Functional profiles of coronal and dentin caries in children

Oral biofilm composition and phenotype in caries-active and caries-free children

Introduction

During development of dental caries, oral biofilms undergo changes in microbial composition and phenotypical traits. The aim of this study was to compare the acid tolerance (AT) of plaque from two groups of children: one with severe caries (CA) and one with no caries experience (CF) and to correlate this to the microbial composition and metabolic profile of the biofilms.

Methods

Dental plaque samples from 20 children (2-5 years) in each group were studied. The AT was analyzed by viability assessment after exposure to an acid challenge (pH 3.5), using LIVE/DEAD® BacLight™ stain and confocal microscopy. Levels of acid tolerance (AT) were evaluated using a scoring system ranging from 1 (no/low AT), to 5 (high/all AT). Metabolic profiles were investigated following a 20 mM glucose pulse for one hour through Nuclear Magnetic Resonance (NMR). Microbial composition was characterized by 16S rRNA Illumina sequencing.

Results

The mean AT score of the CA group (4.1) was significantly higher than that of the CF group (2.6, p < 0.05). When comparing the end-products of glucose metabolism detected after a glucose-pulse, the CA samples showed a significantly higher lactate to acetate, lactate to formate, lactate to succinate and lactate to ethanol ratio than the CF samples (p < 0.05). The bacterial characterization of the samples revealed 25 species significantly more abundant in the CA samples, including species of Streptococcus, Prevotella, Leptotrichia and Veillonella (p < 0.05).

Discussion

Our results show that AT in pooled plaque from the oral cavity of children with severe caries is increased compared to that in healthy subjects and that this can be related to differences in the metabolic activity and microbial composition of the biofilms. Thus, the overall phenotype of dental plaque appears to be a promising indicator of the caries status of individuals. However, longitudinal studies investigating how the AT changes over time in relation to caries development are needed before plaque AT could be considered as a prediction method for the development of dental caries.

Bacterial dynamics in the progression of caries to apical periodontitis in primary teeth of children with severe early childhood caries

Background

Early childhood caries (ECC) are a prevalent chronic disease in young children. However, there has been limited research on the microbiota in different tissue levels of the same tooth in children with ECC. This study aimed to investigate the dynamic changes in bacterial diversity during the progression of Severe Early Childhood Caries (S-ECC) within the same tooth, from the tooth surface to the root canal, by collecting tissue samples from different areas of the affected tooth.

Methods

Twenty primary teeth with periapical periodontitis were selected from 20 children aged 3-5 years, with 100 samples collected from the different layers: uncavitated buccal enamel surface without white spot lesion (surface), the outermost layer of the dentin carious lesion (superficial), the inner layer of carious dentin (deep), necrotic pulp tissue (pulp), and root exudate (exudate). The taxonomy of each OTU representative sequence was analyzed against the 16S rRNA database. Comparisons of alpha diversity between groups were performed. The number of shared and unique genera between groups counted. Beta diversity was contrasted to evaluate differences in bacterial community composition, and the relationships between the microbiota and samples were analyzed. The heatmap analysis of the 30 most abundant genera was used, which highlighted their relative distribution and abundance. The significantly abundant taxa (phylum to genera) of bacteria among the different groups were identified. The differences of relative abundance between bacterial genera among the five groups were analyzed. Significant Spearman correlations were noted, and visualization of the co-occurrence network was conducted.

Results

Bacterial 16S rRNA gene sequencing showed that most genera were present in all layers, with the number of shared genera increasing as the disease advanced. The bacterial communities and core genera in the co-occurrence network changed with progression to severe ECC.

Conclusion

An increase in both the quantity and complexity of bacterial interactions was observed. This study emphasized the importance of paying attention to the relationship between microbial species rather than just checking changes in bacterial species structure when investigating the role of bacteria in disease progression.

