Comparison of oral microbial profiles between children with severe early childhood caries and caries-free children using the human oral microbe identification microarray

Antimicrobial peptide temporin derivatives inhibit biofilm formation and virulence factor expression of Streptococcus mutans

Introduction

Temporin-GHa obtained from the frog Hylarana guentheri showed bactericidal efficacy against Streptococcus mutans. To enhance its antibacterial activity, the derived peptides GHaR and GHa11R were designed, and their antibacterial performance, antibiofilm efficacy and potential in the inhibition of dental caries were evaluated.

Methods

Bacterial survival assay, fluorescent staining assay and transmission electron microscopy observation were applied to explore how the peptides inhibited and killed S. mutans. The antibiofilm efficacy was assayed by examining exopolysaccharide (EPS) and lactic acid production, bacterial adhesion and cell surface hydrophobicity. The gene expression level of virulence factors of S. mutans was detected by qRT-PCR. Finally, the impact of the peptides on the caries induced ability of S. mutans was measured using a rat caries model.

Results

It has been shown that the peptides inhibited biofilm rapid accumulation by weakening the initial adhesion of S. mutans and reducing the production of EPS. Meanwhile, they also decreased bacterial acidogenicity and aciduricity, and ultimately prevented caries development in vivo.

Conclusion

GHaR and GHa11R might be promising candidates for controlling S. mutans infections.

Salivary microbiome diversity in Chinese children with various caries states

OBJECTIVE

This study aimed to explore oral microbiome diversity among children with various caries status based on dmft scores.

METHODS

A total of 320 children aged 3-5 years were recruited, with 66 healthy children and 254 children affected by dental caries. According to dmft scores, these children with dental caries were classified as "mild group" (dmft score 1-3), "moderate group" (dmft score 4-6), and "severe group" (dmft score 7-14). Healthy children with dmft score of 0 served as control group. Illumina MiSeq sequencing was employed to analyze all salivary samples collected from these children.

RESULTS

The salivary microbial diversity among four groups was similar (p > 0.05). A total of five bacterial genera were highly abundant in the control group including Bergeyella, Acidimicrobiales, Acidimicrobiia, Halomonas, and Blautia (p < 0.05). For mild group, there were nine bacterial genera identified to be predominant: Porphyromonadaceae, Porphyromonas, Enterobacteriales, Enterobacteriaceae, Weissella, Leuconostocaceae, Alphaproteobacteria, Stenotrophomonas, and Rhizobiales (p < 0.05). Only one genus, Aggregatibacter was predominant in moderate group (p < 0.05). There were six bacterial genera (Alistipes, Lachnoclostridium, Escherichia-Shigella, Romboutsia, Sphingomonadales, and Denitratisoma) enriched in severe group (p < 0.05).

CONCLUSION

Oral microbial profile was different in children with various caries status based on dmft scores.

CLINICAL RELEVANCE

The results might be beneficial to deeply understand microbiological diversity of early childhood caries (ECC) at various stages and inform effective strategies for ECC prevention.

Salivary microbiome and metabolome analysis of severe early childhood caries

BACKGROUND

Severe early childhood caries (SECC) is an inflammatory disease with complex pathology. Although changes in the oral microbiota and metabolic profile of patients with SECC have been identified, the salivary metabolites and the relationship between oral bacteria and biochemical metabolism remains unclear. We aimed to analyse alterations in the salivary microbiome and metabolome of children with SECC as well as their correlations. Accordingly, we aimed to explore potential salivary biomarkers in order to gain further insight into the pathophysiology of dental caries.

METHODS

We collected 120 saliva samples from 30 children with SECC and 30 children without caries. The microbial community was identified through 16S ribosomal RNA (rRNA) gene high-throughput sequencing. Additionally, we conducted non-targeted metabolomic analysis through ultra-high-performance liquid chromatography combined with quadrupole time-of-flight mass spectrometry to determine the relative metabolite levels and their correlation with the clinical caries status.

RESULTS

There was a significant between-group difference in 8 phyla and 32 genera in the microbiome. Further, metabolomic and enrichment analyses revealed significantly altered 32 salivary metabolites in children with dental caries, which involved pathways such as amino acid metabolism, pyrimidine metabolism, purine metabolism, ATP-binding cassette transporters, and cyclic adenosine monophosphate signalling pathway. Moreover, four in vivo differential metabolites (2-benzylmalate, epinephrine, 2-formaminobenzoylacetate, and 3-Indoleacrylic acid) might be jointly applied as biomarkers (area under the curve = 0.734). Furthermore, the caries status was correlated with microorganisms and metabolites. Additionally, Spearman's correlation analysis of differential microorganisms and metabolites revealed that Veillonella, Staphylococcus, Neisseria, and Porphyromonas were closely associated with differential metabolites.

CONCLUSION

This study identified different microbial communities and metabolic profiles in saliva, which may be closely related to caries status. Our findings could inform future strategies for personalized caries prevention, detection, and treatment.

Understanding the Predictive Potential of the Oral Microbiome in the Development and Progression of Early Childhood Caries

BACKGROUND

Early childhood caries (ECC) is the most common chronic disease in young children and a public health problem worldwide. It is characterized by the presence of atypical and fast progressive caries lesions. The aggressive form of ECC, severe early childhood caries (S-ECC), can lead to the destruction of the whole crown of most of the deciduous teeth and cause pain and sepsis, affecting the child's quality of life. Although the multifactorial etiology of ECC is known, including social, environmental, behavioral, and genetic determinants, there is a consensus that this disease is driven by an imbalance between the oral microbiome and host, or dysbiosis, mediated by high sugar consumption and poor oral hygiene. Knowledge of the microbiome in healthy and caries status is crucial for risk monitoring, prevention, and development of therapies to revert dysbiosis and restore oral health. Molecular biology tools, including next-generation sequencing methods and proteomic approaches, have led to the discovery of new species and microbial biomarkers that could reveal potential risk profiles for the development of ECC and new targets for anti-caries therapies. This narrative review summarized some general aspects of ECC, such as definition, epidemiology, and etiology, the influence of oral microbiota in the development and progression of ECC based on the current evidence from genomics, transcriptomic, proteomic, and metabolomic studies and the effect of antimicrobial intervention on oral microbiota associated with ECC.

CONCLUSION

The evaluation of genetic and proteomic markers represents a promising approach to predict the risk of ECC before its clinical manifestation and plan efficient therapeutic interventions for ECC in its initial stages, avoiding irreversible dental cavitation.

Dental caries and their microbiomes in children: what do we do now?

