Molecular epidemiology and spatial distribution of Selenomonas spp. in subgingival biofilms

Selenomonas sputigena acts as a pathobiont mediating spatial structure and biofilm virulence in early childhood caries

Streptococcus mutans has been implicated as the primary pathogen in childhood caries (tooth decay). While the role of polymicrobial communities is appreciated, it remains unclear whether other microorganisms are active contributors or interact with pathogens. Here, we integrate multi-omics of supragingival biofilm (dental plaque) from 416 preschool-age children (208 males and 208 females) in a discovery-validation pipeline to identify disease-relevant inter-species interactions. Sixteen taxa associate with childhood caries in metagenomics-metatranscriptomics analyses. Using multiscale/computational imaging and virulence assays, we examine biofilm formation dynamics, spatial arrangement, and metabolic activity of Selenomonas sputigena, Prevotella salivae and Leptotrichia wadei, either individually or with S. mutans. We show that S. sputigena, a flagellated anaerobe with previously unknown role in supragingival biofilm, becomes trapped in streptococcal exoglucans, loses motility but actively proliferates to build a honeycomb-like multicellular-superstructure encapsulating S. mutans, enhancing acidogenesis. Rodent model experiments reveal an unrecognized ability of S. sputigena to colonize supragingival tooth surfaces. While incapable of causing caries on its own, when co-infected with S. mutans, S. sputigena causes extensive tooth enamel lesions and exacerbates disease severity in vivo. In summary, we discover a pathobiont cooperating with a known pathogen to build a unique spatial structure and heighten biofilm virulence in a prevalent human disease.

Pre-treatment oral microbiome analysis and salivary Stephan curve kinetics in white spot lesion development in orthodontic patients wearing fixed appliances. A pilot study

BACKGROUND

White spot lesions (WSLs) are a formidable challenge during orthodontic treatment, affecting patients regardless of oral hygiene. Multifactorial in nature, amongst potential contributors to their development are the microbiome and salivary pH. The aim of our pilot study is to determine if pre-treatment differences in salivary Stephan curve kinetics and salivary microbiome features correlate with WSL development in orthodontic patients with fixed appliances. We hypothesize that non-oral hygiene determined differences in saliva could be predictive of WSL formation in this patient population through analysis of salivary Stephan curve kinetics, and that these differences would further manifest as changes in the oral microbiome.

METHODS

In this prospective cohort study, twenty patients with initial simplified oral hygiene index scores of "good" that were planning to undergo orthodontic treatment with self-ligating fixed appliances for at least 12 months were enrolled. At pre-treatment stage, saliva was collected for microbiome analysis, and at 15-minute intervals after a sucrose rinse over 45 min for Stephan curve kinetics.

RESULTS

50% of patients developed a mean 5.7 (SEM: 1.2) WSLs. There were no differences in saliva microbiome species richness, Shannon alpha diversity or beta diversity between the groups. Capnocytophaga sputigena exclusively and Prevotella melaninogenica predominantly were found in WSL patients, while Streptococcus australis was negatively correlated with WSL development. Streptococcus mitis and Streptococcus anginosus were primarily present in healthy patients. There was no evidence to support the primary hypothesis.

CONCLUSIONS

While there were no differences in salivary pH or restitution kinetics following a sucrose challenge and no global microbial differences in WSL developers, our data showed change in salivary pH at 5 min associated with an abundance of acid-producing bacteria in saliva. The results suggest salivary pH modulation as a management strategy to inhibit the abundance of caries initiators. Our study may have uncovered the earliest predecessors to WSL/caries development.

Selenomonas sputigena Interactions with Gingival Epithelial Cells That Promote Inflammation

Increased prevalence and abundance of Selenomonas sputigena have been associated with periodontitis, a chronic inflammatory disease of tooth-supporting tissues, for more than 50 years. Over the past decade, molecular surveys of periodontal disease using 16S and shotgun metagenomic sequencing approaches have confirmed the disease association of classically recognized periodontal pathogens such as Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia while highlighting previously underappreciated organisms such as Filifactor alocis and S. sputigena. Despite abundant clinical association between S. sputigena and periodontal disease, we have little to no understanding of its pathogenic potential, and virulence mechanisms have not been studied. In this study, we sought to characterize the response of gingival epithelial cells to infection with S. sputigena. Here, we show that S. sputigena attaches to gingival keratinocytes and induces expression and secretion of cytokines and chemokines associated with inflammation and leukocyte recruitment. We demonstrate that S. sputigena induces signaling through Toll-like receptor 2 (TLR2) and TLR4 but evades activation of TLR5. Cytokines released from S. sputigena-infected keratinocytes induced monocyte and neutrophil chemotaxis. These results show that S. sputigena-host interactions have the potential to contribute to bacterially driven inflammation and tissue destruction, the hallmark of periodontitis. Characterization of previously unstudied pathogens may provide novel approaches to develop therapeutics to treat or prevent periodontal disease.

Maintaining oral health for a hundred years and more? - An analysis of microbial and salivary factors in a cohort of centenarians

Aim

To investigate associations between oral health-related conditions and the oral microbiome in a representative study sample of centenarians.

Materials and methods

Clinical and microbial parameters from 54 centenarians were assessed in the Heidelberg Dental Centenarian Study. Plaque and salivary samples were collected, and the microbiota was characterized by 16S rRNA gene sequencing.

