Oral Microbiome Metabolism: From "Who Are They?" to "What Are They Doing?"

Predicted functional and taxonomic analysis of subgingival biofilm of grade C periodontitis in young patients under maintenance therapy

BACKGROUND

In Grade C periodontitis in young patients (PerioC-Y), the functional roles of the subgingival community after years of periodontal treatment are still underexplored. This study evaluated the taxonomic and predicted functional content of the subgingival microbiome of PerioC-Y patients under supportive periodontal therapy (SPT).

METHODS

Clinical and microbiological data from subgingival biofilm were assessed from 10 PerioC-Y patients at two time points: at baseline and after 5.7±1.3 years of SPT. This was compared to 15 patients without a history of periodontitis. The V1-V3 and V4-V5 regions of the 16S rRNA were sequenced using the Illumina Miseq. Microbial composition was evaluated by the core microbiome, and alpha- and beta-diversity. The microbiome functional content was predicted using Picrust2, and the gene differential abundance was analyzed with DESeq2.

RESULTS

Clinical improvements were seen in PerioC-Y-SPT. Differences in β-diversity between PerioC-Y and Health were observed (Health x PerioC-Y-baseline, p = 0.02; Health x PerioC-Y-SPT, p = 0.05). Moreover, although β-diversity did not statistically change between baseline and SPT in PerioC-Y, the microbial correlation evidenced increased Streptococcus and decreased Treponema network contributions during SPT. Based on predicted functional data, treatment induced a reduction in genes related to flagellar protein and signal transduction in PerioC-Y. However, compared to healthy individuals, some genes remained more highly abundant in PerioC-Y-SPT, such as quorum sensing and efflux pump transporters.

CONCLUSION

Despite clinical improvements and a shift in taxonomic composition, the PerioC-Y patients' periodontal treatment was not enough to reach a similar microbiome to patients without disease experience. Some functional content in this biofilm remained altered in PerioC-Y regardless of disease control. This article is protected by copyright. All rights reserved.

Relationship between Saliva and Sublingual Immunotherapy

The demand for allergen specific immunotherapy (AIT), especially sublingual immunotherapy (SLIT), is increasing because of its efficacy in inducing clinical remission of allergic diseases and its low risk of side effects. Since not all patients that undergo SLIT demonstrate an improvement in allergic symptoms, the development of biomarkers to predict the outcome and adjuvants for SLIT is desired. Saliva is the first target with which tablets used in SLIT come into contact, and salivary pH, chemical properties or microbiome composition are reported to possibly be associated with the outcome of SLIT. Antibodies such as IgG4 and IgA not only in the serum but also in the saliva are increased after SLIT and may also be associated with the efficacy of SLIT. The development of the metagenomic sequencing technique makes it possible to determine the microbiome composition and ratio of each bacterium, and researchers can investigate the relationships between specific bacteria and the immune response. Some bacteria are reported to improve the SLIT outcome and have the potential to be used as biomarkers for the selection of patients and as adjuvants in SLIT. Here, we introduce biomarkers for SLIT and present recent findings regarding the relationship between saliva and SLIT.

Transcriptional Activity of Predominant Streptococcus Species at Multiple Oral Sites Associate With Periodontal Status

Background

Streptococcus species are predominant members of the oral microbiota in both health and diseased conditions. The purpose of the present study was to explore if different ecological characteristics, such as oxygen availability and presence of periodontitis, associates with transcriptional activity of predominant members of genus Streptococcus. We tested the hypothesis that genetically closely related Streptococcus species express different transcriptional activities in samples collected from environments with critically different ecological conditions determined by site and inflammatory status.

Methods

Metagenomic and metatranscriptomic data was retrieved from 66 oral samples, subgingival plaque (n=22), tongue scrapings (n=22) and stimulated saliva (n=22) collected from patients with periodontitis (n=11) and orally healthy individuals (n=11). Species-specific transcriptional activity was computed as Log2(RNA/DNA), and transcriptional activity of predominant Streptococcus species was compared between multiple samples collected from different sites in the same individual, and between individuals with different oral health status.

Results

The predominant Streptococcus species were identified with a site-specific colonization pattern of the tongue and the subgingival plaque. A total of 11, 4 and 2 pathways expressed by S. parasanguinis, S. infantis and S. salivarius, respectively, were recorded with significantly higher transcriptional activity in saliva than in tongue biofilm in healthy individuals. In addition, 18 pathways, including pathways involved in synthesis of peptidoglycan, amino acid biosynthesis, glycolysis and purine nucleotide biosynthesis expressed by S. parasanguinis and 3 pathways expressed by S. salivarius were identified with significantly less transcriptional activity in patients with periodontitis.

Conclusion

Data from the present study significantly demonstrates the association of site-specific ecological conditions and presence of periodontitis with transcriptional activity of the predominant Streptococcus species of the oral microbiota. In particular, pathways expressed by S. parasanguinis being involved in peptidoglycan, amino acid biosynthesis, glycolysis, and purine nucleotide biosynthesis were identified to be significantly associated with oral site and/or inflammation status.

The oral microbiome: Role of key organisms and complex networks in oral health and disease

States of oral health and disease reflect the compositional and functional capacities of, as well as the interspecies interactions within, the oral microbiota. The oral cavity exists as a highly dynamic microbial environment that harbors many distinct substrata and microenvironments that house diverse microbial communities. Specific to the oral cavity, the nonshedding dental surfaces facilitate the development of highly complex polymicrobial biofilm communities, characterized not only by the distinct microbes comprising them, but cumulatively by their activities. Adding to this complexity, the oral cavity faces near-constant environmental challenges, including those from host diet, salivary flow, masticatory forces, and introduction of exogenous microbes. The composition of the oral microbiome is shaped throughout life by factors including host genetics, maternal transmission, as well as environmental factors, such as dietary habits, oral hygiene practice, medications, and systemic factors. This dynamic ecosystem presents opportunities for oral microbial dysbiosis and the development of dental and periodontal diseases. The application of both in vitro and culture-independent approaches has broadened the mechanistic understandings of complex polymicrobial communities within the oral cavity, as well as the environmental, local, and systemic underpinnings that influence the dynamics of the oral microbiome. Here, we review the present knowledge and current understanding of microbial communities within the oral cavity and the influences and challenges upon this system that encourage homeostasis or provoke microbiome perturbation, and thus contribute to states of oral health or disease.

Identification & correlation of bacterial diversity in oral cancer and long-term tobacco chewers- A case-control pilot study

Introduction. Squamous cell carcinoma is a highly aggressive type of oral cancer (OC). It is the most common cancer among men, and accounts for almost 90 % of all oral cancers in India. Consumption of tobacco is a leading factor contributing to maximum oral cancer incidences as per the WHO.Hypothesis/Gap statement. Researchers reported a direct association of microorganisms with dysbiosis in various oral lesions including oral cancer. However, there is a dearth of information related to compositional changes in the oral microbiome in long-term tobacco chewers and the Indian oral cancer population.Aim. The aim of this study was to identify and correlate the bacterial diversity in the oral cavity of tobacco chewers, patients with oral cancer and healthy subjects in the Indian population.Methods. Oral rinse samples were collected for ten subjects in each group followed by DNA extraction. The variable regions of the bacterial 16S rRNA gene (V6-V8) were amplified, sequenced, processed, and analysed using QIIME2 platform to assess alpha and beta diversity between the study groups.Results. This pilot study showed genus Streptococcus dominated the control group (18.54 %), and the abundance decreased in tobacco and OC group (9.63 and 5.45% respectively); whereas genus Prevotella dominated the tobacco and OC group (21.01 and 26.03% respectively). A shift in abundance of microbiome was observed from control population to oral cancer via the tobacco chewing population. Maximum alpha diversity of oral microbiome was found in Indian tobacco chewers. Beta diversity of tobacco chewers was similar to both the healthy population as well as oral cancer patients suggesting transitioning of the oral microbiome from healthy to oral cancer microbiome via the tobacco chewers microbiome.Conclusion. The data provides evidence of oral bacterial dysbiosis due to tobacco chewing habits that can further lead to progression towards cancer.

Low-Dose Doxycycline Treatment Normalizes Levels of Some Salivary Metabolites Associated with Oral Microbiota in Patients with Primary Sjögren's Syndrome

Saliva is a complex oral fluid, and plays a major role in oral health. Primary Sjögren’s syndrome (pSS), as an autoimmune disease that typically causes hyposalivation. In the present study, salivary metabolites were studied from stimulated saliva samples (n = 15) of female patients with pSS in a group treated with low-dose doxycycline (LDD), saliva samples (n = 10) of non-treated female patients with pSS, and saliva samples (n = 14) of healthy age-matched females as controls. Saliva samples were analyzed with liquid chromatography mass spectrometry (LC-MS) based on the non-targeted metabolomics method. The saliva metabolite profile differed between pSS patients and the healthy control (HC). In the pSS patients, the LDD treatment normalized saliva levels of several metabolites, including tyrosine glutamine dipeptide, phenylalanine isoleucine dipeptide, valine leucine dipeptide, phenylalanine, pantothenic acid (vitamin B5), urocanic acid, and salivary lipid cholesteryl palmitic acid (CE 16:0), to levels seen in the saliva samples of the HC. In conclusion, the data showed that pSS is associated with an altered saliva metabolite profile compared to the HC and that the LLD treatment normalized levels of several metabolites associated with dysbiosis of oral microbiota in pSS patients. The role of the saliva metabolome in pSS pathology needs to be further studied to clarify if saliva metabolite levels can be used to predict or monitor the progress and treatment of pSS.