The oral cavity is an unique ecosystem formed by different structures, tissues, and a complex microbial community formed by hundreds of different species of bacteria, fungi, viruses, phages, and the candidate phyla radiation (CPR) group, all living in symbiosis with healthy individuals. In an opposite state, dental caries is a biofilm-mediated dysbiosis that involves changes in the core microbiome composition and function, which leads to the demineralization of tooth tissues due to the fermentation of dietary carbohydrates, producing acid by select oral bacteria. The cariogenic biofilm is typically characterized by bacterial species with the ability of adhering to the saliva-coated tooth surface, production of exopolysaccharides-rich matrix (which will limit the diffusion of acidic products of carbohydrate fermentation), and the ability of surviving in this acidic environment. Besides years of research and dental treatment, dental caries remains the most common chronic disease in children worldwide. This article aims to bring an insightful discussion about important questions that remain unanswered in the Cariology and Oral Microbiology fields, to move Science forward, characterize the interrelationships of these communities, and understand mechanistic functions between microorganisms and the host, therefore leading to translatable knowledge that benefits the provision of care to our pediatric patients.

Can metagenomics unravel the impact of oral bacteriome in human diseases?

Oral microbial ecosystems are vital in maintaining the health of the oral cavity and the entire body. Oral microbiota is associated with the progression of oral diseases such as dental caries, periodontal diseases, head and neck cancer, and several systemic diseases such as cardiovascular disease, rheumatoid arthritis, adverse pregnancy outcomes, diabetes, lung infection, colorectal cancer, and pancreatic cancer. Buccal mucosa, tongue dorsum, hard palate, saliva, palatine tonsils, throat, keratinized gingiva, supra-gingival plaque, subgingival plaque, dentures, and lips are microbial habitats of the oral cavity. Porphyromonas gingivalis may have a role in the development of periodontal diseases, oral cancer, diabetes, and atherosclerotic disease. Fusobacterium nucleatum showed a higher abundance in periodontal diseases, oral and colon cancer, adverse pregnancy outcomes, diabetes, and rheumatoid arthritis. The higher abundance of Prevotella intermedia is typical in periodontal diseases, rheumatoid arthritis, and adverse pregnancy outcome. S. salivarius displayed higher abundance in both dental caries and OSCC. Oral bacteria may influence systemic diseases through inflammation by releasing pro inflammatory cytokines. Identification of oral bacteria using culture-dependent approaches and next-generation sequencing-based metagenomic approaches is believed to significantly identify the therapeutic targets and non-invasive diagnostic indicators in different human diseases. Oral bacteria in saliva could be exploited as a non-invasive diagnostic indicator for the early detection of oral and systemic disorders. Other therapeutic approaches such as the use of probiotics, green tea polyphenol, cold atmospheric plasma (CAP) therapy, antimicrobial photodynamic therapy, and antimicrobial peptides are used to inhibit the growth of biofilm formation by oral bacteria.

Comparison of the Oral Microbiota Structure among People from the Same Ethnic Group Living in Different Environments

The characteristics of the oral microbiota may depend on oral health, age, diet, and geography, but the influence of the geographic setting on the oral microbiota has received limited attention. The characteristics of oral microbiota have been reported to differ between urban and rural environments. In order to minimize the influence of genetic background, we recruited 54 volunteers from the same ethnic group, living in urban and rural areas of Gansu Province, China. We collected dental plaque samples and divided them into four groups according to the participant's area of residence and dental caries status. We sequenced the 16S rRNA of these samples using the Pacific Biosciences sequencing platform and analyzed the correlation between the geographic area and the characteristics of the oral microbiota. Analysis of the alpha and beta diversity revealed that there were significant differences in diversity and composition of dental plaque microflora among the four groups. Cluster analysis revealed that geographic area played an important role in determining the oral microbiota. Network analysis of oral microorganisms showed that geographic differences had major influence on the composition characteristics and internal structure of oral microorganisms. We found that some dominant strains which may play a key role in maintaining oral health, such as Streptococcus oralis, Capnocytophaga sputigena, Porphyromonas catoniae, Corynebacterium matruchotii, Haemophilus parainfluenzae, and Prevotella loescheii, were less affected by the geographic setting. These results provide a deeper understanding of factors influencing the composition of the oral microbiota and could contribute to early diagnosis and effective prevention of dental caries in different settings.

Multimodal Data Integration Reveals Mode of Delivery and Snack Consumption Outrank Salivary Microbiome in Association With Caries Outcome in Thai Children

Early childhood caries (ECC) is not only the most common chronic childhood disease but also disproportionately affects underserved populations. Of those, children living in Thailand have been found to have high rates of ECC and severe ECC. Frequently, the cause of ECC is blamed on a handful of cariogenic organisms, such as Streptococcus mutans and Streptococcus sobrinus. However, ECC is a multifactorial disease that results from an ecological shift in the oral cavity from a neutral pH (~7.5) to an acidic pH (&lt;5.5) environment influenced by the host individual’s biological, socio-behavioral, and lifestyle factors. Currently, there is a lack of understanding of how risk factors at various levels influence the oral health of children at risk. We applied a statistical machine learning approach for multimodal data integration (parallel and hierarchical) to identify caries-related multiplatform factors in a large cohort of mother-child dyads living in Chiang Mai, Thailand (N=177). Whole saliva (1 mL) was collected from each individual for DNA extraction and 16S rRNA sequencing. A set of maternal and early childhood factors were included in the data analysis. Significantly, vaginal delivery, preterm birth, and frequent sugary snacking were found to increase the risk for ECC. The salivary microbial diversity was significantly different in children with ECC or without ECC. Results of linear discriminant analysis effect size (LEfSe) analysis of the microbial community demonstrated that S. mutans, Prevotella histicola, and Leptotrichia hongkongensis were significantly enriched in ECC children. Whereas Fusobacterium periodonticum was less abundant among caries-free children, suggesting its potential to be a candidate biomarker for good oral health. Based on the multimodal data integration and statistical machine learning models, the study revealed that the mode of delivery and snack consumption outrank salivary microbiome in predicting ECC in Thai children. The biological and behavioral factors may play significant roles in the microbial pathobiology of ECC and warrant further investigation.

Oral Microbiome: Streptococcus mutans/Caries Concordant-Discordant Children

Dental caries remains the most common chronic disease in children, and the respective etiology is not fully understood. Though Streptococcus mutans is an important factor in the initiation and progression of caries, its presence is not always associated with the disease. The existence of caries discordant populations, in which S. mutans counts do not correlate with caries experience, poses a challenging problem. This study explored the possible correlation of S. mutans and other microorganism levels on caries-associated ecology of caries-concordant and discordant populations. A total of forty-seven children were analyzed in this study and stratified into four clinical groups based on their S. mutans levels in saliva (HS/LS: High/low S. mutans) and caries experience. Streptococcus mutans levels were determined by culture-based selective plating. The salivary microbiome of caries concordant and discordant populations was investigated by 16S rRNA gene sequencing and downstream bioinformatics analysis. The salivary microbial communities significantly clustered based on S. mutans levels and independent of their caries experience. In addition to S. mutans levels, significant differences in the abundance of other species were observed between HS and LS groups. Interestingly, disease-associated species such as Veillonella dispar, Streptococcus spp., and Prevotella spp. were significantly increased in HS groups and may contribute, in combination with S. mutans, to the caries progression. Furthermore, health-associated species exhibited higher abundance in the LS groups, such as Veillonella rogosae, Haemophilus sp., and Alloprevotella spp. but their possible contribution to the caries process remains to be elucidated. This study provides evidence that S. mutans may play a role in shaping the salivary microbial community. Our results highlight that future caries research should consider additional species as health/disease microbial markers in conjunction with S. mutans to improve diagnosis and caries management of the caries-discordant population.

