplemented with Concentrate Feed and/or Rumen-Protected Lysine and Methionine

Simple Summary

Ruminal microorganisms, especially bacteria, play a vital role in utilizing fibrous material in ruminants. The yak is a bovid on the Qinghai-Tibet Plateau that traditionally only grazes natural pasture all year. During lactation, energy intake of yaks is often well below requirements, and yaks lose body weight. Today, to mitigate body weight losses during lactation, suckling yaks are often offered supplementary feed. This study examined the effect of dietary supplements on rumen bacteria in lactating yak. The yaks were offered supplementary concentrate feed (C), rumen-protected Lys and Met (RPA), or both (RPA+C). The ratio of the relative abundance of Firmicutes to Bacteroidetes in RPA+C was greater than in the RPA group, while there was no difference between C and RPA+C. The intakes of supplements resulted in a number of alterations in the abundances of bacteria at the genus level. When supplemented with C, yaks increased the concentration of ruminal total volatile fatty acids (VFAs), acetate, and butyrate. These results demonstrate that supplementary feed: (1) alters the composition of rumen microbiota and VFAs of lactating yaks; and (2) can be used to manipulate the composition of rumen microbiota.

Abstract

Traditionally, yaks graze only natural pasture all year round without supplements. Forage intake of lactating yaks is below energy and protein requirements, even in the summer, and suckling yaks lose a substantial amount of significant body weight. Today, to mitigate the loss in body weight, supplementary feed is being offered to lactating yaks. However, the effects of supplementary feed on ruminal bacterial communities in lactating yaks is unknown. In the current study, we examined the effect of supplementary feed on ruminal microbiota, using 16S rRNA sequencing, and on volatile fatty acids (VFAs). Twenty-four lactating yaks of similar body weight (218 ± 19.5 kg) and grazing natural pasture were divided randomly into four groups and received different supplements: (1) rumen-protected amino acids (RPA); (2) concentrate feed (C); (3) RPA plus C (RPA+C); and (4) no supplements (control-CON). The concentrations of total VFAs, acetate, and butyrate were greater (p < 0.05) when supplemented with concentrate feed (C and RPA+C) than without concentrate feed (CON and RPA). Bacteroidetes (B) and Firmicutes (F) were the dominant ruminal bacterial phyla in all groups. The ratio of relative abundance of F:B in RPA+C was greater than in the RPA group, while there was no difference between CON and RPC (interaction, p = 0.026). At the genus level, the relative abundances of Absconditabacteriales_SR1, Bacteroidales-RF16-group, Bacteroidales_BS11_gut_group, Prevotellaceae, and Rikenellaceae_RC9_gut_group were lesser (p < 0.05) with supplementary concentrate feed (C and RPA+C) than without concentrate feed (CON and RPA), whereas Butyrivibrio_2 and Pseudobutyrivibrio were greater (p < 0.05) with supplementary rumen-protected amino acids (RPA and RPA+C) than without rumen-protected amino acids (CON and C). These results demonstrate that supplementary feed: (1) alters the composition of rumen microbiota and concentrations of ruminal VFAs in lactating yaks; and (2) can be used to manipulate the composition of rumen microbiota.

Comprehensive Analysis of Risk Factors for Periodontitis Focusing on the Saliva Microbiome and Polymorphism

Few studies have exhaustively assessed relationships among polymorphisms, the microbiome, and periodontitis. The objective of the present study was to assess associations simultaneously among polymorphisms, the microbiome, and periodontitis. We used propensity score matching with a 1:1 ratio to select subjects, and then 22 individuals (mean age ± standard deviation, 60.7 ± 9.9 years) were analyzed. After saliva collection, V3-4 regions of the 16S rRNA gene were sequenced to investigate microbiome composition, alpha diversity (Shannon index, Simpson index, Chao1, and abundance-based coverage estimator) and beta diversity using principal coordinate analysis (PCoA) based on weighted and unweighted UniFrac distances. A total of 51 single-nucleotide polymorphisms (SNPs) related to periodontitis were identified. The frequencies of SNPs were collected from Genome-Wide Association Study data. The PCoA of unweighted UniFrac distance showed a significant difference between periodontitis and control groups (p < 0.05). There were no significant differences in alpha diversity and PCoA of weighted UniFrac distance (p > 0.05). Two families (Lactobacillaceae and Desulfobulbaceae) and one species (Porphyromonas gingivalis) were observed only in the periodontitis group. No SNPs showed significant expression. These results suggest that periodontitis was related to the presence of P. gingivalis and the families Lactobacillaceae and Desulfobulbaceae but not SNPs.

