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

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.

Phenotype and Tissue Residency of Lymphocytes in the Murine Oral Mucosa

The oral mucosa is a critical barrier tissue that harbors a series of distinct immune cell subsets. Immune surveillance in the oral mucosa is important for both local and systemic immunity because the oral cavity is a heavily utilized route of pathogen entry and also serves as site of pathogen propagation. Nonetheless, composition and phenotype of the lymphocyte pool in the oral mucosa have remained poorly characterized. Utilizing a newly established protocol for mucosal immune cell isolation, here, we report that the oral mucosa features a unique cellular composition of immune cells, which differed not only from secondary lymphoid organs but also from mucosal tissues in the gut and lung. We observed profound accumulation of CD11b⁺Ly6C^lo monocytes in the oral mucosa that were maintained independently of T- and B-lymphocytes. Unlike the gut mucosa, the oral mucosa neither contained CD8αα T cells nor was it enriched for CD103⁺CD69⁺ tissue-resident memory CD8 T cells. In fact, a major fraction of T cells circulated and trafficked through the mucosa as revealed by treatment with the S1P1 receptor antagonist, FTY720, a potent inhibitor of lymphocyte migration. Collectively, these results provide a comprehensive picture of immune cells in the oral mucosa as an active site of lymphocyte recruitment and surveillance.

The oral cavity microbiota: between health, oral disease, and cancers of the aerodigestive tract

Many studies show that the human microbiome plays a critical role in the chronic pathologies of obesity, inflammatory bowel diseases, and diabetes. More recently, the interaction between cancer and the microbiome has been highlighted. Most studies have focused on the gut microbiota because it represents the most extensive bacterial community, and the body of evidence correlating it with gut syndromes is increasing. However, in the strict sense, the gastrointestinal (GI) tract begins in the oral cavity, and special attention should be paid to the specific flora of this cavity. This study reviewed the current knowledge about the various microbial ecosystems of the upper part of the GI tract and discussed their potential link to carcinogenesis. The overall composition of the microbial communities, as well as the presence or absence of "key species", in relation to carcinogenesis is addressed. Alterations in the oral microbiota can potentially be used to predict the risk of cancer. Molecular advances and the further monitoring of the microbiota will increase our understanding of the role of the microbiota in carcinogenesis and open new perspectives for future therapeutic and prophylactic modalities.

Amino acid composition and amino acid-metabolic network in supragingival plaque

Dental plaque metabolizes both carbohydrates and amino acids. The former can be degraded to acids mainly, while the latter can be degraded to various metabolites, including ammonia, acids and amines, and associated with acid-neutralization, oral malodor and tissue inflammation. However, amino acid metabolism in dental plaque is still unclear. This study aimed to elucidate what kinds of amino acids are available as metabolic substrates and how the amino acids are metabolized in supragingival plaque, by a metabolome analysis. Amino acids and the related metabolites in supragingival plaque were extracted and quantified comprehensively by CE-TOFMS. Plaque samples were also incubated with amino acids, and the amounts of ammonia and amino acid-related metabolites were measured. The concentration of glutamate was the highest in supragingival plaque, while the ammonia-production was the highest from glutamine. The obtained metabolome profile revealed that amino acids are degraded through various metabolic pathways, including deamination, decarboxylation and transamination and that these metabolic systems may link each other, as well as with carbohydrate metabolic pathways in dental plaque ecosystem. Moreover, glutamine and glutamate might be the main source of ammonia production, as well as arginine, and contribute to pH-homeostasis and counteraction to acid-induced demineralization in supragingival plaque.

The use of bacteriophages to biocontrol oral biofilms

Infections induced by oral biofilms include caries, as well as periodontal, and peri-implant disease, and may influence quality of life, systemic health, and expenditure. As bacterial biofilms are highly resistant and resilient to conventional antibacterial therapy, it has been difficult to combat these infections. An innovative alternative to the biocontrol of oral biofilms could be to use bacteriophages or phages, the viruses of bacteria, which are specific, non-toxic, self-proliferating, and can penetrate into biofilms. Phages for Actinomyces naeslundii, Aggregatibacter actinomycetemcomitans, Enterococcus faecalis, Fusobacterium nucleatum, Lactobacillus spp., Neisseria spp., Streptococcus spp., and Veillonella spp. have been isolated and characterised. Recombinant phage enzymes (lysins) have been shown to lyse A. naeslundii and Streptococcus spp. However, only a tiny fraction of available phages and their lysins have been explored so far. The unique properties of phages and their lysins make them promising but challenging antimicrobials. The genetics and biology of phages have to be further explored in order to determine the most effective way of applying them. Studying the effect of phages and lysins on multispecies biofilms should pave the way for microbiota engineering and microbiota-based therapy.