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.

Exploring the Interplay Between Oral Diseases, Microbiome, and Chronic Diseases Driven by Metabolic Dysfunction in Childhood

Oral childhood diseases, such as caries and gingivitis, have much more than a local impact on the dentition and tooth surrounding tissues, which can affect systemic conditions. While the mouth is frequently exposed to microbial stressors that can contribute to an inflammatory state in the entire body, chronic disorders can also interfere with oral health. Sharing common risk factors, a dynamic interplay can be driven between 1. dental caries, gingivitis, and type I diabetes mellitus, 2. early childhood caries and obesity, and 3. caries and cardiovascular diseases. Considering that there are ~2.2 billion children worldwide and that childhood provides unique opportunities for intervention targeting future health promotion, this review is of prime importance and aimed to explore the relationship between the oral microbiome and oral chronic diseases driven by metabolic dysfunction in childhood.

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.

Geographic Variation Did Not Affect the Predictive Power of Salivary Microbiota for Caries in Children With Mixed Dentition

Dental caries is one of the most prevalent chronic oral diseases, affecting approximately half of children worldwide. The microbial composition of dental caries may depend on age, oral health, diet, and geography, yet the effect of geography on these microbiomes is largely underexplored. Here, we profiled and compared saliva microbiota from 130 individuals aged 6 to 8 years old, representing both healthy children (H group) and children with caries-affected (C group) from two geographical regions of China: a northern city (Qingdao group) and a southern city (Guangzhou group). First, the saliva microbiota exhibited profound differences in diversity and composition between the C and H groups. The caries microbiota featured a lower alpha diversity and more variable community structure than the healthy microbiota. Furthermore, the relative abundance of several genera (e.g., Lactobacillus, Gemella, Cryptobacterium and Mitsuokella) was significantly higher in the C group than in the H group (p<0.05). Next, geography dominated over disease status in shaping salivary microbiota, and a wide array of salivary bacteria was highly predictive of the individuals’ city of origin. Finally, we built a universal diagnostic model based on 14 bacterial species, which can diagnose caries with 87% (AUC=86.00%) and 85% (AUC=91.02%) accuracy within each city and 83% accuracy across cities (AUC=92.17%). Although the detection rate of Streptococcus mutans in populations is not very high, it could be regarded as a single biomarker to diagnose caries with decent accuracy. These findings demonstrated that despite the large effect size of geography, a universal model based on salivary microbiota has the potential to diagnose caries across the Chinese child population.

Firmicutes Levels in the Mouth Reflect the Gut Condition With Respect to Obesity and Early Childhood Caries

The present cross-sectional study investigated whether Firmicutes (F) and Bacteroidetes (B) levels in the mouth reflected the gut condition in obesity and early childhood caries (ECC). Eighty preschoolers (3-5 years) were equally assigned into four groups: 1. obese + ECC, 2. obese + caries-free (CF), 3. eutrophic + ECC, and 4. eutrophic + CF. Nutritional status and ECC were assessed based on the WHO criteria. Dental biofilm and fecal samples were collected for F and B quantification using RT-PCR analysis. Data were evaluated using three-way-ANOVA and Pearson’s correlation (α = 0.05). Regardless of the anatomical location effect (p = 0.22), there were higher values for F in the obese children + ECC compared with those in obese + caries-free (CF) in both mouth and gut (p < 0.05). The correlation for F at these sites was negative in obese children + ECC (r = −0.48; p = 0.03) and positive in obese children + CF (r=0.50; p = 0.03). Bacteroidetes were influenced by ECC (p = 0.03) and the anatomical location (p = 0.00), and the levels tended to be higher in the mouth of the obese children + ECC (p = 0.04). The F/B ratio was higher in the gut and was affected by the anatomical location (p = 0.00). This preliminary study suggested that modulated by ECC, counts of oral Firmicutes reflected corresponding condition in the gut of obese preschoolers. In addition, we first evidenced that the Firmicutes phylum behave differently according to the nutritional status and caries experience and that supragingival biofilm and gut could share levels of similarity.

Analysis of oral microbial dysbiosis associated with early childhood caries

Background

"Core microbes" play a key role in the development of caries and lead to microbial disorders. Our goal was to detect the core microbes associated with the microbiota imbalance in early childhood caries (ECC).

Methods

Fifteen caries-free children and fifteen high-caries (DMFT ≥ 10) children aged 4–6 years old were recruited according to the diagnostic criteria of caries suggested by the WHO. The 16S rRNA genes from samples of plaque in saliva were amplified by PCR, and the PCR products were sequenced by the Illumina Miseq platform. The sequencing results were analyzed by professional software to determine the composition and structure of the saliva microorganisms.

Results

There were statistically significant differences between the groups regarding the relative abundance of Streptococcus mutans (Wilcoxon rank-sum test, P < 0.05). No significant difference was found between the groups regarding other species or functional genes.

Conclusion

S. mutans, together with other pathogens, may play a prominent role and act as "core microbes" in the occurrence and development of early childhood caries.

Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques

BACKGROUND

An individual's microbiome changes over the course of its lifetime, especially during infancy, and again in old age. Confounding factors such as diet and healthcare make it difficult to disentangle the interactions between age, health, and microbial changes in humans. Animal models present an excellent opportunity to study age- and sex-linked variation in the microbiome, but captivity is known to influence animal microbial abundance and composition, while studies of free-ranging animals are typically limited to studies of the fecal microbiome using samples collected non-invasively. Here, we analyze a large dataset of oral, rectal, and genital swabs collected from 105 free-ranging rhesus macaques (Macaca mulatta, aged 1 month-26 years), comprising one entire social group, from the island of Cayo Santiago, Puerto Rico. We sequenced 16S V4 rRNA amplicons for all samples.

RESULTS

Infant gut microbial communities had significantly higher relative abundances of Bifidobacterium and Bacteroides and lower abundances of Ruminococcus, Fibrobacter, and Treponema compared to older age groups, consistent with a diet high in milk rather than solid foods. The genital microbiome varied widely between males and females in beta-diversity, taxonomic composition, and predicted functional profiles. Interestingly, only penile, but not vaginal, microbiomes exhibited distinct age-related changes in microbial beta-diversity, taxonomic composition, and predicted functions. Oral microbiome composition was associated with age, and was most distinctive between infants and other age classes.

