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

Human Papillomavirus, Human Immunodeficiency Virus, and Oral Microbiota Interplay in Nigerian Youth (HOMINY): A Prospective Cohort Study Protocol

INTRODUCTION

Persistent oral infections with high-risk human papillomavirus (HR-HPV) are a potential cause of most oropharyngeal cancers (OPCs). Oral HR-HPV infection and persistence are significantly higher in people living with HIV (PLWH). Most data on oral HR-HPV in PLWH come from developed countries or adult cohorts. This study aims to investigate oral HR-HPV susceptibility and persistence among children and adolescents living with HIV (CALHIV) and to understand the roles of perinatal HIV exposure, infection, antiretroviral treatment, and the oral microbiome.

METHODS AND ANALYSIS

This prospective cohort study is ongoing at the University of Benin Teaching Hospital (UBTH), Nigeria, involving mother-child pairs followed at 6-month intervals for 2 years. Participants include children aged 9-18 and their mothers aged 18 and above. The study targets 690 adolescents in three groups: 230 CALHIV, 230 HIV-exposed but uninfected and 230 HIV-unexposed and uninfected. Oral rinse, saliva, buccal swabs and supragingival plaque samples are collected at each visit. Blood samples are tested for HIV, Hepatitis B virus (HBV) and Hepatitis C virus (HCV), with CD4, CD8 and full blood counts performed. Oral HPV is assessed for incidence, persistence, and clearance. Statistical analyses to look for associations between cohort baseline characteristics and findings will be conducted using univariable and multivariable models for repeated data and high-dimensional microbiome data. All statistical tests will be two-sided; a p value <0.05 will indicate significance. Multiple comparisons will be adjusted using the False Discovery Rate (FDR) correction to control for Type I error.

ETHICS AND DISSEMINATION

The study was approved by Rutgers State University (Pro2022000949) and the UBTH (ADM/E22/A/VOL. VII/14813674). Informed consent was obtained from all parents/guardians.

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.

The oral microbiota and its relationship to dental calculus and caries

OBJECTIVES

In this review, we provide an overview of the composition of the microbiota associated with these two dental pathologies, caries and tartar, highlighting the microbial profiles associated with each pathology.

DESIGN

This literature review was carried out by a manual search of two electronic databases, PubMed and Web of Science (WOS), using specific keywords to the two oral pathologies dental caries and calculus.

RESULTS

The oral microbial community is known for its complexity, and comprises hundreds of species of different micro-organisms. Many of them, under the influence of endogenous and exogenous factors, can play a role in the onset and development of oral pathologies. Analysis of the microbial profiles of caries and dental calculus revealed that Streptococcus mutans and Lactobacillus species are abundant in the oral microbiota associated with caries whereas their presence is less reported in dental calculus. However, the three pathogens known as the "red complex", namely Porphyromonas, Tannarella and Treponema, which are associated with the development of periodontal pathology, are strongly present in the dental calculus microbiome.

CONCLUSION

The microbiota composition associated with dental caries and calculus highlights specific microbial signatures for each of the two oral pathologies, underscoring their differences and microbiological complexity, while the possible relationship between the formation of dental calculus and the development of caries remains unclear.

Metagenomic and transcriptomic profiling of the hypoglycemic and hypotriglyceridemic actions of Tremella fuciformis-derived polysaccharides in high-fat-diet- and streptozotocin-treated mice

Mushroom polysaccharides have great anti-diabetes potential. The fruiting body of Tremella fuciformis is rich in polysaccharides. However, few studies have been performed to date on T. fuciformis-derived polysaccharides (TPs) in terms of anti-diabetes potential. Our previous studies showed that novel TPs with medium molecular weights exhibited the highest anti-skin aging activities among the tested samples in D-galactose-treated mice. In the present study, the effects of these novel TPs, named TP, on high-fat-diet- and streptozotocin-treated mice were assessed, and their potential biological mechanisms were explored by metagenomic and transcriptomic analyses. Oral administration of TP markedly reduced blood glucose and TG levels, alleviated emaciation, improved anti-oxidant capacity, and protected the functions of β-cells at a dose of 100 mg kg-1 in diabetic mice. Meanwhile, the taxonomic compositions and functional properties of fecal microbiota were altered considerably by TP, as evidenced by partial restoration of the imbalanced gut microbiota and the higher abundances of Bacteroides, Phocaeicola, Bifidobacterium, and Alistipes compared to the model mice, corresponding to the upregulation of four enriched KEGG pathways of microbial communities such as the digestive system, cardiovascular disease, parasitic infectious disease, and cell growth and death. Further transcriptomic analysis of liver tissues identified 35 enriched KEGG pathways associated with metabolism and cellular signaling processes in response to TP. These results demonstrated the biological mechanisms underlying the hypoglycemic and hypotriglyceridemic activities of TP. The findings expanded our understanding of the anti-diabetic mechanisms for mushroom polysaccharides and provided new clues for future studies.