Results

Diversity and structure of the oral microbiome were mainly influenced by the presence of natural teeth and the number of decayed, missing, and filled teeth (0.028 ≤ p ≤ 0.001 in plaque and salivary samples). Centenarians with less caries experience possessed a more diverse oral microbiome. Moreover, the number of dental visits also showed a significant influence on the microbial composition. Most centenarians presented with hyposalivation (mean stimulated flow rate = 0.84 ± 0.55 ml/min), a low buffering capacity, and an acidic pH. The latter was between 5.0 and 5.8 in 46.3% of cases, and we observed that an increased salivary pH correlated with higher alpha-diversity in both salivary and plaque samples.

Conclusion

The microbiome diversity correlated significantly with successful oral aging. In addition, regular dental visits were a beneficial factor. However, diversity can be negatively influenced by hyposalivation, associated with pH changes due to aging effects.

Electronic Cigarette Use Promotes a Unique Periodontal Microbiome

Electronic cigarettes (e-cigs) have become prevalent as an alternative to conventional cigarette smoking, particularly in youth. E-cig aerosols contain unique chemicals which alter the oral microbiome and promote dysbiosis in ways we are just beginning to investigate. We conducted a 6-month longitudinal study involving 84 subjects who were either e-cig users, conventional smokers, or nonsmokers. Periodontal condition, cytokine levels, and subgingival microbial community composition were assessed, with periodontal, clinical, and cytokine measures reflecting cohort habit and positively correlating with pathogenic taxa (e.g., Treponema, Saccharibacteria, and Porphyromonas). α-Diversity increased similarly across cohorts longitudinally, yet each cohort maintained a unique microbiome. The e-cig microbiome shared many characteristics with the microbiome of conventional smokers and some with nonsmokers, yet it maintained a unique subgingival microbial community enriched in Fusobacterium and Bacteroidales (G-2). Our data suggest that e-cig use promotes a unique periodontal microbiome, existing as a stable heterogeneous state between those of conventional smokers and nonsmokers and presenting unique oral health challenges. IMPORTANCE Electronic cigarette (e-cig) use is gaining in popularity and is often perceived as a healthier alternative to conventional smoking. Yet there is little evidence of the effects of long-term use of e-cigs on oral health. Conventional cigarette smoking is a prominent risk factor for the development of periodontitis, an oral disease affecting nearly half of adults over 30 years of age in the United States. Periodontitis is initiated through a disturbance in the microbial biofilm communities inhabiting the unique space between teeth and gingival tissues. This disturbance instigates host inflammatory and immune responses and, if left untreated, leads to tooth and bone loss and systemic diseases. We found that the e-cig user's periodontal microbiome is unique, eliciting unique host responses. Yet some similarities to the microbiomes of both conventional smokers and nonsmokers exist, with strikingly more in common with that of cigarette smokers, suggesting that there is a unique periodontal risk associated with e-cig use.

Friends with Benefits: An Inside Look of Periodontal Microbes' Interactions Using Fluorescence In Situ Hybridization-Scoping Review

Fluorescence in situ hybridization (FISH) has proven to be particularly useful to describe the microbial composition and spatial organization of mixed microbial infections, as it happens in periodontitis. This scoping review aims to identify and map all the documented interactions between microbes in periodontal pockets by the FISH technique. Three electronic sources of evidence were consulted in search of suitable articles up to 7 November 2020: MEDLINE (via PubMed), Scopus (Elsevier: Amsterdam, The Netherlands), and Web of Science (Clarivate Analytics: Philadelphia, PA, USA) online databases. Studies that showed ex vivo and in situ interactions between, at least, two microorganisms were found eligible. Ten papers were included. Layered or radially ordered multiple-taxon structures are the most common form of consortium. Strict or facultative anaerobic microorganisms are mostly found in the interior and the deepest portions of the structures, while aerobic microorganisms are mostly found on the periphery. We present a model of the microbial spatial organization in sub- and supragingival biofilms, as well as how the documented interactions can shape the biofilm formation. Despite the already acquired knowledge, available evidence regarding the structural composition and interactions of microorganisms within dental biofilms is incomplete and large-scale studies are needed.

Subgingival Microbiome and Specialized Pro-Resolving Lipid Mediator Pathway Profiles Are Correlated in Periodontal Inflammation

