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

The short-term impact of comprehensive caries treatment on the supragingival microbiome of severe early childhood caries

BACKGROUND

Children affected by severe early childhood caries (S-ECC) usually need comprehensive caries treatment due to the extensive of caries. How the oral microbiome changes after caries therapy within the short-term warrant further study.

AIM

This study aimed to investigate the short-term impact of comprehensive caries treatment on the supragingival plaque microbiome of S-ECC children.

DESIGN

Thirty-three children aged 2-4 years with severe caries (dt > 7) were recruited. Comprehensive caries treatment was performed under general anesthesia in one session and included restoration, pulp treatment, extraction, and fluoride application. Supragingival plaque was sampled pre- and 1-month posttreatment. The genomic DNA of the supragingival plaque was extracted, and bacterial 16S ribosomal RNA gene sequencing was performed.

RESULTS

Our data showed that the microbial community evenness significantly decreased posttreatment. Furthermore, comprehensive caries treatment led to more diverse microbial structures among the subjects. The interbacterial interactions reflected by the microbial community's co-occurrence network tended to be less complex posttreatment. Caries treatment increased the relative abundance of Corynebacterium matruchotii, Corynebacterium durum, Actinomyces naeslundii, and Saccharibacteria HMT-347, as well as Aggregatibacter HMT-458 and Haemophilus influenzae. Meanwhile, the relative abundance of Streptococcus mutans, three species from Leptotrichia, Neisseria bacilliformis, and Provotella pallens significantly decreased posttreatment.

CONCLUSION

Our results suggested that comprehensive caries treatment may contribute to the reconstruction of a healthier supragingival microbiome.

Genetically engineered phages and engineered phage-derived enzymes to destroy biofilms of antibiotics resistance bacteria

"An impregnable stronghold where one or more warrior clans can evade enemy attacks" may serve as a description of bacterial biofilm on a smaller level than human conflicts. Consider this hypothetical conflict: who would emerge victorious? The occupants of secure trenches or those carrying out relentless assault? Either faction has the potential for triumph; the defenders will prevail if they can fortify the trench with unwavering resolve, while the assailants will succeed if they can devise innovative means to breach the trench. Hence, bacterial biofilms pose a significant challenge and are formidable adversaries for medical professionals, often leading to the failure of antibiotic treatments in numerous hospital infections. Phage engineering has become the foundation for the targeted enhancement of various phage properties, facilitating the eradication of biofilms. Researchers across the globe have studied the impact of engineered phages and phage-derived enzymes on biofilms formed by difficult-to-treat bacteria. These novel biological agents have shown promising results in addressing biofilm-related challenges. The compilation of research findings highlights the impressive capabilities of engineered phages in combating antibiotic-resistant bacteria, superbugs, and challenging infections. Specifically, these engineered phages exhibit enhanced biofilm destruction, penetration, and prevention capabilities compared to their natural counterparts. Additionally, the engineered enzymes derived from phages demonstrate improved effectiveness in addressing bacterial biofilms. As a result, these novel solutions, which demonstrate high penetration, destruction, and inhibition of biofilms, can be regarded as a viable option for addressing infectious biofilms in the near future.

Epigallocatechin gallate reduces the virulence of cariogenic Streptococcus mutans biofilm by affecting the synthesis of biofilm matrix components

INTRODUCTION

There have been reports on the effects of epigallocatechin gallate (EGCG) against Streptococcus mutans viability and acidogenesis. However, the effects of EGCG on the virulence of S. mutans biofilm development have yet to be fully investigated using validated cariogenic biofilm models.

OBJECTIVE

Thus, this study aimed to evaluate the effects of EGCG on S. mutans biofilm virulence using a validated cariogenic model and clinically relevant treatment regimens, twice a day for 1.5 min.

METHODS

Effects of EGCG on bacterial viability, polyssacharide synthesis and biofilm acidogenesis were evaluated. The morphology and 3D structure of the biofilms were evaluated by scanning electron (SEM) and confocal laser scanning microscopy, respectively.

RESULTS

No significant change in S. mutans viability or culture medium pH were observed when comparing EGCG-treated and NaCl-treated biofilms. EGCG significantly reduced the accumulation of soluble and insoluble polysaccharides, resulting in the formation of a biofilm with interspaced exopolysaccharide-microcolony complexes unevenly distributed on enamel. The SEM images of the biofilm treated with EGCG depict multilayers of cells arranged in short chains of microorganisms adhered to an unstructured matrix, which is not continuous and does not enmesh or protect the microorganisms entirely. Importantly, confocal images demonstrated that treatment with EGCG affected the 3D structure and organization of S. mutans biofilm, which presented a biofilm matrix more confined to the location of the microcolonies.

CONCLUSION

In conclusion, EGCG lowered the virulence of S. mutans matrix-rich biofilm by reducing the synthesis of biofilm matrix components, altering the biofilm matrix structure, organization, and distribution.

Effects of Nitrate and Nitrite on Plaque pH Decrease and Nitrite-Producing and -Degrading Activities of Plaque in vitro

INTRODUCTION

The purpose of this study was to investigate the effects of nitrate and nitrite on the pH-lowering activity of human plaque, the nitrite-producing and -degrading activities of human plaque, and their correlation.

METHODS

Nitrate and nitrite were added to human plaque suspensions collected from the buccal aspect of maxillary molars of patients visiting a general dental clinic, and changes in pH were measured with and without glucose addition. Nitrite-producing and -degrading activities were evaluated by adding nitrate and nitrite to the plaque suspension and measuring the increase and decrease in nitrite with Griess reagent, respectively.

RESULTS

The addition of nitrate inhibited both endogenous and glucose-induced plaque pH-lowering. The addition of glucose enhanced the production of nitrite from nitrate by about 3.3-fold. The addition of nitrite also inhibited endogenous plaque pH-lowering, but the addition of glucose promoted nitrite degradation by only about 1.1-fold. Nitrite-producing activity was positively correlated with age, but not with nitrite-degrading activity.

CONCLUSION

This study revealed that nitrite was produced from nitrate and inhibited the pH-lowering activity of human plaque, which may contribute to caries control. Both nitrite-producing and -degrading activities occurred in human plaque, but no correlation was found between them. Furthermore, nitrite production was enhanced by glucose metabolism, which may function as a self-regulatory mechanism (resilience) to prevent excessive acidification by glucose metabolism.

Curcumin inhibits growth of Porphyromonas gingivalis by arrest of bacterial dipeptidyl peptidase activity

Background

Curcumin is a multi-functional polyphenol with anti-bacterial and anti-inflammatory effects and may have potential for treatment of periodontal diseases. The present study was conducted to examine the molecular basis of the anti-bacterial effect of curcumin against Porphyromonas gingivalis using metabolome analysis.

Materials and Methods

P. gingivalis were incubated with 10 µg/mL curcumin, and then metabolites were analyzed with CE-TOF/MS. Expression levels of sigma factors were also evaluated using RT-PCR assays. The activities of dipeptidyl peptidases (DPPs) were assessed by examining the degradation reactions of MCA-labeled peptides.

Results

The relative amounts of various glycogenic amino acids were significantly decreased when P. gingivalis was incubated with curcumin. Furthermore, the metabolites on the amino acid degradation pathway, including high-energy compounds such as ATP, various intermediate metabolites of RNA/DNA synthesis, nucleoside sugars and amino sugars were also decreased. Additionally, the expression levels of sigma-54 and sigma-70 were significantly decreased, and the same results as noted following nutrient starvation. Curcumin also significantly suppressed the activities of some DPPs, while the human DPP-4 inhibitors markedly inhibited the growth of P. gingivalis and activities of the DPPs.

Conclusions

Curcumin suppresses the growth of P. gingivalis by inhibiting DPPs and also interferes with nucleic acid synthesis and central metabolic pathways, beginning with amino acid metabolism.

Exploring the root canal microbiome in previously treated teeth: A comparative study of diversity and metabolic pathways across two geographical locations

AIM

To analyse and compare the root canal microbiome present in root-filled teeth of two different geographical populations, and to study their functional potential using a next-generation sequencing approach.

METHODOLOGY

Sequencing data obtained from surgical specimens from previously treated teeth with periapical bone loss from Spain and USA were included in the study. Taxa were classified using SILVA v.138 database. Differences in genera abundances among the 10 most abundant genera were evaluated using a Kruskal-Wallis test. Alpha diversity indices were calculated in mothur. The Shannon and Chao1 indices were used. Analyses of similarity (ANOSIM) to determine differences in community composition were done in mothur, with Bonferroni correction for multiple comparisons. p-Values < .05 were considered statistically significant. Identification of enriched bacteria function prediction in the study groups (KEGG pathways) was carried out by linear discriminant analysis effect size (LEfSe) via Python 3.7.6.

RESULTS

A greater alpha-diversity (Shannon and Chao1 indices) was observed from samples obtained in Spain (p = .002). Geography showed no significant effects on community composition via an ANOSIM using Bray-Curtis dissimilarities (R = 0.03, p = .21). Bacterial functional analysis prediction obtained by PICRUSt showed that 5.7% KEGG pathways differed between the Spain and US samples.