Omics for deciphering oral microecology

The human oral microbiome harbors one of the most diverse microbial communities in the human body, playing critical roles in oral and systemic health. Recent technological innovations are propelling the characterization and manipulation of oral microbiota. High-throughput sequencing enables comprehensive taxonomic and functional profiling of oral microbiomes. New long-read platforms improve genome assembly from complex samples. Single-cell genomics provides insights into uncultured taxa. Advanced imaging modalities including fluorescence, mass spectrometry, and Raman spectroscopy have enabled the visualization of the spatial organization and interactions of oral microbes with increasing resolution. Fluorescence techniques link phylogenetic identity with localization. Mass spectrometry imaging reveals metabolic niches and activities while Raman spectroscopy generates rapid biomolecular fingerprints for classification. Culturomics facilitates the isolation and cultivation of novel fastidious oral taxa using high-throughput approaches. Ongoing integration of these technologies holds the promise of transforming our understanding of oral microbiome assembly, gene expression, metabolites, microenvironments, virulence mechanisms, and microbe-host interfaces in the context of health and disease. However, significant knowledge gaps persist regarding community origins, developmental trajectories, homeostasis versus dysbiosis triggers, functional biomarkers, and strategies to deliberately reshape the oral microbiome for therapeutic benefit. The convergence of sequencing, imaging, cultureomics, synthetic systems, and biomimetic models will provide unprecedented insights into the oral microbiome and offer opportunities to predict, prevent, diagnose, and treat associated oral diseases.

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.

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.

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

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

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.

Symbiotic relationship between Prevotella denticola and Streptococcus mutans enhances virulence of plaque biofilms

OBJECTIVES

This study aimed to explore that whether interactions between Prevotella denticola and Streptococcus mutans could promote the establishment of hypervirulent biofilms on teeth surface and eventually influence the occurrence and development of caries.

DESIGN

Based on single-species biofilms of either P. denticola or S. mutans, and dual-species biofilms of both bacteria, we compared the virulence properties associated with cariogenicity in vitro, including carbohydrate metabolism and acid productivity, synthesis of extracellular polysaccharides, biomass and architecture of biofilms, level of enamel demineralization and expression of virulence genes associated with carbohydrate metabolism and adhesion in S. mutans.

RESULTS

The data demonstrated that, compared to single-species of above two taxa, dual-species produced lactate by metabolizing carbohydrates at a higher level during the observation period. Moreover, dual-species biofilms accrued more biomass and exhibited more dense microcolonies and abundant extracellular matrix. And it's noticeable that the level of enamel demineralization in dual-species biofilms was more augmented than that of single-species. In addition, the presence of P. denticola induced the expression of virulence genes gtfs and gbpB in S. mutans.

CONCLUSIONS

Symbiotic relationship between P. denticola and S. mutans enhances caries-associated virulence of plaque biofilms, which might provide new strategies for effective prevention and treatment of caries.

Understanding human health through metatranscriptomics

Metatranscriptomics has revolutionized our ability to explore and understand transcriptional programs in microbial communities. Moreover, it has enabled us to gain deeper and more specific insight into the microbial activities in human gut, respiratory, oral, and vaginal communities. Perhaps the most important contribution of metatranscriptomics arises, however, from the analyses of disease-associated communities. We review the advantages and disadvantages of metatranscriptomics analyses in understanding human health and disease. We focus on human tissues low in microbial biomass and conditions associated with dysbiotic microbiota. We conclude that a more widespread use of metatranscriptomics and increased knowledge on microbe activities will uncover critical interactions between microbes and host in human health and provide diagnostic basis for culturing-independent, direct functional pathogen identification.