Failure of resolution pathways in periodontitis is reflected in levels of specialized pro-resolving lipid mediators (SPMs) and SPM pathway markers but their relationship with the subgingival microbiome is unclear. This study aimed to analyze and integrate lipid mediator level, SPM receptor gene expression and subgingival microbiome data in subjects with periodontitis vs. healthy controls. The study included 13 periodontally healthy and 15 periodontitis subjects that were evaluated prior to or after non-surgical periodontal therapy. Samples of gingival tissue and subgingival plaque were collected prior to and 8 weeks after non-surgical treatment; only once in the healthy group. Metabololipidomic analysis was performed to measure levels of SPMs and other relevant lipid mediators in gingiva. qRT-PCR assessed relative gene expression (2-ΔΔCT) of known SPM receptors. 16S rRNA sequencing evaluated the relative abundance of bacterial species in subgingival plaque. Correlations between lipid mediator levels, receptor gene expression and bacterial abundance were analyzed using the Data Integration Analysis for Biomarker discovery using Latent cOmponents (DIABLO) and Sparse Partial Least Squares (SPLS) methods. Profiles of lipid mediators, receptor genes and the subgingival microbiome were distinct in the three groups. The strongest correlation existed between lipid mediator profile and subgingival microbiome profile. Multiple lipid mediators and bacterial species were highly correlated (correlation coefficient ≥0.6) in different periodontal conditions. Comparing individual correlated lipid mediators and bacterial species in periodontitis before treatment to healthy controls revealed that one bacterial species, Corynebacterium durum, and five lipid mediators, 5(S)6(R)-DiHETE, 15(S)-HEPE, 7-HDHA, 13-HDHA and 14-HDHA, were identified in both conditions. Comparing individual correlated lipid mediators and bacterial species in periodontitis before treatment to after treatment revealed that one bacterial species, Anaeroglobus geminatus, and four lipid mediators, 5(S)12(S)-DiHETE, RvD1, Maresin 1 and LTB4, were identified in both conditions. Four Selenomonas species were highly correlated with RvD1, RvE3, 5(S)12(S)-DiHETE and proinflammatory mediators in the periodontitis after treatment group. Profiles of lipid mediators, receptor gene and subgingival microbiome are associated with periodontal inflammation and correlated with each other, suggesting inflammation mediated by lipid mediators influences microbial composition in periodontitis. The role of correlated individual lipid mediators and bacterial species in periodontal inflammation have to be further studied.

Quality Control in Diagnostic Fluorescence In Situ Hybridization (FISH) in Microbiology

This overview addresses fluorescence in situ hybridization (FISH) in a diagnostic microbiology setting with its associated problems and pitfalls and how to control them, but also the advantages and opportunities the method offers. This article focuses mainly on diagnostic FISH assays on tissue sections and on techniques and experiences in our laboratory. FISH in a routine diagnostic setting in microbiology requires strict quality control measures to ensure consistent high-quality and reliable assay results. Here, for the first time, we define quality control requirements for microbiological diagnostic FISH applications and discuss their impact and possible future developments of the FISH technique for infection diagnostics. We focus on diagnosis of biofilm-associated infections including infective endocarditis, oral biofilms, and device-associated infections as well as infections due to fastidious or yet uncultured microorganisms like Treponema spp., Tropheryma whipplei, Bartonella, Coxiella burnetii, or Brachyspira.

FISH Variants

FISH has gained an irreplaceable place in microbiology because of its ability to detect and locate a microorganism, or a group of organisms, within complex samples. However, FISH role has evolved drastically in the last few decades and its value has been boosted by several advances in signal intensity, imaging acquisitions, automation, method robustness, and, thus, versatility. This has resulted in a range of FISH variants that gave researchers the ability to access a variety of other valuable information such as complex population composition, metabolic activity, gene detection/quantification, or subcellular location of genetic elements. In this chapter, we will review the more relevant FISH variants, their intended use, and how they address particular challenges of classical FISH.

Metatranscriptomic analyses of the oral microbiome

Although the composition of the oral human microbiome is now well studied, regulation of genes within oral microbial communities remains mostly uncharacterized. Current concepts of periodontal disease and caries highlight the importance of oral biofilms and their role as etiological agents of those diseases. Currently, there is increased interest in exploring and characterizing changes in the composition and gene-expression profiles of oral microbial communities. These efforts aim to identify changes in functional activities that could explain the transition from health to disease and the reason for the chronicity of those infections. It is now clear that the functions of distinct species within the subgingival microbiota are intimately intertwined with the rest of the microbial community. This point highlights the relevance of examining the expression profile of specific species within the subgingival microbiota in the case of periodontal disease or caries lesions, in the context of the other members of the biofilm in vivo. Metatranscriptomic analysis of the oral community is the starting point for identifying environmental signals that modulate the shift in metabolism of the community from commensal to dysbiotic. These studies give a snapshot of the expression patterns of microbial communities and also allow us to determine triggers to diseases. For example, in the case of caries, studies have unveiled a potential new pathway of sugar metabolism, namely the use of sorbitol as an additional source of carbon by Streptococcus mutans; and in the case of periodontal disease, high levels of extracellular potassium could be a signal of disease. Longitudinal studies are needed to identify the real markers of the initial stages of caries and periodontal disease. More information on the gene-expression profiles of the host, along with the patterns from the microbiome, will lead to a clearer understanding of the modulation of health and disease. This review presents a summary of these initial studies, which have opened the door to a new understanding of the dynamics of the oral community during the dysbiotic process in the oral cavity.

Do patients with aggressive and chronic periodontitis exhibit specific differences in the subgingival microbial composition? A systematic review

BACKGROUND

The 2017 World Workshop on the Classification of Periodontal and Peri-Implant Diseases and Conditions grouped the diseases previously recognized as chronic (CP) or aggressive (AgP) periodontitis under a single category named periodontitis. The rationale for this decision was the lack of specific patterns of immune-inflammatory response or microbial profiles associated with CP or AgP. However, no previous studies have compiled the results of all studies comparing subgingival microbial data between these clinical conditions. Thus, this systematic review aimed to answer the following focused question: "Do patients with AgP periodontitis present differences in the subgingival microbiota when compared with patients with CP?"

METHODS

A systematic review was conducted according to the PRISMA statement. The MEDLINE, EMBASE, and Cochrane databases were searched up to June 2019 for studies of any design (except case reports, case series, and reviews) comparing subgingival microbial data from patients with CP and AgP.