On the ecosystemic network of saliva in healthy young adults

A dysbiotic state is believed to be a key factor in the onset of oral disease. Although oral diseases have been studied for decades, our understanding of oral health, the boundaries of a healthy oral ecosystem and ecological shift toward dysbiosis is still limited. Here, we present the ecobiological heterogeneity of the salivary ecosystem and relations between the salivary microbiome, salivary metabolome and host-related biochemical salivary parameters in 268 healthy adults after overnight fasting. Gender-specific differences in the microbiome and metabolome were observed and were associated with salivary pH and dietary protein intake. Our analysis grouped the individuals into five microbiome and four metabolome-based clusters that significantly related to biochemical parameters of saliva. Low salivary pH and high lysozyme activity were associated with high proportions of streptococcal phylotypes and increased membrane-lipid degradation products. Samples with high salivary pH displayed increased chitinase activity, higher abundance of Veillonella and Prevotella species and higher levels of amino acid fermentation products, suggesting proteolytic adaptation. An over-specialization toward either a proteolytic or a saccharolytic ecotype may indicate a shift toward a dysbiotic state. Their prognostic value and the degree to which these ecotypes are related to increased disease risk remains to be determined.

The Microbiome and Blood Pressure: Can Microbes Regulate Our Blood Pressure?

The surfaces of the human body are heavily populated by a highly diverse microbial ecosystem termed the microbiota. The largest and richest among these highly heterogeneous populations of microbes is the gut microbiota. The collection of microbes and their genes, called the microbiome, has been studied intensely through the past few years using novel metagenomics, metatranscriptomics, and metabolomics approaches. This has enhanced our understanding of how the microbiome affects our metabolic, immunologic, neurologic, and endocrine homeostasis. Hypertension is a leading cause of cardiovascular disease worldwide; it contributes to stroke, heart disease, kidney failure, premature death, and disability. Recently, studies in humans and animals have shown that alterations in microbiota and its metabolites are associated with hypertension and atherosclerosis. In this review, we compile the recent findings and hypotheses describing the interplay between the microbiome and blood pressure, and we highlight some prospects by which utilization of microbiome-related techniques may be incorporated to better understand the pathophysiology and treatment of hypertension.

The dental calculus metabolome in modern and historic samples

INTRODUCTION

Dental calculus is a mineralized microbial dental plaque biofilm that forms throughout life by precipitation of salivary calcium salts. Successive cycles of dental plaque growth and calcification make it an unusually well-preserved, long-term record of host-microbial interaction in the archaeological record. Recent studies have confirmed the survival of authentic ancient DNA and proteins within historic and prehistoric dental calculus, making it a promising substrate for investigating oral microbiome evolution via direct measurement and comparison of modern and ancient specimens.

OBJECTIVE

We present the first comprehensive characterization of the human dental calculus metabolome using a multi-platform approach.

METHODS

Ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) quantified 285 metabolites in modern and historic (200 years old) dental calculus, including metabolites of drug and dietary origin. A subset of historic samples was additionally analyzed by high-resolution gas chromatography-MS (GC-MS) and UPLC-MS/MS for further characterization of metabolites and lipids. Metabolite profiles of modern and historic calculus were compared to identify patterns of persistence and loss.

RESULTS

Dipeptides, free amino acids, free nucleotides, and carbohydrates substantially decrease in abundance and ubiquity in archaeological samples, with some exceptions. Lipids generally persist, and saturated and mono-unsaturated medium and long chain fatty acids appear to be well-preserved, while metabolic derivatives related to oxidation and chemical degradation are found at higher levels in archaeological dental calculus than fresh samples.

CONCLUSIONS

The results of this study indicate that certain metabolite classes have higher potential for recovery over long time scales and may serve as appropriate targets for oral microbiome evolutionary studies.

Annual review of selected scientific literature: Report of the committee on scientific investigation of the American Academy of Restorative Dentistry

STATEMENT OF PROBLEM

It is clear the contemporary dentist is confronted with a blizzard of information regarding materials and techniques from journal articles, advertisements, newsletters, the internet, and continuing education events. While some of that information is sound and helpful, much of it is misleading at best.