Oral Microbiome and Dental Caries Development

Dental caries remains the most prevalent oral disease worldwide. The development of dental caries is highly associated with the microbiota in the oral cavity. Microbiological research of dental caries has been conducted for over a century, with conventional culture-based methods and targeted molecular methods being used in order to identify the microorganisms related to dental caries. These methods' major limitation is that they can identify only part of the culturable microorganisms in the oral cavity. Introducing sequencing-based technology and bioinformatics analysis has boosted oral microbiome research and greatly expanded the understanding of complex oral microbiology. With the continuing revolution of molecular technologies and the accumulated sequence data of the oral microbiome, researchers have realized that microbial composition alone may be insufficient to uncover the relationship between caries and the microbiome. Most updated evidence has coupled metagenomics with transcriptomics and metabolomics techniques in order to comprehensively understand the microbial contribution to dental caries. Therefore, the objective of this article is to give an overview of the research of the oral microbiome and the development of dental caries. This article reviews the classical concepts of the microbiological aspect of dental caries and updates the knowledge of caries microbiology with the results of current studies on the oral microbiome. This paper also provides an update on the caries etiological theory, the microorganisms related to caries development, and the shifts in the microbiome in dental caries development.

Optimization and Evaluation of the 30S-S11 rRNA Gene for Taxonomic Profiling of Oral Streptococci

Dental caries is a multifactorial disease driven by interactions between the highly complex microbial biofilm community and host factors like diet, oral hygiene habits, and age. The oral streptococci are one of the most dominant members of the plaque biofilm and are implicated in disease but also in maintaining oral health. Current methods used for studying the supragingival plaque community commonly sequence portions of the16S rRNA gene, which often cannot taxonomically resolve members of the streptococcal community past the genus level due to their sequence similarity. The goal of this study was to design and evaluate a more reliable and cost-effective method to identify oral streptococci at the species level by applying a new locus, the 30S-S11 rRNA gene, for high-throughput amplicon sequencing. The study results demonstrate that the newly developed single-copy 30S-S11 gene locus resolved multiple amplicon sequence variants (ASVs) within numerous species, providing much improved taxonomic resolution over 16S rRNA V4. Moreover, the results reveal that different ASVs within a species were found to change in abundance at different stages of caries progression. These findings suggest that strains of a single species may perform distinct roles along a biochemical spectrum associated with health and disease. The improved identification of oral streptococcal species will provide a better understanding of the different ecological roles of oral streptococci and inform the design of novel oral probiotic formulations for prevention and treatment of dental caries. IMPORTANCE The microbiota associated with the initiation and progression of dental caries has yet to be fully characterized. Although much insight has been gained from 16S rRNA hypervariable region DNA sequencing, this approach has several limitations, including poor taxonomic resolution at the species level. This is particularly relevant for oral streptococci, which are abundant members of oral biofilm communities and major players in health and caries disease. Here, we develop a new method for taxonomic profiling of oral streptococci based on the 30S-S11 rRNA gene, which provides much improved resolution over 16S rRNA V4 (resolving 10 as opposed to 2 species). Importantly, 30S-S11 can resolve multiple amplicon sequence variants (ASVs) within species, providing an unprecedented insight into the ecological progression of caries. For example, our findings reveal multiple incidences of different ASVs within a species with contrasting associations with health or disease, a finding that has high relevance toward the informed design of prebiotic and probiotic therapy.

Taxonomic and functional alterations in the salivary microbiota of children with and without severe early childhood caries (S-ECC) at the age of 3

Background

Primary dental caries is the most prevalent oral disease among preschool children, which can cause severe damage to teeth and even affect the mental well-being of children. Various studies have demonstrated that the oral microbiome plays a pivotal role in the onset and development of dental caries. However, it remains uncertain about the key microbial markers associated with caries, owing to the limited evidence.

Methods

Fifteen S-ECC children and fifteen healthy controls were selected from three-year-old children in this study. Their clinical data and oral saliva samples were collected. Shotgun sequencing was conducted to investigate the microbial differences and the relevant functions between the two groups.

Results

We observed no apparent difference in oral microbial community diversity between the two groups. Still, at the genus/species levels, several characteristic genera/species such as Propionibacterium, Propionibacterium acidifaciens, Prevotella denticola, Streptococcus mutans and Actinomyces sp. oral taxon 448/414 increased significantly in S-ECC children, compared with the oral health group. Furthermore, we found that functional pathways involving glycolysis and acid production, such as starch and sucrose metabolism, fructose and mannose metabolism, glycolysis/gluconeogenesis, were prominently up-regulated in the high-caries group.