CONCLUSIONS

The taxonomic assessment alone does not fully capture the microbiome's differences from two different geographical locations. Carbohydrate and amino acid metabolism were enriched in samples from Spain, while samples from USA had a higher representation of pathways related to nitrogen, propanoate metabolism, and secretion systems.

Identification of keystone taxa in root canals and periapical lesions of post-treatment endodontic infections: Next generation microbiome research

AIM

The aim of this study was to analyse and compare the microbiome present in root canals and periapical lesions of teeth with post-treatment infections, and to identify the presence of keystone taxa in both habitats using next-generation sequencing analysis.

METHODOLOGY

Apices and periapical lesions of patients with post-treatment apical periodontitis were surgically extracted. Specimens were cryo-pulverized, bacterial DNA was extracted, and the V3-V4 hypervariable regions of the 16S rRNA gene were sequenced using the Illumina Miseq platform. Bioinformatic analysis was carried out with Mothur software, whilst diversity indices were obtained using operational taxonomic units (OTUs). The diversity indices were compared with the Kruskal-Wallis test, and community composition differences were explored with Permutational Multivariate Analysis of Variance (PERMANOVA). A bacterial functional study was performed with the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis. Co-occurrence network analyses were performed using the Sparse Correlations for Compositional data (SparCC). Eigencentrality, clr-based abundance and ubiquitousness were applied to infer keystone taxa. P values <.05 were considered statistically significant.

RESULTS

Thirty-two apices and thirty-nine periapical lesions were sequenced and analysed. A similar alpha-diversity (p < .05) and community composition (p = .91) was observed for apices and lesion samples. The most abundant OTUs identified amongst all samples included Fusobacterium nucleatum, Prevotella loescheii, Streptococcus intermedius, Porphyromonas gingivalis, Parvimonas micra, Synergistetes bacterium, Tannerella forsythia and Peptostreptococcus stomatis. The metabolic pathways with >0.81% abundances included membrane transport, genetic information processing and metabolic pathways. F. nucleatum was identified as a keystone taxon as it showed ubiquitousness, an eigenvector centrality value of 0.83 and a clr-based abundance >4.

CONCLUSIONS

The microbiome in apices and periapical lesions of post-treatment endodontic infections showed a similar diversity and taxonomic composition. Co-occurrence network analyses at OTU level identified F. nucleatum as a keystone taxon candidate in these infections.

Genome-wide association study identifies host genetic variants influencing oral microbiota diversity and metabolic health

The microbial communities of the oral cavity are important elements of oral and systemic health. With emerging evidence highlighting the heritability of oral bacterial microbiota, this study aimed to identify host genome variants that influence oral microbial traits. Using data from 16S rRNA gene amplicon sequencing, we performed genome-wide association studies with univariate and multivariate traits of the salivary microbiota from 610 unrelated adults from the Danish ADDITION-PRO cohort. We identified six single nucleotide polymorphisms (SNPs) in human genomes that showed associations with abundance of bacterial taxa at different taxonomical tiers (P < 5 × 10-8). Notably, SNP rs17793860 surpassed our study-wide significance threshold (P < 1.19 × 10-9). Additionally, rs4530093 was linked to bacterial beta diversity (P < 5 × 10-8). Out of these seven SNPs identified, six exerted effects on metabolic traits, including glycated hemoglobin A1c, triglyceride and high-density lipoprotein cholesterol levels, the risk of type 2 diabetes and stroke. Our findings highlight the impact of specific host SNPs on the composition and diversity of the oral bacterial community. Importantly, our results indicate an intricate interplay between host genetics, the oral microbiota, and metabolic health. We emphasize the need for integrative approaches considering genetic, microbial, and metabolic factors.

The effect of different sweeteners on the oral microbiome: a randomized clinical exploratory pilot study

Introduction

The aim of the study was to evaluate the modulating effects of five commonly used sweetener (glucose, inulin, isomaltulose, tagatose, trehalose) containing mouth rinses on the oral microbiome.

Methods

A single-centre, double-blind, parallel randomized clinical trial was performed with healthy, 18-55-year-old volunteers (N = 65), who rinsed thrice-daily for two weeks with a 10% solution of one of the allocated sweeteners. Microbiota composition of supragingival dental plaque and the tongue dorsum coating was analysed by 16S RNA gene amplicon sequencing of the V4 hypervariable region (Illumina MiSeq). As secondary outcomes, dental plaque red fluorescence and salivary pH were measured.

Results

Dental plaque microbiota changed significantly for two groups: inulin (F = 2.0239, p = 0.0006 PERMANOVA, Aitchison distance) and isomaltulose (F = 0.67, p = 0.0305). For the tongue microbiota, significant changes were observed for isomaltulose (F = 0.8382, p = 0.0452) and trehalose (F = 1.0119, p = 0.0098). In plaque, 13 species changed significantly for the inulin group, while for tongue coating, three species changed for the trehalose group (ALDEx2, p < 0.1). No significant changes were observed for the secondary outcomes.

Conclusion

The effects on the oral microbiota were sweetener dependant with the most pronounced effect on plaque microbiota. Inulin exhibited the strongest microbial modulating potential of the sweeteners tested. Further full-scale clinical studies are required.

Tongue coating metabolic profiles of intra-oral halitosis patients

OBJECTIVE

This study focused on the metabolic characteristics of tongue coating in patients with intra-oral halitosis (IOH) to investigate potential diagnostic biomarkers for IOH.

METHODS

Oral healthy participants were enrolled in this study. Halitosis was evaluated with an organoleptic assessment, a Halimeter®, and an OralChroma™. Tongue coating samples were collected from 18 halitosis patients and 18 healthy controls. Liquid chromatography-mass spectrometry was conducted to reveal the IOH-related metabolic variations in tongue coating.

RESULTS

A total of 2214 metabolites were obtained. Most metabolites were shared between the two groups. A total of 274 upregulated metabolites, such as paramethasone acetate and indole-3-acetic acid, and 43 downregulated metabolites, including deoxyadenosine and valyl-arginine, were detected in the halitosis group. Functional analysis indicated that several metabolic pathways, including arginine biosynthesis, arginine and proline metabolism, histidine metabolism, and lysine degradation were significantly enriched in the IOH group. The least absolute shrinkage and selection operator logistic regression analysis revealed that paramethasone acetate, {1-[2-(4-carbamimidoyl-benzoylamino)-propionyl]-piperidin-4-yloxy}-acetic acid, indole-3-acetic acid, and valyl-arginine were remarkably associated with IOH.

CONCLUSIONS

This study revealed the metabolites present in tongue coating and identified effective biomarkers, providing essential insights into the prediction, pathogenesis, and diagnosis of IOH.

High-Throughput Combined Analysis of Saliva Microbiota and Metabolomic Profile in Chinese Periodontitis Patients: A Pilot Study

The onset and progression of periodontitis involves complicated interactions between the dysbiotic oral microbiota and disrupted host immune-inflammatory response, which can be mirrored by the changes in salivary metabolites profile. This pilot study sought to examine the saliva microbiome and metabolome in the Chinese population by the combined approach of 16s rRNA sequencing and high-throughput targeted metabolomics to discover potential cues for host-microbe metabolic interactions. Unstimulated whole saliva samples were collected from eighteen Stage III and IV periodontitis patients and thirteen healthy subjects. Full-mouth periodontal parameters were recorded. The taxonomic composition of microbiota was obtained by 16s rRNA sequencing, and the metabolites were identified and measured by ultra-high performance liquid chromatography and mass spectrometry-based metabolomic analysis. The oral microbiota composition displayed marked changes where the abundance of 93 microbial taxa differed significantly between the periodontitis and healthy group. Targeted metabolomics identified 103 differential metabolites between the patients and healthy individuals. Functional enrichment analysis demonstrated the upregulation of protein digestion and absorption, histidine metabolism, and nicotinate and nicotinamide metabolism pathways in the dysbiotic microbiota, while the ferroptosis, tryptophan metabolism, glutathione metabolism, and carbon metabolism pathways were upregulated in the patients. Correlation analysis confirmed positive relationships between the clinical parameters, pathogen abundances, and disease-related metabolite levels. The integral analysis of the saliva microbiome and metabolome yielded an accurate presentation of the dysbiotic oral microbiome and functional alterations in host-microbe metabolism. The microbial and metabolic profiling of the saliva could be a potential tool in the diagnosis, prognosis evaluation, and pathogenesis study of periodontitis.

Sucrose rinse modulates the salivary behavior of carbonic anhydrase VI and its buffering capacity: a longitudinal study in 4 to 6.5-year-old children

Background

Carbonic anhydrase VI (CA VI) is crucial in regulating oral pH and predicting susceptibility to dental caries. The hypothesis posits that caries activity may alter the CA VI function, diminishing its capacity to regulate pH effectively and potentially exacerbating cariogenic challenges. This 1-year cohort study sought to investigate the enzymatic activity of salivary CA VI and buffering capacity following a 20% sucrose rinse in 4 to 6.5-year-old children.