RESULTS

A total of 488 articles were identified and 56 were included. Thirteen studies found Aggregatibacter actinomycetemcomitans elevated in AgP in comparison with CP, while Fusobacterium nucleatum, Parvimonas micra, and Campylobacter rectus were elevated in AgP in a few studies. None of these species were elevated in CP. However, the number of studies not showing statistically significant differences between CP and AgP was always higher than that of studies showing differences.

CONCLUSION

These results suggested an association of A. actinomycetemcomitans with AgP, but neither this species nor the other species studied to date were unique to or could differentiate between CP and AgP (PROSPERO #CRD42016039385).

Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis

Microbial communities are complex and dynamic, composed of hundreds of taxa interacting across multiple spatial scales. Advances in sequencing and imaging technology have led to great strides in understanding both the composition and the spatial organization of these complex communities. In the human mouth, sequencing results indicate that distinct sites host microbial communities that not only are distinguishable but to a meaningful degree are composed of entirely different microbes. Imaging suggests that the spatial organization of these communities is also distinct. Together, the literature supports the idea that most oral microbes are site specialists. A clear understanding of microbiota structure at different sites in the mouth enables mechanistic studies, informs the generation of hypotheses, and strengthens the position of oral microbiology as a model system for microbial ecology in general.

Flagellin Glycoproteomics of the Periodontitis Associated Pathogen Selenomonas sputigena Reveals Previously Not Described O-glycans and Rhamnose Fragment Rearrangement Occurring on the Glycopeptides

Flagellated, Gram-negative, anaerobic, crescent-shaped Selenomonas species are colonizers of the digestive system, where they act at the interface between health and disease. Selenomonas sputigena is also considered a potential human periodontal pathogen, but information on its virulence factors and underlying pathogenicity mechanisms is scarce. Here we provide the first report of a Selenomonas glycoprotein, showing that S. sputigena produces a diversely and heavily O-glycosylated flagellin C9LY14 as a major cellular protein, which carries various hitherto undescribed rhamnose- and N-acetylglucosamine linked O-glycans in the range from mono- to hexasaccharides. A comprehensive glycomic and glycoproteomic assessment revealed extensive glycan macro- and microheterogeneity identified from 22 unique glycopeptide species. From the multiple sites of glycosylation, five were unambiguously identified on the 437-amino acid C9LY14 protein (Thr149, Ser182, Thr199, Thr259, and Ser334), the only flagellin protein identified. The O-glycans additionally showed modifications by methylation and putative acetylation. Some O-glycans carried hitherto undescribed residues/modifications as determined by their respective m/z values, reflecting the high diversity of native S. sputigena flagellin. We also found that monosaccharide rearrangement occurred during collision-induced dissociation (CID) of protonated glycopeptide ions. This effect resulted in pseudo Y1-glycopeptide fragment ions that indicated the presence of additional glycosylation sites on a single glycopeptide. CID oxonium ions and electron transfer dissociation, however, confirmed that just a single site was glycosylated, showing that glycan-to-peptide rearrangement can occur on glycopeptides and that this effect is influenced by the molecular nature of the glycan moiety. This effect was most pronounced with disaccharides. This study is the first report on O-linked flagellin glycosylation in a Selenomonas species, revealing that C9LY14 is one of the most heavily glycosylated flagellins described to date. This study contributes to our understanding of the largely under-investigated surface properties of oral bacteria. The data have been deposited to the ProteomeXchange with identifier PXD005859.

Furcation Therapy With Enamel Matrix Derivative: Effects on the Subgingival Microbiome

BACKGROUND

Although enamel matrix derivative (EMD) has been used to promote periodontal regeneration, little is known of its effect on the microbiome. Therefore, this investigation aims to identify changes in periodontal microbiome after treatment with EMD using a deep-sequencing approach.

METHODS

Thirty-nine patients with mandibular Class II buccal furcation defects were randomized to beta-tricalcium-phosphate/hydroxyapatite graft (BONE group), EMD+BONE, or EMD alone. Plaque was collected from furcation defects at baseline and 3 and 6 months post-treatment. Bacterial DNA was analyzed using terminal restriction fragment length polymorphism and 16S pyrotag sequencing, resulting in 169,000 classifiable sequences being compared with the Human Oral Microbiome Database. Statistical comparisons were made using parametric tests.

RESULTS

At baseline, a total of 422 species were identified from the 39 defects, belonging to Fusobacterium, Pseudomonas, Streptococcus, Filifactor, and Parvimonas. All three regenerative procedures predictably altered the disease-associated microbiome, with a restitution of health-compatible species. However, EMD and BONE+EMD groups demonstrated more long-term reductions in a higher number of species than the BONE group (P <0.05), especially disease-associated species, e.g., Selenomonas noxia, F. alocis, and Fusobacterium.

CONCLUSIONS

EMD treatment predictably alters a dysbiotic subgingival microbiome, decreasing pathogen richness and increasing commensal abundance. Further investigations are needed to investigate how this impacts regenerative outcomes.