Porphyromonas gingivalis, the most influential pathogen in red-complex bacteria: A cross-sectional study on the relationship between bacterial count and clinical periodontal status in Japan

BACKGROUND

Porphyromonas gingivalis is a key pathogen in microbiota associated with periodontitis. The purpose of the present study was to assess the association between salivary counts of red-complex bacteria and clinical periodontal status in a Japanese population.

METHODS

A total of 977 subjects who visited a general dental clinic in Japan from 2003 to 2006 were enrolled in the study. Stimulated saliva was obtained, and the amounts of major periodontal bacteria were measured using real-time polymerase chain reaction. Probing pocket depth (PPD), bleeding on probing (BOP), and each subject's average proximal bone crest level (BCL) on dental radiographs were measured.

RESULTS

The number of P. gingivalis strongly associated with percentage of 4 mm or more PPD sites, BOP positive percentage, and 1.5 mm or more BCL sites. The detection of P. gingivalis with Treponema denticola and/or Tannerella forsythia showed a high rate of three positive clinical parameters, whereas the only P. gingivalis detected group and those without P. gingivalis had a low rate of three positive clinical parameters.

CONCLUSION

Among red-complex bacteria, the amount of P. gingivalis showed the strongest association with the severity of periodontal condition, and co-occurrence of P. gingivalis with T. denticola and/or T. forsythia showed heightened progression of periodontitis.

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.

The oralome and its dysbiosis: New insights into oral microbiome-host interactions

The oralome is the summary of the dynamic interactions orchestrated between the ecological community of oral microorganisms (comprised of up to approximately 1000 species of bacteria, fungi, viruses, archaea and protozoa - the oral microbiome) that live in the oral cavity and the host. These microorganisms form a complex ecosystem that thrive in the dynamic oral environment in a symbiotic relationship with the human host. However, the microbial composition is significantly affected by interspecies and host-microbial interactions, which in turn, can impact the health and disease status of the host. In this review, we discuss the composition of the oralome and inter-species and host-microbial interactions that take place in the oral cavity and examine how these interactions change from healthy (eubiotic) to disease (dysbiotic) states. We further discuss the dysbiotic signatures associated with periodontitis and caries and their sequalae, (e.g., tooth/bone loss and pulpitis), and the systemic diseases associated with these oral diseases, such as infective endocarditis, atherosclerosis, diabetes, Alzheimer's disease and head and neck/oral cancer. We then discuss current computational techniques to assess dysbiotic oral microbiome changes. Lastly, we discuss current and novel techniques for modulation of the dysbiotic oral microbiome that may help in disease prevention and treatment, including standard hygiene methods, prebiotics, probiotics, use of nano-sized drug delivery systems (nano-DDS), extracellular polymeric matrix (EPM) disruption, and host response modulators.

Characterization of the Oral Microbiome of Medicated Type-2 Diabetes Patients

Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease that is becoming a significant global health care problem. Several studies have shown that people with diabetes are more susceptible to oral problems, such as periodontitis and, although the causes are still inconclusive, oral microbiota is considered to play a major role in oral health. This study aimed to characterize the oral microbiome of a sample representing T2DM patients from Portugal and exploit potential associations between some microorganisms and variables like teeth brushing, smoking habits, average blood sugar levels, medication and nutrient intake. By sequencing the hypervariable regions V3-V4 of the 16S rRNA gene in 50 individuals belonging to a group of diabetes patients and a control group, we found a total of 232 taxa, from which only 65% were shared between both groups. No differences were found in terms of alpha and beta diversity between categories. We did not find significant differences in the oral microbiome profiles of control and diabetes patients. Only the class Synergistia and the genus TG5, which are related to periodontitis, were statistically more frequent in the control group. The similar microbiome profiles of medicated diabetics and the control group indicates that the relationship between the T2DM and the oral microbiome might be more related to either the lifestyle/diet rather than diabetes per se. Moreover, this study provides, for the first time, insights into the oral microbiome of a population with a high prevalence of diabetes.