Method

This research involved 46 volunteers categorized into three groups based on their caries status after follow-up: caries-free (CFee), arrested caries (CArrested), and caries active (CActive). Children underwent visible biofilm examination and saliva collection for salivary flow rate, buffering capacity, and CA VI analyses before and after a 20% sucrose rinse.

Results

A reduction in the buffering capacity was observed after sucrose rinse in all groups. The CA VI activity decreased significantly in CFee and CArrested groups after sucrose rinse, although it did not change in the CActive group. An improvement in the buffering capacity and salivary flow rate was found at follow-up when compared with the baseline. After 1-year follow-up, buffering capacity and salivary flow rate increased in all groups, whilst the CA VI activity reduced only in CFree and CArrested children.

Conclusion

Sucrose rinse universally reduces the salivary buffering capacity, while caries activity may disrupt CA VI activity response during a cariogenic challenge. After a year, increased salivary flow enhances buffering capacity but not CA VI activity in caries-active children.

Dynamic hydrogel-metal-organic framework system promotes bone regeneration in periodontitis through controlled drug delivery

Periodontitis is a prevalent chronic inflammatory disease, which leads to gradual degradation of alveolar bone. The challenges persist in achieving effective alveolar bone repair due to the unique bacterial microenvironment's impact on immune responses. This study explores a novel approach utilizing Metal-Organic Frameworks (MOFs) (comprising magnesium and gallic acid) for promoting bone regeneration in periodontitis, which focuses on the physiological roles of magnesium ions in bone repair and gallic acid's antioxidant and immunomodulatory properties. However, the dynamic oral environment and irregular periodontal pockets pose challenges for sustained drug delivery. A smart responsive hydrogel system, integrating Carboxymethyl Chitosan (CMCS), Dextran (DEX) and 4-formylphenylboronic acid (4-FPBA) was designed to address this problem. The injectable self-healing hydrogel forms a dual-crosslinked network, incorporating the MOF and rendering its on-demand release sensitive to reactive oxygen species (ROS) levels and pH levels of periodontitis. We seek to analyze the hydrogel's synergistic effects with MOFs in antibacterial functions, immunomodulation and promotion of bone regeneration in periodontitis. In vivo and in vitro experiment validated the system's efficacy in inhibiting inflammation-related genes and proteins expression to foster periodontal bone regeneration. This dynamic hydrogel system with MOFs, shows promise as a potential therapeutic avenue for addressing the challenges in bone regeneration in periodontitis.

Species-level characterization of saliva and dental plaque microbiota reveals putative bacterial and functional biomarkers of periodontal diseases in dogs

Periodontal diseases are among the most common bacterial-related pathologies affecting the oral cavity of dogs. Nevertheless, the canine oral ecosystem and its correlations with oral disease development are still far from being fully characterized. In this study, the species-level taxonomic composition of saliva and dental plaque microbiota of 30 healthy dogs was investigated through a shallow shotgun metagenomics approach. The obtained data allowed not only to define the most abundant and prevalent bacterial species of the oral microbiota in healthy dogs, including members of the genera Corynebacterium and Porphyromonas, but also to identify the presence of distinct compositional motifs in the two oral microniches as well as taxonomical differences between dental plaques collected from anterior and posterior teeth. Subsequently, the salivary and dental plaque microbiota of 18 dogs affected by chronic gingival inflammation and 18 dogs with periodontitis were compared to those obtained from the healthy dogs. This analysis allowed the identification of bacterial and metabolic biomarkers correlated with a specific clinical status, including members of the genera Porphyromonas and Fusobacterium as microbial biomarkers of a healthy and diseased oral status, respectively, and genes predicted to encode for metabolites with anti-inflammatory properties as metabolic biomarkers of a healthy status.

Influence of Biofilm Maturity on the Antibacterial Efficacy of Cold Atmospheric Plasma in Oral Microcosm Biofilms

As biofilms mature, biomass and extracellular polysaccharide (EPS) content increases, enhancing pathogenicity. Therefore, this study aimed to evaluate the antibacterial efficacy of cold atmospheric plasma (CAP) against oral microcosm biofilms and the influence of biofilm maturity on treatment. Oral microcosm biofilms were cultured on hydroxyapatite disks for 2 and 6 days. Based on the treatment and biofilm maturity, these were subsequently allocated into six groups (N = 19 each): Groups 1 and 2 were incubated with distilled water for 1 min; Groups 3 and 4 were treated with CAP for 2 min, and Groups 5 and 6 were treated with 0.12% chlorhexidine gluconate for 1 min. Groups 1, 3, and 5 represent 2-day biofilms, and Groups 2, 4, and 6 represent 6-day biofilms. Treatments were repeated daily for 5 days. Antibacterial efficacy was analyzed by measuring oral biofilms' red fluorescence intensity (RatioR/G) and quantifying EPS content and bacterial viability. The RatioR/G was 1.089-fold and 1.104-fold higher in Groups 4 and 6 than in Groups 3 and 5 following antibacterial treatment, respectively (p < 0.001). EPS content increased by 1.71-fold in Group 6 than in Group 5 (p < 0.001). Bacterial survival rate was the lowest in Group 3 (p = 0.005). These findings underscore the relevance of CAP treatment in maintaining antibacterial efficacy regardless of the biofilm development stage, highlighting its potential utility in oral care.

Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users

Tobacco use significantly influences the oral microbiome. However, less is known about how different tobacco products specifically impact the oral microbiome over time. To address this knowledge gap, we characterized the oral microbiome of cigarette users, smokeless tobacco users, and non-users over 4 months (four time points). Buccal swab and saliva samples (n = 611) were collected from 85 participants. DNA was extracted from all samples and sequencing was carried out on an Illumina MiSeq, targeting the V3-V4 region of the 16S rRNA gene. Cigarette and smokeless tobacco users had more diverse oral bacterial communities, including a higher relative abundance of Firmicutes and a lower relative abundance of Proteobacteria, when compared to non-users. Non-users had a higher relative abundance of Actinomyces, Granulicatella, Haemophilus, Neisseria, Oribacterium, Prevotella, Pseudomonas, Rothia, and Veillonella in buccal swab samples, compared to tobacco users. While the most abundant bacterial genera were relatively constant over time, some species demonstrated significant shifts in relative abundance between the first and last time points. In addition, some opportunistic pathogens were detected among tobacco users including Neisseria subflava, Bulleidia moorei and Porphyromonas endodontalis. Overall, our results provide a more holistic understanding of the structure of oral bacterial communities in tobacco users compared to non-users.

Effects of glucose and lactate on Streptococcus mutans abundance in a novel multispecies oral biofilm model

The oral microbiome plays an important role in protecting oral health. Here, we established a controlled mixed-species in vitro biofilm model and used it to assess the impact of glucose and lactate on the ability of Streptococcus mutans, an acidogenic and aciduric species, to compete with commensal oral bacteria. A chemically defined medium was developed that supported the growth of S. mutans and four common early colonizers of dental plaque: Streptococcus gordonii, Actinomyces oris, Neisseria subflava, and Veillonella parvula. Biofilms containing the early colonizers were developed in a continuous flow bioreactor, exposed to S. mutans, and incubated for up to 7 days. The abundance of bacteria was estimated by quantitative polymerase chain reaction (qPCR). At high glucose and high lactate, the pH in bulk fluid rapidly decreased to approximately 5.2, and S. mutans outgrew other species in biofilms. In low glucose and high lactate, the pH remained above 5.5, and V. parvula was the most abundant species in biofilms. By contrast, in low glucose and low lactate, the pH remained above 6.0 throughout the experiment, and the microbial community in biofilms was relatively balanced. Fluorescence in situ hybridization confirmed that all species were present in the biofilm and the majority of cells were viable using live/dead staining. These data demonstrate that carbon source concentration is critical for microbial homeostasis in model oral biofilms. Furthermore, we established an experimental system that can support the development of computational models to predict transitions to microbial dysbiosis based on metabolic interactions.IMPORTANCEWe developed a controlled (by removing host factor) dynamic system metabolically representative of early colonization of Streptococcus mutans not measurable in vivo. Hypotheses on factors influencing S. mutans colonization, such as community composition and inoculation sequence and the effect of metabolite concentrations, can be tested and used to predict the effect of interventions such as dietary modifications or the use of toothpaste or mouthwash on S. mutans colonization. The defined in vitro model (species and medium) can be simulated in an in silico model to explore more of the parameter space.

A novel method for sampling subgingival microbiome: a comparative metatranscriptomic study

The subgingival microbiome has been implicated in oral and systemic diseases such as periodontitis and Alzheimer's disease. However, subgingival sampling is challenging. We developed a novel method of sampling the subgingival microbiome by rotationally swabbing the supragingival area, named subgingival-P (for proxy) samples. We sampled and metatranscriptomically analyzed subgingival and subgingival-P samples of three different teeth in 20 individuals. The subgingival-P samples were comparable to the subgingival samples in the relative abundances of microorganisms and microbial gene expression levels. Our data demonstrate that the novel method of collecting and analyzing the subgingival-P samples can act as a proxy for the subgingiva, paving the way for large and diverse studies investigating the role of the subgingival microbiome in health and disease.