Members of the Oral Microbiota Are Associated with IL-8 Release by Gingival Epithelial Cells in Healthy Individuals

The triggers for the onset of oral diseases are still poorly understood. The aim of this study was to characterize the oral bacterial community in healthy humans and its association with nutrition, oral hygiene habits, and the release of the inflammatory marker IL-8 from gingival epithelial cells (GECs) with and without stimulation by bacterial endotoxins to identify possible indicator operational taxonomic units (OTUs) associated with inflammatory marker status. GECs from 21 healthy participants (13 females, 8 males) were incubated with or without addition of bacterial lipopolysaccharides (LPSs), and the oral microbiota was profiled using 16S rRNA gene-targeted sequencing. The basal IL-8 release after 6 h was between 9.9 and 98.2 pg/ml, and bacterial communities were characteristic for healthy oral microbiota. The composition of the oral microbiota was associated with basal IL-8 levels, the intake of meat, tea, white wine, sweets and the use of chewing gum, as well as flossing habits, allergies, gender and body mass index. Additionally, eight OTUs were associated with high basal levels of IL-8 and GEC response to LPS, with high basal levels of IL-8, and 1 with low basal levels of IL8. The identification of indicator bacteria in healthy subjects with high levels of IL-8 release is of importance as they may be promising early warning indicators for the possible onset of oral diseases.

Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review

Early identification of microbial pathogens is essential for rational and conservative antibiotic use especially in the case of known regional resistance patterns. Here, we describe fluorescence in situ hybridization (FISH) as one of the rapid methods for easy identification of microbial pathogens, and its advantages and disadvantages for the diagnosis of pathogens in human infections in the laboratory diagnostic routine. Binding of short fluorescence-labeled DNA or nucleic acid-mimicking PNA probes to ribosomes of infectious agents with consecutive analysis by fluorescence microscopy allows identification of bacterial and eukaryotic pathogens at genus or species level. FISH analysis leads to immediate differentiation of infectious agents without delay due to the need for microbial culture. As a microscopic technique, FISH has the unique potential to provide information about spatial resolution, morphology and identification of key pathogens in mixed species samples. On-going automation and commercialization of the FISH procedure has led to significant shortening of the time-to-result and increased test reliability. FISH is a useful tool for the rapid initial identification of microbial pathogens, even from primary materials. Among the rapidly developing alternative techniques, FISH serves as a bridging technology between microscopy, microbial culture, biochemical identification and molecular diagnostic procedures.

Detection and comparison of Selenomonas sputigena in subgingival biofilms in chronic and aggressive periodontitis patients

Background:

With the advent of DNA-based culture-independent techniques, a constantly growing number of Selenomonas phylotypes have been detected in patients with destructive periodontal diseases. However, the prevalence levels that have been determined in different studies vary considerably.

Aim:

The present study was undertaken to detect and compare the presence of Selenomonas sputigena in the subgingival plaque samples from generalized aggressive periodontitis (GAP), chronic generalized periodontitis, and periodontally healthy patients using conventional polymerase chain reaction (PCR) technique.

Materials and Methods:

A total of 90 patients were categorized as periodontally healthy individuals (Group I, n = 30), chronic generalized periodontitis (Group II, n = 30), and GAP (Group III, n = 30). The clinical parameters were recorded and subgingival plaque samples were collected. These were then subjected to conventional PCR analysis.

Statistical Analysis Used:

Kruskal–Wallis ANOVA test was used for multiple group comparisons followed by Mann–Whitney U-test for pairwise comparison.

Results:

On comparison between three groups, all the clinical parameters were found to be statistically highly significant. Comparing Groups I-II and I-III, the difference in detection was found to be statistically highly significant whereas in Groups II-III, it was statistically nonsignificant. On comparison of S. sputigena detected and undetected patients to clinical parameters in various study groups, the difference was found to be nonsignificant.

Conclusion:

S. sputigena was found to be significantly associated with chronic and aggressive periodontitis. Although the difference in its detection frequency in both groups was statistically nonsignificant when compared clinically, S. sputigena was more closely associated with the GAP.

Peri-implant and periodontal microbiome diversity in aggressive periodontitis patients: a pilot study

AIM

To investigate the bacterial microbiome in periodontal and peri-implant biofilms deriving from aggressive periodontitis patients (AgP) in conditions of health and disease.

MATERIAL AND METHODS

Ninety-one plaque samples were collected from 18 patients previously diagnosed and treated for AgP. The samples were taken from (i) 24 residual periodontal pockets (TD) (n = 6 patients), (ii) 24 healthy periodontal sites (TH) (n = 6 patients), (iii) 24 dental sites from the same implant patients (TM) (n = 6 patients), (iv) 5 peri-implantitis sites (II) (n = 2 patients), (v) 6 peri-mucositis sites (IM) (n = 2 patients) and (vi) 8 healthy implant sites (IH) (n = 2 patients). All subjects underwent periodontal clinical and radiographic assessments. Bacterial DNA was extracted, PCR amplified using 16S rRNA gene V5-V7 primers (barcoded amplicons 785F;1175R), purified, pooled at equimolar concentrations and sequenced (MiSeq, Illumina) yielding 250 bp paired-end reads. The 16S rRNA reads were filtered, assembled and analysed.

RESULTS

The genera Propionibacterium, Paludibacter, Staphylococcus, Filifactor, Mogibacterium, Bradyrhizobium and Acinetobacter were unique to peri-implant sites (P = 0.05). In TM samples, different proportions and bacterial spp. were found when compared with the same patients' samples at implant sites. Specifically, Actinomyces (P = 0.013) and Corynebacterium (P = 0.030) genera showed to be significantly more abundant in the TM group when compared to the II. The highest phylogenetic diversity was observed in residual periodontal pocket sites (TD). Increased annual tooth loss rate and residual pocketing was related to high proportions of the genera Actinomyces, Porphyromonas, Prevotella, Streptococcus, Actinomycetaceae, TM7-3, Selenomonas, and Dialister, Treponema, Parvimonas and Peptostreptococcus in the TD group.