CONCLUSIONS

Across all three body regions, with notable exceptions in the penile microbiome, while infants were distinctly different from other age groups, microbiomes of adults were relatively invariant, even in advanced age. While vaginal microbiomes were exceptionally stable, penile microbiomes were quite variable, especially at the onset of reproductive age. Relative invariance among adults, including elderly individuals, is contrary to findings in humans and mice. We discuss potential explanations for this observation, including that age-related microbiome variation seen in humans may be related to changes in diet and lifestyle. Video abstract.

Comparative analysis of oral microbiome from Zang and Han populations living at different altitudes

OBJECTIVES

The aim of this study was to obtain greater insight into the environmental and genetic factors affecting the oral microbiome.

DESIGN

To this end, we investigated the oral microbiome composition in Han and Zang populations living at different altitudes. The saliva microbiome in 115 individuals from Zang and Han populations living at different altitudes was analyzed using the 16 s rRNA gene sequencing method on the Illumina MiSeq platform. The dominant species in the oral microbiome were verified by quantitative real-time polymerase chain reaction (qPCR) analysis.

RESULTS

The Han population, living at an altitude of 500 m, had higher microbiome diversity than the Zang population living at altitudes of 3000-4000 m. People living at 3000 m had a higher relative abundance of Leptothrix genus, but people living at 500 m had a higher relative abundance of Capnocytophaga genus according to Lefse difference analysis (P < 0.05). Compared to the Zang population, the Han population had higher relative abundances of Porphyromonas and Treponema genus organisms, especially Porphyromonas (P < 0.001). qPCR analysis confirmed that people living at high altitudes had the highest relative abundance of Porphyromonas gingivalis (P < 0.01).

CONCLUSIONS

This study showed that both genetics and the environment had significant influences on the oral microbiome composition. The study proposed a meaningful research direction to explore the relationship between different ethnic and altitude groups and oral diseases, such as periodontal diseases.

Carbon source utilization patterns in dental plaque and microbial responses to sucrose, lactose, and phenylalanine consumption in severe early childhood caries

Background

Severe early childhood caries (S-ECC) is mainly caused by the interaction of microbiota and environmental factors. However, the metabolic profiles of S-ECC microbial communities and the community-level microbial responses to carbohydrates and amino acids are poorly understood.

Methods

We collected supragingival plaques from 15 caries-free (CF) and 14 S-ECC children. Cultivation on Biolog AN microplates together with next-generation sequencing was used to analyze sole carbon source utilization patterns and microbial responses to sucrose, lactose and phenylalanine.

Results

S-ECC plaques had greater overall metabolic activity than those of CF ones. Comparing with CF, S-ECC plaques utilized more sucrose and lactose but less phenylalanine and then had greater response to carbohydrates. A remarkable increase of non-mutans Streptococci was observed in sucrose and lactose consumption. Lactose led to less differently distributed taxa than sucrose in both CF and S-ECC groups. Sucrose made the originally different S-ECC and CF communities eventually became similar to each other, but they remained dissimilar in lactose.

Conclusion

S-ECC plaques had more active interaction with cariogenic carbohydrates like sucrose and lactose than healthy plaques. We supported lactose has less cariogenicity compared with sucrose from microbial community structural aspect. Phenylalanine may have a potentially inhibitory effect on caries development.

Oral microbiome: possible harbinger for children's health

The human microbiome functions as an intricate and coordinated microbial network, residing throughout the mucosal surfaces of the skin, oral cavity, gastrointestinal tract, respiratory tract, and reproductive system. The oral microbiome encompasses a highly diverse microbiota, consisting of over 700 microorganisms, including bacteria, fungi, and viruses. As our understanding of the relationship between the oral microbiome and human health has evolved, we have identified a diverse array of oral and systemic diseases associated with this microbial community, including but not limited to caries, periodontal diseases, oral cancer, colorectal cancer, pancreatic cancer, and inflammatory bowel syndrome. The potential predictive relationship between the oral microbiota and these human diseases suggests that the oral cavity is an ideal site for disease diagnosis and development of rapid point-of-care tests. The oral cavity is easily accessible with a non-invasive collection of biological samples. We can envision a future where early life salivary diagnostic tools will be used to predict and prevent future disease via analyzing and shaping the infant’s oral microbiome. In this review, we present evidence for the establishment of the oral microbiome during early childhood, the capability of using childhood oral microbiome to predict future oral and systemic diseases, and the limitations of the current evidence.

Co-occurrence of yeast, streptococci, dental decay, and gingivitis in the post-partum period: results of a longitudinal study

Objective: The interactions between yeast and streptococci species that lead to dental decay and gingivitis are poorly understood. Our study describes these associations among a cohort of 101 post-partum women enrolled in the Center for Oral Health Research in Appalachia, 2012–2013.

Methods: All eligible women without dental caries were included (n = 21) and the remainder were randomly sampled to represent the total number of decayed, missing, and filled teeth (DMFT) at enrollment. We used amplicon sequencing and qPCR of saliva from 2, 6, 12 and 24 visits to determine microbiome composition.

Results: Active decay and generalized gingivitis were strongly predictive of each other. Using adjusted marginal models, Candida albicans and Streptococcus mutans combined were associated with active decay (OR = 3.13; 95% CI 1.26, 7.75). However, C. albicans alone (OR = 2.33; 95% CI: 0.81, 6.75) was associated with generalized gingivitis, but S. mutans alone was not (OR = 0.55; 95% CI: 0.21, 1.44). Models including microbiome community state types (CSTs) showed CSTs positively associated with active decay were negatively associated with generalized gingivitis.

Discussion: C. albicans is associated with active decay and generalized gingivitis, but whether one or both are present depends on the structure of the co-existing microbial community.

The effect of brushing with Salvadora persica (miswak) sticks on salivary Streptococcus mutans and plaque levels in children: a clinical trial

Background

The aim of the randomized double-blinded clinical trial was to evaluate the effect of tooth brushing with Salvadora persica (miswak) sticks on Streptococcus mutans count and the mean plaque score relative to brushing with fluoridated tooth paste (FTP).

Methods

Our sample included 94 healthy, high caries-risk, 8 to 9-year-old students recruited from a government school, in Jeddah, Saudi Arabia between February and April 2016. Subjects were randomly grouped into test (provided with miswak sticks) and control groups (provided with FTP and soft brushes). Both groups were introduced to a preparatory period (PPP) of 3 weeks. Plaque score and saliva sampling were conducted prior to the PPP and in follow-up visits by a single, calibrated and blinded dentist.

Results

Both groups showed a statistically significant decrease in the mean plaque score across the study (P = 0.007 and P = 0.001, respectively). In addition, subjects in the test group with abundant S. sanguinis increased from zero to six after 3 months.