Unlocking the potential of probiotic administration in caries management: a systematic review

BACKGROUND

The use of prebiotics and/or probiotic bacteria with the potential to modulate the oral ecosystem may play an important role in the prevention and management of dental caries. To assess the evidence of the potential of pre/probiotics both in the prevention and treatment of dental caries, we focused on the PICO question "In individuals with caries, after probiotic administration, is there an improvement in outcomes directly related to caries risk and development?".

METHODS

An extensive systematic search was conducted in electronic databases PubMed, Web of Science, Scopus and Cochrane, to identify articles with relevant data. This systematic review included trials performed in Humans; published in English; including the observation of patients with caries, with clear indication of the probiotic used and measuring the outcomes directly involved with the cariogenic process, including the quantification of bacteria with cariogenic potential. To evaluate the methodological quality of the studies, the critical assessment tool from the Joanna Briggs Institute was used.

RESULTS

Eight hundred and fifty articles, potentially relevant, were identified. Following PRISMA guidelines 14 articles were included in this systematic review. Outcomes such as reduction of cariogenic microorganism counts, salivary pH, buffer capacity, and caries activity were assessed. The probiotic most often referred with beneficial results in dental caries outcomes is Lacticaseibacillus rhamnosus. Regarding the most used administration vehicle, in studies with positive effects on the caries management, probiotic supplemented milk could be considered the best administration vehicle.

CONCLUSIONS

Evidence suggests a beneficial effect of probiotic supplemented milk (Lacticaseibacillus rhamnosus) as an adjuvant for caries prevention and management. However, comparable evidence is scarce and better designed and comparable studies are needed.

Application of omics technologies in cariology research: A critical review with bibliometric analysis

OBJECTIVES

To review the application of omics technologies in the field of cariology research and provide critical insights into the emerging opportunities and challenges.

DATA & SOURCES

Publications on the application of omics technologies in cariology research up to December 2022 were sourced from online databases, including PubMed, Web of Science and Scopus. Two independent reviewers assessed the relevance of the publications to the objective of this review.

STUDY SELECTION

Studies that employed omics technologies to investigate dental caries were selected from the initial pool of identified publications. A total of 922 publications with one or more omics technologies adopted were included for comprehensive bibliographic analysis. (Meta)genomics (676/922, 73 %) is the predominant omics technology applied for cariology research in the included studies. Other applied omics technologies are metabolomics (108/922, 12 %), proteomics (105/922, 11 %), and transcriptomics (76/922, 8 %).

CONCLUSION

This study identified an emerging trend in the application of multiple omics technologies in cariology research. Omics technologies possess significant potential in developing strategies for the detection, staging evaluation, risk assessment, prevention, and management of dental caries. Despite the numerous challenges that lie ahead, the integration of multi-omics data obtained from individual biological samples, in conjunction with artificial intelligence technology, may offer potential avenues for further exploration in caries research.

CLINICAL SIGNIFICANCE

This review presented a comprehensive overview of the application of omics technologies in cariology research and discussed the advantages and challenges of using these methods to detect, assess, predict, prevent, and treat dental caries. It contributes to steering research for improved understanding of dental caries and advancing clinical translation of cariology research outcomes.

Structure, variation and assembly of body-wide microbiomes in endangered crested ibis Nipponia nippon

Limited knowledge of bird microbiome in the all-body niche hinders our understanding of host-microbial relationships and animal health. Here, we characterized the microbial composition of the crested ibis from 13 body sites, representing the cloaca, oral, feather and skin habitats, and explored assembly mechanism structuring the bacterial community of the four habitats respectively. The bacterial community characteristics were distinct among the four habitats. The skin harboured the highest alpha diversity and most diverse functions, followed by feather, oral and cloaca. Individual-specific features were observed when the skin and feathers were concentrated independently. Skin and feather samples of multiple body sites from the same individual were more similar than those from different individuals. Although a significant proportion of the microbiota in the host (85.7%-96.5%) was not derived from the environmental microbiome, as body sites became more exposed to the environment, the relative importance of neutral processes (random drift or dispersal) increased. Neutral processes were the most important contributor in shaping the feather microbiome communities (R2  = .859). A higher percentage of taxa (29.3%) on the skin were selected by hosts compared to taxa on other body habitats. This study demonstrated that niche speciation and partial neutral processes, rather than environmental sources, contribute to microbiome variation in the crested ibis. These results enhance our knowledge of baseline microbial diversity in birds and will aid health management in crested ibises in the future.

Manipulating the diseased oral microbiome: the power of probiotics and prebiotics

Dental caries and periodontal disease are amongst the most prevalent global disorders. Their aetiology is rooted in microbial activity within the oral cavity, through the generation of detrimental metabolites and the instigation of potentially adverse host immune responses. Due to the increasing threat of antimicrobial resistance, alternative approaches to readdress the balance are necessary. Advances in sequencing technologies have established relationships between disease and oral dysbiosis, and commercial enterprises seek to identify probiotic and prebiotic formulations to tackle preventable oral disorders through colonisation with, or promotion of, beneficial microbes. It is the metabolic characteristics and immunomodulatory capabilities of resident species which underlie health status. Research emphasis on the metabolic environment of the oral cavity has elucidated relationships between commensal and pathogenic organisms, for example, the sequential metabolism of fermentable carbohydrates deemed central to acid production in cariogenicity. Therefore, a focus on the preservation of an ecological homeostasis in the oral environment may be the most appropriate approach to health conservation. In this review we discuss an ecological approach to the maintenance of a healthy oral environment and debate the potential use of probiotic and prebiotic supplementation, specifically targeted at sustaining oral niches to preserve the delicately balanced microbiome.

Salivary metabolomics in patients with oral lichen planus: a preliminary study based on NMR spectroscopy

OBJECTIVES

The present preliminary study aimed to investigate the salivary metabolic profile in patients with asymptomatic oral lichen planus (OLP) using nuclear magnetic resonance (NMR) spectroscopy.

MATERIAL AND METHODS

Stimulated whole mouth saliva (SWMS) samples were collected from 15 reticular OLP female patients and 15 from age- and sex-matched controls (HCs). A total of 23 metabolites were identified and quantified. Mann-Whitney's U test was used to compare the determined concentration salivary metabolite concentrations between OLP patients and the healthy controls.

RESULTS

The concentration of acetate, methylamine, and pyruvate was elevated, whereas the concentration of tyrosine was decreased in the saliva of OLP patients compared with HCs. To identify a combination of metabolites, multivariate discrimination function analysis (DFA) was conducted. DFA analysis have shown that the most powerful discrimination between the groups was achieved when methylamine and tyrosine were considered as combined biomarkers.

CONCLUSIONS

Salivary tyrosine was of particular interest and a promising finding for the screening of OLP and its progression. Further longitudinal studies are required to establish it as a reliable salivary biomarker in OLP.

CLINICAL RELEVANCE

The salivary metabolic profiling can describe the pathologic characteristics of OLP on non-invasive saliva samples and NMR analysis. Salivary metabolites provide details to considered early detectors and to impact oral health of OLP patients.

The Evolving Microbiome of Dental Caries

Dental caries is a significant oral and public health problem worldwide, especially in low-income populations. The risk of dental caries increases with frequent intake of dietary carbohydrates, including sugars, leading to increased acidity and disruption of the symbiotic diverse and complex microbial community of health. Excess acid production leads to a dysbiotic shift in the bacterial biofilm composition, demineralization of tooth structure, and cavities. Highly acidic and acid-tolerant species associated with caries include Streptococcus mutans, Lactobacillus, Actinomyces, Bifidobacterium, and Scardovia species. The differences in microbiotas depend on tooth site, extent of carious lesions, and rate of disease progression. Metagenomics and metatranscriptomics not only reveal the structure and genetic potential of the caries-associated microbiome, but, more importantly, capture the genetic makeup of the metabolically active microbiome in lesion sites. Due to its multifactorial nature, caries has been difficult to prevent. The use of topical fluoride has had a significant impact on reducing caries in clinical settings, but the approach is costly; the results are less sustainable for high-caries-risk individuals, especially children. Developing treatment regimens that specifically target S. mutans and other acidogenic bacteria, such as using nanoparticles, show promise in altering the cariogenic microbiome, thereby combatting the disease.

Current concepts in the pathogenesis of periodontitis: from symbiosis to dysbiosis

The primary etiological agent for the initiation and progression of periodontal disease is the dental plaque biofilm which is an organized aggregation of microorganisms residing within a complex intercellular matrix. The non-specific plaque hypothesis was the first attempt to explain the role of the dental biofilm in the pathogenesis of periodontal diseases. However, the introduction of sophisticated diagnostic and laboratory assays has led to the realisation that the development of periodontitis requires more than a mere increase in the biomass of dental plaque. Indeed, multispecies biofilms exhibit complex interactions between the bacteria and the host. In addition, not all resident microorganisms within the biofilm are pathogenic, since beneficial bacteria exist that serve to maintain a symbiotic relationship between the plaque microbiome and the host’s immune-inflammatory response, preventing the emergence of pathogenic microorganisms and the development of dysbiosis. This review aims to highlight the development and structure of the dental plaque biofilm and to explore current literature on the transition from a healthy (symbiotic) to a diseased (dysbiotic) biofilm in periodontitis and the associated immune-inflammatory responses that drive periodontal tissue destruction and form mechanistic pathways that impact other systemic non-communicable diseases.