Conclusions

Our study showed that dental caries in children were associated with the alterations in the oral microbiota at the composition and functional levels, which may potentially inspire the exploration of microbial diagnosis or therapeutic treatments.

Prevotella species as oral residents and infectious agents with potential impact on systemic conditions

Oral Prevotella are known as anaerobic commensals on oral mucosae and in dental plaques from early life onwards, including pigmented P. melaninogenica, P. nigrescens, and P. pallens and non-pigmented Prevotella species. Many Prevotella species contribute to oral inflammatory processes, being frequent findings in dysbiotic biofilms of periodontal diseases (P. intermedia, P. nigrescens), cariotic lesions (P. denticola, Alloprevotella (formerly Prevotella) tannerae), endodontic infections (P. baroniae, P. oris, P. multisaccharivorax), and other clinically relevant oral conditions. Over the years, several novel species have been recovered from the oral cavity without knowledge of their clinical relevance. Within this wide genus, virulence properties and other characteristics like biofilm formation seemingly vary in a species- and strain-dependent manner, as shown for the P. intermedia group organisms (P. aurantiaca, P. intermedia, P. nigrescens, and P. pallens). Oral Prevotella species are identified in various non-oral infections and chronic pathological conditions. Here, we have updated the knowledge of the genus Prevotella and the role of Prevotella species as residents and infectious agents of the oral cavity, as well as their detection in non-oral infections, but also gathered information on their potential link to cancers of the head and neck, and other systemic disorders.

Streptococcus mutans-associated bacteria in dental plaque of severe early childhood caries

Background

Streptococcus mutans (S. mutans) is a potential pathogenic bacteria of dental caries. However, the level of S. mutans is low in some children with severe early childhood caries (SECC)

Aim

To evaluate the effect of S. mutans level on dental microbiome and cariogenesis.

Methods

The oral microbiota was compared between caries-free group (CF) and SECC group.16S rRNA gene sequencing was used for S. mutans level bacterial community analysis. The candidate bacteria that were closely related with S. mutans abundance were identified and confirmed by absolute quantitative real-time PCR in clinical dental plaque samples from CF and SECC groups.

Results

Through in-depth analysis of dental plaque microorganism, Leptotrichia, Selenomonas and Prevotella_7 were found in the S. mutans-low group (p < 0.05) and Porphyromonas, Selenomonas_3 were found in the S. mutans-high group (p < 0.05). Through quantitative real-time PCR, Leptotrichia, Selenomonas and Prevotella_7 were identified as the potential biomarkers of SECC when S. mutans was at a low level.

Conclusion

Leptotrichia, Selenomonas and Prevotella_7 are identified as potential biomarkers in SECC with a low abundance or without S. mutans. Our study may shed light on the understanding of caries occurrence in SECC with low abundance of S. mutans.

Abbreviations

S. mutans, Streptococcus mutans; CF, caries-free; SECC, severe early childhood caries; ECC, early childhood caries; rRNA, ribosome RNA; qPCR, Quantitative real-time PCR; OTUs, operational taxonomic units; ANOVA, analysis of variance; LDA, Linear discriminant analysis; LEfSe, Linear discriminant analysis effect size; COG, Groups of proteins; NMDS, Non-MetricMulti-Dimensional Scaling; IL-1β, interleukin −1β; IL-6, interleukin-6; IL-8, interleukin-8; IL-10, interleukin-10.