Leukoplakia in the Oral Cavity and Oral Microbiota: A Comprehensive Review

Simple Summary

The aim of this narrative review is to better understand the role of the oral microbiota in oral cavity leukoplakia. We provide a comprehensive review, exhaustively summarizing the steps taken in this field.

Abstract

We reviewed the current published literature on the impact of oral microbiota on oral cavity leukoplakia (OLK), aiming at clarifying its role in disease transformation. The analysis unveiled that bacterial richness and diversity in the oral cavity tend to be decreased in OLK compared to healthy controls, with a reduction in the prevalent commensals, such as Streptococci, and elevation of anaerobes. Moreover, Fusobacterium nucleatum, Porphyromonas gingivalis and Prevotella intermedia are recurrent findings, and they already have been linked to periodontal disease. These microbial community changes may also represent a marker for the transition from OLK to oral squamous cell carcinoma. Unfortunately, the reviewed studies present several limitations, making an objective comparison difficult. To overcome these biases, longitudinal studies are necessary.

Proteomic response in Streptococcus gordonii DL1 biofilm cells during attachment to salivary MUC5B

Background

Salivary mucin MUC5B seems to promote biodiversity in dental biofilms, and thereby oral health, for example, by inducing synergistic ‘mucolytic’ activities in a variety of microbial species that need to cooperate for the release of nutrients from the complex glycoprotein. Knowledge of how early colonizers interact with host salivary proteins is integral to better understand the maturation of putatively harmful oral biofilms and could provide key insights into biofilm physiology.

Methods

The early oral colonizer Streptococcus gordonii DL1 was grown planktonically and in biofilm flow cell systems with uncoated, MUC5B or low-density salivary protein (LDP) coated surfaces. Bacterial cell proteins were extracted and analyzed using a quantitative mass spectrometry-based workflow, and differentially expressed proteins were identified.

Results and conclusions

Overall, the proteomic profiles of S. gordonii DL1 were similar across conditions. Six novel biofilm cell proteins and three planktonic proteins absent in all biofilm cultures were identified. These differences may provide insights into mechanisms for adaptation to biofilm growth in this species. Salivary MUC5B also elicited specific responses in the biofilm cell proteome. These regulations may represent mechanisms by which this mucin could promote colonization of the commensal S. gordonii in oral biofilms.

Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users

INTRODUCTION

Smoked, and especially smokeless, tobacco are major causes of oral cancer globally. Here, we examine the oral bacteriome of smokers and of smokeless tobacco users, in comparison to healthy controls, using 16S rRNA gene sequencing.

METHODS

Oral swab samples were collected from smokers, smokeless tobacco users, and healthy controls (n = 44). Microbial DNA was extracted and the 16S rRNA gene profiled using the Illumina MiSeq platform. Sequencing reads were processed using DADA2, and taxonomical classification was performed using the phylogenetic placement method. Differentially abundant taxa were identified using DESeq2, while functional metagenomes based on KEGG orthology abundance were inferred using LIMMA.

RESULTS

A significantly higher microbial diversity was observed in smokeless tobacco users and smokers relative to controls (P < 0.05). Compositional differences in microbial communities were observed in all comparisons with healthy controls (PERMANOVA P < 0.05) but not between smokers and smokeless tobacco users. Levels of Fusobacterium spp., Saccharibacterium spp., and members of Shuttleworthia were elevated in smokers when compared to controls (BH adj P < 0.01). In addition, the relative abundance of three bacterial taxa belonging to genera Fusobacterium spp., Catonella, and Fretibacterium spp. was significantly increased in smokeless tobacco users relative to controls (BH adj P < 0.01). Major functional pathways significantly increased in smokeless tobacco users relative to both controls, and smokers were similar and involved amino acid metabolism including glutamate and aspartate biosynthesis and degradation (log FC > 1.5; BH adj P < 0.01).

CONCLUSIONS

A distinct taxonomic and functional profile of oral microbiome in smokers and smokeless tobacco users as compared to healthy controls implicates a significant role of microbes and their metabolites in diseases associated with tobacco use including oral cancer.

CLINICAL RELEVANCE

Future efforts in preventive, diagnostic, curative, and prognostic strategies for diseases associated with tobacco use in smokers and smokeless tobacco users could incorporate the oral microbiome.

Impact of Oral Microbiota on Flavor Perception: From Food Processing to In-Mouth Metabolization

Flavor perception during food intake is one of the main drivers of food acceptability and consumption. Recent studies have pointed to the oral microbiota as an important factor modulating flavor perception. This review introduces general characteristics of the oral microbiota, factors potentially influencing its composition, as well as known relationships between oral microbiota and chemosensory perception. We also review diverse evidenced mechanisms enabling the modulation of chemosensory perception by the microbiota. They include modulation of the chemosensory receptors activation by microbial metabolites but also modification of receptors expression. Specific enzymatic reactions catalyzed by oral microorganisms generate fragrant molecules from aroma precursors in the mouth. Interestingly, these reactions also occur during the processing of fermented beverages, such as wine and beer. In this context, two groups of aroma precursors are presented and discussed, namely, glycoside conjugates and cysteine conjugates, which can generate aroma compounds both in fermented beverages and in the mouth. The two entailed families of enzymes, i.e., glycosidases and carbon-sulfur lyases, appear to be promising targets to understand the complexity of flavor perception in the mouth as well as potential biotechnological tools for flavor enhancement or production of specific flavor compounds.

The Role of Periodontopathogens and Oral Microbiome in the Progression of Oral Cancer. A Review

Chronic periodontal disease and oral bacteria dysbiosis can lead to the accumulation of genetic mutations that eventually stimulate Oral Squamous Cell Cancer (OSCC). The annual incidence of OSCC is increasing significantly, and almost half of the cases are diagnosed in an advanced stage. Worldwide there are more than 380,000 new cases diagnosed every year, and a topic of extensive research in the last few years is the alteration of oral bacteria, their compositional changes and microbiome. This review aims to establish the relationship between bacterial dysbiosis and OSCC. Several bacteria implicated in periodontal disease, including Fusobacterium nucleatum, Porphyromonas gingivalis, Prevotella intermedia, and some Streptococcus species, promote angiogenesis, cell proliferation, and alteration in the host defense process; these same bacteria have been present in different stages of OSCC. Our review showed that genes involved in bacterial chemotaxis, the lipopolysaccharide (LPS) of the cell wall membrane of gram negatives bacteria, were significantly increased in patients with OSCC. Additionally, some bacterial diversity, particularly with Firmicutes, and Actinobacteria species, has been identified in pre-cancerous stage samples. This review suggests the importance of an early diagnosis and more comprehensive periodontal therapy for patients by the dental care professional.

The Extracellular Metabolome Stratifies Low and High Risk Potentially Premalignant Oral Keratinocytes and Identifies Citrate as a Potential Non-Invasive Marker of Tumour Progression

Simple Summary

The early detection of oral cancer is a high priority, as improvements in this area could lead to greater cure rates and reduced disability due to extensive surgery. Oral cancer is very difficult to detect in over 70% of cases as it develops unseen until quite advanced, sometimes rapidly. Therefore, the development of markers in body fluids (liquid biopsies) indicative of cancerous changes have a high priority. We show here that small molecules called metabolites can distinguish between non-diseased oral cells and two types of cells found in oral cells on the road to cancer. Although our investigation is preliminary, some of the metabolites have already been detected in the saliva (split) of oral cancer patients, and could eventually help detect oral cancer development at an earlier stage.

Abstract

Premalignant oral lesions (PPOLs) which bypass senescence (IPPOL) have a much greater probability of progressing to malignancy, but pre-cancerous fields also contain mortal PPOL keratinocytes (MPPOL) that possess tumour-promoting properties. To identify metabolites that could potentially separate IPPOL, MPPOL and normal oral keratinocytes non-invasively in vivo, we conducted an unbiased screen of their conditioned medium. MPPOL keratinocytes showed elevated levels of branch-chain amino acid, lipid, prostaglandin, and glutathione metabolites, some of which could potentially be converted into volatile compounds by oral bacteria and detected in breath analysis. Extracellular metabolites were generally depleted in IPPOL, and only six were elevated, but some metabolites distinguishing IPPOL from MPPOL have been associated with progression to oral squamous cell carcinoma (OSCC) in vivo. One of the metabolites elevated in IPPOL relative to the other groups, citrate, was confirmed by targeted metabolomics and, interestingly, has been implicated in cancer growth and metastasis. Although our investigation is preliminary, some of the metabolites described here are detectable in the saliva of oral cancer patients, albeit at a more advanced stage, and could eventually help detect oral cancer development earlier.