Low Carbohydrate, High Fat Diet Alters the Oral Microbiome without Negating the Nitrite Response to Beetroot Juice Supplementation

A low carbohydrate, high fat (LCHF) diet in athletes increases fat oxidation but impairs sports performance, potentially due to impaired exercise economy. Dietary nitrate supplementation can improve exercise economy via an increase in nitric oxide production, which is initiated by the reduction of nitrate to nitrite within the oral cavity. This reaction is dependent on the presence of nitrate-reducing oral bacteria, which can potentially be altered by dietary changes, including a LCHF diet. This study explored the effect of a LCHF diet on the oral microbiome and subsequent changes to plasma nitrite concentration following nitrate supplementation. Following five days of LCHF or high carbohydrate (HCHO) control dietary intervention, highly trained male race walkers consumed 140 mL beetroot juice containing 8.4 mmol nitrate; they then provided (a) blood samples for plasma nitrate and nitrite analysis and (b) saliva samples for 16S rRNA sequencing of the oral microbiome. The LCHF diet (n = 13) reduced oral bacterial diversity and changed the relative abundance of the genera Neisseria (+10%), Fusobacteria (+3%), Prevotella (-9%), and Veillonella (-4%), with no significant changes observed following the HCHO diet (n = 11). Following beetroot juice ingestion, plasma nitrite concentrations were higher for the LCHF diet compared to the HCHO diet (p = 0.04). However, the absence of an interaction with the trial (pre-post) (p = 0.71) suggests that this difference was not due to the dietary intervention. In summary, we found an increase in plasma nitrate and nitrite concentrations in response to nitrate supplementation independent of diet. This suggests the oral microbiome is adaptive to dietary changes and can maintain a nitrate reduction capacity despite a decrease in bacterial diversity following the LCHF diet.

Evaluation of Human Dental Plaque Lactic Acid Bacilli for Probiotic Potential and Functional Analysis in Relevance to Oral Health

Members of the lactic acid bacillus group are well-known probiotics and primarily isolated from fermented food, dairy products, intestinal and gut environment of human. Since probiotics from the human source are preferred, there exists a huge repertoire of lactobacilli in the human oral cavity which could prove a much better niche to be exploited for these beneficial microorganisms. Therefore, in this study, four lactobacilli strains, including strain DISK7, reported earlier, isolated from dental plaque samples of a healthy humans were evaluated for their probiotic potential. Strains displayed 99.9% of 16S rRNA gene sequence identity with species of the genera Lactobacillus and Limosilactobacillus. All strains showed lactic acid production, tolerance to low pH and antibiotic sensitivity. Variations were observed among strains in their aggregation ability, biofilm formation, bile salt resistance and cholesterol degradation. Further, we analyzed the interaction of strains with other oral commensals and opportunistic pathogens in co-culture experiments. Isolates DISK7 and DISK26 exhibited high co-aggregation (> 70%) with secondary colonizers, Streptococcus pyogenes and Veillonella parvula, respectively, but their aggregation ability was decreased with opportunistic pathogens. Furthermore, strains showed a substantial increase in biofilm in co-culture with other Lactobacillus isolates, indicating their ability to proliferate commensal bacteria in the oral environment. These microbes continually evolve in terms of niche adaptation as evidenced in genome analysis. The highlight of the investigation is the isolation and evaluation of the probiotic lactobacilli from the human oral cavity, which could prove a much better niche to be exploited for the effective commercialization of these beneficial microbes. Taken together, probiotic properties and interaction with commensal bacteria, these isolates exhibit the huge potential to be developed as alternative bioresource agents for maintenance of oral health.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-023-01108-2.

The bacterial species profiles of the lingual and salivary microbiota differ with basic tastes sensitivity in human

Taste perception is crucial and impairments, which can be linked to pathologies, can lead to eating disorders. It is triggered by taste compounds stimulating receptors located on the tongue. However, the tongue is covered by a film containing saliva and microorganisms suspected to modulate the taste receptor environment. The present study aimed to elucidate the links between taste sensitivity (sweetness, sourness, bitterness, saltiness, umami) and the salivary as well as the tongue microbiota using shotgun metagenomics. 109 bacterial species were correlated with at least one taste. Interestingly, when a species was correlated with at least two tastes, the correlations were unidirectional, indicating a putative global implication. Some Streptococcus, SR1 and Rickenellaceae species correlated with five tastes. When comparing both ecosystems, saliva appears to be a better taste predictor than tongue. This work shows the implication of the oral microbiota in taste and exhibits specificities depending on the ecosystem considered.

Spatiotemporal monitoring of a periodontal multispecies biofilm model: demonstration of prebiotic treatment responses

Biofilms are complex polymicrobial communities which are often associated with human infections such as the oral disease periodontitis. Studying these complex communities under controlled conditions requires in vitro biofilm model systems that mimic the natural environment as close as possible. This study established a multispecies periodontal model in the drip flow biofilm reactor in order to mimic the continuous flow of nutrients at the air-liquid interface in the oral cavity. The design is engineered to enable real-time characterization. A community of five bacteria, Streptococcus gordonii-GFPmut3*, Streptococcus oralis-GFPmut3*, Streptococcus sanguinis-pVMCherry, Fusobacterium nucleatum, and Porphyromonas gingivalis-SNAP26 is visualized using two distinct fluorescent proteins and the SNAP-tag. The biofilm in the reactor develops into a heterogeneous, spatially uniform, dense, and metabolically active biofilm with relative cell abundances similar to those in a healthy individual. Metabolic activity, structural features, and bacterial composition of the biofilm remain stable from 3 to 6 days. As a proof of concept for our periodontal model, the 3 days developed biofilm is exposed to a prebiotic treatment with L-arginine. Multifaceted effects of L-arginine on the oral biofilm were validated by this model setup. L-arginine showed to inhibit growth and incorporation of the pathogenic species and to reduce biofilm thickness and volume. Additionally, L-arginine is metabolized by Streptococcus gordonii-GFPmut3* and Streptococcus sanguinis-pVMCherry, producing high levels of ornithine and ammonium in the biofilm. In conclusion, our drip flow reactor setup is promising in studying spatiotemporal behavior of a multispecies periodontal community.ImportancePeriodontitis is a multifactorial chronic inflammatory disease in the oral cavity associated with the accumulation of microorganisms in a biofilm. Not the presence of the biofilm as such, but changes in the microbiota (i.e., dysbiosis) drive the development of periodontitis, resulting in the destruction of tooth-supporting tissues. In this respect, novel treatment approaches focus on maintaining the health-associated homeostasis of the resident oral microbiota. To get insight in dynamic biofilm responses, our research presents the establishment of a periodontal biofilm model including Streptococcus gordonii, Streptococcus oralis, Streptococcus sanguinis, Fusobacterium nucleatum, and Porphyromonas gingivalis. The added value of the model setup is the combination of simulating continuously changing natural mouth conditions with spatiotemporal biofilm profiling using non-destructive characterization tools. These applications are limited for periodontal biofilm research and would contribute in understanding treatment mechanisms, short- or long-term exposure effects, the adaptation potential of the biofilm and thus treatment strategies.

Dysbiosis of oral microbiome persists after dental treatment-induced remission of periodontal disease and dental caries

IMPORTANCE

We characterized the oral conditions, salivary microbiome, and metabolome after dental treatment by investigating the state after treatment completion and transition to self-care. Dental treatment improved oral health conditions, resulting in oral disease remission; however, the imbalanced state of the salivary microbiome continued even after remission. Although the results of this study are preliminary, owing to the small number of participants in each group when compared to larger cohort studies, they indicate that the risk of disease may remain higher than that of healthy participants, thereby demonstrating the importance of removing dental plaque containing disease-related bacteria using appropriate care even after treatment completion. We also identified bacterial species with relative abundances that differed from those of healthy participants even after remission of symptoms, which may indicate that the maturation of certain bacterial species must be controlled to improve the oral microbiome and reduce the risk of disease recurrence.