The Crosstalk Between Saliva Bacteria and Fungi in Early Childhood Caries

Early childhood caries (ECC) is the most prevalent oral disease in children, which greatly affects the quality of life and health condition of the patients. Although co-infection of oral streptococci and fungi has been well recognized in the development of ECC, the correlation between other core members of oral mycobiome and ECC progression remains unclear. In the current study, saliva samples obtained from severe ECC (SECC), ECC, and caries-free children were collected, and both V3–V4 16S rRNA and ITS1 rRNA gene amplicon sequencing were performed to investigate the salivary bacterial and fungal profiles. Significant alteration of salivary fungal community in SECC/ECC children was observed compared with the caries-free control. The typing analysis determined the fungal community into five fungal types, which influenced the structure of salivary bacteria. By performing Spearman correlation analysis, carious phenotypes were positively related to Fusobacterium but negatively linked to Neocosmospora, and a significant correlation of cross-kingdom taxonomic pairs was identified. Our work demonstrated the interactions between oral bacteria and fungi at the community level, which may advance our knowledge on the etiological role of bacteria/fungi in the development of ECC and promote better management of this disease.

Diversity of site-specific microbes of occlusal and proximal lesions in severe- early childhood caries (S-ECC)

BACKGROUND

Severe-early childhood caries (S-ECC) a global problem of significant concern, commonly manifest on the occlusal, and proximal surfaces of affected teeth. Despite the major ecological differences between these two niches the compositional differences, if any, in the microbiota of such lesions is unknown.

METHODS

Deep-dentine caries samples from asymptomatic primary molars of children with S-ECC (n 19) belonging to caries-code 5/6, (ICDAS classification) were evaluated. Employing two primer pools, we amplified and compared the bacterial 16S rRNA gene sequences of the seven hypervariable regions (V2-V4 and V6-V9) using NGS-based assay.

RESULTS

Bray-Curtisevaluation indicated that occlusal lesions (OL) had a more homogeneous community than the proximal lesions (PL) with significant compositional differences at the species level (p = 0.01; R- 0.513). Together, the occlusal and proximal niches harbored 263 species, of which 202 (76.8%) species were common to both , while 49 (18.6%) and 12 (4.6%) disparate species were exclusively isolated from the proximal and occlusal niches, respectively. The most commonl genera at both niches included Streptococcus, Prevotella, and Lactobacillus. S. mutans was predominant in PL (p ≤ 0.05), and Atopobium parvulum (p = 0.01) was predominant in OL.

CONCLUSIONS

Distinct differences exist between the caries microbiota of occlusal and proximal caries in S-ECC.

Metagenomic and Metatranscriptomic Insight Into Oral Biofilms in Periodontitis and Related Systemic Diseases

The oral microbiome is one of the most complex microbial communities in the human body and is closely related to oral and systemic health. Dental plaque biofilms are the primary etiologic factor of periodontitis, which is a common chronic oral infectious disease. The interdependencies that exist among the resident microbiota constituents in dental biofilms and the interaction between pathogenic microorganisms and the host lead to the occurrence and progression of periodontitis. Therefore, accurately and comprehensively detecting periodontal organisms and dissecting their corresponding functional activity characteristics are crucial for revealing periodontitis pathogenesis. With the development of metagenomics and metatranscriptomics, the composition and structure of microbial communities as well as the overall functional characteristics of the flora can be fully profiled and revealed. In this review, we will critically examine the currently available metagenomic and metatranscriptomic evidence to bridge the gap between microbial dysbiosis and periodontitis and related systemic diseases.

Comparative Microbial Profiles of Caries and Black Extrinsic Tooth Stain in Primary Dentition