The role of Saccharibacteria (TM7) in the subginival microbiome as a predictor for secondary cardiovascular events

BACKGROUND

The composition of the subgingival microbiota is of great importance in both oral and systemic diseases. However, a possible association of the oral microbiome and cardiovascular (CV) outcome has not yet been considered in a complex model. The primary objective of the study (DRKS-ID: DRKS00015776) was to assess differences in complex subgingival bacterial composition, depending on the CV outcome in patients undergoing Coronary Artery Bypass Grafting Surgery (CABG).

MATERIAL AND METHODS

We conducted a longitudinal cohort study enrolling 102 CV patients. After a one-year follow-up, the postoperative outcome was evaluated applying MACCE (Major Adverse Cardiac and Cerebrovascular Events) criteria. The complex oral microbiome was evaluated depending on CV outcome. The mathematical data processing included Qiime 2 software workflow and DADA2 pipeline as well as Human Oral Microbiome Database (HOMD) and Greengenes database classification. For identifying biomarkers distinguishing patients suffering from secondary CV events, the Cox Proportional Hazard Model for survival analysis was applied.

RESULTS

In total, 19,418 Operational Taxonomic Units (OTU) were mapped according to the HOMD and Greengenes database. No significant differences in alpha and beta diversity were linked to CV outcomes (Shannon index; Principal Coordinates Analysis). No biomarker predicting secondary CV events were identified applying the area under the receiver operating characteristic curve (AUC) model. However, in survival analysis, one biomarker of Saccharibacteria phylum (class: TM7-3, order: CW040, family: F16) was associated with the incidence of a secondary CV event (p = 0.016).

CONCLUSIONS

For the first time, a subgingival biomarker has been identified that supports a cardiovascular prognosis in CV patients undergoing coronary artery bypass grafting.

A Longitudinal Study of the Human Oropharynx Microbiota Over Time Reveals a Common Core and Significant Variations With Self-Reported Disease

Our understanding of human microbial communities, in particular in regard to diseases is advancing, yet the basic understanding of the microbiome in healthy subjects over time remains limited. The oropharynx is a key target for colonization by several important human pathogens. To understand how the oropharyngeal microbiome might limit infections, and how intercurrent infections might be associated with its composition, we characterized the oropharyngeal microbiome of 18 healthy adults, sampled weekly over a 40-weeks using culture-independent molecular techniques. We detected nine phyla, 202 genera and 1438 assignments on OTU level, dominated by Firmicutes, Bacteroidetes, and Proteobacteria on phylum level. Individual microbiomes of participants were characterized by levels of high alpha diversity (mean = 204.55 OTUs, sd = 35.64), evenness (19.83, sd = 9.74) and high temporal stability (mean Pearson's correlation between samples of 0.52, sd = 0.060), with greater differences in microbiome community composition between than within individuals. Significant changes in community composition were associated with disease states, suggesting that it is possible to detect specific changes in OTU abundance and community composition during illness. We defined the common core microbiota by varying occurrence and abundance thresholds showing that individual core microbiomes share a substantial number of OTUs across participants, chiefly Streptococci and Veillonella. Our results provide insights into the microbial communities that characterize the healthy human oropharynx, community structure and variability, and provide new approaches to define individual and shared cores. The wider implications of this result include the potential for modeling the general dynamics of oropharynx microbiota both in health and in response to antimicrobial treatments or probiotics.