CONCLUSION

Within the limitations of this pilot study, the periodontal and peri-implant microbiome presents a dissimilar taxonomic composition across different niches within AgP patients. The host response, the habitat structure and the vast coexistence of strains and species surrounding implants and teeth in health and disease are likely to be shaping the heterogeneous composition of the subgingival biofilms. The TM7 phylum was found only in TD cases. The investigation of the impact of periodontal and peri-implant keystone species on these complex ecosystems in states of health and disease seems to be essential.

Biogeography of a human oral microbiome at the micron scale

The spatial organization of complex natural microbiomes is critical to understanding the interactions of the individual taxa that comprise a community. Although the revolution in DNA sequencing has provided an abundance of genomic-level information, the biogeography of microbiomes is almost entirely uncharted at the micron scale. Using spectral imaging fluorescence in situ hybridization as guided by metagenomic sequence analysis, we have discovered a distinctive, multigenus consortium in the microbiome of supragingival dental plaque. The consortium consists of a radially arranged, nine-taxon structure organized around cells of filamentous corynebacteria. The consortium ranges in size from a few tens to a few hundreds of microns in radius and is spatially differentiated. Within the structure, individual taxa are localized at the micron scale in ways suggestive of their functional niche in the consortium. For example, anaerobic taxa tend to be in the interior, whereas facultative or obligate aerobes tend to be at the periphery of the consortium. Consumers and producers of certain metabolites, such as lactate, tend to be near each other. Based on our observations and the literature, we propose a model for plaque microbiome development and maintenance consistent with known metabolic, adherence, and environmental considerations. The consortium illustrates how complex structural organization can emerge from the micron-scale interactions of its constituent organisms. The understanding that plaque community organization is an emergent phenomenon offers a perspective that is general in nature and applicable to other microbiomes.

Aggressive Periodontitis: microbes and host response, who to blame?

A paradigm shift several decades ago elucidated that aggressive periodontitis (AgP) was not a degenerative disorder but a rapid progressive form of plaque-induced inflammatory periodontal disease. Ensuing years of research have led to linkage analysis identification of specific genetic defects responsible for AgP in some families and to the finding that subgingival detection of A. actinomycet-emcomitans JP2 clone is a predictive factor for disease onset and progression. However, rather disappointingly, these ‘proven’ risk factors are only detected in a small subset of AgP cases. Recent advances are leading to a new paradigm shift, with the realization that genetically-driven dysbiotic changes in the subgingival microbiota may predispose to a cascade of events leading to the rapid periodontal tissue destruction seen in AgP. This review tries to dissect the existing literature on the host response-microbial axis of AgP and to propose possible pathogenic pathways in line with current theories.

Microbiology of aggressive periodontitis

For decades, Aggregatibacter actinomycetemcomitans has been considered the most likely etiologic agent in aggressive periodontitis. Implementation of DNA-based microbiologic methodologies has considerably improved our understanding of the composition of subgingival biofilms, and advanced open-ended molecular techniques even allow for genome mapping of the whole bacterial spectrum in a sample and characterization of both the cultivable and not-yet-cultivable microbiota associated with periodontal health and disease. Currently, A. actinomycetemcomitans is regarded as a minor component of the resident oral microbiota and as an opportunistic pathogen in some individuals. Its specific JP2 clone, however, shows properties of a true exogenous pathogen and has an important role in the development of aggressive periodontitis in certain populations. Still, limited data exist on the impact of other microbes specifically in aggressive periodontitis. Despite a wide heterogeneity of bacteria, especially in subgingival samples collected from patients, bacteria of the red complex in particular, and those of the orange complex, are considered as potential pathogens in generalized aggressive periodontitis. These types of bacterial findings closely resemble those found for chronic periodontitis, representing a mixed polymicrobial infection without a clear association with any specific microorganism. In aggressive periodontitis, the role of novel and not-yet-cultivable bacteria has not yet been elucidated. There are geographic and ethnic differences in the carriage of periodontitis-associated microorganisms, and they need to be taken into account when comparing study reports on periodontal microbiology in different study populations. In the present review, we provide an overview on the colonization of potential periodontal pathogens in childhood and adolescence, and on specific microorganisms that have been suspected for their role in the initiation and progression of aggressive forms of periodontal disease.

Development of a polymerase chain reaction assay for the rapid detection of the oral pathogenic bacterium, Selenomonas noxia

Background

In recent studies, periodontal health has been linked to being overweight and/or obese. Among common oral bacteria, Selenomonas noxia has been implicated in converting periodontal health to disease, and Selenomonas species have also been found in gastric ulcers. The objective of this study was to develop and validate a quantitative polymerase chain reaction (qPCR) assay for the specific and rapid detection of S. noxia.

Methods

Two oligonucleotide primer pairs and one probe were designed and tested to determine optimal amplification signal with three strains of S. noxia. The PCR assay was tested against fourteen non-target organisms, including closely related oral Selenomonads, one phylogenetically closely related bacterium, and two commonly isolated oral bacteria.

Results

One of the primer sets was more sensitive at detecting the target organism and was selected for optimization and validation experiments. The designed primers and probe amplified the target organism with 100 % specificity. PCR inhibition was observed with an internal positive control, and inhibition was resolved by diluting the DNA extract.