Oral microbiota of adolescents with dental caries: A systematic review

OBJECTIVE

This systematic review summarizes the current knowledge on the association between the oral microbiota and dental caries in adolescents.

DESIGN

An electronic search was carried out across five databases. Studies were included if they conducted research on generally healthy adolescents, applied molecular-based microbiological analyses and assessed caries status. Data extraction was performed by two reviewers and the Newcastle-Ottawa Scale was applied for quality assessment.

RESULTS

In total, 3935 records were reviewed which resulted in a selection of 20 cross-sectional studies (published 2005-2022) with a sample size ranging from 11 to 614 participants including adolescents between 11 and 19 years. The studies analyzed saliva, dental biofilm or tongue swabs with Checkerboard DNA-DNA hybridization, (q)PCR or Next-Generation Sequencing methods. Prevotella denticola, Scardoviae Wiggsiae, Streptococcus sobrinus and Streptococcus mutans were the most frequently reported species presenting higher abundance in adolescents with caries. The majority of the studies reported that the microbial diversity was similar between participants with and without dental caries.

CONCLUSION

This systematic review is the first that shows how the oral microbiota composition in adolescents appears to differ between those with and without dental caries, suggesting certain taxa may be associated with increased caries risk. However, there is a need to replicate and expand these findings in larger, longitudinal studies that also focus on caries severity and take adolescent-specific factors into account.

Elimination of Pathogen Biofilms via Postbiotics from Lactic Acid Bacteria: A Promising Method in Food and Biomedicine

Pathogenic biofilms provide a naturally favorable barrier for microbial growth and are closely related to the virulence of pathogens. Postbiotics from lactic acid bacteria (LAB) are secondary metabolites and cellular components obtained by inactivation of fermentation broth; they have a certain inhibitory effect on all stages of pathogen biofilms. Postbiotics from LAB have drawn attention because of their high stability, safety dose parameters, and long storage period, which give them a broad application prospect in the fields of food and medicine. The mechanisms of eliminating pathogen biofilms via postbiotics from LAB mainly affect the surface adhesion, self-aggregation, virulence, and QS of pathogens influencing interspecific and intraspecific communication. However, there are some factors (preparation process and lack of target) which can limit the antibiofilm impact of postbiotics. Therefore, by using a delivery carrier and optimizing process parameters, the effect of interfering factors can be eliminated. This review summarizes the concept and characteristics of postbiotics from LAB, focusing on their preparation technology and antibiofilm effect, and the applications and limitations of postbiotics in food processing and clinical treatment are also discussed.

Effects of Sjogren's syndrome and high sugar diet on oral microbiome in patients with rampant caries: a clinical study

OBJECTIVE

The purpose of this study was to assess the composition of the oral microbial flora of adults with rampant caries in China to provide guidance for treatment.

PATIENTS AND METHODS

Sixty human salivary and supragingival plaque samples were collected. They were characterized into four groups: patients with rampant caries with Sjogren's syndrome (RC-SS) or high-sugar diet (RC-HD), common dental caries (DC), and healthy individuals (HP). The 16S rRNA V3-V4 region of the bacterial DNA was detected by Illumina sequencing. PCoA based on OTU with Bray-Curtis algorithm, the abundance of each level, LEfSe analysis, network analysis, and PICRUSt analysis were carried out between the four groups and two sample types. Clinical and demographic data were compared using analysis of variance (ANOVA) or the nonparametric Kruskal-Wallis rank-sum test, depending on the normality of the data, using GraphPad Prism 8 (P < 0.05).

RESULTS

OTU principal component analysis revealed a significant difference between healthy individuals and those with RC-SS. In the saliva of patients with rampant caries, the relative abundance of Firmicutes increased significantly at the phylum level. Further, Streptocpccus, Veillonella, Prevotella, and Dialister increased, while Neisseria and Haemophilus decreased at the genus level. Veillonella increased in the plaque samples of patients with rampant caries.