Dependency of hydration and growth conditions on the mechanical properties of oral biofilms

Within the oral cavity, dental biofilms experience dynamic environments, in part due to changes in dietary content, frequency of intake and health conditions. This can impact bacterial diversity and morpho-mechanical properties. While phenotypic properties of oral biofilms are closely related to their composition, these can readily change according to dynamic variations in the growth environment and nutrient availability. Understanding the interlink between phenotypic properties, variable growth conditions, and community characterization is an essential requirement to develop structure–property relationships in oral-biofilms. In this study, the impact of two distinct growth media types with increasing richness on the properties of oral biofilms was assessed through a new combination of in-vitro time-lapse biophysical methods with microbiological assays. Oral biofilms grown in the enriched media composition presented a decrease in their pH, an increase in soluble EPS production, and a severe reduction in bacterial diversity. Additionally, enriched media conditions presented an increase in biofilm volumetric changes (upon hydration) as well as a reduction in elastic modulus upon indentation. With hydration time considered a major factor contributing to changes in biofilm mechanical properties, we have shown that it is less associated than media richness. Future investigations can now use this time-lapse approach, with a clearer focus on the extracellular matrix of oral biofilms dictating their morpho-mechanical properties.

The secretion of cytokines by peripheral blood mononuclear cells of patients with periodontitis and healthy controls when exposed to H2S

Background: Hydrogen sulfide(H2S) is a bacterial metabolite produced as a result of bacterial growth in subgingival pockets, suggested to partake in the pathogenesis of periodontitis. H2S has previously been shown to induce the secretion of the pro-inflammatory cytokines IL-1β and IL-18 via the NLRP3 inflammasome in monocytes. Objective: To investigate the non-NLRP3 inflammasome-dependent immunological response of human peripheral blood mononuclear cells (PBMCs) of periodontitis patients and healthy controls exposed to H2S in vitro. Methods: PBMCs of periodontitis patients(N = 31) and healthy controls(N = 32) were exposed to 1 mM sodium hydrosulfide (NaHS) at 37°C for 24 h and the secretion of cytokines was compared to resting cells. TNF-α, IFN-γ, IL-6, IL-8, IL-12p40, IL-12p70, IL-17, MCP-1, and IL-1Ra secretions were measured with Bio-Plex Pro™ Human Cytokine Assay. Results: H2S triggered the secretion of the pro-inflammatory IFN-γ, IL-6, IL-17, TNF-α, IL-12p40, and IL-12p70, while the reverse was seen for IL-1Ra. In addition, a higher basal secretion of IFN-γ, IL-6, IL-12p70, IL-17 and MCP-1 was seen from PBMCs of periodontitis patients compared to healthy controls. Conclusion: The bacterial metabolite H2S triggers the secretion of pro-inflammatory cytokines from PBMCs and may thus have a prominent role in the host-bacteria interplay in periodontitis.

Bacterial Composition and Metabolomics of Dental Plaque From Adolescents

Supragingival dental plaque samples were collected from 40 Swedish adolescents, including 20 with caries lesions (CAR) and 20 caries-free (CF). Fresh plaque samples were subjected to an ex vivo acid tolerance (AT) test where the proportion of bacteria resistant to an acid shock was evaluated through confocal microscopy and live/dead staining, and the metabolites produced were quantified by ¹H Nuclear Magnetic Resonance (¹H NMR). In addition, DNA was extracted and the 16S rRNA gene was sequenced by Illumina sequencing, in order to characterize bacterial composition in the same samples. There were no significant differences in AT scores between CAR and CF individuals. However, 7 out of the 10 individuals with highest AT scores belonged to the CAR group. Regarding bacterial composition, Abiotrophia, Prevotella and Veillonella were found at significantly higher levels in CAR individuals (p=0.0085, 0.026 and 0.04 respectively) and Rothia and Corynebacterium at significantly higher levels in CF individuals (p=0.026 and 0.003). The caries pathogen Streptococcus mutans was found at low frequencies and was absent in 60% of CAR individuals. Random-forest predictive models indicate that at least 4 bacterial species or 9 genera are needed to distinguish CAR from CF adolescents. The metabolomic profile obtained by NMR showed a significant clustering of organic acids with specific bacteria in CAR and/or high AT individuals, being Scardovia wiggsiae the species with strongest associations. A significant clustering of ethanol and isopropanol with health-associated bacteria such as Rothia or Corynebacterium was also found. Accordingly, several relationships involving these compounds like the Ethanol : Lactate or Succinate : Lactate ratios were significantly associated to acid tolerance and could be of predictive value for caries risk. We therefore propose that future caries risk studies would benefit from considering not only the use of multiple organisms as potential microbial biomarkers, but also their functional adaptation and metabolic output.

Do Gut Microbes Taste?

Gut microbiota has emerged as a major metabolically active organ with critical functions in both health and disease. The trillions of microorganisms hosted by the gastrointestinal tract are involved in numerous physiological and metabolic processes including modulation of appetite and regulation of energy in the host spanning from periphery to the brain. Indeed, bacteria and their metabolic byproducts are working in concert with the host chemosensory signaling pathways to affect both short- and long-term ingestive behavior. Sensing of nutrients and taste by specialized G protein-coupled receptor cells is important in transmitting food-related signals, optimizing nutrition as well as in prevention and treatment of several diseases, notably obesity, diabetes and associated metabolic disorders. Further, bacteria metabolites interact with specialized receptors cells expressed by gut epithelium leading to taste and appetite response changes to nutrients. This review describes recent advances on the role of gut bacteria in taste perception and functions. It further discusses how intestinal dysbiosis characteristic of several pathological conditions may alter and modulate taste preference and food consumption via changes in taste receptor expression.

Comparison of the modulatory effects of three structurally similar potential prebiotic substrates on an in vitro multi-species oral biofilm

Previous research identified potential prebiotic substrates for oral health like the structural analogues N-acetyl-D-mannosamine (NADM) and N-acetyl-D-glucosamine (NADG). The main hypothesis of the current study was twofold. Firstly, it was hypothesized that the modulatory effects of NADM are not limited to changes in multi-species oral biofilm composition, but also include effects on metabolism, virulence, and inflammatory potential. Secondly, the presence and orientation of their N-acetyl group could play a role. Therefore, a comparison was made between the effects of NADM, NADG and D-(+)-mannose on multi-species oral biofilms. Besides a beneficial compositional shift, NADM-treated biofilms also showed an altered metabolism, a reduced virulence and a decreased inflammatory potential. At a substrate concentration of 1 M, these effects were pronounced for all biofilm aspects, whereas at ~ 0.05 M (1%_(w/v)) only the effects on virulence were pronounced. When comparing between substrates, both the presence and orientation of the N-acetyl group played a role. However, this was generally only at 1 M and dependent on the biofilm aspect. Overall, NADM was found to have different effects at two concentrations that beneficially modulate in vitro multi-species oral biofilm composition, metabolism, virulence and inflammatory potential. The presence and orientation of the N-acetyl group influenced these effects.

Metabolic phenotyping of saliva to identify possible biomarkers of periodontitis using proton nuclear magnetic resonance

AIM

The aim of this study was to propose biomarker candidates for periodontitis via untargeted metabolomics analysis.

MATERIALS AND METHODS

Metabolic profiling was performed using saliva samples from 92 healthy controls (H) and 129 periodontitis patients (P) in the discovery cohort using proton nuclear magnetic resonance spectroscopy. Random forest was applied to identify metabolites that significantly differentiated the control group from the periodontitis group. Candidate metabolites were then validated in an independent validation cohort.

RESULTS

In the discovery set, the metabolic profiles of the P group were clearly separated from those of the H group. A total of 31 metabolites were identified in saliva, and 7 metabolites were selected as candidate biomarkers. These metabolites were further confirmed in the validation set. Ethanol, taurine, isovalerate, butyrate, and glucose were finally confirmed as biomarkers. Furthermore, the biomarker panel showed more than 0.9 of the area under curve value in both discovery and validation sets, indicating that panels were more effective than individual metabolites for diagnosing periodontitis.

CONCLUSIONS

We identified five metabolite biomarkers that discriminated patients with periodontitis from healthy controls in two independent cohorts. These biomarkers have the potential for periodontal screening, detection of periodontitis, and monitoring of the outcome of periodontal therapy.

Salivary metabolites associated with a 5-year tooth loss identified in a population-based setting

BACKGROUND

Periodontitis is among the most common chronic diseases worldwide, and it is one of the main reasons for tooth loss. Comprehensive profiling of the metabolite content of the saliva can enable the identification of novel pathways associated with periodontitis and highlight non-invasive markers to facilitate time and cost-effective screening efforts for the presence of periodontitis and the prediction of tooth loss.