PURPOSE

This review identifies and discusses the most important scientific findings regarding outcomes of dental treatment to assist the practitioner in making evidence-based choices. This review was conducted to assist the busy dentist in keeping abreast of the latest scientific information regarding the clinical practice of dentistry.

MATERIAL AND METHODS

Each of the authors, who are considered experts in their disciplines, was asked to peruse the scientific literature published in 2015 in their discipline and review the articles for important information that may have an impact on treatment decisions. Comments on experimental methodology, statistical evaluation, and overall validity of the conclusions are included in many of the reviews.

RESULTS

The reviews are not meant to stand alone but are intended to inform the interested reader about what has been discovered in the past year. The readers are then invited to go to the source if they wish more detail.

CONCLUSIONS

Analysis of the scientific literature published in 2015 is divided into 7 sections, dental materials, periodontics, prosthodontics, occlusion and temporomandibular disorders, sleep-disordered breathing, cariology, and implant dentistry.

Oral Bacterial Acid-Base Metabolism in Caries Screening: A Proof-Of-Concept Study

The objective of this cross-sectional study was to clinically validate an array of biochemical tests for oral acid/alkali generation as caries screening instruments. 185 adult subjects (mean 33.6±10.6 years) were examined clinically for dental caries using the ICDAS criteria. Bitewing radiographs were used to confirm interproximal surfaces of posterior teeth. For the purposes of this study, subjects were classified as "caries-active" if they had at least one untreated caries lesion with ICDAS 4 or higher. Pooled supragingival plaque and unstimulated saliva samples were collected and assayed for pH changes from sucrose and urea metabolism using colorimetric tests. The validity of each test to discriminate between "caries-inactive" and "caries-active" subjects was assessed and compared to a commercial bacteriological caries-screening test using roc regression and logistic regression models. The AUCs of the plaque-urea (PU: 0.59 (0.51, 0.67)), plaque-urea-glucose (PUG: 0.59 (0.51, 0.67)) and saliva-urea-glucose (SUG: 0.59 (0.51, 0.67)) tests did not differ significantly from the bacteriological tests (CRT-mutans: 0.62 (0.54, 0.70); CRT-lactobacillus: 0.63 (0.56, 0.71) (P>0.05), but the plaque-glucose (SG), saliva-glucose (SG), saliva-urea (SU) and saliva-plaque-glucose (SPG) tests had significantly smaller AUCs (P<0.05). The AUCs for the PU, PUG, SUG, and the CRT-mutans tests were higher in subjects who had no existing dental restorations (PU: 0.90 (0.77, 1.04); PUG: 0.90 (0.79, 1.01); SUG: 0.89 (0.69, 1.08); CRT-mutans: 0.90 (0.73, 1.08)). The incorporation of the biochemical tests into a multidimensional bacteriological/psychosocial caries screening model significantly increased its diagnostic values (Se+Sp: 160.6, AUC: 0.846). In conclusion, as a proof of concept, the results of this study indicate that measuring the ability of dental plaque and saliva to metabolize urea together with the ability to generate acid from sugars may have a promising role in caries screening either independently, or as part of a multidimensional biological test.

Occlusal Caries: Biological Approach for Its Diagnosis and Management

The management of occlusal caries still remains a major challenge for researchers as well as for general practitioners. The present paper reviews and discusses the most up-to-date knowledge and evidence of the biological principles guiding diagnosis, risk assessment, and management of the caries process on occlusal surfaces. In addition, it considers the whole spectrum of the caries process on occlusal surfaces, ranging from the molecular ecology of occlusal biofilms to the management of deep occlusal caries lesions. Studies using molecular methods with focus on biofilms in relation to occlusal caries should explore the relationship between the function and the structural composition of these biofilms to understand the role of occlusal biofilms in caries development. State-of-the-art measures to evaluate risk for occlusal caries lesion activity, caries incidence, and progression should include the assessment of the occlusal biofilm and the stage of tooth eruption. Careful clinical examination of non-cavitated lesions, including assessment of the lesion activity status, remains the major tool to determine the immediate treatment need and to follow on the non-operative treatment outcome. Even medium occlusal caries lesions in the permanent dentition may be treated by non-invasive fissure sealing. By extending the criteria for non-invasive treatments, traditional restoration of occlusal surfaces can be postponed or even avoided, and the dental health in children and adolescents can be improved. Selective removal (incomplete) to soft dentin in deep carious lesions has greater success rates than stepwise excavation. Selective (complete) removal to firm dentin has a lower success rate due to increased pulp exposure.