HPV-Related Oropharyngeal Cancer and Biomarkers Based on Epigenetics and Microbiome Profile

H uman papillomavirus (HPV) is considered the main cause of the increasing incidence rates of oropharyngeal squamous cell carcinoma (OPSCC), and soon, the global burden of HPV-related OPSCC is predicted to exceed that of cervical cancer. Moreover, a different molecular profile for HPV-related OPSCC has been described, opening new promising targeted therapies and immunotherapy approaches. Epigenetic and microbiome-based exploration of biomarkers has gained growing interest with a view to the primary oropharyngeal cancer (OPC) screening. Understanding the role of the epigenetic mechanism and the changes that occur during pathogenesis shows appreciable progress in recent years. The different methylation status of DNA and miRNAs demonstrates the value of possible biomarkers discriminating even in different stages of dysplasia. Through whole-genome bisulfite sequencing, differentially methylated regions (DMRs) hold the key to recover missing information. O n the other hand, the microbiota investigation signifies a new biomarker approach for the evaluation of OPC. Along with known cofactors playing a major role in microbiota differentiation, HPV-related cases must be explored further for better understanding. The dynamic approach of the shotgun metagenomic sequencing will robustly fill the gap especially in species/strain level and consequently to biomarker detection. The constantly growing incidence of HPV-related OPC should lead us in further investigation and understanding of the unique features of the disease, more accurate diagnostic methods, along with the development and implementation of new, targeted therapies. This paper comprehensively reviews the significance of biomarkers based on epigenetics and microbiome profile in the accuracy of the diagnosis of the HPV-related cancer in the oropharynx.

The Role of the Oral Microbiota Related to Periodontal Diseases in Anxiety, Mood and Trauma- and Stress-Related Disorders

The prevalence of anxiety, mood and trauma- and stress-related disorders are on the rise; however, efforts to develop new and effective treatment strategies have had limited success. To identify novel therapeutic targets, a comprehensive understanding of the disease etiology is needed, especially in the context of the holobiont, i.e., the superorganism consisting of a human and its microbiotas. Much emphasis has been placed on the role of the gut microbiota in the development, exacerbation, and persistence of psychiatric disorders; however, data for the oral microbiota are limited. The oral cavity houses the second most diverse microbial community in the body, with over 700 bacterial species that colonize the soft and hard tissues. Periodontal diseases encompass a group of infectious and inflammatory diseases that affect the periodontium. Among them, periodontitis is defined as a chronic, multi-bacterial infection that elicits low-grade systemic inflammation via the release of pro-inflammatory cytokines, as well as local invasion and long-distance translocation of periodontal pathogens. Periodontitis can also induce or exacerbate other chronic systemic inflammatory diseases such as atherosclerosis and diabetes and can lead to adverse pregnancy outcomes. Recently, periodontal pathogens have been implicated in the etiology and pathophysiology of neuropsychiatric disorders (such as depression and schizophrenia), especially as dysregulation of the immune system also plays an integral role in the etiology and pathophysiology of these disorders. This review will discuss the role of the oral microbiota associated with periodontal diseases in anxiety, mood and trauma- and stress-related disorders. Epidemiological data of periodontal diseases in individuals with these disorders will be presented, followed by a discussion of the microbiological and immunological links between the oral microbiota and the central nervous system. Pre-clinical and clinical findings on the oral microbiota related to periodontal diseases in anxiety, mood and trauma- and stress-related phenotypes will be reviewed, followed by a discussion on the bi-directionality of the oral-brain axis. Lastly, we will focus on the oral microbiota associated with periodontal diseases as a target for future therapeutic interventions to alleviate symptoms of these debilitating psychiatric disorders.