METHODS

We first investigated cross-sectional associations of 13 oral health variables with saliva levels of 562 metabolites, measured by untargeted mass spectrometry among a sub-sample (n = 938) of the Study of Health in Pomerania (SHIP-2) using linear regression models adjusting for common confounders. We took forward any candidate metabolite associated with at least two oral variables, to test for an association with a 5-year tooth loss over and above baseline oral health status using negative binomial regression models.

RESULTS

We identified 84 saliva metabolites that were associated with at least one oral variable cross-sectionally, for a subset of which we observed robust replication in an independent study. Out of 34 metabolites associated with more than two oral variables, baseline saliva levels of nine metabolites were positively associated with a 5-year tooth loss. Across all analyses, the metabolites 2-pyrrolidineacetic acid and butyrylputrescine were the most consistent candidate metabolites, likely reflecting oral dysbiosis. Other candidate metabolites likely reflected tissue destruction and cell proliferation.

CONCLUSIONS

Untargeted metabolic profiling of saliva replicated metabolic signatures of periodontal status and revealed novel metabolites associated with periodontitis and future tooth loss.

Metabolites of the Oral Microbiome: Important Mediators of Multi-Kingdom Interactions

The oral cavity hosts over 700 different microbial species that produce a rich reservoir of bioactive metabolites critical to oral health maintenance. Over the last two decades, new insights into the oral microbiome and its importance in health and disease have emerged mainly due to the discovery of new oral microbial species using next-generation sequencing (NGS). This advancement has revolutionized the documentation of unique microbial profiles associated with different niches and health/disease states within the oral cavity and the relation of the oral bacteria to systemic diseases. However, less work has been done to identify and characterize the unique oral microbial metabolites that play critical roles in maintaining equilibrium between the various oral microbial species and their human hosts. This article discusses the most significant microbial metabolites produced by these diverse communities of oral bacteria that can either foster health or contribute to disease. Finally, we shed light on how advances in genomics and genome mining can provide a high throughput platform for discovering novel bioactive metabolites derived from the human oral microbiome to tackle emerging human infections and systemic diseases.

Effect of TiF4/NaF and chitosan solutions on the development of enamel caries under a microcosm biofilm model

OBJECTIVES

To evaluate the effect of experimental solutions containing TiF₄/NaF and chitosan on bacterial species and on enamel caries prevention.

METHODS

Microcosm biofilm was produced from human saliva mixed with McBain saliva (0.2% sucrose) on bovine enamel for five days, under 5% CO₂ and 37 °C. From the second day until the end, the treatments were applied (1 × 60 s/day): (1) NaF (500 ppm F^-, positive control); (2) TiF₄ and NaF (TiF₄: 190 ppm Ti⁴⁺ and 300 ppm F^-; NaF: 190 ppm F^-); (3) similar to 2 plus 0.5% chitosan (Ch 500 mPas, 75% deacetylation); (4) phosphate buffer solution (negative control); and (5) 0.5% chitosan (Ch 500 mPas, 75% deacetylation). CFU counting was performed for total microorganism, total streptococcus, total lactobacillus and Streptococcus mutans. Enamel demineralization was measured by transverse microradiography-TMR. The data were compared using ANOVA/Tukey or Kruskal-Wallis/Dunn tests (p < .050).

RESULTS

No differences were found between the treatments with respect to CFU counting (ANOVA, p > .050). Enamel treated with TiF₄/NaF plus chitosan solution presented the lowest demineralization compared to the negative control and pure chitosan solution. On the other hand, this experimental solution did not significantly differ from TiF₄/NaF and NaF solutions, being all of them able to significantly reduce mineral loss (50-74%), but only TiF₄/NaF plus chitosan reduced lesion depth (55%) compared to the negative control (p = .001).

CONCLUSION

TiF₄/NaF plus chitosan solution had no antimicrobial effect, but it was able to reduce enamel caries development in 79% compared to control under this model.

CLINICAL SIGNIFICANCE

This study showed that TiF₄/NaF plus chitosan solution had no antimicrobial effect, but it was able to reduce enamel caries development under a microcosm biofilm model.

Identification of Salivary Microorganisms and Metabolites Associated with Halitosis

Halitosis is mainly caused by the action of oral microbes. The purpose of this study was to investigate the differences in salivary microbes and metabolites between subjects with and without halitosis. Of the 52 participants, 22 were classified into the halitosis group by the volatile sulfur compound analysis on breath samples. The 16S rRNA gene amplicon sequencing and metabolomics approaches were used to investigate the difference in microbes and metabolites in saliva of the control and halitosis groups. The profiles of microbiota and metabolites were relatively different between the halitosis and control groups. The relative abundances of Prevotella, Alloprevotella, and Megasphaera were significantly higher in the halitosis group. In contrast, the relative abundances of Streptococcus, Rothia, and Haemophilus were considerably higher in the control group. The levels of 5-aminovaleric acid and n-acetylornithine were significantly higher in the halitosis group. The correlation between identified metabolites and microbiota reveals that Alloprevotella and Prevotella might be related to the cadaverine and putrescine pathways that cause halitosis. This study could provide insight into the mechanisms of halitosis.

Oral Microbiome in Relation to Periodontitis Severity and Systemic Inflammation

Systemic inflammation induced by periodontitis is suggested to be the link between periodontitis and cardiovascular disease. The aim of this work was to explore the oral microbiome in periodontitis in relation to disease severity and systemic inflammation. The saliva and subgingival microbiome from periodontal pocket samples of patients with severe (n = 12) and mild periodontitis (n = 13) were analyzed using metagenomic shotgun sequencing. The taxa and pathways abundances were quantified. The diversity was assessed and the abundances to phenotype associations were performed using ANCOM and linear regression. A panel of inflammatory markers was measured in blood and was associated with taxa abundance. The microbial diversity and species richness did not differ between severe and mild periodontitis in either saliva or periodontal pockets. However, there were significant differences in the microbial composition between severe and mild periodontitis in the subgingival microbiome (i.e., pocket samples) and, in a lower grade, in saliva, and this is positively associated with systemic inflammatory markers. The “red complex” and “cluster B” abundances in periodontal pockets were strongly associated with inflammatory markers interleukin-6 and the white blood cell count. Our data suggest that systemic inflammation in severe periodontitis may be driven by the oral microbiome and may support the indirect (inflammatory) mechanism for the association between periodontitis and cardiovascular disease.

Regulation of Bone Cell Differentiation and Activation by Microbe-Associated Molecular Patterns

Gut microbiota has emerged as an important regulator of bone homeostasis. In particular, the modulation of innate immunity and bone homeostasis is mediated through the interaction between microbe-associated molecular patterns (MAMPs) and the host pattern recognition receptors including Toll-like receptors and nucleotide-binding oligomerization domains. Pathogenic bacteria such as Porphyromonas gingivalis and Staphylococcus aureus tend to induce bone destruction and cause various inflammatory bone diseases including periodontal diseases, osteomyelitis, and septic arthritis. On the other hand, probiotic bacteria such as Lactobacillus and Bifidobacterium species can prevent bone loss. In addition, bacterial metabolites and various secretory molecules such as short chain fatty acids and cyclic nucleotides can also affect bone homeostasis. This review focuses on the regulation of osteoclast and osteoblast by MAMPs including cell wall components and secretory microbial molecules under in vitro and in vivo conditions. MAMPs could be used as potential molecular targets for treating bone-related diseases such as osteoporosis and periodontal diseases.

Patterns of salivary microbiota injury and oral mucositis in recipients of allogeneic hematopoietic stem cell transplantation

Oral mucositis (OM) is a common debilitating dose-limiting toxicity of cancer treatment, including hematopoietic stem cell transplantation (HSCT). We hypothesized that the oral microbiome is disturbed during allogeneic HSCT, partially accounting for the variability in OM severity. Using 16S ribosomal RNA gene sequence analysis, metabolomic profiling, and computational methods, we characterized the behavior of the salivary microbiome and metabolome of 184 patients pre- and post-HSCT. Transplantation was associated with a decrease in oral α diversity in all patients. In contrast to the gut microbiome, an association with overall survival was not detected. Among 135 patients given methotrexate for graft-versus-host disease prophylaxis pre-HSCT, Kingella and Atopobium abundance correlated with future development of severe OM. Posttransplant, Methylobacterium species were significantly enriched in patients with severe OM. Moreover, the oral microbiome and metabolome of severe OM patients underwent distinct changes post-HSCT, compared with patients with no or mild OM. Changes in specific metabolites were well explained by microbial composition, and the common metabolic pathway was the polyamines pathway, which is essential for epithelial homeostasis. Together, our findings suggest that salivary microbial composition and metabolites are associated with the development of OM, offering new insights on pathophysiology and potential avenues of intervention.