Analysis of Bacterial Activity in Sound and Cariogenic Biofilm: A Pilot in vivo Study

Dental caries is a multifactorial disease with many associated microbial taxa, but only a few are notably contributing to acidogenicity. The ribosome number and the corresponding 16S ribosomal RNA (rRNA) concentration are considered a molecular indicator for general metabolic activity of bacteria, as they are elevated with increased anabolic and catabolic activities. We hypothesize that the activity of aciduric/acidogenic bacterial taxa, reflected by a rise in ribosomal counts, could resolve differences between plaque biofilm from sound surfaces and caries lesions. The included subjects were allocated to two groups: caries-free (CF) or caries-active (CA). CF subjects presented one donor site, namely one sound surface (CFS, n = 10), whereas CA subjects presented two donor sites: a cavitated lesion with an ICDAS score of 5-6 (CAC, n = 13), and a sound reference surface (CAS, n = 13). Four aciduric/acidogenic bacterial taxa (Streptococcus mutans, lactobacilli, Bifidobacterium dentium, and Scardovia wiggsiae) and one asaccharolytic taxon (fusobacteria) as a contrast were selected. 16S rRNA and 16S rRNA genes were quantified by quantitative PCR. Based on these parameters, bacterial and ribosomal counts, as well as relative activities were calculated as the quotient of relative ribosomal abundance and relative genome abundance. Caries-associated bacteria showed the highest relative activity in caries lesions (e.g. lactobacilli CAC: 177.5 ± 46.0%) and lower activities on sound surfaces (e.g. lactobacilli CAS: 96.3 ± 31.5%), whereas asaccharolytic fusobacteria were most active on sound surfaces and less active in caries lesions (CFS: 275.7 ± 171.1%; CAS: 205.8 ± 114.3%; CAC: 51.1 ± 19.0%). Thus, the present study suggests different activity patterns for biofilms from CF and CA individuals.

Metabolic traits of pathogenic streptococci

Invasive and noninvasive diseases caused by facultative pathogenic streptococci depend on their equipment with virulence factors and on their ability to sense and adapt to changing nutrients in different host environments. The knowledge of the principal metabolic mechanisms which allow these bacteria to recognize and utilize nutrients in host habitats is a prerequisite for our understanding of streptococcal pathogenicity and the development of novel control strategies. This review aims to summarize and compare the central carbohydrate metabolic and amino acid biosynthetic pathways of a selected group of streptococcal species, all belonging to the naso-oropharyngeal microbiome in humans and/or animals. We also discuss the urgent need of comprehensive metabolomics approaches for a better understanding of the streptococcal metabolism during host-pathogen interaction.

Ecological Hypothesis of Dentin and Root Caries

Recent advances regarding the caries process indicate that ecological phenomena induced by bacterial acid production tilt the de- and remineralization balance of the dental hard tissues towards demineralization through bacterial acid-induced adaptation and selection within the microbiota - from the dynamic stability stage to the aciduric stage via the acidogenic stage [Takahashi and Nyvad, 2008]. Dentin and root caries can also be partly explained by this hypothesis; however, the fact that these tissues contain a considerable amount of organic material suggests that protein degradation is involved in caries formation. In this review, we compiled relevant histological, biochemical, and microbiological information about dentin/root caries and refined the hypothesis by adding degradation of the organic matrix (the proteolytic stage) to the abovementioned stages. Bacterial acidification not only induces demineralization and exposure of the organic matrix in dentin/root surfaces but also activation of dentin-embedded and salivary matrix metalloproteinases and cathepsins. These phenomena initiate degradation of the demineralized organic matrix in dentin/root surfaces. While a bacterial involvement has never been confirmed in the initial degradation of organic material, the detection of proteolytic/amino acid-degrading bacteria and bacterial metabolites in dentin and root caries suggests a bacterial digestion and metabolism of partly degraded matrix. Moreover, bacterial metabolites might induce pulpitis as an inflammatory/immunomodulatory factor. Root and dentin surfaces are always at risk of becoming demineralized in the oral cavity, and exposed organic materials can be degraded by host-derived proteases contained in saliva and dentin itself. New approaches to the prevention and treatment of root/dentin caries are required.

