Comparative Analysis of the Microbial Profiles in Supragingival Plaque Samples Obtained From Twins With Discordant Caries Phenotypes and Their Mothers

Streptococcus mutans and Caries: A Systematic Review and Meta-Analysis

It has been questioned whether Streptococcus mutans can still be considered the major etiological agent for caries. The main argument is that most evidence has been based on single-species identification. The composition of the oral microbiome was not analyzed. This systemic review aims to assess the prevalence and abundance of S. mutans in caries-active (CA) and caries-free (CF) subjects based on clinical studies in which the microbiome was investigated. Three databases (PubMed, Cochrane, Embase) were searched until May 22, 2023, for eligible publications that included CA and CF subjects and reported the detection of both S. mutans and the oral microbial community, using DNA-based methods. The clinical and microbial outcomes were summarized and further analyzed using a random-effects model. Of 22 eligible studies, 3 were excluded due to the high risk of bias. In the remaining 19 studies, 16 reported the prevalence of S. mutans, 11 reported its relative abundance, and 8 reported both parameters. The prevalence of S. mutans in CA was either similar to (n = 4) or higher than (n = 12) the CF group. The reported relative abundance in CA was higher than CF in all 11 studies, although the values varied from 0.001% to 5%. Meta-analysis confirmed the significance of these findings. The summary of microbial community data did not reveal other caries-associated bacterial genera/species than S. mutans. In conclusion, the collected evidence based on microbiome studies suggests a strong association between the prevalence and abundance of S. mutans and caries experience. While the cariogenic role of S. mutans in the oral ecosystem should be recognized, its actual function warrants further exploration.

Imbalance of oral microbiome homeostasis: the relationship between microbiota and the occurrence of dental caries

BACKGROUND

Streptococcus mutans is recognized as a key pathogen responsible for the development of dental caries. With the advancement of research on dental caries, the understanding of its pathogenic mechanism has gradually shifted from the theory of a single pathogenic bacterium to the theory of oral microecological imbalance. Acidogenic and aciduric microbial species are also recognized to participate in the initiation and progression of dental caries. This study is designed to elucidate the relationship between oral microbiome dysregulation and the initiation of dental caries.

RESULTS

16 S rRNA gene sequencing of saliva and dental plaque from the Specific Pathogen Free Control group and the Specific Pathogen Free sucrose diet group revealed that a sucrose diet significantly influenced the composition of the oral microbiome. At the phylum level, the dominant microbial communities in both groups of mice were Firmicutes, Proteobacteria, Unclassified Bacteria, Actinobacteria, and Bacteroidetes. At the genus level, statistical analysis identified significant differences in the abundance of 18 genera between the two groups. The relative abundance of the Gemella genus was significantly increased in the SPF Sucrose group. The SPF Control group and the Germ-free Control group have no differential bacterial genera in the oral microbiome. Micro-CT examination of the mandibles revealed the development of dental caries in both the SPF Sucrose group and the Germ-free Sucrose group.

CONCLUSIONS

This study indicates that a dysbiotic microbial community can lead to the development of caries. Lays the foundation for further research into the etiology of dental caries.

The microbiome alterations of supragingival plaque among adolescents using clear aligners: a metagenomic sequencing analysis

BACKGROUND

White spot lesions (WSLs) may develop in adolescents undergoing clear aligner (CA) therapy with poor oral hygiene. The specific effects of CAs on the microbial composition and functional characteristics of supragingival plaques remain unclear. The present study investigated the shift in the supragingival microbial community induced by CAs in adolescents through metagenomic technology.

METHODS

Fifteen adolescents (12-15 years old) with Invisalign appliances were recruited. Supragingival plaque specimens were obtained twice, before treatment (T1) and three months after treatment (T2). All the bacterial plaque specimens were analyzed for microbial communities and functions using metagenomic analyses.