Extrinsic black tooth stain (BS) is a common oral disease associated with lower caries experience in preschool children, although the microbiotic features contributing to the low risk of caries in this group remain elusive. In this study, we aimed at identifying the dominant bacteria in dental plaque to indicate the incidence of caries in the primary dentition. Subjects were divided into 3 groups based on the clinical examination: group CF, children without pigment who had no caries lesions or restorations (n = 18); group CS, children who were diagnosed with severe early childhood caries (n = 17); and group BS, children with pigment (black extrinsic stain) without caries or restorations (n = 15). The total microbial genomic DNA was extracted and subjected to bacterial 16S ribosomal RNA gene sequencing using an Illumina HiSeq platform. The differential dominant bacteria were determined using Wilcoxon rank-sum testing and linear discriminant analysis effect size (LEfSe). Co-occurrence network analysis was performed using sparse correlations for compositional data, calculation and functional features were predicted using PICRUSt. Interestingly, our results showed that the relative abundance of Pseudopropionibacterium, Actinomyces, Rothia, and Cardiobacterium was from high to low and that of Porphyromonas was low to high in the BS, CF, and CS groups, consistent with the clinical incidence of caries in the 3 groups. Moreover, an increased level of Selenomonas_3, Fusobacterium, and Leptotrichia was associated with high caries prevalence. We found that the interactions among genera in the BS and CS plaque communities are less complex than those in the CF communities at the taxon level. Functional features, including cofactor and vitamin metabolism, glycan biosynthesis and metabolism, and translation, significantly increased in caries plaque samples. These bacterial competition- and commensalism-induced changes in microbiota would result in a change of their symbiotic function, finally affecting the balance of oral microflora.

Freitas-Fernandes L, Fidalgo TKS, Tadeu Lopes R, Valente AP, R. Arnold R, de Aguiar Ribeiro A. The bacterial microbiome and metabolome in caries progression and arrest

Aim: This in vivo experimental study investigated bacterial microbiome and metabolome longitudinal changes associated with enamel caries lesion progression and arrest. Methods: We induced natural caries activity in three caries-free volunteers prior to four premolar extractions for orthodontic reasons. The experimental model included placement of a modified orthodontic band on smooth surfaces and a mesh on occlusal surfaces. We applied the caries-inducing protocol for 4- and 6-weeks, and subsequently promoted caries lesion arrest via a 2-week toothbrushing period. Lesions were verified clinically and quantitated via micro-CT enamel density measurements. The biofilm microbial composition was determined via 16S rRNA gene Illumina sequencing and NMR spectrometry was used for metabolomics. Results: Biofilm maturation and caries lesion progression were characterized by an increase in Gram-negative anaerobes, including Veillonella and Prevotella. Streptococcus was associated caries lesion progression, while a more equal distribution of Streptococcus, Bifidobacterium, Atopobium, Prevotella, Veillonella, and Saccharibacteria (TM7) characterized arrest. Lactate, acetate, pyruvate, alanine, valine, and sugars were more abundant in mature biofilms compared to newly formed biofilms. Conclusions: These longitudinal bacterial microbiome and metabolome results provide novel mechanistic insights into the role of the biofilm in caries progression and arrest and offer promising candidate biomarkers for validation in future studies.

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

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

Dental plaque microbiota profiles of children with caries-free and caries-active dentition

OBJECTIVE

Microbiota comparisons between healthy and diseased dental tissues have accentuated the importance of cultivating and identifying bacterial species that play a role in the initiation and progression of dental caries. The objective of this study was to evaluate the bacterial community composition in caries-active and caries-free children.

METHODS

Supragingival plaque samples were collected from 64 caries-active and 64 caries-free Middle Eastern children. The hypervariable V3-V4 of the bacterial 16S rRNA gene was sequenced with Human Oral Microbe Identification using Next Generation Sequencing. Microbial community structure and composition analyses were performed by processing operational taxonomic units. Bioinformatic analyses, including analysis of similarity, alpha and beta diversities, and principal coordinate analysis, were carried out.

RESULTS

Diversity indices did not find differences between the caries-active and caries-free groups (p > 0.05). Similarity analysis demonstrated that the microbiota composition did not differ between the two groups. Comparative analysis at the species level revealed a significantly higher relative abundance of Leptotrichia shahii, Prevotella melaninogenica, Veillonella dispar, Leptotrichia HOT 498, and Streptococcus mutans in caries-active children (p < 0.05). Corynebacterium matruchotii, Lautropia mirabilis, Neisseria elongata, and Corynebacterium durum were relatively more abundant in the caries-free group (p < 0.05). Species belonging to the Leptotrichia, Prevotella, and Veillonella genera were significantly predominant in the caries-active subjects.