Association of oral microbiota profile with sugar-sweetened beverages consumption in school-aged children

Evidence that common beverage consumption is associated with oral ecosystem. However, little is known about the effect of sugar-sweetened beverages (SSBs) on composition and functional potential of childhood oral microbiota. We aim to examine associations between SSBs consumption with oral microbiota diversity and function among school-aged children. Oral microbiota in buccal swab samples was collected from 180 children (11.3 ± 0.6 years) from an ongoing child growth and development cohort established in 2016, using 16S rDNA gene sequencing. Higher SSBs consumption (≥1 serving/day) was associated with lower oral microbiota richness and diversity. Children with higher SSBs consumption showed decreased abundance of genus Fusobacterium, Lachnoanaerobaculum, Soonwooa, Tannerella and Moraxella (p < 0.05). However, more SSBs intake selectively increases the dominance of aciduric bacteria (Neisseria and Streptococcus), which can lead to dental caries and other oral problems. Furthermore, PICRUSt analysis illustrated that oral microbiota was more conducive to the pathway activated of protein export (p = 0.020), D-glutamine and D-glutamate metabolism (p = 0.013), and pantothenate and CoA biosynthesis (p = 0.004), indicating vigorous microbial metabolism in oral bacterial community in higher SSBs intake groups. Overall, our finding suggests that higher SSBs consumption may disturb oral microecology and reduce diversity of microbiota during childhood, stimulating an increase in cariogenic genera, which contributes to increased susceptibility of SSBs-related oral diseases.

The Effect of Solutions Containing Extracts of Vochysia tucanorum Mart., Myrcia bellaCambess., Matricaria chamomilla L. and Malva sylvestris L. on Cariogenic Bacterial Species and Enamel Caries Development

This study evaluated the effect of experimental solutions containing plant extracts on bacterial species and enamel caries prevention. Microcosm biofilm was produced from human saliva mixed with McBain saliva (0.2% sucrose) on bovine enamel for 5 days (3 days under anaerobiosis and 2 days under aerobiosis) at 37°C. From the 2nd day, the following treatments were applied (1 × 60 s/day): Vochysia tucanorum (10 mg/mL); Myrcia bella (5 mg/mL); Matricaria chamomilla (80 mg/mL); Malva sylvestris, fluoride, and xylitol (Malvatricin Plus®); 0.12% chlorhexidine (CHX, PerioGard®); and PBS (negative control). The medium pH was measured. Quantitative polymerase chain reaction was performed for the detection of Streptococcus mutans and Lactobacillus spp. Enamel demineralization was measured by spectral-domain optical coherence tomography. The data were compared by means of the Kruskal-Wallis/Dunn, two-way ANOVA/Bonferroni, and ANOVA/Tukey tests (p < 0.05). The pH decreased after sucrose exposure; only CHX reestablished pH >5.5 by the last day. CHX also eliminated Lactobacillusspp., but the other treatments did not differ significantly from PBS. Malvatricin Plus® and CHX eliminated S. mutans, but the other treatments did not differ from PBS. Similar results were seen concerning the reduction of lesion depth and reflectivity. The experimental natural-extract solutions were ineffective against cariogenic bacteria and in preventing the development of enamel caries.

The predictive power of saliva electrolytes exceeds that of saliva microbiomes in diagnosing early childhood caries

Early childhood caries (ECC) is one of the most prevalent chronic diseases affecting children worldwide, and thus its etiology, diagnosis, and prognosis are of particular clinical significance. This study aims to test the ability of salivary microbiome and electrolytes in diagnosing ECC, and their interplays within the same population. We here simultaneously profiled salivary microbiome and biochemical components of 331 children (166 caries-free (H group) and 165 caries-active children (C group)) aged 4-6 years. We identified both salivary microbial and biochemical dysbiosis associated with ECC. Remarkably, K⁺, Cl^-, NH₄⁺, Na⁺, SO₄^2-, Ca²⁺, Mg²⁺, and Br^- were enriched while pH and NO₃^- were depleted in ECC. Moreover, the dmft index (ECC severity) positively correlated with Cl^-, NH₄⁺, Ca²⁺, Mg²⁺, Br^-, while negatively with pH and NO₃^-. Furthermore, machine-learning classification models were constructed based on these biomarkers from saliva microbiota, or electrolytes (and pH). Unexpectedly, the electrolyte-based classifier (AUROC = 0.94) outperformed microbiome-based (AUROC = 0.70) one and the composite-based one (with both microbial and biochemical data; AUC = 0.89) in predicting ECC. Collectively, these findings indicate ECC-associated alterations and interplays in the oral microbiota, electrolytes and pH, underscoring the necessity of developing diagnostic models with predictors from salivary electrolytes.

Regulatory involvement of the PerR and SloR metalloregulators in the Streptococcus mutans oxidative stress response

Streptococcus mutans is a commensal of the human oral microbiome that can promote dental caries under conditions of dysbiosis. This study investigates metalloregulators and their involvement in the S. mutans oxidative stress response. Oxidative stress in the human mouth can derive from temporal increases in reactive oxygen species (ROS) after meal consumption and from endogenous bacterial ROS-producers that colonize the dentition. We hypothesize that the S. mutans PerR (SMU.593) and SloR (SMU.186) metalloregulatory proteins contribute to the regulation of oxidative stress genes and their products. Expression assays with S. mutans UA159 wild type cultures exposed to H₂O₂ reveal that H₂O₂ upregulates perR, and that PerR represses sloR transcription upon binding directly to Fur and PerR consensus sequences within the sloR operator. In addition, the results of Western blot experiments implicate the Clp proteolytic system in SloR degradation under conditions of H₂O₂-stress. To reveal a potential role for SloR in the H₂O₂-resistant phenotype of S. mutans GMS802 (a perR-deficient strain), we generated a sloR/perR double knockout mutant, GMS1386, where we observed upregulation of the tpx and dpr antioxidant genes. These results are consistent with GMS802 H₂O₂ resistance and with a role for PerR as a transcriptional repressor. Cumulatively, these findings support a reciprocal relationship between PerR and SloR during the S. mutans oxidative stress response and begin to elucidate the fitness strategies that evolved to foster S. mutans persistence in the transient environments of the human oral cavity.IMPORTANCEIn 2020, untreated dental caries, especially in the permanent dentition, ranked among the most prevalent infectious diseases worldwide, disproportionately impacting individuals of low socioeconomic status. Untreated caries can lead to systemic health problems and has been associated with extended school and work absences, inappropriate use of emergency departments, and an inability for military forces to deploy. Together with public health policy, research aimed at alleviating S. mutans -induced tooth decay is important because it can improve oral health (and overall health), especially in underserved populations. This research, focused on S. mutans metalloregulatory proteins and their gene targets, is significant because it can promote virulence gene control in an important oral pathogen, and contribute to the development of an anti-caries therapeutic that can reduce tooth decay.

Potential prebiotic substrates modulate composition, metabolism, virulence and inflammatory potential of an in vitro multi-species oral biofilm

Background: Modulation of the commensal oral microbiota constitutes a promising preventive/therapeutic approach in oral healthcare. The use of prebiotics for maintaining/restoring the health-associated homeostasis of the oral microbiota has become an important research topic.

Aims: This study hypothesised that in vitro 14-species oral biofilms can be modulated by (in)direct stimulation of beneficial/commensal bacteria with new potential prebiotic substrates tested at 1 M and 1%_(w/v), resulting in more host-compatible biofilms with fewer pathogens, decreased virulence and less inflammatory potential.

Methods: Established biofilms were repeatedly rinsed with N-acetyl-D-glucosamine, α-D-lactose, D-(+)-trehalose or D-(+)-raffinose at 1 M or 1%_(w/v). Biofilm composition, metabolic profile, virulence and inflammatory potential were eventually determined.

Results: Repeated rinsing caused a shift towards a more health-associated microbiological composition, an altered metabolic profile, often downregulated virulence gene expression and decreased the inflammatory potential on oral keratinocytes. At 1 M, the substrates had pronounced effects on all biofilm aspects, whereas at 1%_(w/v) they had a pronounced effect on virulence gene expression and a limited effect on inflammatory potential.

Conclusion: Overall, this study identified four new potential prebiotic substrates that exhibit different modulatory effects at two different concentrations that cause in vitro multi-species oral biofilms to become more host-compatible.

Single DNase or Proteinase Treatment Induces Change in Composition and Structural Integrity of Multispecies Oral Biofilms

Biofilm virulence is mainly based on its bacterial cell surrounding biofilm matrix, which contains a scaffold of exopolysaccharides, carbohydrates, proteins, lipids, and nucleic acids. Targeting these nucleid acids or proteins could enable an efficient biofilm control. Therefore, the study aimed to test the effect of deoxyribonuclease I (DNase I) and proteinase K on oral biofilms. Six-species biofilms (Streptococcus mutans, Streptococcus oralis, Actinomyces oris, Fusobacterium nucleatum, Veillonella dispar, and Candida albicans) were exposed to DNase I (0.001 mg/mL, 0.002 mg/mL) or proteinase K (0.05 mg/mL, 0.1 mg/mL) for 1 h during biofilm formation. After 64 h, biofilms were harvested, quantified by culture analysis and visualized by image analysis using CLSM (confocal laser scanning microscopy). Statistical analysis was performed by ANOVA, followed by the Tukey test at a 5% significance level. The biofilm treatment with proteinase K induced a significant increase of Logs₁₀ counts in S. mutans and a decrease in C. albicans, while biofilm thickness was reduced from 28.5 μm (control) to 9.07 μm (0.05 mg/mL) and 7.4 μm (0.1 mg/mL). Treatment with DNase I had no effect on the total bacterial growth within the biofilm. Targeting proteins of biofilms by proteinase K are promising adjunctive tool for biofilm control.