Periodontal Pathogens' strategies disarm neutrophils to promote dysregulated inflammation

Periodontitis is an irreversible, chronic inflammatory disease where inflammophilic pathogenic microbial communities accumulate in the gingival crevice. Neutrophils are a major component of the innate host response against bacterial challenge, and under homeostatic conditions, their microbicidal functions typically protect the host against periodontitis. However, a number of periodontal pathogens developed survival strategies to evade neutrophil microbicidal functions while promoting inflammation, which provides a source of nutrients for bacterial growth. Research on periodontal pathogens has largely focused on a few established species: Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum, Aggregatibacter actinomycetemcomitans, and Porphyromonas gingivalis. However, advances in culture-independent techniques have facilitated the identification of new bacterial species in periodontal lesions, such as the two Gram-positive anaerobes, Filifactor alocis and Peptoanaerobacter stomatis, whose characterization of pathogenic potential has not been fully described. Additionally, there is not a full understanding of the pathogenic mechanisms used against neutrophils by organisms that are abundant in periodontal lesions. This presents a substantial barrier to the development of new approaches to prevent or ameliorate the disease. In this review, we first summarize the neutrophil functions affected by the established periodontal pathogens listed above, denoting unknown areas that still merit a closer look. Then, we review the literature on neutrophil functions and the emerging periodontal pathogens, F. alocis and P. stomatis, comparing the effects of the emerging microbes to that of established pathogens, and speculate on the contribution of these putative pathogens to the progression of periodontal disease.

Inferring directional relationships in microbial communities using signed Bayesian networks

BACKGROUND

Microbe-microbe and host-microbe interactions in a microbiome play a vital role in both health and disease. However, the structure of the microbial community and the colonization patterns are highly complex to infer even under controlled wet laboratory conditions. In this study, we investigate what information, if any, can be provided by a Bayesian Network (BN) about a microbial community. Unlike the previously proposed Co-occurrence Networks (CoNs), BNs are based on conditional dependencies and can help in revealing complex associations.

RESULTS

In this paper, we propose a way of combining a BN and a CoN to construct a signed Bayesian Network (sBN). We report a surprising association between directed edges in signed BNs and known colonization orders.

CONCLUSIONS

BNs are powerful tools for community analysis and extracting influences and colonization patterns, even though the analysis only uses an abundance matrix with no temporal information. We conclude that directed edges in sBNs when combined with negative correlations are consistent with and strongly suggestive of colonization order.

Alterations and Correlations in Microbial Community and Metabolome Characteristics in Generalized Aggressive Periodontitis

This study aimed to characterize the microbial community and metabolic profiles in generalized aggressive periodontitis (AgP) using 16S ribosomal RNA (rRNA) gene high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS). A total of 146 subgingival plaque samples and 50 gingival crevicular fluid (GCF) samples were collected from 24 patients with AgP and 10 periodontally healthy subjects (PH). Striking differences were observed in subgingival microbiome and GCF metabolomics between patients with AgP and PH, but not between samples with different probing depths (PDs). Metabolomics analysis combined with enrichment analysis showed that periodontitis significantly altered the concentration of compounds associated with biosynthesis of amino acids (e.g., alanine, leucine, isoleucine, and valine), galactose metabolism (e.g., myo-inositol, galactose, glucose, and hexitol), and pyrimidine metabolism (e.g., uracil, uridine, beta alanine, and thymine). Correlation analysis showed that the genera with significant difference between AgP and PH were usually significantly correlated with more metabolites, such as Aggregatibacter, Rothia, Peptostreptococcaceae_[XI][G-5], and Bacteroidaceae_[G-1]. While glucose and oxoproline had the most significant correlations with microorganisms. Our results revealed distinct microbial communities and metabolic profiles between AgP and PH. The significant correlation between microbial taxa and metabolites suggested the possible mechanisms for periodontitis. Our results also provided effective approaches for detecting periodontal disease and managing periodontitis.

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.

Clinical and Microbiological Profiles of Aggressive and Chronic Periodontitis in Congolese Patients: A Cross-sectional Study

Background:

Chronic and aggressive periodontitis were the main forms of periodontitis according to the 1999 classification of periodontal diseases and conditions. Their profile in Congolese patients is still undescribed.

Aim:

The aim of this study was to compare the profile of chronic periodontitis (ChP) with that of aggressive periodontitis (AgP) in Congolese patients.