RESULTS

A total of 2,840,242,722 reads disclosed 180 phyla, 3,975 genera, and 16,497 microbiome species. During the first three months, the microbial community was relatively stable. The genus level revealed a higher relative abundance of Capnocytophaga, Neisseria, and Arachnia in the T2 period. Furthermore, the functional analysis suggested that the relative abundances of folate biosynthesis, biotin metabolism and biofilm formation-vibrio cholerae were increased in the T2 period compared to the T1 period. Finally, virulence factor analysis demonstrated that the relative abundance of genes associated with type IV pili (VF0082) and polar flagella (VF0473) was higher in the T2 period than in the T1 period.

CONCLUSION

In adolescents undergoing CA therapy with poor plaque control, caries progresses quickly within three months and noticeable WSLs develop on the tooth surface. Although the microbial community remained relatively steady and CA therapy did not cause significant changes in the overall functional gene composition in the first three months, virulence factors, including type IV pili and flagella, were more abundant and actively contributed to microorganism adhesion and biofilm formation.

A deep learning feature importance test framework for integrating informative high-dimensional biomarkers to improve disease outcome prediction

Many human diseases result from a complex interplay of behavioral, clinical, and molecular factors. Integrating low-dimensional behavioral and clinical features with high-dimensional molecular profiles can significantly improve disease outcome prediction and diagnosis. However, while some biomarkers are crucial, many lack informative value. To enhance prediction accuracy and understand disease mechanisms, it is essential to integrate relevant features and identify key biomarkers, separating meaningful data from noise and modeling complex associations. To address these challenges, we introduce the High-dimensional Feature Importance Test (HdFIT) framework for machine learning models. HdFIT includes a feature screening step for dimension reduction and leverages machine learning to model complex associations between biomarkers and disease outcomes. It robustly evaluates each feature's impact. Extensive Monte Carlo experiments and a real microbiome study demonstrate HdFIT's efficacy, especially when integrated with advanced models like deep neural networks. Our framework shows significant improvements in identifying crucial features and enhancing prediction accuracy, even in high-dimensional settings.

The oral microbiome of children in health and disease-a literature review

The oral microbiome is a complex community of microorganisms residing in the oral cavity interacting with each other and with the host in a state of equilibrium. Disruptions in this balance can result in both oral and systemic conditions. Historically, studying the oral microbiome faced limitations due to culture-dependent techniques that could not capture the complexity and diversity of the microbial community. The emergence of advanced genomic technologies and the ease of sample collection from the oral cavity has revolutionized the understanding of the oral microbiome, providing valuable insights into the bacterial community in both health and disease. This review explores the oral microbiome in children, discussing its formation and dynamics in both states of health and disease, its role in various conditions such as dental caries, periodontal disease, oral cancer, cleft lip and palate, and explores its connection to several systemic consequences.

Effects of dietary nitrate supplementation on oral health and associated markers of systemic health: a systematic review

Poor oral health can impact an individual's ability to eat and has been associated with an increased risk of non-communicable diseases. While the benefits of nitrate consumption on oral health were first proposed more than 20 years ago, no systematic review has been published examining effects of dietary nitrate on oral health. This systematic review investigated the effects of dietary nitrate on markers of oral health in vivo in randomized controlled trials (RCTs). Five databases (PubMed, The Cochrane Library, CINAHL, MEDLINE, and SPORTDiscus) were searched from inception until March 2023. Nine articles reporting data on 284 participants were included. Dietary nitrate was provided via beetroot juice in most studies. The duration of the interventions ranged from one day to six weeks. Dietary nitrate supplementation increased the relative abundance of several individual bacterial genera including Neisseria and Rothia. Dietary nitrate supplementation increased salivary pH and decreased salivary acidification following consumption of a sugar-sweetened beverage. Furthermore, dietary nitrate supplementation resulted in a decrease in the gingival inflammation index. The results of this systematic review suggest that dietary nitrate could represent a potential nutritional strategy to positively modify oral health by impacting the oral microbiome, altering salivary pH, and minimizing gingival inflammation.

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.

Is there an association between dental caries and genetics? Systematic review and meta-analysis of studies with twins

OBJECTIVE

This review aimed to assess the agreement of dental caries experience between monozygotic (MZ) and dizygotic (DZ) twins.