Conclusions

The qPCR assay designed in this study can be used to specifically detect S. noxia in the clinical setting and in future research involving the enhanced detection of S. noxia. The assay can also be used in epidemiological studies for understanding the role of S. noxia in disease processes including, but not limited to, oral health and obesity of infectious origin.

Quantification of Selenomonas sputigena in Chronic Periodontitis in Smokers Using 16S rDNA Based PCR Analysis

BACKGROUND AND AIM

Selenomonas species have been associated with chronic periodontitis and have been implicated in converting periodontal health to disease. Scanty literature is available in Indian population. Hence, the objective of the study was to detect the prevalence of Selenomonas sputigena in healthy and chronic periodontitis by polymerase chain reaction (PCR) in Indian population and to check whether smoking affects the subgingival microflora of this organism in chronic periodontitis.

MATERIALS AND METHODS

A total of 60 subjects with severe chronic periodontitis with or without smoking and periodontal healthy subjects underwent clinical and microbiological assessment. A deep subgingival plaque sample was collected and genomic DNA was extracted from each sample and analysed for detection of Selnomonas sputigena using PCR. The frequency and quantification of bacteria were also estimated.

RESULTS

All groups differed statistically significant in the frequency of detection of Selenomonas sputigena. On comparison of patients with chronic periodontitis in smokers and non-smokers, there was no statistically significant difference. When the results were quantified, statistically non-significant results were seen among all groups. Plaque index, gingival index, probing pocket depth and clinical attachment level were statistically non-significant in chronic periodontitis with smokers and non-smokers.

CONCLUSION

Prevalence of Selenomonas sputigena showed significant differences with respect to the frequency of detection when comparing the disease group to the healthy population. But no significant difference was seen when the results were quantified. Smoking has no influence on number of Selenomonas sputigena. This study highlights presence as well as quantity of the organism is very important in elucidating its role in causation and progression of the disease.

16S rRNA gene-based metagenomic analysis identifies a novel bacterial co-prevalence pattern in dental caries

Objective:

To identify the prevalence of acidogenic and nonacidogenic bacteria in patients with polycaries lesions, and to ascertain caries specific bacterial prevalence in relation to noncaries controls.

Materials and Methods:

Total genomic DNA extracted from saliva of three adults and four children from the same family were subjected to 16S rRNA gene sequencing analysis on a next generation sequencer, the PGS-Ion Torrent. Those bacterial genera with read counts > 1000 were considered as significant in each of the subject and used to associate the occurrence with caries.

Results and Conclusion:

Sequencing analysis indicated a higher prevalence of Streptococcus, Rothia, Granulicatella, Gemella, Actinomyces, Selenomonas, Haemophilus and Veillonella in the caries group relative to controls. While higher prevalence of Streptococcus, Rothia and Granulicatella were observed in all caries samples, the prevalence of others was observable in 29–57% of samples. Interestingly, Rothia and Selenomonas, which are known to occur within anaerobic environments of dentinal caries and subgingival plaque biofilms, were seen in the saliva of these caries patients. Taken together, the study has identified for the first time a unique co-prevalence pattern of bacteria in caries patients that may be explored as distinct caries specific bacterial signature to predict cariogenesis in high-risk primary and mixed dentition age groups.

Newly identified pathogens associated with periodontitis: a systematic review

There is substantial evidence supporting the role of certain oral bacteria species in the onset and progression of periodontitis. Nevertheless, results of independent-culture diagnostic methods introduced about a decade ago have pointed to the existence of new periodontal pathogens. However, the data of these studies have not been evaluated together, which may generate some misunderstanding on the actual role of these microorganisms in the etiology of periodontitis. The aim of this systematic review was to determine the current weight of evidence for newly identified periodontal pathogens based on the results of "association" studies. This review was conducted and reported in accordance with the PRISMA statement. The MEDLINE, EMBASE, and Cochrane databases were searched up to September 2013 for studies (1) comparing microbial data of subgingival plaque samples collected from subjects with periodontitis and periodontal health and (2) evaluating at least 1 microorganism other than the already-known periodontal pathogens. From 1,450 papers identified, 41 studies were eligible. The data were extracted and registered in predefined piloted forms. The results suggested that there is moderate evidence in the literature to support the association of 17 species or phylotypes from the phyla Bacteroidetes, Candidatus Saccharibacteria, Firmicutes, Proteobacteria, Spirochaetes, and Synergistetes. The phylum Candidatus Saccharibacteria and the Archaea domain also seem to have an association with disease. These data point out the importance of previously unidentified species in the etiology of periodontitis and might guide future investigations on the actual role of these suspected new pathogens in the onset and progression of this infection.