The role of mechanical control of biofilm in the salivary pH after sucrose exposure in children with early childhood caries

This quasi-experimental study sought to investigate if the mechanical control of biofilm (3-times-a-day) modifies the saliva’s ability to buffer the oral environment after 20% sucrose rinse (SR_20%) in children with early childhood caries (ECC). Here, SR_20% reduced the saliva’s pH in both groups and the mechanical control of biofilm had a greater effect on this parameter after SR_20% in CF children. The mechanical control of biofilm evidenced a higher buffering capacity in CF children before SR_20%, which was not observed after SR_20%. Otherwise, the absence of mechanical control of biofilm showed that buffering capacity was comparable in the two groups before SR_20%, whereas after SR_20% the saliva’s buffering capacity of CF children was higher than ECC children. When biofilm was mechanically controlled, carbonic anhydrase VI activity did not change after SR_20% whereas the absence of mechanical control of biofilm reduced this enzyme activity after SR_20%. In conclusion, the mechanical control of biofilm did not change saliva’s ability to buffer the oral environment after SR_20% in children with ECC. On the other hand, CF children appeared to regulate more effectively the saliva’s pH than ECC children while the absence of mechanical control of biofilm mediated their pH-modifying ability after SR_20%.

Role of the oral microbiome, metabolic pathways, and novel diagnostic tools in intra-oral halitosis: a comprehensive update

Halitosis or oral malodor is one of the most common reasons for the patients' visit to the dental clinic, ranking behind only dental caries and periodontitis. In the present times, where social and professional communications are becoming unavoidable, halitosis has become a concern of growing importance. Oral malodor mostly develops due to the putrefaction of substrates by the indigenous bacterial populations. Although culture-based studies have provided adequate information on halitosis, the high throughput omics technologies have amplified the resolution at which oral microbial community can be examined and has led to the detection of a broader range of taxa associated with intra-oral halitosis (IOH). These microorganisms are regulated by the interactions of their ecological processes. Thus to develop effective treatment strategies, it is important to understand the microbial basis of halitosis. In the current review, we provide an update on IOH in context to the role of the oral microbiome, metabolic pathways involved, and novel diagnostic tools, including breathomics. Understanding oral microbiota associated with halitosis from a broader ecological perspective can provide novel insights into one's oral and systemic health. Such information can pave the way for the emergence of diagnostic tools that can revolutionize the early detection of halitosis and various associated medical conditions.

Dynamic Alterations of Oral Microbiota Related to Halitosis in Preschool Children

Objective

This longitudinal study was aimed to evaluate the dynamic shift in oral microbiota during the process of halitosis progression among preschool children.

Methods

The oral examinations, questionnaires and tongue coating specimens were collected at the baseline and 12-month follow-up. All children were oral healthy at the enrollment. At the 12-month follow-up, children who developed halitosis were included to the halitosis group (n = 10). While children who matched the age, gender, kindergarten and without halitosis were included to the control group (n = 10). 16S rRNA gene sequencing was used to reveal the shift of the tongue coating microbiome in these children during the 12- month period with the Human Oral Microbiome Database.

Results

A remarkable shift in relative abundance of specific bacteria was observed prior to halitosis development. The principal coordinates and alpha diversity analyses revealed different shifting patterns of halitosis and the healthy participants’ microbiome structures and bacterial diversity over the 12-month follow-up. Both groups showed variable microbiota community structures before the onset of halitosis. Halitosis-enriched species Prevotella melaninogenica, Actinomyces sp._HMT_180 and Saccharibacteria TM7_G-1_bacterium_HMT_352 were finally selected as biomarkers in the halitosis-onset prediction model after screening, with a prediction accuracy of 91.7%.

Conclusions

The microbiome composition and relative abundance of the tongue coatings in the halitosis and control groups remarkably differed, even prior to the onset of the clinical manifestations of halitosis. The halitosis prediction model constructed on the basis of tongue coating microbiome biomarkers indicated the microbial shifts before the halitosis onset. Therefore, this can be considered for the timely detection and intervention of halitosis in children.

Quantification and gene expression of Lactobacillus casei group species associated with dentinal lesions in early childhood caries

Background

Considering that the Lactobacillus casei group is strongly associated with caries progression, the use of lactobacilli as probiotics must be balanced due to their possible involvement in dental caries.

Objective

This study aimed to detect and quantify L. paracasei, L. rhamnosus, and L. casei group species in the active and arrested dentinal lesions of preschoolers. It also aimed to determine the expression profiles of lactobacilli genes related to adhesion, extracellular polymeric substance regulation, and pyruvate oxidation.

Methods

Total ribonucleic acid (RNA) was extracted from dentinal lesion samples (25 active, 13 arrested) of children between 2 and 5 years of age. The samples were converted to complementary deoxyribonucleic acid (cDNA), and quantitative polymerase chain reaction (qPCR) analyses were performed to quantify and determine the relative abundance (measured by percentage of total bacteria) of L. paracasei, L. rhamnosus, and L. casei group species. The expression profiles of L. paracasei/casei genes (spaC and spxB) and L. rhamnosus genes (spaE and wzb) were assessed. The Student t-test and the Mann-Whitney U test were used for comparisons.

Results

The L. casei group species were found to be part of the viable microbial community in dentinal caries. L. paracasei (p = 0.001), L. rhamnosus (p = 0.022), and L. casei (p = 0.004) group species were abundant in the active dentinal lesions compared to the arrested dentinal lesions. Only the wzb gene (p = 0.006) exhibited a statistically significant difference between the active and arrested lesions in terms of its expression profile; it was expressed to a higher extent in the active dentinal lesions.

Conclusions

The L. casei group species presented in large numbers in the active dentinal caries lesions, indicating that these microorganisms are related to caries activity, and the wzb gene may play an important role in caries progression.

Molecular Strategies Underlying Porphyromonas gingivalis Virulence

The anaerobic Gram-negative bacterium Porphyromonas gingivalis is considered the keystone of periodontitis diseases, a set of inflammatory conditions that affects the tissues surrounding the teeth. In the recent years, the major virulence factors exploited by P. gingivalis have been identified and characterized, including a cocktail of toxins, mainly proteases called gingipains, which promote gingival tissue invasion. These effectors use the Sec pathway to cross the inner membrane and are then recruited and transported across the outer membrane by the type IX secretion system (T9SS). In P. gingivalis, most secreted effectors are attached to anionic lipopolysaccharides (A-LPS), and hence form a virulence coat at the cell surface. P. gingivalis produces additional virulence factors to evade host immune responses, such as capsular polysaccharide, fimbriae and outer membrane vesicles. In addition to periodontitis, it is proposed that this broad repertoire of virulence factors enable P. gingivalis to be involved in diverse human diseases such as rheumatoid arthritis, and neurodegenerative, Alzheimer, and cardiovascular disorders. Here, we review the major virulence determinants of P. gingivalis and discuss future directions to better understand their mechanisms of action.

Antimicrobial effects in oral microenvironments by a novel herbal toothpaste

Objective

This clinical study compared the antibacterial effects after brushing with a novel herbal toothpaste incorporating zinc [test] to a control fluoride toothpaste on anaerobic organisms, gram-negative bacteria and malodor bacteria of dental plaque, tongue scrapings and cheek surfaces.

Methods

This double-blind, two-cell study enrolled 44 adults [age range 19–63 years]. Subjects completed a 1-week washout and provided baseline oral samples i.e. dental plaque, tongue and cheek scrapings for microbiological analysis. Diluted samples for microbiological analyses were plated on agar to enumerate anaerobic organisms, gram-negative bacteria and malodor bacteria representing functional groups of organisms. Subjects were randomized to brush their teeth with either the test or control with the first brushing conducted under supervision in the dental clinic. Post-treatment samples were collected 12 h after 21 day hygiene with assigned toothpaste. After providing these samples, subjects brushed in the dental clinic with additional samples collected 4 h after brushing. Statistical analyses were conducted separately for each organism collected from each oral niche by t-test for within-treatment assessments and analysis of covariance (ANCOVA) for between-treatment comparisons.

Results

Treatment groups demonstrated no significant differences at baseline for anaerobic organisms, gram-negative bacteria and malodor bacteria in any oral niche (p > 0.05). The test demonstrated reductions between 42 and 68% for anaerobic bacteria in oral niches, 12 h after brushing with reductions increasing to 46–80%, 4 h after brushing. Similarly, the test demonstrated reductions between 49 and 61% for gram-negative bacteria of oral niches that increased to 54–69% at the 4 h post-brushing evaluation. Reductions in malodor organisms of 22–42% were noted 12 h after brushing that increased to 60–72%, 4 h after brushing.