Metabolomic Studies of Oral Biofilm, Oral Cancer, and Beyond

Oral diseases are known to be closely associated with oral biofilm metabolism, while cancer tissue is reported to possess specific metabolism such as the ‘Warburg effect’. Metabolomics might be a useful method for clarifying the whole metabolic systems that operate in oral biofilm and oral cancer, however, technical limitations have hampered such research. Fortunately, metabolomics techniques have developed rapidly in the past decade, which has helped to solve these difficulties. In vivo metabolomic analyses of the oral biofilm have produced various findings. Some of these findings agreed with the in vitro results obtained in conventional metabolic studies using representative oral bacteria, while others differed markedly from them. Metabolomic analyses of oral cancer tissue not only revealed differences between metabolomic profiles of cancer and normal tissue, but have also suggested a specific metabolic system operates in oral cancer tissue. Saliva contains a variety of metabolites, some of which might be associated with oral or systemic disease; therefore, metabolomics analysis of saliva could be useful for identifying disease-specific biomarkers. Metabolomic analyses of the oral biofilm, oral cancer, and saliva could contribute to the development of accurate diagnostic, techniques, safe and effective treatments, and preventive strategies for oral and systemic diseases.

Dietary nitrate and nitrite: Benefits, risks, and evolving perceptions

Consumers have an illogical relationship with nitrite (and its precursor, nitrate) in food. Despite a long history of use, nitrite was nearly banned from use in foods in the 1970s due to health concerns related to the potential for carcinogenic nitrosamine formation. Changes in meat processing methods reduced those potential risks, and nitrite continued to be used in foods. Since then, two opposing movements continue to shape how consumers view dietary nitrate and nitrite. The discovery of the profound physiological importance of nitric oxide led to the realization that dietary nitrate contributes significantly to the nitrogen reservoir for nitric oxide formation. Numerous clinical studies have also demonstrated beneficial effects from dietary nitrate consumption, especially in vascular and metabolic health. However, the latest wave of consumer sentiment against food additives, the clean-label movement, has renewed consumer fear and avoidance of preservatives, including nitrite. Education is necessary but may not be sufficient to resolve this disconnect in consumer perception.

Influence of the Inoculum Source on the Cariogenicity of in vitro Microcosm Biofilms

This study investigated the cariogenic potential of biofilms originating from different types of inoculum (saliva and dental plaque) from caries-active and caries-free individuals. Ten volunteers were selected from each caries condition for the paired collection of saliva and dental plaque. Microcosm biofilms were grown in triplicate from each inoculum on enamel specimens in 24-well plates under cariogenic challenge. After 10 days, the biofilms were collected for analysis of outcome variables: percentage of surface hardness change (%SHC) and microbiological composition of biofilms. Statistical analysis was performed using the t test, the linear multivariate analysis model and Pearson's correlation coefficients (α = 0.05). A comparative analysis between microbiological baseline data showed higher counts of mutans streptococci in plaque samples within caries-active individuals; a comparative analysis of colony-forming unit (CFU) counts between individuals with different caries status showed higher counts of acid-tolerant microorganisms and mutans streptococci in dental plaque and of acid-tolerant microorganisms in saliva. After 10 days of biofilm growth, the CFU values for total microorganisms, lactobacilli, mutans streptococci and acid-tolerant bacteria, as well as for SHC, were not statistically significant, considering the type of inoculum and caries condition (p > 0.05). A positive correlation was found for %SHC and CFU counts of acid-tolerant bacteria (r = 0.406) and lactobacilli (r = 0.379). Under the limits of this study, the cariogenic potential of biofilms, formed under identical conditions in vitro, is similar, regardless of baseline differences between the source and type of inoculum.

Oral microbiome, periodontitis and risk of head and neck cancer

A wide range of studies has been successfully exploring the association between the human microenvironment, sustained inflammation, and cancer. Growing evidence has then emerged in this field over the past few years. Nevertheless, reliable data addressing the impact of the oral microbiome and periodontitis on the pathogenesis and risk of head and neck malignancies remain scarce. Hence, this communication focuses on briefly discuss the relationship between the oral microbiome, periodontitis and head and neck cancer based on the current understanding of such a disease-associated scenario.