Materials and Methods:

Thirty-two patients with ChP and 20 with AgP who consulted the dental services at any of the four medical centers in Kinshasa, from April 2017 to April 2018, were enrolled in the cross-sectional study. All patients underwent a full mouth examination, including assessment of the probing pocket depth and clinical attachment level at six sites per tooth. Microbial samples were collected in the deepest pocket in the maxilla and the deepest pocket in the mandible. A deoxyribonucleic acid (DNA) analysis was performed using DNA strip technology. Fisher exact test, the chi-square test, the t test, and the Mann–Whitney test were used for the statistical analysis.

Results:

Patients with AgP were significantly younger than those with ChP (P < 0.001). There was no significant difference in the prevalence of Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, or Prevotella intermedia between the AgP and ChP groups (P > 0.05). Aggregatibacter actinomycetemcomitans was detected in 10% of cases in the AgP group and in none of those in the ChP group (P = 0.143).

Conclusion:

This study shows that the clinical profiles of ChP and AgP are similar in Congolese patients. There were no microbiological differences between these two forms of periodontitis.

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.

Dysbiosis of salivary microbiome and cytokines influence oral squamous cell carcinoma through inflammation

Advanced combinatorial treatments of surgery, chemotherapy, and radiotherapy do not have any effect on the enhancement of a 5-year survival rate of oral squamous cell carcinoma (OSCC). The discovery of early diagnostic non-invasive biomarkers is required to improve the survival rate of OSCC patients. Recently, it has been reported that oral microbiome has a significant contribution to the development of OSCC. Oral microbiome induces inflammatory response through the production of cytokines and chemokines that enhances tumor cell proliferation and survival. The study aims to develop saliva-based oral microbiome and cytokine biomarker panel that screen OSCC patients based on the level of the microbiome and cytokine differences. We compared the oral microbiome signatures and cytokine level in the saliva of OSCC patients and healthy individuals by 16S rRNA gene sequencing targeting the V3/V4 region using the MiSeq platform and cytokine assay, respectively. The higher abundance of Prevotella melaninogenica, Fusobacterium sp., Veillonella parvula, Porphyromonas endodontalis, Prevotella pallens, Dialister, Streptococcus anginosus, Prevotella nigrescens, Campylobacter ureolyticus, Prevotella nanceiensis, Peptostreptococcus anaerobius and significant elevation of IL-8, IL-6, TNF-α, GM-CSF, and IFN-γ in the saliva of patients having OSCC. Oncobacteria such as S. anginosus, V. parvula, P. endodontalis, and P. anaerobius may contribute to the development of OSCC by increasing inflammation via increased expression of inflammatory cytokines such as IL-6, IL-8, TNF-α, IFN-γ, and GM-CSF. These oncobacteria and cytokines panels could potentially be used as a non-invasive biomarker in clinical practice for more efficient screening and early detection of OSCC patients.

Phylum Synergistetes in the oral cavity: A possible contributor to periodontal disease

Microbial contributions to periodontal disease have been under renewed scrutiny with the advent of newer technologies to identify their presence and gene expression at the molecular level. Members of the phylum Synergistetes are some of the more recent bacteria to be associated with periodontal disease. Bacteria classified in this phylum can be found in a wide variety of habitats including both inside and outside of a mammalian host. Members of this phylum have been identified as part of the human microbiome. Indeed, many of the identified phylotypes have yet to be cultivated. Here we consider contributions of three named and formally described species to the oral microbial community and to pathogenesis of periodontal disease.

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.