Conclusions

Salvadora Persica (miswak) and brushing with FTP significantly reduced plaque scores among school children. In addition, Salvadora persica was found to change the proportions of salivary bacteria in favor of species with less risk of inducing caries.

Trial registration

ClinicalTrials.gov ID #: NCT04137393.

Streptococcus mutans isolated from children with severe-early childhood caries form higher levels of persisters

OBJECTIVES

Dental caries is the most common chronic infectious disease in children. Streptococcus mutans, the main cariogenic bacterial species, produces persisters, nongrowing dormant variants of regular cells associated with chronicity of diseases. We hypothesized that the recurrent nature of caries, particularly within populations with high-caries risk, is due partly to specific phenotypic features of S. mutans such as its ability to form persisters. We aimed to investigate the genotypic and phenotypic differences between the S. mutans from children with severe early-childhood caries (S-ECC) and those without caries.

METHODS

S. mutans from plaque samples of caries-free (CF) and S-ECC children were tested for their ability to adapt to a lethal pH in an acid tolerance response assay. The persister levels of S. mutans isolates was quantified in both groups.

RESULTS

S. mutanswas identified in all 23 S-ECC but only 6 of the 21 CF subjects. In most subjects, only one dominant S. mutans genotype was detected. No statistically significant differences in the mean survival percentage of S. mutans were observed between the two groups at a lethal pH of 3.5. However, the dominant genotype within a particular S-ECC subject exhibited a higher percentage of cell survival compared to those in the CF group. In S-ECC patients, S. mutans isolates displayed a ∼15-fold higher persistence phenotype than S. mutans isolates from CF patients.

CONCLUSIONS

The ability of S. mutans to produce high levels of persisters may contribute to part of an individual's ability to control caries disease activity and recurrent lesions.

Sex-specific differences in the salivary microbiome of caries-active children

Background and Objectives: Dental caries is a chronic disease affecting young children and has multi-factorial risk factors. The purpose of this work was to identify sex-specific differences in the salivary microbiota within caries-active children. Design: Saliva specimens were collected from 85 children (boys: 41; girls: 44) between the ages of 2-12 years. Salivary microbial DNA was subjected to PCR amplification using V3-V4 16S rDNA-specific primers and next-generation sequencing. Results: Significant sex differences in salivary microbiota were found between caries-active boys versus caries-active girls. Neisseria flavescens, Rothia aeria, and Haemophilus pittmaniae were found at significantly higher levels in caries-active boys. In contrast, Lactococcus lactis, Selenomonas species HOT 126, Actinobaculum species HOT 183, Veillonella parvula, and Alloprevotella species HOT 473 were found at significantly higher levels in caries-active girls. Conclusion: We have found the acid-generating, cariogenic Lactococcus lactis to be much more abundant in caries-active girls than caries-active boys, indicating that this microorganism may play a more significant role in shaping the cariogenic microbiome in girls. In addition, in caries-active girls, Alloprevotella species HOT 473 was the only species that exhibited both significant sex differences (4.4-fold difference; p=0.0003) as well as high abundance in numbers (1.85% of the total microbial population).

Human genes influence the interaction between Streptococcus mutans and host caries susceptibility: a genome-wide association study in children with primary dentition

Streptococcus mutans is a well-known cause of dental caries, due to its acidogenicity, aciduricity, and ability to synthesize exopolysaccharides in dental plaques. Intriguingly, not all children who carry S. mutans manifest caries, even with similar characteristics in oral hygiene, diet, and other environmental factors. This phenomenon suggests that host susceptibility potentially plays a role in the development of dental caries; however, the association between host genetics, S. mutans, and dental caries remains unclear. Therefore, this study examined the influence of host gene-by-S. mutans interaction on dental caries. Genome-wide association analyses were conducted in 709 US children (<13 years old), using the dbGap database acquired from the center for oral health research in appalachia (COHRA) and the Iowa Head Start programmes (GEIRS). A generalized estimating equation was used to examine the gene-by-S. mutans interaction effects on the outcomes (decayed and missing/filled primary teeth due to caries). Sequentially, the COHRA and GEIRS data were used to identify potential interactions and replicate the findings. Three loci at the genes interleukin 32 (IL32), galactokinase 2 (GALK2), and CUGBP, Elav-like family member 4 (CELF4) were linked to S. mutans carriage, and there was a severity of caries at a suggestive significance level among COHRA children (P < 9 × 10-5), and at a nominal significance level among GEIRS children (P = 0.047-0.001). The genetic risk score that combined the three loci also significantly interacted with S. mutans (P < 0.000 1). Functional analyses indicated that the identified genes are involved in the host immune response, galactose carbohydrate metabolism, and food-rewarding system, which could potentially be used to identify children at high risk for caries and to develop personalized caries prevention strategies.

[Recent achievements in the microbiological etiology of dental caries]

Dental caries is the most common chronic infectious disease of the oral cavity. The bacterium Streptococcus mutans is the sole pathogen that causes this disease. However, substantial evidence suggests that prevention and treatment strategies developed from traditional "cariogenic pathogen theory" are inefficient in reducing the prevalence of dental caries. An increasing number of individuals adopt the ecological view of the microbiota in the pathogenesis of dental caries. Recent technological improvements have enabled the detection and analysis of oral microorganisms, and many studies have focused on this area. The core microbiota is defined as a cluster of microbes playing critical roles in the initial and development phases of dental caries and may provide future direction for microorganism-related etiological studies.

Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease

Small molecules are the primary communication media of the microbial world. Recent bioinformatic studies, exploring the biosynthetic gene clusters (BGCs) which produce many small molecules, have highlighted the incredible biochemical potential of the signaling molecules encoded by the human microbiome. Thus far, most research efforts have focused on understanding the social language of the gut microbiome, leaving crucial signaling molecules produced by oral bacteria and their connection to health versus disease in need of investigation. In this study, a total of 4,915 BGCs were identified across 461 genomes representing a broad taxonomic diversity of oral bacteria. Sequence similarity networking provided a putative product class for more than 100 unclassified novel BGCs. The newly identified BGCs were cross-referenced against 254 metagenomes and metatranscriptomes derived from individuals either with good oral health or with dental caries or periodontitis. This analysis revealed 2,473 BGCs, which were differentially represented across the oral microbiomes associated with health versus disease. Coabundance network analysis identified numerous inverse correlations between BGCs and specific oral taxa. These correlations were present in healthy individuals but greatly reduced in individuals with dental caries, which may suggest a defect in colonization resistance. Finally, corroborating mass spectrometry identified several compounds with homology to products of the predicted BGC classes. Together, these findings greatly expand the number of known biosynthetic pathways present in the oral microbiome and provide an atlas for experimental characterization of these abundant, yet poorly understood, molecules and socio-chemical relationships, which impact the development of caries and periodontitis, two of the world's most common chronic diseases.IMPORTANCE The healthy oral microbiome is symbiotic with the human host, importantly providing colonization resistance against potential pathogens. Dental caries and periodontitis are two of the world's most common and costly chronic infectious diseases and are caused by a localized dysbiosis of the oral microbiome. Bacterially produced small molecules, often encoded by BGCs, are the primary communication media of bacterial communities and play a crucial, yet largely unknown, role in the transition from health to dysbiosis. This study provides a comprehensive mapping of the BGC repertoire of the human oral microbiome and identifies major differences in health compared to disease. Furthermore, BGC representation and expression is linked to the abundance of particular oral bacterial taxa in health versus dental caries and periodontitis. Overall, this study provides a significant insight into the chemical communication network of the healthy oral microbiome and how it devolves in the case of two prominent diseases.