The Complicated Relationship of Short-Chain Fatty Acids and Oral Microbiome: A Narrative Review

The human oral microbiome has emerged as a focal point of research due to its profound implications for human health. The involvement of short-chain fatty acids in oral microbiome composition, oral health, and chronic inflammation is gaining increasing attention. In this narrative review, the results of early in vitro, in vivo, and pilot clinical studies and research projects are presented in order to define the boundaries of this new complicated issue. According to the results, the current research data are disputable and ambiguous. When investigating the role of SCFAs in human health and disease, it is crucial to distinguish between their local GI effects and the systemic influences. Locally, SCFAs are a part of normal oral microbiota metabolism, but the increased formation of SCFAs usually attribute to dysbiosis; excess SCFAs participate in the development of local oral diseases and in oral biota gut colonization and dysbiosis. On the other hand, a number of studies have established the positive impact of SCFAs on human health as a whole, including the reduction of chronic systemic inflammation, improvement of metabolic processes, and decrease of some types of cancer incidence. Thus, a complex and sophisticated approach with consideration of origin and localization for SCFA function assessment is demanded. Therefore, more research, especially clinical research, is needed to investigate the complicated relationship of SCFAs with health and disease and their potential role in prevention and treatment.

Microbial Relationship of Carious Deciduous Molars and Adjacent First Permanent Molars

(1) Epidemiological studies have shown that deciduous molar caries are related to and more severe than permanent molar caries. This study aimed to investigate whether caries subtypes in deciduous molars were associated with caries in first permanent molars and to explore taxonomic and functional profiles of the microbiota involved in different subtypes. (2) 42 mixed-dentition children were recruited and were divided into DMC (carious deciduous molars but caries-free first permanent molars; n = 14), C (carious deciduous and first permanent molars; n = 13), and control (n = 15) groups. Metagenomic sequencing was performed for supragingival plaque samples obtained separately from deciduous and first permanent molars. (3) The microbiota of deciduous molars in the DMC and C groups differed not only in species-based beta diversity but also in compositional and functional profiles. In the C group-like subtype, 14 caries-related species and potential pathways were identified that could be responsible for the caries relationship between the deciduous and permanent molars. In the DMC group-like subtype, the overall functional structure, the levels of Leptotrichia wadei, Streptococcus anginosus, and Stomatobaculum longum and KOs in sugar transporters and fermentation, quorum sensing, and TCA cycle in their first permanent molars surprisingly resembled those of the C group rather than the control group. This suggested that these clinically sound first permanent molars were at a greater risk for caries. (4) Classification of deciduous molar caries according to the microbiota could serve as a caries risk predictor for adjacent first permanent molars.

Mechanisms underlying the effects, and clinical applications, of oral microbiota in lung cancer: current challenges and prospects

The oral cavity contains a site-specific microbiota that interacts with host cells to regulate many physiological processes in the human body. Emerging evidence has suggested that changes in the oral microbiota can increase the risk of lung cancer (LC), and the oral microbiota is also altered in patients with LC. Human and animal studies have shown that oral microecological disorders and/or specific oral bacteria may play an active role in the occurrence and development of LC through direct and/or indirect mechanisms. These studies support the potential of oral microbiota in the clinical treatment of LC. Oral microbiota may therefore be used in the prevention and treatment of LC and to improve the side effects of anticancer therapy by regulating the balance of the oral microbiome. Specific oral microbiota in LC may also be used as screening or predictive biomarkers. This review summarizes the main findings in research on oral microbiome-related LC and discusses current challenges and future research directions.

Oral microbiome mediated inflammation, a potential inductor of vascular diseases: a comprehensive review

The dysbiosis of the oral microbiome and vascular translocation of the periodontopathic microorganism to peripheral blood can cause local and systemic extra-oral inflammation. Microorganisms associated with the subgingival biofilm are readily translocated to the peripheral circulation, generating bacteremia and endotoxemia, increasing the inflammation in the vascular endothelium and resulting in endothelial dysfunction. This review aimed to demonstrate how the dysbiosis of the oral microbiome and the translocation of oral pathogen-induced inflammation to peripheral blood may be linked to cardiovascular diseases (CVDs). The dysbiosis of the oral microbiome can regulate blood pressure and activate endothelial dysfunction. Similarly, the passage of periodontal microorganisms into the peripheral circulation and their virulence factors have been associated with a vascular compartment with a great capacity to activate endothelial cells, monocytes, macrophages, and plaquettes and increase interleukin and chemokine secretion, as well as oxidative stress. This inflammatory process is related to atherosclerosis, hypertension, thrombosis, and stroke. Therefore, oral diseases could be involved in CVDs via inflammation. The preclinic and clinical evidence suggests that periodontal disease increases the proinflammatory markers associated with endothelial dysfunction. Likewise, the evidence from clinical studies of periodontal treatment in the long term evidenced the reduction of these markers and improved overall health in patients with CVDs.

Saliva as Biomarker for Oral and Chronic Degenerative Non-Communicable Diseases

Saliva is a very complex fluid and it is essential to maintain several physiological processes and functions, including oral health, taste, digestion and immunological defenses. Saliva composition and the oral microbiome can be influenced by several factors, like diet and smoking habits, and their alteration can represent an important access point for pathogens and, thus, for systemic illness onset. In this review, we explore the potentiality of saliva as a new tool for the early detection of some pathological conditions, such as oral diseases, chronic degenerative non-communicable diseases, among these chronic kidney disease (CKD). We also examined the possible correlation between oral and systemic diseases and oral and gut microbiota dysbiosis. In particular, we deeply analyzed the relationship between oral diseases and CKD. In this context, some salivary parameters can represent a new device to detect either oral or systemic pathologies. Moreover, the positive modulation of oral and gut microbiota induced by prebiotics, postbiotics, or symbiotics could represent a new possible adjuvant therapy in the clinical management of oral diseases and CKD.

Microbial metabolites in the pathogenesis of periodontal diseases: a narrative review

The purpose of this narrative review is to highlight the importance of microbial metabolites in the pathogenesis of periodontal diseases. These diseases, involving gingivitis and periodontitis are inflammatory conditions initiated and maintained by the polymicrobial dental plaque/biofilm. Gingivitis is a reversible inflammatory condition while periodontitis involves also irreversible destruction of the periodontal tissues including the alveolar bone. The inflammatory response of the host is a natural reaction to the formation of plaque and the continuous release of metabolic waste products. The microorganisms grow in a nutritious and shielded niche in the periodontal pocket, protected from natural cleaning forces such as saliva. It is a paradox that the consequences of the enhanced inflammatory reaction also enable more slow-growing, fastidious, anaerobic bacteria, with often complex metabolic pathways, to colonize and thrive. Based on complex food chains, nutrient networks and bacterial interactions, a diverse microbial community is formed and established in the gingival pocket. This microbiota is dominated by anaerobic, often motile, Gram-negatives with proteolytic metabolism. Although this alternation in bacterial composition often is considered pathologic, it is a natural development that is promoted by ecological factors and not necessarily a true "dysbiosis". Normal commensals are adapting to the gingival crevice when tooth cleaning procedures are absent. The proteolytic metabolism is highly complex and involves a number of metabolic pathways with production of a cascade of metabolites in an unspecific manner. The metabolites involve short chain fatty acids (SCFAs; formic, acetic, propionic, butyric, and valeric acid), amines (indole, scatole, cadaverine, putrescine, spermine, spermidine) and gases (NH₃, CO, NO, H₂S, H₂). A homeostatic condition is often present between the colonizers and the host response, where continuous metabolic fluctuations are balanced by the inflammatory response. While it is well established that the effect of the dental biofilm on the host response and tissue repair is mediated by microbial metabolites, the mechanisms behind the tissue destruction (loss of clinical attachment and bone) are still poorly understood. Studies addressing the functions of the microbiota, the metabolites, and how they interplay with host tissues and cells, are therefore warranted.

The Impact of Alcohol Consumption and Oral Microbiota on Upper Aerodigestive Tract Carcinomas: A Pilot Study

Alcohol consumption is associated with oxidative stress and an increased risk of carcinoma of the upper aero-digestive tract (UADT). Recently, it has been found that some microorganisms in the human oral cavity may locally metabolize ethanol, forming acetaldehyde, a carcinogenic metabolite of alcohol. In a cohort of patients first visited for UADT cancers, we estimated their alcohol consumption by measuring Ethyl Glucuronide/EtG (a long-lasting metabolite of ethanol) in the hair and carbohydrate-deficient transferrin/CDT (short-term index of alcohol intake) in the serum. Moreover, we analyzed, by culture-based methods, the presence of Neisseria subflava, Streptococcus mitis, Candida albicans, and glabrata (microorganisms generating acetaldehyde) in the oral cavity. According to the EtG values, we correlated drinking alcohol with endogenous oxidative stress and the investigated microorganism's presence. We found that 55% of heavy drinkers presented microorganisms generating acetaldehyde locally. Moreover, we found that the presence of oral acetaldehyde-producing bacteria correlates with increased oxidative stress compared to patients without such bacteria. As for the study of alcohol dehydrogenase gene polymorphisms (the enzyme that transforms alcohol to acetaldehyde), we found that only the "CGTCGTCCC" haplotype was more frequent in the general population than in carcinoma patients. This pilot study suggests the importance of estimating alcohol consumption (EtG), the presence of bacteria producing acetaldehyde, and oxidative stress as risk factors for the onset of oral carcinomas.