DATA RESOURCES

This systematic review was performed by reviewers in the databases Embase, MEDLINE-PubMed, Scopus, Web of Science and manual searches and gray literature Google Scholar® and Opengray. Observational studies that evaluated dental caries in twins were included. The risk of bias was analyzed using the Joanna Briggs checklist. Meta-analyses were performed to assess the pooled Odds Ratio to estimate the agreement values of dental caries experience and DMF index between pairs of twins (p < 0.05). To assess the certainty of evidence, the GRADE scale was used.

STUDY SELECTION

2533 studies were identified, of which 19 were included in the qualitative analysis, six in the quantitative synthesis, with two meta-analyses being carried out. Association between genetics and the development of the disease was observed in most studies. In the risk of bias analysis, 47.4% had moderate risk. Higher agreement of dental caries experience was observed in MZ twins than DZ in both dentitions (OR: 5.94; 95% CI: 2.00-17.57). However, there was no difference between the MZ and DZ twin groups in the analysis comparing DMF index agreement (OR: 2.86; 95%CI: 0.25-32.79). The certainty of evidence was considered low and very low for all studies included in meta-analyses.

CONCLUSION

With very low certainty of the evidence, the genetic factor seems to influence the agreement of the caries experience.

CLINICAL RELEVANCE

Understanding the genetic influence on the disease has the potential to contribute to the development of studies that may use biotechnologies for prevention and treatment as well as guide future research involving gene therapies aiming to prevent the occurrence of dental caries.

Correlation between caries activity and salivary microbiota in preschool children

Early childhood caries (ECC) is the most common chronic infectious oral disease in preschool children worldwide. It is closely related to the caries activity (CA) of children. However, the distribution characteristics of oral saliva microbiomes in children with different CA are largely underexplored. The aim of this study was to investigate the microbial community in saliva of preschool children with different CA and caries status, and to analyze the difference of microbial community in saliva of children with different CA and its correlation with ECC. Subjects were divided into 3 groups based on the Cariostat caries activity test: Group H, high CA (n=30); Group M, medium CA (n = 30); Group L, low CA (n=30). Questionnaire survey was used to explore the related influencing factors of CA. According to the caries status (on the basis of decayed mising filled teeth), these subjects were divided into caries-free group (dmft=0, n=19), caries-low group (0 < dmft ≤ 4, n=27) and caries-high group (dmft > 4, n=44). Microbial profiles of oral saliva were analyzed using 16S rRNA gene sequencing. There were significant differences in the microbial structure (P < 0.05). Scardovia and Selenomonas were the biomarkers of both H group and high caries group. The genus Abiotrophia and Lautropia were the biomarkers of both the L group and the low caries group, while the Lactobacillus and Arthrospira spp. were significantly enriched in the M group. The area under the ROC curve of the combined application of dmft score, age, frequency of sugary beverage intake, and the genus Scardovia, Selenomonas, and Campylobacter in screening children with high CA was 0.842. Moreover, function prediction using the MetaCyc database showed that there were significant differences in 11 metabolic pathways of salivary microbiota among different CA groups. Certain bacteria genera in saliva such as Scardovia and Selenomonas may be helpful in screening children with high CA.

Meta-Analysis Using NGS Data: The Veillonella Species in Dental Caries

Objectives: In light of recent technological advances in Next-generation sequencing (NGS) and the accumulation of large, publicly available oral microbiome datasets, the need for meta-analysing data on caries microbiome is becoming feasible and essential. A consensus on the identification of enriched organisms in cariogenic dysbiotic biofilms would be reached. For example, members of the Veillonella genus have been detected in caries biofilms, and may have an underestimated contribution to the dysbiotic process. Hence, we aimed to determine the abundance of Veillonella species in dental caries in studies using NGS data.

Materials and Methods: Analysis was performed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (registered at PROSPERO: CRD42020204150). Studies investigating microbial composition in saliva, dental biofilm, or carious dentin were included. Six databases and grey literature were searched. Two independent reviewers selected the papers and assessed the methodological quality.