CONCLUSION

Both salivary and dental plaque composition were significantly different between healthy individuals and patients with rampant caries. This study provides a microbiological basis for exploring the etiology of rampant caries.

CLINICAL RELEVANCE

This study provides basic information on the flora of the oral cavity in adults with rampant caries in China. These findings could serve as a reference for the treatment of this disease.

How probiotics, prebiotics, synbiotics, and postbiotics prevent dental caries: an oral microbiota perspective

Dental caries, a highly prevalent oral disease, impacts a significant portion of the global population. Conventional approaches that indiscriminately eradicate microbes disrupt the natural equilibrium of the oral microbiota. In contrast, biointervention strategies aim to restore this balance by introducing beneficial microorganisms or inhibiting cariogenic ones. Over the past three decades, microbial preparations have garnered considerable attention in dental research for the prevention and treatment of dental caries. However, unlike related pathologies in the gastrointestinal, vaginal, and respiratory tracts, dental caries occurs on hard tissues such as tooth enamel and is closely associated with localized acid overproduction facilitated by cariogenic biofilms. Therefore, it is insufficient to rely solely on previous mechanisms to delineate the role of microbial preparations in the oral cavity. A more comprehensive perspective should involve considering the concepts of cariogenic biofilms. This review elucidates the latest research progress, mechanisms of action, challenges, and future research directions regarding probiotics, prebiotics, synbiotics, and postbiotics for the prevention and treatment of dental caries, taking into account the unique pathogenic mechanisms of dental caries. With an enhanced understanding of oral microbiota, personalized microbial therapy will emerge as a critical future research trend.

The role of microbial interactions in dental caries: Dental plaque microbiota analysis

OBJECTIVES

Dental caries is a result of the ecological dysfunction of the polymicrobial community on the tooth surface, which evolves through microbial interactions. In this study, we conducted a thorough analysis of the dental plaque microbiome to comprehend its multi-microbial aetiology.

MATERIALS AND METHOD

In this study, plaque was collected from healthy tooth surfaces, shallow carious teeth and deep carious teeth, and bacterial composition and abundance were assessed using 16S rRNA high-throughput sequencing. Random forest and LEfSe were used to profile various microorganisms at each stage. Additionally, we developed a molecular ecological network (MEN) based on random matrix theory (RMT) to examine microbial interactions for the first time.

RESULTS

Our results reveal that Scardovia wiggsiae, Streptococcus mutans, and Propionibacterium acidifaciens may be associated with initial caries, and Propionibacterium acidifaciens differentiates between shallow and deep caries. As caries progressed, the alpha diversity index declined, indicating a decrease in microbial variety. The network topological indices such as centralization betweenness revealed that the caries network had become more complex, involving more microbial interactions. The shallow network revealed a high negative correlation ratio across nodes, indicating that microbes competed heavily. In contrast, the positive correlation ratio of deep network nodes was high, and microorganisms transitioned from a competitive to a synergistic state.

CONCLUSIONS

This study suggests that microbial diversity and interactions are critical to caries progression and that future caries research should give greater consideration to the role of microbial interaction factors in caries progression.

Comprehensive insights into the gallic acid assisted bioleaching process for spent LIBs: Relationships among bacterial functional genes, Co(III) reduction and metal dissolution behavior

Despite the growing demand for resource recovery from spent lithium-ion batteries (LIBs) by bioleaching, low Co leaching efficiency has hindered the development and application of this technology. Therefore, a novel process was designed, combining gallic acid (GA) and mixed culture bioleaching (MCB), to enhance the removal of metals from spent LIBs. Results indicated that the GA + MCB process achieved 98.03% Co and 98.02% Li leaching from spent LIBs, simultaneously reducing the biotoxicity, phytotoxicity and leaching toxicity of spent LIBs under optimal conditions. The results of mechanism analysis demonstrated that functional microorganisms adapted to the leaching system through various strategies, including oxidative stress reduction, DNA damage repair, heavy metal resistance and biofilm formation, maintaining normal physiological activities and the continuous production of biological acid. The biological acid erodes the surface of waste LIBs, causing some Co and a large amount of Li to be released, while also increasing the contact area between GA and Co(III). Therefore, GA is beneficial for reducing insoluble Co(III), forming soluble Co(II). Finally, biological acid can effectively promote Co(II) leaching. Collectively, the results of this study provide valuable insight into the simultaneous enhancement of metal extraction and the mitigation of environmental pollution from spent LIBs.