Comparison of the salivary and dentinal microbiome of children with severe-early childhood caries to the salivary microbiome of caries-free children

BACKGROUND

The main objectives of this study were to describe and compare the microbiota of 1) deep dentinal lesions of deciduous teeth of children affected with severe early childhood caries (S-ECC) and 2) the unstimulated saliva of these children and 3) the unstimulated saliva of caries-free children, and to compare microbiota compositional differences and diversity of taxa in these sampled sites.

METHODS

Children with S-ECC and without S-ECC were recruited. The saliva of all children with and without S-ECC was sampled along with the deep dentinal microbiota from children affected by S-ECC. The salivary microbiota of children affected by S-ECC (n = 68) was compared to that of caries-free children (n = 70), by Illumina MiSeq sequencing of 16S rRNA amplicons. Finally, the caries microbiota of deep dentinal lesions of those children with S-ECC was investigated.

RESULTS

Using two beta diversity metrics (Bray Curtis dissimilarity and UniFrac distance), the caries microbiota was found to be distinct from that of either of the saliva groups (caries-free & caries-active) when bacterial abundance was taken into account. However, when the comparison was made by measuring only presence and absence of bacterial taxa, all three microbiota types separated. While the alpha diversity of the caries microbiota was lowest, the diversity difference between the caries samples and saliva samples was statistically significant (p < 0.001). The major phyla of the caries active dentinal microbiota were Firmicutes (median abundance value 33.5%) and Bacteroidetes (23.2%), with Neisseria (10.3%) being the most abundant genus, followed by Prevotella (10%). The caries-active salivary microbiota was dominated by Proteobacteria (median abundance value 38.2%) and Bacteroidetes (27.8%) with the most abundant genus being Neisseria (16.3%), followed by Porphyromonas (9.5%). Caries microbiota samples were characterized by high relative abundance of Streptococcus mutans, Prevotella spp., Bifidobacterium and Scardovia spp.

CONCLUSIONS

Distinct differences between the caries microbiota and saliva microbiota were identified, with separation of both salivary groups (caries-active and caries-free) whereby rare taxa were highlighted. While the caries microbiota was less diverse than the salivary microbiota, the presence of these rare taxa could be the difference between health and disease in these children.

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

Early childhood caries (ECC), the most frequent disease of oral cavity in preschool children, is the consequence of microbial, genetic, biochemical, socioeconomic, physical, environmental and health-influencing behavioral factors. To investigate the role of the oral microbiome and the impact of host and environmental factors in the occurrence and development of ECC, we studied the supragingival plaques of 14 twin pairs and a set of triplets with discordant caries phenotypes and 15 mothers, applying the Human Oral Microbe Identification using Next Generation Sequencing technique (HOMINGS). A total of 2,293,650 reads revealed 11 phyla, 116 genera, and 139 species of micromiome. Comparative analysis between the caries and caries-free group at species level revealed that the relative abundance of Streptococcus mutans, Lactobacillus fermentum, Actinomyces islaelii, Neisseria sica, and Veilonella dispar was much higher in caries group (P < 0.0001). Furthermore, monozygotic twins exhibited a higher degree of similarity than dizygotic twins. Finally, we analyzed the relationship between environmental factors and the oral microbiome, and our results indicat that the frequency of taking sweet food is associated with ECC. We conclude the following. First, the occurrence of Streptococcus mutans, Lactobacillus fermentum, Neisseria sica, and Veilonella dispar is strongly associated with the occurrence of ECC. Second, host genetic factors influence the oral microbiome composition, while environmental and behavioral factors like the frequency of taking sweet foods have an impact on the distribution of caries-related bacteria.

Early Childhood Caries

Early childhood caries (ECC) is a common childhood disease with highest prevalence found in poor, socially disadvantaged, and minority groups. The main risk factors for ECC are frequent sugar consumption, lack of tooth brushing, and enamel hypoplasia. Contributory factors include environmental and psychosocial stresses that modify caregiver behaviors. Strategies for prevention include preventing mutans streptococci transmission, restricting dietary sugars, tooth brushing, topical fluoride applications, and early dental examinations. This article provides an overview of ECC based on current understanding of its cause, prevention, and management.

Cariogenic microbiome and microbiota of the early primary dentition: A contemporary overview

Recent advances in the field of molecular microbiology provide an unprecedented opportunity to decipher the vast diversity of the oral microbiome in health and disease. Here, we provide a contemporary overview of the oral microbiome and the microbiota of early childhood caries (ECC) with particular reference to newer analytical techniques. A MEDLINE search revealed a total of 20 metagenomic studies describing cariogenic microbiomes of ECC, 10 of which also detailed the healthy microbiomes. In addition, seven studies on site-specific microbiomes, focusing on acidogenic and aciduric microbiota of deep-dentinal lesions, were also reviewed. These studies evaluated plaque and saliva of children aged 1.5-11 years, in cohorts of 12-485 individuals. These studies reveal a very rich and diverse microbial communities, with hundreds of different phylotypes and microbial species, including novel species and phyla such as Scardovia wiggsiae, Slackia exigua, Granulicatella elegans, Firmicutes in the plaque biofilms of children with ECC. On the contrary, bacteria such as Streptococcus cristatus, S. gordonii, S. sanguinis, Corynebacterium matruchotii, and Neisseria flavescens were common in plaque biofilm of noncarious, healthy, tooth surfaces in subjects with caries. The review illustrates the immense complexity and the diversity of the human oral microbiota of the cariogenic plaque microbiome in ECC, and the daunting prospect of its demystification.

Salivary antioxidant capacity of children with severe early childhood caries before and after complete dental rehabilitation

OBJECTIVE

There is a need to determine whether total antioxidant capacity (TAC) in severe early childhood caries (S-ECC) is an indicator of inflammatory response to the lesion or a marker of the disease. This study compared TAC levels in children with ECC before and after dental treatment and compared the results with those of caries-free children.

DESIGN

Prospective study.

SETTING

A teaching hospital.