Results: Searches retrieved 1,323 titles, from which 38 studies were included in a qualitative synthesis, comprising a total of 1,374 caries and 745 caries-free individuals. Most studies analysed 16S rRNA amplicons, and only 5 studies used shotgun metagenomics and metatranscriptomics. A geographical bias was observed. The methodological quality was downrated in 81.5% of the studies due to the lack of criteria for defining cases and standard criteria used for measurement of the condition in a reliable way. Six studies on early childhood caries (ECC) were meta-analysed, confirming a significant enrichment of Veillonella spp. in caries-associated biofilms (but not saliva) when compared to caries-free controls [mean difference: 2.22 (0.54–3.90); p = 0.01].

Conclusions:Veillonella spp. is more abundant in individuals suffering with ECC when compared to caries-free controls (very low evidence certainty), and should be considered for further studies to observe their metabolism in dental caries. There is an urgent need for a consensus in methodologies used to allow for more rigorous comparison between NGS studies, particularly including clinical data and details of caries diagnosis, as they are currently scarce. Inconsistent reporting on the NGS data affected the cross-study comparison and the biological connexions of the relative abundances on caries microbiome.

Metagenomic Analysis of Dental Plaque on Pit and Fissure Sites With and Without Caries Among Adolescents

Caries is one of the most prevalent infectious diseases worldwide and is driven by the dysbiosis of dental biofilms adhering to tooth surfaces. The pits and fissured surfaces are the most susceptible sites of caries. However, information on the taxonomic composition and functional characteristics of the plaque microbiota in the pit and fissure sites is very limited. This study aimed to use metagenomic sequencing analyses to investigate the relationship between the plaque microbiome in the pit and fissure site and caries in adolescents. A total of 20 adolescents with active pit and fissure surface caries were involved as well as 20 age-matched, caries-free teenagers for control tests. Plaque samples were collected from the pit and fissure site and were subjected to metagenomic analyses, in which the microbial communities were investigated. Our results showed that the microbiota diversity was similar between those two groups. At the species level, the relative abundances of A. gerencseriae, P. acidifaciens, P. multisaccharivorax, S. oralis, S. mutans, and P. denticolens were higher in the caries-active group. N. elongata, C. hominis, and A. johnsonii were relatively more abundant in the caries-free groups. Functional analysis suggested that the metabolic pathway was the most abundant pathway, and the functional traits of the level 2 pathways included amino acid metabolism, metabolism of cofactors, and vitamins and carbohydrate metabolism. Our results also revealed that the caries group displayed several alterations in metabolic pathways, including enriched functions in carbohydrate digestion and absorption. This study suggested that in addition to the specific anatomical structures of the pit and fissured surfaces, the fundamental differences in the plaque microbiome may also be related to the susceptibility of pit and fissure caries.

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

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

Cariogenic and oral health taxa in the oral cavity among children and adults: A scoping review

OBJECTIVE

To review published oral microbiome studies and create a comprehensive list of bacterial species found in saliva and dental plaque among healthy children and adults associated with presence of carious lesions and caries-free state (oral health).

DESIGN

This review followed PRISMA-ScR guidelines. We searched published studies querying PUBMED and EMBASE using the following keywords: (plaque OR saliva) AND caries AND (next generation sequencing OR checkerboard OR 16s rRNA or qPCR). Studies were limited to human studies published in English between January 1, 2010 and June 24, 2020 that included > 10 caries-active and > 10 caries-free participants, and assessed the entire bacterial community.

RESULTS

Our search strategy identified 298 articles. After exclusion criteria, 22 articles remained; we considered 2 studies that examined saliva and plaque as separate studies, for a total of 24 studies. Species associated with caries or oral health varied widely among studies reviewed, with notable differences by age and biologic sample type. No bacterial species was associated with caries in all studies. Streptococcus mutans was found more frequently among those with caries (14/24 (58.3 %)) and Fusobacterium periodonticum was found more frequently among those that were caries-free (5/24 (20.8 %)).