CONCLUSION

In view of the lack of a clear association between Corynebacterium spp. and dental caries status in the literature, the predominance of these species in caries-free children warrants further research to understand their possible role in a health-associated microbial community.

CLINICAL SIGNIFICANCE

Understanding the relationship between specific bacteria present in dental biofilms and health and disease is essential for preventing and combating dental caries. Using advanced next generation sequencing techniques, the present study demonstrated the complexity of the caries microbiome and identified species/genera whose virulence or protective properties should be further explored.

Omics and interspecies interaction

Interspecies interactions are key determinants in biofilm behavior, ecology, and architecture. The cellular responses of microorganisms to each other at transcriptional, proteomic, and metabolomic levels ultimately determine the characteristics of biofilm and the corresponding implications for health and disease. Advances in omics technologies have revolutionized our understanding of microbial community composition and their activities as a whole. Large-scale analyses of the complex interaction between the many microbial species residing within a biofilm, however, are currently still hampered by technical and bioinformatics challenges. Thus, studies of interspecies interactions have largely focused on the transcriptional and proteomic changes that occur during the contact of a few prominent species, such as Porphyromonas gingivalis, Streptococcus mutans, Candida albicans, and a few others, with selected partner species. Expansion of available tools is necessary to grow the revealing, albeit limited, insight these studies have provided into a profound understanding of the nature of individual microbial responses to the presence of others. This will allow us to answer important questions including: Which intermicrobial interactions orchestrate the myriad of cooperative, synergistic, antagonistic, manipulative, and other types of relationships and activities in the complex biofilm environment, and what are the implications for oral health and disease?

Metatranscriptomic analyses of the oral microbiome

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

Pulp Fibroblast Contribution to the Local Control of Pulp Inflammation via Complement Activation

Upon traumatic injuries or carious lesions, the elimination of bacteria infiltrating the pulp is recognized as a prerequisite for initiating the regeneration process. Complement is a major system involved in initiating the inflammatory reaction and the subsequent bacteria elimination. This plasma system of above 35 proteins is synthesized by the liver and some immune cells. It is activated by 3 pathways: the classical, alternative, and lectin pathways that can be triggered by physical injuries, infection, and biomaterials. Recent data have shown that the pulp fibroblast represents a unique nonimmune cell type able to synthesize Complement proteins. Indeed, after physical injuries/bacteria stimulation, the pulp fibroblast has been shown to synthesize and to activate the complement system leading to the production of biologically active molecules such as C5a, C3b, and the membrane attack complex. This local secretion represents a rapid and efficient mechanism for eliminating bacteria invading the pulp, thus supporting complement activation from the plasma. Pulp fibroblast-secreted Complement proteins allow cariogenic bacteria direct lysis via membrane attack complex formation on their surface, phagocytic cell recruitment by producing C5a and cariogenic bacteria opsonization by C3b fixation on their surface, stimulating cariogenic bacteria phagocytosis. Overall, this review highlights that, in addition to initiating the inflammatory reaction, pulp fibroblasts also provide a powerful control of this inflammation via local Complement activation. The pathogen elimination capacity by fibroblast-produced complement demonstrates that this system is a strong local actor in arresting bacterial progression into the dental pulp.

Antimicrobial Peptide GH12 Prevents Dental Caries by Regulating Dental Plaque Microbiota