Co-localized or randomly distributed? Pair cross correlation of in vivo grown subgingival biofilm bacteria quantified by digital image analysis

The polymicrobial nature of periodontal diseases is reflected by the diversity of phylotypes detected in subgingival plaque and the finding that consortia of suspected pathogens rather than single species are associated with disease development. A number of these microorganisms have been demonstrated in vitro to interact and enhance biofilm integration, survival or even pathogenic features. To examine the in vivo relevance of these proposed interactions, we extended the spatial arrangement analysis tool of the software daime (digital image analysis in microbial ecology). This modification enabled the quantitative analysis of microbial co-localization in images of subgingival biofilm species, where the biomass was confined to fractions of the whole-image area, a situation common for medical samples. Selected representatives of the disease-associated red and orange complexes that were previously suggested to interact with each other in vitro (Tannerella forsythia with Fusobacterium nucleatum and Porphyromonas gingivalis with Prevotella intermedia) were chosen for analysis and labeled with specific fluorescent probes via fluorescence in situ hybridization. Pair cross-correlation analysis of in vivo grown biofilms revealed tight clustering of F. nucleatum/periodonticum and T. forsythia at short distances (up to 6 µm) with a pronounced peak at 1.5 µm. While these results confirmed previous in vitro observations for F. nucleatum and T. forsythia, random spatial distribution was detected between P. gingivalis and P. intermedia in the in vivo samples. In conclusion, we successfully employed spatial arrangement analysis on the single cell level in clinically relevant medical samples and demonstrated the utility of this approach for the in vivo validation of in vitro observations by analyzing statistically relevant numbers of different patients. More importantly, the culture-independent nature of this approach enables similar quantitative analyses for “as-yet-uncultured” phylotypes which cannot be characterized in vitro.

Levels of Selenomonas species in generalized aggressive periodontitis

BACKGROUND AND OBJECTIVE

To compare the levels of Selenomonas sputigena and uncultivated/unrecognized Selenomonas species in subgingival biofilms from periodontally healthy subjects and from subjects with generalized aggressive periodontitis.

MATERIAL AND METHODS

Fifteen periodontally healthy subjects and 15 subjects with generalized aggressive periodontitis were recruited and their clinical periodontal parameters were evaluated. Nine subgingival plaque samples were collected from each subject and all were individually analyzed for the levels of 10 bacterial taxa, including cultured and uncultivated/unrecognized microorganisms, using the RNA-oligonucleotide quantification technique. Between-group differences in the levels of the test taxa were determined using the Mann-Whitney U-test.

RESULTS

  Subjects with generalized aggressive periodontitis showed significantly higher mean counts of Porphyromonas gingivalis, S. sputigena and the Mitsuokella sp. Human Oral Taxon (HOT) 131 (previously described as Selenomonas sp. oral clone CS002), while higher mean counts of Actinomyces gerencseriae and Streptococcus sanguinis were found in periodontally healthy subjects (p < 0.01). Selenomonas sp. HOT 146 was only detected in the generalized aggressive periodontitis group. In the generalized aggressive periodontitis group, the levels of P. gingivalis and S. sputigena were higher in deep sites (probing depth ≥ 5 mm) than in shallow sites (probing depth ≤ 3 mm) (p < 0.01). Furthermore, in subjects with generalized aggressive periodontitis, sites with probing depth of ≤ 3 mm harbored higher levels of these two species than sites with the same probing depth in periodontally healthy subjects. There were positive correlations between probing depth and the levels of P. gingivalis (r = 0.77; p < 0.01), S. sputigena (r = 0.60; p < 0.01) and Selenomonas dianae (previously described as Selenomonas sp. oral clone EW076) (r = 0.42, p < 0.05).

CONCLUSION

S. sputigena and Mitsuokella sp. HOT 131 may be associated with the pathogenesis of generalized aggressive periodontitis, and their role in the onset and progression of this infection should be investigated further.

Preliminary characterization of the oral microbiota of Chinese adults with and without gingivitis

BACKGROUND

Microbial communities inhabiting human mouth are associated with oral health and disease. Previous studies have indicated the general prevalence of adult gingivitis in China to be high. The aim of this study was to characterize in depth the oral microbiota of Chinese adults with or without gingivitis, by defining the microbial phylogenetic diversity and community-structure using highly paralleled pyrosequencing.

METHODS

Six non-smoking Chinese, three with and three without gingivitis (age range 21-39 years, 4 females and 2 males) were enrolled in the present cross-sectional study. Gingival parameters of inflammation and bleeding on probing were characterized by a clinician using the Mazza Gingival Index (MGI). Plaque (sampled separately from four different oral sites) and salivary samples were obtained from each subject. Sequences and relative abundance of the bacterial 16 S rDNA PCR-amplicons were determined via pyrosequencing that produced 400 bp-long reads. The sequence data were analyzed via a computational pipeline customized for human oral microbiome analyses. Furthermore, the relative abundances of selected microbial groups were validated using quantitative PCR.

RESULTS

The oral microbiomes from gingivitis and healthy subjects could be distinguished based on the distinct community structures of plaque microbiomes, but not the salivary microbiomes. Contributions of community members to community structure divergence were statistically accessed at the phylum, genus and species-like levels. Eight predominant taxa were found associated with gingivitis: TM7, Leptotrichia, Selenomonas, Streptococcus, Veillonella, Prevotella, Lautropia, and Haemophilus. Furthermore, 98 species-level OTUs were identified to be gingivitis-associated, which provided microbial features of gingivitis at a species resolution. Finally, for the two selected genera Streptococcus and Fusobacterium, Real-Time PCR based quantification of relative bacterial abundance validated the pyrosequencing-based results.

CONCLUSIONS

This methods study suggests that oral samples from this patient population of gingivitis can be characterized via plaque microbiome by pyrosequencing the 16 S rDNA genes. Further studies that characterize serial samples from subjects (longitudinal study design) with a larger population size may provide insight into the temporal and ecological features of oral microbial communities in clinically-defined states of gingivitis.