PATIENT SELECTION

Salivary samples were obtained from 20 children aged 5 years and diagnosed with S-ECC, and 20 age- and sex-matched controls.

INTERVENTION DETAILS

Complete dental rehabilitation under general anesthesia was performed on the children with S-ECC, and follow-up salivary samples were obtained one week and three months postoperatively. TAC was measured using a commercially available Oxygen Radical Absorbance Antioxidant Assay measurement kit (Zen-Bio ORAC™, AMS Biotechnology, Abington, UK).

OUTCOME MEASURES

Differences between children with and without dental caries were tested using the Mann-Whitney U test; differences before and after dental treatment were analyzed using Friedman test followed by Wilcoxon sign-rank test with Bonferroni correction to compensate for multiple comparisons.

RESULTS

Median TAC (1.54 mcg/L, CI 1.15-1.92) of the control group was significantly lower than that of the treated group prior to treatment (p = 0.003). Treatment of the dental lesions significantly reduced TAC of the treated group, and no significant differences were observed between the test and control groups at either one week (p = 0.076) recall or three-month recall (p = 0.096). TAC in children posttreatment was significantly reduced compared to their pretreatment values (p < 0.001).

CONCLUSION

Total antioxidant capacity in the saliva of children with severe early childhood caries undergoes significant reduction following treatment of the carious lesions.

Association between Oral Candida and Bacteriome in Children with Severe ECC

Candida albicans is an opportunistic fungal organism frequently detected in the oral cavity of children with severe early childhood caries (S-ECC). Previous studies suggested the cariogenic potential of C. albicans, in vitro and in vivo, and further demonstrated its synergistic interactions with Streptococcus mutans. In combination, the 2 organisms are associated with higher caries severity in a rodent model. However, it remains unknown whether C. albicans influences the composition and diversity of the entire oral bacterial community to promote S-ECC onset. With 16s rRNA amplicon sequencing, this study analyzed the microbiota of saliva and supragingival plaque from 39 children (21 S-ECC and 18 caries-free [CF]) and 33 mothers (17 S-ECC and 16 CF). The results revealed that the presence of oral C. albicans is associated with a highly acidogenic and acid-tolerant bacterial community in S-ECC, with an increased abundance of plaque Streptococcus (particularly S. mutans) and certain Lactobacillus/Scardovia species and salivary/plaque Veillonella and Prevotella, as well as decreased levels of salivary/plaque Actinomyces. Concurrent with this microbial community assembly, the activity of glucosyltransferases (cariogenic virulence factors secreted by S. mutans) in plaque was significantly elevated when C. albicans was present. Moreover, the oral microbial community composition and diversity differed significantly by disease group (CF vs. S-ECC) and sample source (saliva vs. plaque). Children and mothers within the CF and S-ECC groups shared microbiota composition and diversity, suggesting a strong maternal influence on children's oral microbiota. Altogether, this study underscores the importance of C. albicans in association with the oral bacteriome in the context of S-ECC etiopathogenesis. Further longitudinal studies are warranted to examine how fungal-bacterial interactions modulate the onset and severity of S-ECC, potentially leading to novel anticaries treatments that address fungal contributions.

Oral microbiomes: more and more importance in oral cavity and whole body

Microbes appear in every corner of human life, and microbes affect every aspect of human life. The human oral cavity contains a number of different habitats. Synergy and interaction of variable oral microorganisms help human body against invasion of undesirable stimulation outside. However, imbalance of microbial flora contributes to oral diseases and systemic diseases. Oral microbiomes play an important role in the human microbial community and human health. The use of recently developed molecular methods has greatly expanded our knowledge of the composition and function of the oral microbiome in health and disease. Studies in oral microbiomes and their interactions with microbiomes in variable body sites and variable health condition are critical in our cognition of our body and how to make effect on human health improvement.

Salivary proteins and microbiota as biomarkers for early childhood caries risk assessment

Early childhood caries (ECC) is a term used to describe dental caries in children aged 6 years or younger. Oral streptococci, such as Streptococcus mutans and Streptococcus sorbrinus, are considered to be the main etiological agents of tooth decay in children. Other bacteria, such as Prevotella spp. and Lactobacillus spp., and fungus, that is, Candida albicans, are related to the development and progression of ECC. Biomolecules in saliva, mainly proteins, affect the survival of oral microorganisms by multiple innate defensive mechanisms, thus modulating the oral microflora. Therefore, the protein composition of saliva can be a sensitive indicator for dental health. Resistance or susceptibility to caries may be significantly correlated with alterations in salivary protein components. Some oral microorganisms and saliva proteins may serve as useful biomarkers in predicting the risk and prognosis of caries. Current research has generated abundant information that contributes to a better understanding of the roles of microorganisms and salivary proteins in ECC occurrence and prevention. This review summarizes the microorganisms that cause caries and tooth-protective salivary proteins with their potential as functional biomarkers for ECC risk assessment. The identification of biomarkers for children at high risk of ECC is not only critical for early diagnosis but also important for preventing and treating the disease.

Saliva and tooth biofilm bacterial microbiota in adolescents in a low caries community

The oral cavity harbours a complex microbiome that is linked to dental diseases and serves as a route to other parts of the body. Here, the aims were to characterize the oral microbiota by deep sequencing in a low-caries population with regular dental care since childhood and search for association with caries prevalence and incidence. Saliva and tooth biofilm from 17-year-olds and mock bacteria communities were analysed using 16S rDNA Illumina MiSeq (v3-v4) and PacBio SMRT (v1-v8) sequencing including validity and reliability estimates. Caries was scored at 17 and 19 years of age. Both sequencing platforms revealed that Firmicutes dominated in the saliva, whereas Firmicutes and Actinobacteria abundances were similar in tooth biofilm. Saliva microbiota discriminated caries-affected from caries-free adolescents, with enumeration of Scardovia wiggsiae, Streptococcus mutans, Bifidobacterium longum, Leptotrichia sp. HOT498, and Selenomonas spp. in caries-affected participants. Adolescents with B. longum in saliva had significantly higher 2-year caries increment. PacBio SMRT revealed Corynebacterium matruchotii as the most prevalent species in tooth biofilm. In conclusion, both sequencing methods were reliable and valid for oral samples, and saliva microbiota was associated with cross-sectional caries prevalence, especially S. wiggsiae, S. mutans, and B. longum; the latter also with the 2-year caries incidence.