Identification of Potential Oral Microbial Biomarkers for the Diagnosis of Periodontitis

Periodontitis is a chronic and multifactorial inflammatory disease that can lead to tooth loss. At present, the diagnosis for periodontitis is primarily based on clinical examination and radiographic parameters. Detecting the periodontal pathogens at the subgingival plaque requires skilled professionals to collect samples. Periodontal pathogens are also detected on various mucous membranes in patients with periodontitis. In this study, we characterized the oral microbiome profiles from buccal mucosa and supragingival space in a total of 272 healthy subjects as a control group, and periodontitis patients as a disease group. We identified 13 phyla, 193 genera, and 527 species and determined periodontitis-associated taxa. Porphyromonas gingivalis, Tannerella forsythia, Treponema denticolar, Filifactor alocis, Porphyromonas endodontalis, Fretibacterium fastiosum and Peptostreptococcus species were significantly increased in both the buccal mucosa and the supragingival space in periodontitis patients. The identified eight periodontitis-associated bacterial species were clinically validated in an independent cohort. We generated the prediction model based on the oral microbiome profiles using five machine learning algorithms, and validated its capability in predicting the status of patients with periodontitis. The results showed that the oral microbiome profiles from buccal mucosa and supragingival space can represent the microbial composition of subgingival plaque and further be utilized to identify potential microbial biomarkers for the diagnosis of periodontitis. Besides, bacterial community interaction network analysis found distinct patterns associated with dysbiosis in periodontitis. In summary, we have identified oral bacterial species from buccal and supragingival sites which can predict subgingival bacterial composition and can be used for early diagnosis of periodontitis. Therefore, our study provides an important basis for developing easy and noninvasive methods to diagnose and monitor periodontitis.

Comparison of the Microbiota and Inorganic Anion Content in the Saliva of Patients with Gastroesophageal Reflux Disease and Gastroesophageal Reflux Disease-Free Individuals

The oral cavity is one of the most complex microbial environments; however, the complex nature of the salivary microbiota and the level of inorganic anions in the saliva of subjects with and without gastroesophageal reflux disease (GERD) are poorly understood. The primary goals of this pilot research were to assess differences in salivary bacterial community composition and inorganic anion concentrations between patients with GERD and GERD-free people. Thus, the salivary microbiota within both groups was dominated by these genera: Streptococcus, Prevotella, Porphyromonas, Veillonella, Neisseria, Haemophilus, Fusobacterium, Rothia, and Leptotrichia. However, the relative abundances of the genera Actinomyces, Atopobium, Stomatobaculum, Ruminococcaceae_[G-2], Veillonella, and Leptotrichia were significantly higher in the saliva samples of patients with GERD, while the genera Porphyromonas, Gemella, Peptostreptococcus, and Neisseria were less abundant in this group. The concentrations of chloride, phosphate, and sulphate ions in the human saliva varied among all subjects and sampling time. These results broaden our knowledge of the salivary microbial community composition and chemistry of saliva of patients with GERD and GERD-free individuals.

Nanofibers as drug-delivery systems for infection control in dentistry

INTRODUCTION

Due to the complexity of different oral infections, new anti-infective nanotechnological approaches have been emerging for dentistry in recent years. These strategies may contribute to antimicrobial molecules delivery, tissue regeneration, and oral health maintenance by acting in a more specific site and not being cytotoxic. In this context, nanofibers appear as versatile structures and might act both in the release of antimicrobial molecules and as a scaffold for new tissue formation.

AREAS COVERED

This review addresses the application of different nanofibers as new strategies for the delivery of antimicrobial molecules for dentistry. Here, we present the main polymers used to construct nanofibers, methods of production and mainly their antimicrobial activity against microorganisms commonly responsible for the usual dental infections. These biomaterials may be associated to restorative materials, prostheses, and mucoadhesive structures. Besides, nanofibers can be used for endodontic or periodontal therapy, or even on implant surfaces.

EXPERT OPINION

A wide variety of studies report the potential application of anti-infective nanofibers in the oral cavity. Although there are still several barriers between in vitro and in vivo studies, these new formulations appear as promising new therapies for dentistry.