Conclusions

In comparison to control, brushing with a novel herbal toothpaste demonstrated significant reductions in functional bacterial groups from distinct oral niches 12 h after brushing with additional microbial reductions 4 h after brushing.

Evidence for Proline Utilization by Oral Bacterial Biofilms Grown in Saliva

Within the mouth bacteria are starved of saccharides as their main nutrient source between meals and it is unclear what drives their metabolism. Previously oral in vitro biofilms grown in saliva have shown proteolytic degradation of salivary proteins and increased extracellular proline. Although arginine and glucose have been shown before to have an effect on oral biofilm growth and activity, there is limited evidence for proline. Nuclear magnetic resonance (NMR) spectroscopy was used to identify extracellular metabolites produced by bacteria in oral biofilms grown on hydroxyapatite discs. Biofilms were inoculated with stimulated whole mouth saliva and then grown for 7 days using sterilized stimulated whole mouth saliva supplemented with proline, arginine or glucose as a growth-medium. Overall proline had a beneficial effect on biofilm growth-with significantly fewer dead bacteria present by biomass and surface area of the biofilms (p < 0.05). Where arginine and glucose significantly increased and decreased pH, respectively, the pH of proline supplemented biofilms remained neutral at pH 7.3-7.5. SDS-polyacrylamide gel electrophoresis of the spent saliva from proline and arginine supplemented biofilms showed inhibition of salivary protein degradation of immature biofilms. NMR analysis of the spent saliva revealed that proline supplemented biofilms were metabolically similar to unsupplemented biofilms, but these biofilms actively metabolized proline to 5-aminopentanoate, butyrate and propionate, and actively utilized glycine. This study shows that in a nutrient limited environment, proline has a beneficial effect on in vitro oral biofilms grown from a saliva inoculum.

Propionate and Alzheimer's Disease

Propionate, a short-chain fatty acid, serves important roles in the human body. However, our review of the current literature suggests that under certain conditions, excess levels of propionate may play a role in Alzheimer's disease (AD). The cause of the excessive levels of propionate may be related to the Bacteroidetes phylum, which are the primary producers of propionate in the human gut. Studies have shown that the relative abundance of the Bacteroidetes phylum is significantly increased in older adults. Other studies have shown that levels of the Bacteroidetes phylum are increased in persons with AD. Studies on the diet, medication use, and propionate metabolism offer additional potential causes. There are many different mechanisms by which excess levels of propionate may lead to AD, such as hyperammonemia. These mechanisms offer potential points for intervention.

Aroma release during wine consumption: Factors and analytical approaches

During wine consumption, aroma compounds are released from the wine matrix and are transported to the olfactory receptor in vivo, leading to retronasal perception which can affect consumer acceptance. During this process, in addition to the influence of the wine matrix compositions, some physiological factors can significantly influence aroma release leading to altered concentrations of the aroma compounds that reach the receptors. Therefore, this review is focused on the impact of multiple factors, including the physiology and wine matrix, on the aroma released during wine tasting. Moreover, to reflect the pattern of volatiles that reach the olfactory receptors during wine consumption, some analytical approaches have been described for in vitro and in vivo conditions.

Evaluation of Saliva Stability for NMR Metabolomics: Collection and Handling Protocols

Maintaining a salivary metabolic profile upon sample collection and preparation is determinant in metabolomics. Nuclear magnetic resonance (NMR) spectroscopy was used to identify metabolite changes during short-term storage, at room temperature (RT)/4 °C/-20 °C, and after sample preparation, at RT/4 °C (mimicking typical clinical/laboratory settings). Interestingly, significant metabolic inter-individual and inter-day variability were noted, probably determining sample stability to some extent. After collection, no changes were noted at -20 °C (at least for 4 weeks). RT storage induced decreases in methylated macromolecules (6 h); lactate (8 h); alanine (12 h); galactose, hypoxanthine, pyruvate (24 h); sarcosine, betaine, choline, N-acetyl-glycoproteins (48 h), while acetate increased (48 h). Less, but different, changes were observed at 4 °C, suggesting different oral and microbial status at different temperatures (with a possible contribution from inter-individual and inter-day variability), and identifying galactose, hypoxanthine, and possibly, choline esters, as potential general stability indicators. After preparation, addition of NaN3 did not impact significantly on saliva stabilization, neither at RT nor at 4 °C, although its absence was accompanied by slight increases in fucose (6.5 h) and proline (8 h) at RT, and in xylose (24 h) at 4 °C. The putative metabolic origins of the above variations are discussed, with basis on the salivary microbiome. In summary, after collection, saliva can be stored at RT/4 °C for up to 6 h and at -20 °C for at least 4 weeks. Upon preparation for NMR analysis, samples are highly stable at 25 °C up to 8 h and at 4 °C up to 48 h, with NaN3 addition preventing possible early changes in fucose, proline (6-8 h), and xylose (24 h) levels.

Antibacterial effect of a brominated self-etch adhesive on carious dentin - An in vivo study

OBJECTIVES

This in vivo study compared the antibacterial effect of a self-etch adhesive with and without the brominated monomer 12-methacryloyloxydodecyl-pyridinium bromide (MDPB) on carious dentin after selective caries removal.

METHODS

10 patients showing deep primary carious lesions at two posterior teeth without pulpal symptoms were included. At visit I, carious tissue was selectively removed and carious dentin was sampled with a sterile roundbur (Komet No. 18). One cavity was restored with composite (SDR, Ceram X; DENTSPLY DeTrey) using an MDPB-containing self-etch adhesive (Clearfil Protect Bond, Kuraray Noritake; PB). The other restoration served as a control (Clearfil SE Bond II, Kuraray Noritake; SE). At visit II after 8 weeks, carious dentin was sampled again. Bacterial growth in carious dentin was differentiated using microbial cultivation. Bacterial DNA from intact cells and cell-free DNA were quantified using 16S rRNA gene-based real-time PCR and the microbial community composition was analyzed by amplicon deep-sequencing. Wilcoxon test was applied for statistical analysis.

RESULTS

Both treatments showed a decrease of intact bacterial cells in carious dentin at visit II compared to visit I (PB: visit I: 1.1*10⁶, visit II: 1.7*10⁵ (p = 0.03); SE: visit I: 1.1*10⁷, visit II = 2.4*10⁵ (p = 0.002)). No statistically significant reduction of cell-free bacterial DNA was detected (PB: visit I: 6.1*10⁵, visit II: 1.6*10⁵ (p = 0.08); SE: visit I: 5.3*10⁵, visit II: 2.9*10⁵ (p = 0.10)). The decrease of intact cell-derived (p = 0.371) and cell-free DNA (p = 0.455) did not differ significantly between PB and SE. Lactobacillus was most abundant within the microbial community at both visits. Alpha-diversity was not affected by treatment and samples showed high intra- and interindividual diversity.

CONCLUSION AND CLINICAL SIGNIFICANCE

Both self-etch adhesives have an antibacterial effect due to a decrease of bacterial DNA after selective caries removal. However, the results do not reveal any additional antibacterial effect by MDPB. The study is registered with the German Clinical Trials Register (DRKS00011532).

Alternation of supragingival microbiome in patients with cirrhosis of different Child-Pugh scores

OBJECTIVES

The aim of this study was to analyze the differences in the taxonomy and functions of oral microbiome between patients with and without cirrhosis.

MATERIALS AND METHODS

In this study, V4-16S rDNA amplicon sequencing was used to compare the difference of supragingival microbiome in 42 patients and 12 healthy individuals.

RESULTS

Overall, 3,223,529 clean reads were generated, with an average of 59,694 ± 1,548 clean reads per sample. A total of 30 phyla, 78 classes, 116 orders, 167 families, 228 genera, and 114 species were detected in the 54 samples. The differences were detected among groups at each taxonomical level. Functional prediction showed that patients with cirrhosis had a significant higher proportion of the genes associated with carbohydrate transport and metabolism, defense mechanisms, infectious diseases, membrane transport, etc. compared with healthy individuals (p < .05).

CONCLUSIONS

In conclusion, significant differences were observed in compositions and predictive functions of the supragingival microbiome between patients with cirrhosis and that in healthy people. These findings will provide a new insight into the understanding of pathogenesis, diagnosis, prognosis, and therapy of cirrhosis.