Microbiome Associated with Severe Caries in Canadian First Nations Children

Young Indigenous children in North America suffer from a higher degree of severe early childhood caries (S-ECC) than the general population, leading to speculation that the etiology and characteristics of the disease may be distinct in this population. To address this knowledge gap, we conducted the first microbiome analysis of an Indigenous population using modern molecular techniques. We investigated the caries-associated microbiome among Canadian First Nations children with S-ECC. Thirty First Nations children <72 mo of age with S-ECC and 20 caries-free children were recruited in Winnipeg, Canada. Parents or caregivers completed a questionnaire on general and dental health, diet, and demographics. The plaque microbiome was investigated by sequencing the 16S rRNA gene. Sequences were clustered into operational taxonomic units and taxonomy assigned via the Human Oral Microbiome Database, then analyzed at the community level with alpha and beta diversity measures. Compared with those who were caries free, children with S-ECC came from households with lower income; they were more likely to live in First Nations communities and were more likely to be bottle-fed; and they were weaned from the bottle at a later age. The microbial communities of the S-ECC and caries-free groups did not differ in terms of species richness or phylogenetic diversity. Beta diversity analysis showed that the samples significantly clustered into groups based on caries status. Twenty-eight species-level operational taxonomic units were significantly different between the groups, including Veillonella HOT 780 and Porphyromonas HOT 284, which were 4.6- and 9-fold higher, respectively, in the S-ECC group, and Streptococcus gordonii and Streptococcus sanguinis, which were 5- and 2-fold higher, respectively, in the caries-free group. Extremely high levels of Streptococcus mutans were detected in the S-ECC group. Overall, First Nations children with S-ECC have a significantly different plaque microbiome than their caries-free counterparts, with the S-ECC group containing higher levels of known cariogenic organisms.

The microbiome of the lung and its extracellular vesicles in nonsmokers, healthy smokers and COPD patients

Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disease, and bacterial infection plays a role in its pathogenesis. Bacteria secrete nanometer-sized extracellular vesicles (EVs), which may induce more immune dysfunction and inflammation than the bacteria themselves. We hypothesized that the microbiome of lung EVs might have distinct characteristics depending on the presence of COPD and smoking status. We analyzed and compared the microbiomes of 13 nonsmokers with normal spirometry, 13 smokers with normal spirometry (healthy smokers) and 13 patients with COPD by using 16S ribosomal RNA gene sequencing of surgical lung tissue and lung EVs. Subjects were matched for age and sex in all groups and for smoking levels in the COPD and healthy smoker groups. Each group included 12 men and 1 woman with the same mean age of 65.5 years. In all groups, EVs consistently showed more operational taxonomic units (OTUs) than lung tissue. In the healthy smoker and COPD groups, EVs had a higher Shannon index and a lower Simpson index than lung tissue and this trend was more prominent in the COPD group. Principal component analysis (PCA) showed clusters based on sample type rather than participants' clinical characteristics. Stenotrophomonas, Propionibacterium and Alicyclobacillus were the most commonly found genera. Firmicutes were highly present in the EVs of the COPD group compared with other samples or groups. Our analysis of the lung microbiome revealed that the bacterial communities present in the EVs and in the COPD group possessed distinct characteristics with differences in the OTUs, diversity indexes and PCA clustering.

Exploration of Human Salivary Microbiomes--Insights into the Novel Characteristics of Microbial Community Structure in Caries and Caries-Free Subjects

Recently, high-throughput sequencing has improved the understanding of the microbiological etiology of caries, but the characteristics of the microbial community structure in the human oral cavity with and without caries are not completely clear. To better understand these characteristics, Illumina MiSeq high-throughput sequencing was utilized to analyze 20 salivary samples (10 caries-free and 10 caries) from subjects from the same town in Dongxiang, Gansu, China. A total of 5,113 OTUs (Operational Taxonomic Units, 97% cutoff) were characterized in all of the salivary samples obtained from the 20 subjects. A comparison of the two groups revealed that (i) the predominant phyla were constant between the two groups; (ii) the relative abundance of the genera Veillonella, Bifidobacterium, Selenomonas, Olsenella, Parascardovia, Scardovia, Chryseobacterium, Terrimonas, Burkholderia and Sporobacter was significantly higher in the group with caries (P < 0.05); and (iii) four genera with low relative abundance (< 0.01% on average), including two characteristic genera in caries (Chryseobacterium and Scardovia), significantly influenced the microbial community structure at the genus and OTU levels. Moreover, via co-occurrence and principal component analyses, the co-prevalence of the pathogenic genera was detected in the caries samples, but in the caries-free samples, the function of clustered genera was more random. This result suggests that a synergistic effect may be influencing the assembly of the caries microbial community, whereas competition may play a more dominant role in governing the microbial community in the caries-free group. Our findings regarding the characteristics of the microbial communities of the groups with and without caries might improve the understanding of the microbiological etiology of caries and might improve the prevention and cure of caries in the future.

The Microbiome in Populations with a Low and High Prevalence of Caries

The oral microbiota was compared between Romanian adolescents with a high prevalence of caries and no dental care and Swedish caries-active and caries-free adolescents in caries prevention programs and with a low prevalence of caries. Biofilm samples were analyzed by FLX+ pyrosequencing of the V1 to V4 hypervariable regions of the 16S rRNA gene and polymerase chain reaction (PCR)/quantitative PCR (qPCR) for Streptococcus mutans and Streptococcus sobrinus. Sequences obtained blasted to 9 phyla, 66 genera, and 401 human oral taxa (HOT) in the 16S rRNA Human Oral Microbiome Database, of which 295 were represented by ≥20 sequences. The Romanian adolescents had more sequences in Firmicutes and fewer in Actinobacteria phyla and more sequences in the genera Bacteroidetes [G-3], Porphyromonas, Abiotrophia, Filifactor, Peptostreptococcaceae [11][G-4], Pseudoramibacter, Streptococcus, and Neisseria and fewer in Actinomyces, Selenomonas, Veillonella, Campylobacter, and TM7 [G-1] than the Swedish groups. Multivariate modeling employing HOT, S. sobrinus and S. mutans (PCR/qPCR), and sugar snacks separated Romanian from Swedish adolescents. The Romanian adolescents' microbiota was characterized by a panel of streptococci, including S. mutans, S. sobrinus, and Streptococcus australis, and Alloprevotella, Leptotrichia, Neisseria, Porphyromonas, and Prevotella. The Swedish adolescents were characterized by sweet snacks, and those with caries activity were also characterized by Prevotella, Actinomyces, and Capnocytophaga species and those free of caries by Actinomyces, Prevotella, Selenomonas, Streptococcus, and Mycoplasma. Eight species including Streptococcus mitis and Streptococcus species HOT070 were prevalent in Romanian and Swedish caries-active subjects but not caries-free subjects. In conclusion, S. mutans and S. sobrinus correlated with Romanian adolescents with caries and with limited access to dental care, whereas S. mutans and S. sobrinus were detected infrequently in Swedish adolescents in dental care programs. Swedish caries-active adolescents were typically colonized by Actinomyces, Selenomonas, Prevotella, and Capnocytophaga. Hence, the role of mutans streptococci as a primary caries pathogen appears less pronounced in populations with prevention programs compared to populations lacking caries treatment and prevention strategies.