Multistability and hysteresis in states of oral microbiota: Is it impacting the dental clinical cohort studies?

INTRODUCTION

Microbiome from a "healthy cohort" is used as a reference for comparison to cases and intervention. However, the studies with cohort-based clinical research have not sufficiently accounted for the multistability in oral microbial community. The screening is limited to phenotypic features with marked variations in microbial genomic markers. Herein, we aimed to assess the stability of the oral microbiome across time from an intervention-free "healthy" cohort.

METHODS

We obtained 33 supragingival samples of 11 healthy participants from the biobank. For each participant, we processed one sample as baseline (T0) and two samples spaced at 1-month (T1) and 3-month (T2) intervals for 16S ribosomal RNA gene sequencing analysis.

RESULTS

We observed that taxonomic profiling had a similar pattern of dominant genera, namely, Rothia, Prevotella, and Hemophilus, at all time points. Shannon diversity revealed a significant increase from T0 (p < .05). Bray Curtis dissimilarity was significant (R = -.02, p < .01) within the cohort at each time point. Community stability had negative correlation to synchrony (r = -.739; p = .009) and variance (r = -.605; p = .048) of the species. Clustering revealed marked differences in the grouping patterns between the three time points. For all time points, the clusters presented a substantially dissimilar set of differentially abundant taxonomic and functional biomarkers.

CONCLUSION

Our observations indicate towards the presence of multistable states within the oral microbiome in an intervention-free healthy cohort. For a conclusive and meaningful long-term reference, dental clinical research should account for multistability in the personalized therapy approach to improve the identification and classification of reliable markers.

Culturing the Human Oral Microbiota, Updating Methodologies and Cultivation Techniques

Recent years have been marked by a paradigm shift in the study of the human microbiota, with a re-emergence of culture-dependent approaches. Numerous studies have been devoted to the human microbiota, while studies on the oral microbiota still remain limited. Indeed, various techniques described in the literature may enable an exhaustive study of the microbial composition of a complex ecosystem. In this article, we report different methodologies and culture media described in the literature that can be applied to study the oral microbiota by culture. We report on specific methodologies for targeted culture and specific culture techniques and selection methodologies for cultivating members of the three kingdoms of life commonly found in the human oral cavity, namely, eukaryota, bacteria and archaea. This bibliographic review aims to bring together the various techniques described in the literature, enabling a comprehensive study of the oral microbiota in order to demonstrate its involvement in oral health and diseases.

Oral mitis group streptococci: A silent majority in our oral cavity

Members of the oral mitis group streptococci including Streptococcus oralis, Streptococcus sanguinis, and Streptococcus gordonii are the most abundant inhabitants of human oral cavity and dental plaque, and have been implicated in infectious complications such as bacteremia and infective endocarditis. Oral mitis group streptococci are genetically close to Streptococcus pneumoniae; however, they do not produce cytolysin (pneumolysin), which is a key virulence factor of S. pneumoniae. Similar to S. pneumoniae, oral mitis group streptococci possess several cell surface proteins that bind to the cell surface components of host mammalian cells. S. sanguinis expresses long filamentous pili that bind to the matrix proteins of host cells. The cell wall-anchored nuclease of S. sanguinis contributes to the evasion of the neutrophil extracellular trap by digesting its web-like extracellular DNA. Oral mitis group streptococci produce glucosyltransferases, which synthesize glucan (glucose polymer) from sucrose of dietary origin. Neuraminidase (NA) is a virulent factor in oral mitis group streptococci. Influenza type A virus (IAV) relies on viral NA activity to release progeny viruses from infected cells and spread the infection, and NA-producing oral streptococci elevate the risk of IAV infection. Moreover, oral mitis group streptococci produce hydrogen peroxide (H₂ O₂ ) as a by-product of sugar metabolism. Although the concentrations of streptococcal H₂ O₂ are low (1-2 mM), they play important roles in bacterial competition in the oral cavity and evasion of phagocytosis by host macrophages and neutrophils. In this review, we intended to describe the diverse pathogenicity of oral mitis group streptococci.

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.