The Effect of Lactobacillus salivarius SGL03 on Clinical and Microbiological Parameters in Periodontal Patients

The destruction of periodontal tissues during periodontitis is the result of the immune-inflammatory reactions to the bacteria of dental biofilm. Probiotics may reduce dysbiosis by the modification of the dental microbiome, which can influence the immune-inflammatory mechanisms. The aim of this study was to estimate the clinical and microbiological parameters, before and after 30 days of application of the dietary supplement containing Lactobacillus salivarius SGL03 or placebo. The study was conducted in 51 patients with stage I or II periodontitis during the maintenance phase of treatment. The clinical parameters and the number of colony forming units (CFU) of bacteria in supragingival plaque were assessed before and after 30 days of the oral once daily administration of the dietary supplement in the form of suspension containing L. salivarius SGL03 or placebo. There were no changes in the PI scores between and within the groups. The value of BOP decreased in both groups. In the study group the significant reduction of the mean pocket depth was revealed (from 2.5 to 2.42, p = 0,027) but without the difference between the groups. There were no significant changes in the number of bacteria within the groups. In the control, but not the study group, positive correlations were observed between the clinical parameters (variables) and the number of bacteria. The use of the dietary supplement containing L. salivarius SGL03 may reduce pocket depth despite the lack of changes in other clinical parameters and the number of bacteria in supragingival plaque.

Analysis of relative bacterial activity and lactate dehydrogenase gene expression of caries-associated bacteria in a site-specific natural biofilm: an ex vivo study

Objectives

Detecting bacterial activity is considered a promising approach to monitor shifts from symbiosis to dysbiosis in oral microbiome. The present study aimed at investigating both the relative bacterial activity and the lactate dehydrogenase (ldh) gene expression of caries-associated bacteria in a site-specific natural biofilm.

Material and methods

Sixty subjects (age, mean ± SE: 30.1 ± 1.4) were allocated to two groups: caries-free subjects (CF) or caries-active subjects (CA). CF presented one sound surface (CFS, n = 30). CA presented two donor sites: a cavitated caries lesion (CAC, n = 30) and a sound reference surface (CAS, n = 30). Real-time quantitative PCR (q-PCR) on species or genus level and total bacteria was performed targeting the 16S gene, the 16S rRNA, the ldh gene, and the ldh mRNA (increasing 16S ribosomal RNA copy numbers can function as an indicator of increased energy metabolism). As the 16S rRNA abundance represents the number of ribosomes, while the 16S gene abundance represents the number of genomes, the quotient of the relative abundances functions as a measure for the relative bacterial activity (%).

Results

Both lactobacilli and S. mutans showed the highest relative bacterial activity in CAC ((mean ± SE) 218 ± 60% and 61 ± 16%, respectively) and the lowest values for both sound reference surfaces (69 ± 48%; 8 ± 3%). Significant differences were found between CAC and CAS as well as between CAC and CFS for both lactobacilli and S. mutans (p < 0.05). The ldh gene expression of lactobacilli and S. mutans only showed moderate values in CAC (1.90E+03 ± 2.11E+03; 2.08E+04 ± 4.44E+04 transcripts/μl) and CFS (2.04E+03 ± 2.74E+03; 8.16E+03 ± 6.64E+03 transcripts/μl); consequently no significant differences were detected.

Conclusion and clinical relevance

Caries-associated bacteria (lactobacilli and S. mutans) showed the highest relative bacterial activity in plaque of cavitated lesions, the lowest in sound surfaces, allowing the detection of a significant activity shift in health and disease for caries-active patients. However, no significant differences in ldh gene expression could be determined.

Establishment of microcosm biofilm models that reproduce a cariogenic diet intake

Biofilms were developed from human saliva on bovine enamel discs in four experimental conditions to investigate dental caries development: feast and famine (M1), abundance and scarcity (M2), three meals daily (M3), and three meals plus two snacks daily (M4). The main difference between these models was the diet for microbial growth. The evaluations included verifying the pH of the spent culture media and analyzing the enamel discs for demineralization (microhardness and roughness) and biofilms (biomass, viable populations of mutans streptococci, and total microbiota). Two major behaviors were observed: M1 and M2 promoted an acidic environment, while M3 and M4 maintained pH values closer to neutral. The demineralization process was slower in the neutral groups but more pronounced in M3, while a greater increase in microbiota and biomass was observed over time for both neutral groups. Thus, the M3 model was better at mimicking the oral environment that leads to demineralization.

Bacteria associated with periodontal disease are also increased in health

Background

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

Material and Methods

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

Results

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

Conclusions

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

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

Taxonomic profiling and functional characterization of the healthy human oral bacterial microbiome from the north Indian urban sub-population

Poor oral health has broad consequences that can be seen at personal as well as societal levels, especially in developing countries like India. We have limited information on the healthy oral cavity's inhabitant microorganisms that play a crucial role in overall oral health. In a comprehensive culture-independent approach, the bacterial composition of healthy human oral cavities was determined from a sub-population of northern India. During this study, 20 mouthwash-derived metagenomes were explored for identifying bacterial diversity using the 16S rRNA hypervariable V3 region with the MiSeq Illumina platform. On the taxonomy assignment of operational taxonomic units (OTUs), 20 assigned phyla and 162 genera were recovered among the participants. The mean relative abundance revealed that Streptococcus was the dominant genera among the participants. However, at inter-individual analysis, Neisseria and Haemophilus exhibited first-order dominance among five and three healthy individuals, respectively. Correlation studies indicate that Streptococcus shares a strong relationship with Rothia, Corynebacterium, Prevotella, and Veillonella, whereas it was negatively correlated with Neisseria, Aggregatibacter, Porphyromonas, and Fusobacteria like Gram-negative bacteria. Bacterial diversity showed insignificant differences at the level of age and gender within and between the participants. The results support several of the major findings of previous reports on the healthy oral microbiome of the Indian population, however, the present investigation further illustrates that demographic region leaves an impact on overall bacterial composition. The study will assist in a better understanding of the oral microbiome from region-specific Indian population that was otherwise highly under-represented.

Nitrite-producing oral microbiome in adults and children

Recently, it was suggested that the nitrite (NO₂^-) produced from NO₃^- by oral bacteria might contribute to oral and general health. Therefore, we aimed to clarify the detailed information about the bacterial NO₂-production in the oral biofilm. Dental plaque and tongue-coating samples were collected, then the NO₂-producing activity was measured. Furthermore, the composition of the NO₂^--producing bacterial population were identified using the Griess reagent-containing agar overlay method and molecular biological method. NO₂^--producing activity per mg wet weight varied among individuals but was higher in dental plaque. Additionally, anaerobic bacteria exhibited higher numbers of NO₂^--producing bacteria, except in the adults' dental plaque. The proportion of NO₂^--producing bacteria also varied among individuals, but a positive correlation was found between NO₂^--producing activity and the number of NO₂^--producing bacteria, especially in dental plaque. Overall, the major NO₂^--producing bacteria were identified as Actinomyces, Schaalia, Veillonella and Neisseria. Furthermore, Rothia was specifically detected in the tongue coatings of children. These results suggest that dental plaque has higher NO₂^--producing activity and that this activity depends not on the presence of specific bacteria or the bacterial compositions, but on the number of NO₂^--producing bacteria, although interindividual differences were detected.

Nitrite Production from Nitrate and Its Link with Lactate Metabolism in Oral Veillonella spp

Veillonella species are among the major anaerobes in the oral cavity and are frequently detected in both caries lesions and healthy oral microbiomes. They possess the ability to utilize lactate and convert nitrate (NO₃ ^-) into nitrite (NO₂ ^-). Recently, interest in NO₂ ^- has increased rapidly because of its beneficial effects on oral and general health; i.e., it inhibits the growth and metabolism of oral pathogenic bacteria, such as Streptococcus mutans, and lowers systemic blood pressure. However, there is only limited information about the biochemical characteristics of NO₂ ^- production by Veillonella species. We found that NO₃ ^- did not inhibit the growth of Veillonella atypica or Veillonella parvula, and it inhibited the growth of Streptococcus mutans only at a high concentration (100 mM). However, NO₂ ^- inhibited the growth of Streptococcus mutans at a low concentration (0.5 mM), while a higher concentration of NO₂ ^- (20 mM) was needed to inhibit the growth of Veillonella species. NO₂ ^- production by Veillonella species was increased by environmental factors (lactate, acidic pH, and anaerobic conditions) and growth conditions (the presence of NO₃ ^- or NO₂ ^-) and was linked to anaerobic lactate metabolism. A stoichiometric evaluation revealed that NO₃ ^- is reduced to NO₂ ^- by accepting reducing power derived from the oxidization of lactate. These findings suggest that the biochemical characteristics of NO₂ ^- production from NO₃ ^- and its linkage with lactate metabolism in oral Veillonella species may play a key role in maintaining good oral and general health.IMPORTANCE The prevalence of dental caries is still high around the world. Dental caries is initiated when the teeth are exposed to acid, such as lactic acid, produced via carbohydrate metabolism by acidogenic microorganisms. Veillonella species, which are among the major oral microorganisms, are considered to be beneficial bacteria due to their ability to convert lactic acid to weaker acids and to produce NO₂ ^- from NO₃ ^-, which is thought to be good for both oral and general health. Therefore, it is clear that there is a need to elucidate the biochemical characteristics of NO₂ ^- production in Veillonella species. The significance of our research is that we have found that lactate metabolism is linked to NO₂ ^- production by Veillonella species in the environment found in the oral cavity. This study suggests that Veillonella species are potential candidates for maintaining oral and general health.