Due to the complex microecology and microenvironment of dental plaque, novel caries prevention strategies require modulating the microbial communities ecologically and reducing the cariogenic properties effectively. Antimicrobial peptide GH12 reduced the lactic acid production and exopolysaccharide (EPS) synthesis of a Streptococcus mutans biofilm and a three-species biofilm in vitro in previous studies. However, the anticaries effects and microecological effects of GH12 remained to be investigated in a complex biofilm model in vitro and an animal caries model in vivo In the present study, GH12 at 64 mg/liter showed the most effective inhibition of lactic acid production, EPS synthesis, pH decline, and biofilm integrity of human dental plaque-derived multispecies biofilms in vitro, and GH12 at 64 mg/liter was therefore chosen for use in subsequent in vitro and in vivo assays. When treated with 64-mg/liter GH12, the dental plaque-derived multispecies biofilms sampled from healthy volunteers maintained its microbial diversity and showed a microbial community structure similar to that of the control group. In the rat caries model with a caries-promoting diet, 64-mg/liter GH12 regulated the microbiota of dental plaque, in which the abundance of caries-associated bacteria was decreased and the abundance of commensal bacteria was increased. In addition, 64-mg/liter GH12 significantly reduced the caries scores of sulcal and smooth surface caries in all locations. In conclusion, GH12 inhibited the cariogenic properties of dental plaque without perturbing the dental plaque microbiota of healthy individuals and GH12 regulated the dysbiotic microbial ecology and arrested caries development under cariogenic conditions.IMPORTANCE The anticaries effects and microecological regulation effects of the antimicrobial peptide GH12 were evaluated systematically in vitro and in vivo GH12 inhibited the cariogenic virulence of dental plaque without overintervening in the microbial ecology of healthy individuals in vitro GH12 regulated the microbial ecology of dental plaque to a certain extent in vivo under cariogenic conditions, increased the proportion of commensal bacteria, and decreased the abundance of caries-associated bacteria. GH12 significantly suppressed the incidence and severity of dental caries in vivo This study thus describes an alternative antimicrobial therapy for dental caries.

Quantitative Analysis of Salivary Oral Bacteria Associated with Severe Early Childhood Caries and Construction of Caries Assessment Model

To construct a saliva-based caries risk assessment model, saliva samples from 176 severe early childhood caries (S-ECC) children and 178 healthy (H) children were screened by real-time PCR-based quantification of the selected species, including Streptococcus mutans, Prevotella pallens, Prevotella denticola and Lactobacillus fermentum. Host factors including caries status, dmft indices, age, gender, and geographic origin were assessed in their influence on abundance of the targeted species, which revealed host caries status as the dominant factor, followed by dmft indices (both P < 0.01). Moreover, levels of S. mutans and P. denticola in the S-ECC group were significantly higher than those in the healthy group (P < 0.001 for S. mutans and P < 0.01 for P. denticola). Interestingly, the co-occurrence network of these targeted species in the S-ECC group differed from that from the healthy group. Finally, based on the combined change pattern of S. mutans and P. pallens, we constructed an S-ECC diagnosis model with an accuracy of 72%. This saliva-based caries diagnosis model is of potential value for circumstances where sampling dental plague is difficult.

Oral microbiomes in children with asthma and dental caries

OBJECTIVE

Recently, a significant association between dental caries and the severity of bronchial asthma in children has been revealed. This finding indicates a possible relationship between the oral microbiome and the pathogenesis of asthma. The purpose of our study was to estimate differences in the dental plaque microbiota of asthmatic children with and without dental caries by 16S rDNA sequencing.

MATERIAL AND METHODS

Dental plaque samples were obtained with a spoon excavator from the occlusal surface of one deciduous tooth (the second mandibular left molar in caries-free children and the most affected tooth in caries-affected children). Total DNA was extracted from dental plaque. DNA libraries were analysed by 16S rRNA gene sequencing on the MiSeq (Illumina) platform.

RESULTS

There were no significant differences in the composition of bacterial communities from both caries-affected and caries-free children with asthma. The "caries-enriched" genus was Veillonella (Veillonellaceae, Selenomonadales, Negativicutes). Relative abundance of Neisseria was significantly higher in caries-free children with asthma (p < 0.05).

CONCLUSIONS

The most significant difference in compared bacterial communities was a higher relative abundance of Veillonella in caries-affected plaques that suggests its involvement in pathogenesis of caries. Potential respiratory pathogens are present in oral cavity of both caries-affected and caries-free asthmatic children.