CONCLUSION

No bacterial species was associated with caries or oral health across all studies supporting multiple pathways to cariogenesis. However, the variation may be due to sampling at different time points during caries development, varying methods of specimen sampling, storage, sequencing or analysis or differences in host factors such as age.

Machine Learning Study in Caries Markers in Oral Microbiota from Monozygotic Twin Children

In recent years, the etiology of caries has evolved from a simplistic infectious perspective based on Streptococcus mutans and/or Lactobacillus activity, to a multifactorial disease involving a complex oral microbiota, the human genetic background and the environment. The aim of this work was to identify bacterial markers associated with early caries using massive 16S rDNA. To minimize the other factors, the composition of the oral microbiota of twins in which only one of them had caries was compared with their healthy sibling. Twenty-one monozygotic twin pairs without a previous diagnosis of caries were recruited in the context of their orthodontic treatment and divided into two categories: (1) caries group in which only one of the twins had caries; and (2) control group in which neither of the twins had caries. Each participant contributed a single oral lavage sample in which the bacterial composition was determined by 16S rDNA amplification and further high-throughput sequencing. Data analysis included statistical comparison of alpha and beta diversity, as well as differential taxa abundance between groups. Our results show that twins of the control group have a closer bacterial composition than those from the caries group. However, statistical differences were not detected and we were unable to find any particular bacterial marker by 16S rDNA high-throughput sequencing that could be useful for prevention strategies. Although these results should be validated in a larger population, including children from other places or ethnicities, we conclude that the occurrence of caries is not related to the increase of any particular bacterial population.

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.

Oral microbiota and dental caries data from monozygotic and dizygotic twin children

There are recent studies which aimed to detect the inheritance on the etiology of dental caries exploring oral composition. We present data on the oral microbiota and its relation with dental caries and other factors in monozygotic (MZ) and dizygotic (DZ) twin children. Following clinical investigation, DNA samples were collected and isolated from saliva of 198 patients (49 MZ and 50 DZ twins) with an average age of 9.7 ± 2.7 years. Salivary bacterial microbiota analysis was performed using high throughput amplicon sequencing method targeting V3-V4 region of the 16S rRNA gene. A total of 8,297,859 raw reads corresponding to 41,908 reads per sample were obtained on average. The QIIME2-deblur workflow was used for 16S rRNA amplicon analysis. Microbiome similarity analyses between twins (based on Bray-Curtis dissimilarity, weighted and unweighted Unifrac distances) showed that monozygotic twins share more bacterial microbial content compared to dizygotic twins. This is a large microbial community dataset of MZ and DZ twins with or without dental findings which can be further used for children oral microbiome profile explorations.

Measurement(s)	Oral Microbiome • DNA • dental health
Technology Type(s)	twin design • amplicon sequencing • Examination
Factor Type(s)	zygosity status • age • sex
Sample Characteristic - Organism	Microbiota • Homo sapiens
Sample Characteristic - Environment	saliva

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12987797

Heritability of Oral Microbiota and Immune Responses to Oral Bacteria

Maintaining a symbiotic oral microbiota is essential for oral and dental health, and host genetic factors may affect the composition or function of the oral microbiota through a range of possible mechanisms, including immune pathways. The study included 836 Swedish twins divided into separate groups of adolescents (n = 418) and unrelated adults (n = 418). Oral microbiota composition and functions of non-enzymatically lysed oral bacteria samples were evaluated using 16S rRNA gene sequencing and functional bioinformatics tools in the adolescents. Adaptive immune responses were assessed by testing for serum IgG antibodies against a panel of common oral bacteria in adults. In the adolescents, host genetic factors were associated with both the detection and abundance of microbial species, but with considerable variation between species. Host genetic factors were associated with predicted microbiota functions, including several functions related to bacterial sucrose, fructose, and carbohydrate metabolism. In adults, genetic factors were associated with serum antibodies against oral bacteria. In conclusion, host genetic factors affect the composition of the oral microbiota at a species level, and host-governed adaptive immune responses, and also affect the concerted functions of the oral microbiota as a whole. This may help explain why some people are genetically predisposed to the major dental diseases of caries and periodontitis.