Effect of anaerobic or/and microaerophilic atmosphere on microcosm biofilm formation and tooth demineralization

OBJECTIVE

Microcosm biofilms can reproduce the complexity of a dental biofilm. However, different forms of cultivation have been used. The impact of the culture atmosphere on the development of microcosm biofilms and their potential to cause tooth demineralization has not yet been deeply studied. This study analyzes the effects of three experimental cultivation models (microaerophile vs. anaerobiosis vs. experimental mixed) on the colony-forming units (CFU) of the cariogenic microorganisms and tooth demineralization.

METHODOLOGY

90 bovine enamel and 90 dentin specimens were distributed into different atmospheres: 1) microaerophilia (5 days, 5% CO2); 2) anaerobiosis (5 days, jar); 3) mixed (2 days microaerophilia and 3 days anaerobiosis), which were treated with 0.12% chlorhexidine (positive control - CHX) or Phosphate-Buffered Saline (negative control - PBS) (n=15). Human saliva and McBain's saliva containing 0.2% sucrose were used for microcosm biofilm formation, for 5 days. From the second day to the end of the experiment, the specimens were treated with CHX or PBS (1x1 min/day). Colony-forming units (CFU) were counted, and tooth demineralization was analyzed using transverse microradiography (TMR). Data were subjected to two-way ANOVA and Tukey's or Sidak's test (p<0.05).

RESULTS

CHX was able to reduce total microorganism's CFU compared to PBS (differences of 0.3-1.48 log10 CFU/mL), except for anaerobiosis and microaerophilia in enamel and dentin biofilm, respectively. In the case of dentin, no effect of CHX on Lactobacillus spp. was observed. CHX significantly reduced enamel demineralization compared to PBS (78% and 22% reductions for enamel and dentin, respectively). Enamel mineral loss did not differ when compared with the other atmospheres; however, the enamel lesion depth was greater under anaerobiosis. Dentin mineral loss was lower under anaerobiosis when compared with the other atmospheres.

CONCLUSION

The type of atmosphere has, in general, little influence on the cariogenic ability of the microcosm biofilm.

The role of the oral microbiome in obesity and metabolic disease: potential systemic implications and effects on taste perception

Obesity and its metabolic sequelae still comprise a challenge when it comes to understanding mechanisms, which drive these pandemic diseases. The human microbiome as a potential key player has attracted the attention of broader research for the past decade. Most of it focused on the gut microbiome while the oral microbiome has received less attention. As the second largest niche, the oral microbiome is associated with a multitude of mechanisms, which are potentially involved in the complex etiology of obesity and associated metabolic diseases. These mechanisms include local effects of oral bacteria on taste perception and subsequent food preference as well as systemic effects on adipose tissue function, the gut microbiome and systemic inflammation. This review summarizes a growing body of research, pointing towards a more prominent role of the oral microbiome in obesity and associated metabolic diseases than expected. Ultimately, our knowledge on the oral microbiome may support the development of new patient oriented therapeutic approaches inevitable to relieve the health burden of metabolic diseases and to reach long-term benefits in patients´ lives.

Biomaterial engineering surface to control polymicrobial dental implant-related infections: focusing on disease modulating factors and coatings development

INTRODUCTION

Peri-implantitis is the leading cause of dental implant loss and is initiated by a polymicrobial dysbiotic biofilm formation on the implant surface. The destruction of peri-implant tissue by the host immune response and the low effectiveness of surgical or non-surgical treatments highlight the need for new strategies to prevent, modulate and/or eliminate biofilm formation on the implant surface. Currently, several surface modifications have been proposed using biomolecules, ions, antimicrobial agents, and topography alterations.

AREAS COVERED

Initially, this review provides an overview of the etiopathogenesis and host- and material-dependent modulating factors of peri-implant disease. In addition, a critical discussion about the antimicrobial surface modification mechanisms and techniques employed to modify the titanium implant material is provided. Finally, we also considered the future perspectives on the development of antimicrobial surfaces to narrow the bridge between idea and product and favor the clinical application possibility.

EXPERT OPINION

Antimicrobial surface modifications have demonstrated effective results; however, there is no consensus about the best modification strategy and in-depth information on the safety and longevity of the antimicrobial effect. Modified surfaces display recurring challenges such as short-term effectiveness, the burst release of drugs, cytotoxicity, and lack of reusability. Stimulus-responsive surfaces seem to be a promising strategy for a controlled and precise antimicrobial effect, and future research should focus on this technology and study it from models that better mimic clinical conditions.

Effect of silver diamine fluoride upon the microbial community of carious lesions: A scoping review

OBJECTIVES

To explore the effects of silver diamine fluoride (SDF) on the microbial community of carious lesions.

DATA

Original studies evaluating the effect of SDF treatment on the microbial community of human carious lesions were included.

SOURCES

A systematic search of English-language publications was performed in PubMed, EMBASE, Scopus, and Web of Science. Gray literature was searched in ClinicalTrials.gov and Google Scholar.

STUDY SELECTION/RESULTS

This review included seven publications reporting the effects of SDF on microbial community of dental plaque or carious dentin, including the microbial biodiversity, relative abundance of microbial taxa, and predicted functional pathways of the microbial community. The studies on microbial community of dental plaque reported that SDF did not have a significant effect on both the within-community species diversity (alpha-diversity) and inter-community microbial compositional dissimilarity (beta-diversity) of the plaque microbial communities. However, SDF changed the relative abundance of 29 bacterial species of plaque community, inhibited carbohydrate transportation and interfered with the metabolic functions of the plaque microbial community. A study on the microbial community in dentin carious lesions reported that SDF affected its beta-diversity and changed the relative abundance of 14 bacterial species.

CONCLUSION

SDF showed no significant effects on the biodiversity of the plaque microbial community but changed the beta-diversity of the carious dentin microbial community. SDF could change the relative abundance of certain bacterial species in the dental plaque and the carious dentin. SDF could also affect the predicted functional pathways of the microbial community.

CLINICAL SIGNIFICANCE

This review provided comprehensive evidence on the potential effect of SDF treatment on the microbial community of carious lesions.

A decade of progress: bibliometric analysis of trends and hotspots in oral microbiome research (2013-2022)

Background

Over the past decade, a plethora of studies have delved into the oral microbiome. Our objective was to evaluate the trends in oral microbiome research employing a quantitative approach.

Materials and methods

We extracted clinical studies on the oral microbiome published between 2013 and 2022 from the Web of Science database, yielding 3024 articles. The assembled literature was visually scrutinized using VOSviewer 1.6.18, Citespace 6.1.6, Pajek, Scimago Graphica, and other specialized software to assess authors, institutions, countries, journals, co-cited literature, keywords, genes, and diseases.

Results

Our analysis identified a total of 3024 articles. The volume and rate of annual publications steadily increased, with research interest in the oral microbiome progressively intensifying. The United States, China, and the UK contributed the highest number of publications. Growth rates of publications varied among countries over time. The Forsyth Institute emerged as the most collaborative institution, boasting the highest number of relevant papers (135) and securing the top rank, followed by Sichuan University and Harvard University. Paster Bruce J, Zhou Xuedong, and He Xuesong were pioneers in the field of oral microbiome research. This analysis demonstrates that the homeostatic balance of the oral microbiome, advanced microbial sequencing technology, connections with gut microbiota, and tumorigenesis, including oral cancer, have become emerging topics in the oral microbiome field.

Conclusions

This study delineated a comprehensive landscape of hotspots and frontiers in oral microbiome research, thus facilitating the identification of interdisciplinary advancements. We sincerely hope that our bibliometric analysis will enable researchers to leverage the oral microbiome to ultimately improve human oral health.

Decreased retronasal olfaction and taste perception in obesity are related to saliva biochemical and microbiota composition

Understanding the individual factors that modulate flavor perception is a central issue for the development of personalized diets strategies to fight obesity. This study aimed to investigate differences in flavor perception between adults with normal weight and those with obesity, as well as some potential biological factors related to these differences. To do that, liking and flavor perception intensity were measured against retronasal olfactory (pineapple, butter, tropical and chocolate) and taste attributes (sweetness, umami and bitter) in 77 individuals grouped as normalweight or obese, according to their body mass index (BMI). Unstimulated saliva was collected from all participants and characterized in terms of salivary flow, total protein content, total antioxidant capacity, total esterase activity and bacterial composition through 16S rDNA amplicon sequencing. The results showed that participants displayed differences in flavor perception according to their BMI group. Thus, the group with obesity showed significant lower liking and intensity scores for low calorie related food aroma (pineapple and tropical), lower taste intensity scores for sweet and umami, and a higher acceptability for umami than the group with normal weight. Significant differences between BMI groups were observed for salivary biochemical variables and specific bacterial taxa, some of which were significantly correlated to flavor intensity. This work suggests for the first time the existence of an oral-brain axis that might contribute to the development or perpetuation of obesity, which opens new and interesting avenues of research.