The Oral Microbiome Impacts the Link between Sugar Consumption and Caries: A Preliminary Study

Background: The excessive and frequent intake of refined sugar leads to caries. However, the relationship between the amount of sugar intake and the risk of caries is not always consistent. Oral microbial profile and function may impact the link between them. This study aims to identify the plaque microbiota characteristics of caries subjects with low (CL) and high (CH) sugar consumption, and of caries-free subjects with low (FL) and high sugar (FH) consumption. Methods: A total of 40 adolescents were enrolled in the study, and supragingival plaque samples were collected and subjected to metagenomic analyses. The caries status, sugar consumption, and oral-health behaviors of the subjects were recorded. Results: The results indicate that the CL group showed a higher abundance of several cariogenic microorganisms Lactobacillus, A. gerencseriae, A. dentails, S. mutans, C. albicans, S. wiggsiae and P. acidifaciens. C. gingivalis, and P. gingivalis, which were enriched in the FH group. In terms of gene function, the phosphotransferase sugar uptake system, phosphotransferase system, and several two-component responses–regulator pairs were enriched in the CL group. Conclusion: Overall, our data suggest the existence of an increased cariogenic microbial community and sugar catabolism potential in the CL group, and a healthy microbial community in the FH group, which had self-stabilizing functional potential.

Site- and Time-Dependent Compositional Shifts in Oral Microbiota Communities

Objectives

The oral microbiota plays a significant role in oral health. The present study aims to characterize variations in the oral microbiota relative to the collection site, the dynamics of biofilm accumulation, and inherent inter-individual differences.

Methods

Whole stimulated saliva and tooth biofilm samples from the 16 defined tooth regions were collected after 1, 2, or 3 days without oral hygiene (accumulation time) in six healthy adults with no signs of active caries or periodontal disease. The routines and conditions before and between sample collections were carefully standardized. Genomic DNA was extracted, and the V3-V4 regions of the 16S rRNA gene were amplified by PCR and sequenced on an Illumina MiSeq platform. Sequences were quality controlled, amplicon sequence variants (ASVs) were clustered, and taxonomic allocation was performed against the expanded Human Oral Microbiome Database (eHOMD). Microbial community profiles were analyzed by multivariate modeling and a linear discriminant analysis (LDA) effect size (LEfSe) method.

Results

The overall species profile in saliva and tooth biofilm differed between participants, as well as sample type, with a significantly higher diversity in tooth biofilm samples than saliva. On average, 45% of the detected species were shared between the two sample types. The microbiota profile changed from the most anterior to the most posterior tooth regions regardless of whether sampling was done after 1, 2, or 3 days without oral hygiene. Increasing accumulation time led to higher numbers of detected species in both the saliva and region-specific tooth biofilm niches.

Conclusion

The present study confirms that the differences between individuals dominate over sample type and the time abstaining from oral hygiene for oral microbiota shaping. Therefore, a standardized accumulation time may be less important for some research questions aiming at separating individuals. Furthermore, the amount of DNA is sufficient if at least two teeth are sampled for microbiota characterization, which allows a site-specific characterization of, for example, caries or periodontitis.

Effects of Bleaching Associated with Er:YAG and Nd:YAG Laser on Enamel Structure and Bacterial Biofilm Formation

OBJECTIVE

To compare the effects of bleaching associated with Er:YAG and Nd:YAG laser on enamel structure and mixed biofilm formation on teeth surfaces.

MATERIALS AND METHODS

Sixty-eight enamel samples were randomly divided into four groups (n = 17), control, Opalescence Boost only, Opalescence Boost plus Er: YAG laser, and Opalescence Boost plus Nd:YAG laser. The structure was observed using SEM after bleaching. Subsequently, the treated enamel samples were also cultured in suspensions of Streptococcus mutans, Streptococcus sanguis, Actinomyces viscosus, and Fusobacterium nucleatum (Fn) for 24 and 48 h. Biofilm formation was quantified by crystal violet staining, and the structure was visualized by confocal laser scanning microscopy. The data were analyzed using the Kruskal-Wallis method.

RESULTS

The enamel structure significantly changed after bleaching. There was no obvious difference in the biofilm formation after 24 h; however, after 48 hours, the amount of biofilm increased significantly. Remarkably, the amount was significantly higher on enamel bleached only, however, there was no significant difference between samples bleached with Er:YAG or Nd:YAG laser compared to the control.

CONCLUSIONS

Bleaching only appeared to markedly promote biofilm formation after 48 h, and the biofilms on samples bleached with Er:YAG or Nd:YAG laser did not change significantly, showing that bleaching with Er:YAG or Nd:YAG laser can be safely applied in clinical practice.