Involvement of Cathepsins in Innate and Adaptive Immune Responses in Periodontitis

Periodontitis is an infectious disease whereby the chronic inflammatory process of the periodontium stimulated by bacterial products induces specific host cell responses. The activation of the host cell immune system upregulates the production of inflammatory mediators, comprising cytokines and proteolytic enzymes, which contribute to inflammation and bone destruction. It has been well known that periodontitis is related to systemic inflammation which links to numerous systemic diseases, including diabetes and arteriosclerosis. Furthermore, periodontitis has been reported in association with neurodegenerative diseases such as Alzheimer's disease (AD) in the brain. Regarding immune responses and inflammation, cathepsin B (CatB) plays pivotal role for the induction of IL-1β, cathepsin K- (CatK-) dependent active toll-like receptor 9 (TLR9) signaling, and cathepsin S (CatS) which involves in regulating both TLR signaling and maturation of the MHC class II complex. Notably, both the production and proteolytic activities of cathepsins are upregulated in chronic inflammatory diseases, including periodontitis. In the present review, we focus on the roles of cathepsins in the innate and adaptive immune responses within periodontitis. We believe that understanding the roles of cathepsins in the immune responses in periodontitis would help to elucidate the therapeutic strategies of periodontitis, thus benefit for reduction of systemic diseases as well as neurodegenerative diseases in the global aging society.

Tracking the functional meaning of the human oral-microbiome protein-protein interactions

The interactome - the network of protein-protein interactions (PPIs) within a cell or organism - is technically difficult to assess. Bioinformatic tools can, not only, identify potential PPIs that can be later experimentally validated, but also be used to assign functional meaning to PPIs. Saliva's potential as a non-invasive diagnostic fluid is currently being explored by several research groups. But, in order to fully attain its potential, it is necessary to achieve the full characterization of the mechanisms that take place within this ecosystem. The onset of omics technologies, and specifically of proteomics, delivered a huge set of data that is largely underexplored. Quantitative information relative to proteins within a given context (for example a given disease) can be used by computational algorithms to generate information regarding PPIs. These PPIs can be further analyzed concerning their functional meaning and used to identify potential biomarkers, therapeutic targets, defense and pathogenicity mechanisms. We describe a computational pipeline that can be used to identify and analyze PPIs between human and microbial proteins. The pipeline was tested within the scenario of human PPIs of systemic (Zika Virus infection) and of oral conditions (Periodontal disease) and also in the context of microbial interactions (Candida-Streptococcus) and showed to successfully predict functionally relevant PPIs. The pipeline can be applied to different scientific areas, such as pharmacological research, since a functional meaningful PPI network can provide insights on potential drug targets, and even new uses for existing drugs on the market.

Comparison of Subgingival and Buccal Mucosa Microbiome in Chronic and Aggressive Periodontitis: A Pilot Study

Periodontal microorganisms not only colonize subgingival pockets, but also are detected on various mucous membranes in patients with periodontitis. The object of this pilot study was, using the next-generation sequencing of 16S RNA gene, to characterize the microbiota in two oral habitats (buccal mucosas and subgingival pockets) in patients with different forms of periodontitis. Thirty-two buccal swab samples and 113 subgingival samples were obtained from eleven subjects with chronic periodontitis (ChP), twelve subjects with aggressive periodontitis (AgP), and nine periodontally healthy individuals (HP). Using Miseq Sequencing of 16S rRNA gene, we found that the subgingival and buccal mucosa microbiome of ChP and AgP patients both differed from HP. Meanwhile, Veillonella, Treponema, Filifactor, Fretibacterium, Peptostreptococcaceae_[XI][G-6], Peptostreptococcaceae_[XI][G-5], Bacteroidetes_[G-5], Bacteroidetes_[G-3], Peptostreptococcaceae_[XI][G-4], Peptostreptococcaceae_[XI][G-2] significantly increased both in buccal and subgingival plaque samples in periodontitis subjects (ChP and AgP) compared with HP. Moreover, the results based on the Unweighted UniFrac distance showed that buccal and subgingival plaque samples from the same individuals show higher community divergence than same habitats from different subject samples. This study demonstrated that the microbiome of buccal mucosa can be influenced by periodontitis. However, subgingival and buccal mucosa microbiome seem to be characterized by species-specific colonization patterns. This pilot study provides a glimpse at the changes of subgingival and buccal mucosa associated with periodontitis from a holistic view. Further studies should be taken to illuminate the interplay between these detected changes and periodontitis development.