Oral Microbiome Community Composition in Head and Neck Squamous Cell Carcinoma

The impact of the oral microbiome on head and neck cancer pathogenesis and outcomes requires further study. 16s rRNA was isolated and amplified from pre-treatment oral wash samples for 52 cases and 102 controls. The sequences were binned into operational taxonomic units (OTUs) at the genus level. Diversity metrics and significant associations between OTUs and case status were assessed. The samples were binned into community types using Dirichlet multinomial models, and survival outcomes were assessed by community type. Twelve OTUs from the phyla Firmicutes, Proteobacteria, and Acinetobacter were found to differ significantly between the cases and the controls. Beta-diversity was significantly higher between the cases than between the controls (p < 0.01). Two community types were identified based on the predominant sets of OTUs within our study population. The community type with a higher abundance of periodontitis-associated bacteria was more likely to be present in the cases (p < 0.01), in older patients (p < 0.01), and in smokers (p < 0.01). Significant differences between the cases and the controls in community type, beta-diversity, and OTUs indicate that the oral microbiome may play a role in HNSCC.

Microbiome and metabolome associated with white spot lesions in patients treated with clear aligners

White spot lesions (WSLs) have long been a noteworthy complication during orthodontic treatment. Recently, an increasing number of orthodontists have found that adolescents undergoing orthodontic treatment with clear aligners are at a higher risk of developing WSLs. The oral microbiota and metabolites are considered the etiologic and regulatory factors of WSLs, but the specific impact of clear aligners on the oral microbiota and metabolites is unknown. This study investigated the differences in the salivary microbiome and metabolome between adolescents with and without WSLs treated with clear aligners. Fifty-five adolescents (aged 11-18) with Invisalign appliances, 27 with and 28 without WSLs, were included. Saliva samples were analyzed using 16S rRNA gene sequencing and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS); the data were further integrated for Spearman correlation analysis. The relative abundances of 14 taxa, including Actinobacteria, Actinomycetales, Rothia, Micrococcaceae, Subdoligranulum, Capnocytophaga, Azospira, Olsenella, Lachnoanaerobaculum, and Abiotrophia, were significantly higher in the WSL group than in the control group. Metabolomic analysis identified 27 potential biomarkers, and most were amino acids, including proline and glycine. The metabolites were implicated in 6 metabolic pathways, including alanine, aspartate and glutamate metabolism; glycine, serine and threonine metabolism; and aminoacyl-tRNA biosynthesis. There was a correlation between the salivary microbial and metabolomic datasets, reflecting the impact of clear aligners on the metabolic activity of the oral flora. A concordant increase in the levels of Lachnoanaerobaculum, Rothia, Subdoligranulum and some amino acids had predictive value for WSL development. In summary, when adolescents undergo long-term clear aligner therapy with poor oral hygiene habits, clear aligners can disrupt the balance of the oral microecosystem and lead to oral microbiota dysbiosis, thereby increasing the risk of developing WSLs. Our findings might contribute to the understanding of the pathogenesis of WSLs and provide candidate biomarkers for the diagnosis and treatment of WSLs associated with clear aligners.

Longitudinal transkingdom gut microbial approach towards decompensation in outpatients with cirrhosis

OBJECTIVE

First decompensation development is a critical milestone that needs to be predicted. Transkingdom gut microbial interactions, including archaeal methanogens, may be important targets and predictors but a longitudinal approach is needed.

DESIGN

Cirrhosis outpatients who provided stool twice were included. Group 1: compensated, group 2: 1 decompensation (decomp), group 3: >1 decompensationwere followed and divided into those who remained stable or decompensated. Bacteria, viral and archaeal presence, α/β diversity and taxa changes over time adjusted for clinical variables were analysed. Correlation networks between kingdoms were analysed.

RESULTS

157 outpatients (72 group 1, 33 group 2 and 52 group 3) were followed and 28%-47% developed outcomes. Baseline between those who remained stable/developed outcome: While no α/β diversity differences were seen, commensals were lower and pathobionts were higher in those who decompensated. After decompensation: those experiencing their first decompensation showed greater decrease in α/β-diversity, bacterial change (↑Lactobacillus spp, Streptococcus parasanguinis and ↓ beneficial Lachnospiraceae and Eubacterium hallii) and viral change (↑Siphoviridae, ↓ Myoviridae) versus those with further decompensation. Archaea: 19% had Methanobacter brevii, which was similar between/within groups. Correlation networks: Baseline archaeal-viral-bacterial networks were denser and more homogeneous in those who decompensated versus the rest. Archaea-bacterial correlations collapsed post first decompensation. Lactobacillus phage Lc Nu and C2-like viruses were negatively linked with beneficial bacteria.

CONCLUSION

In this longitudinal study of cirrhosis outpatients, the greatest transkingdom gut microbial changes were seen in those reaching the first decompensation, compared with subsequent decompensating events. A transkingdom approach may refine prediction and provide therapeutic targets to prevent cirrhosis progression.

Dysbiome and Its Role in Surgically Relevant Medical Disease

Several surgically relevant conditions are directly or indirectly influenced by the human microbiome. Different microbiomes may be found within, or along, specific organs and intra-organ variation is common. Such variations include those found along the course of the gastrointestinal tract as well as those on different regions of the skin. A variety of physiologic stressors and care interventions may derange the native microbiome. A deranged microbiome is termed a dysbiome and is characterized by decreased diversity and an increase in the proportion of potentially pathogenic organisms; the elaboration of virulence factors coupled with clinical consequences defines a pathobiome. Specific conditions such as Clostridium difficile colitis, inflammatory bowel disease, obesity, and diabetes mellitus are tightly linked to a dysbiome or pathobiome. Additionally, massive transfusion after injury appears to derange the gastrointestinal microbiome as well. This review explores what is known about these surgically relevant clinical conditions to chart how non-surgical interventions may support surgical undertakings or potentially reduce the need for operation.

Mucin glycans drive oral microbial community composition and function

Human microbiome composition is closely tied to health, but how the host manages its microbial inhabitants remains unclear. One important, but understudied, factor is the natural host environment: mucus, which contains gel-forming glycoproteins (mucins) that display hundreds of glycan structures with potential regulatory function. Leveraging a tractable culture-based system to study how mucins influence oral microbial communities, we found that mucin glycans enable the coexistence of diverse microbes, while resisting disease-associated compositional shifts. Mucins from tissues with unique glycosylation differentially tuned microbial composition, as did isolated mucin glycan libraries, uncovering the importance of specific glycan patterns in microbiome modulation. We found that mucins shape microbial communities in several ways: serving as nutrients to support metabolic diversity, organizing spatial structure through reduced aggregation, and possibly limiting antagonism between competing taxa. Overall, this work identifies mucin glycans as a natural host mechanism and potential therapeutic intervention to maintain healthy microbial communities.

BZINB Model-Based Pathway Analysis and Module Identification Facilitates Integration of Microbiome and Metabolome Data

Integration of multi-omics data is a challenging but necessary step to advance our understanding of the biology underlying human health and disease processes. To date, investigations seeking to integrate multi-omics (e.g., microbiome and metabolome) employ simple correlation-based network analyses; however, these methods are not always well-suited for microbiome analyses because they do not accommodate the excess zeros typically present in these data. In this paper, we introduce a bivariate zero-inflated negative binomial (BZINB) model-based network and module analysis method that addresses this limitation and improves microbiome-metabolome correlation-based model fitting by accommodating excess zeros. We use real and simulated data based on a multi-omics study of childhood oral health (ZOE 2.0; investigating early childhood dental caries, ECC) and find that the accuracy of the BZINB model-based correlation method is superior compared to Spearman's rank and Pearson correlations in terms of approximating the underlying relationships between microbial taxa and metabolites. The new method, BZINB-iMMPath, facilitates the construction of metabolite-species and species-species correlation networks using BZINB and identifies modules of (i.e., correlated) species by combining BZINB and similarity-based clustering. Perturbations in correlation networks and modules can be efficiently tested between groups (i.e., healthy and diseased study participants). Upon application of the new method in the ZOE 2.0 study microbiome-metabolome data, we identify that several biologically-relevant correlations of ECC-associated microbial taxa with carbohydrate metabolites differ between healthy and dental caries-affected participants. In sum, we find that the BZINB model is a useful alternative to Spearman or Pearson correlations for estimating the underlying correlation of zero-inflated bivariate count data and thus is suitable for integrative analyses of multi-omics data such as those encountered in microbiome and metabolome studies.

Oral microbiome variations related to ageing: possible implications beyond oral health

The global population is getting older due to a combination of longer life expectancy and declining birth rates. Growing evidence suggests that the oral microbiota composition and distribution may have a profound effect on how well we age. The purpose of this study was to investigate age-related oral microbiome variations of supragingival plaque and buccal mucosa samples in the general population in Latvia. Our results indicated significant difference between supragingival plaque bacterial profiles of three age groups (20-40; 40-60; 60 + years). Within supragingival plaque samples, age group 20-40 showed the highest bacterial diversity with a decline during the 40-60 age period and uprise again after the age of 60. Among other differences, the important oral commensal Neisseria had declined after the age of 40. Additionally, prevalence of two well-documented opportunistic pathogens Streptococcus anginosus and Gemella sanguinis gradually rose with age within our samples. Furthermore, supragingival plaque and buccal mucosa samples significantly differed in overall bacterial composition.