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

Risk of Severe Early Childhood Caries over Time in Low-Income Preschoolers

INTRODUCTION

Early childhood caries (ECC), and the progression to severe ECC (S-ECC), is a serious oral health issue, leading to acute pain, sepsis, tooth loss, and compromised quality of life. Although the association between sociodemographic factors and ECC has been widely discussed, it remains unclear whether the same association exists between inequality and S-ECC.

OBJECTIVES

To investigate the impact of low income on the oral health of preschool children and explore any additional risk factors for developing ECC and S-ECC during follow-up.

METHODS

The study used Taipei Child Development Screening Program data from 2014 to 2019. It included children aged 3 to 5 y who had more than 2 oral exams and completed baseline oral health questionnaires. Low-income children were matched 1:4 with controls by age and gender. Evaluation of ECC and S-ECC used the dmft index during follow-up exams. Generalized estimating equations (GEEs) assessed the impact of household income on ECC and S-ECC risk over time.

RESULTS

Of the 895 participants, 179 were from low-income households. We revealed a significantly higher risk of developing S-ECC (adjusted odds ratio [aOR] 1.99; 95% confidence interval [CI] 1.25-3.17) in children from low-income households, with no significantly increased of risk of developing ECC. Children who consumed sugary beverages >4 times per week showed elevated risks of developing both ECC (aOR 1.77; 95% CI 1.07-2.94) and S-ECC (aOR 1.89; 95% CI 1.13-3.17). Protective factors included children with mothers with a college education (S-ECC: aOR 0.50; 95% CI 0.32-0.79).

CONCLUSION

Children from low-income households have a significant risk of developing S-ECC compared with children from non-low-income households during follow-up. Factors contributing to this risk include lower maternal education, poor maternal oral health, and increased consumption of sugar-sweetened beverages. Policymakers should develop health measures to reduce the prevalence of ECC and S-ECC in children from low-income households whose mothers have lower educational levels and poor oral health.Knowledge Transfer Statement:The results of this study highlight the significant S-ECC risk among preschool children from low-income households in Taipei, with other risk factors including higher consumption of sugar-sweetened beverages, lower maternal education, and poor maternal oral health. Policymakers can use our findings to develop targeted policy and behavioral interventions to reduce S-ECC in vulnerable populations.

Efficacy of silver diamine fluoride (SDF) in arresting dentin caries against inter-kingdom biofilms of Streptococcus mutans and Candida albicans

OBJECTIVES

To compare, in vitro, the efficacy of three proprietary silver diamine fluoride (SDF) products in mitigating progression of dentinal caries induced by an inter-kingdom, dual-species, bacterial-yeast biofilm.

METHODS

Human dentin blocks were demineralized to create artificial caries lesions and randomized into three SDF test groups: Saforide, Topamine, T-SDF, and an aqueous control (n = 26 per group). After application of foregoing SDF variants, the blocks were incubated with Streptococcus mutans and Candida albicans for 24 h for biofilm development, and subsequently subjected to a microbe-induced, pH-cycling process for 7 days, to mimic the oral eco-system. The biofilm cell viability and surface topography were assessed by colony-forming units (CFUs) and scanning electron microscopy respectively. The lesion depth and mineral density were evaluated by micro-computer tomography. SDF precipitate and matrix-to-mineral ratio were evaluated by X-ray diffraction and Fourier transform infrared spectroscopy, respectively. Standard, accepted methodology was used for all these evaluations and procedures.

RESULTS

After pH cycling, the SDF groups demonstrated comparable inhibition of the biofilm relative to the control. the log CFU of S. mutans for Saforide, Topamine, T-SDF, and control were 6.69±0.73, 6.48±0.56, 6.63±0.66, and 8.01±0.45, respectively. For C. albicans, the log CFU were 4.86±0.44, 4.72±0.53, 4.92±0.29, and 5.60±0.27, respectively. The log CFU of S. mutans and C. albicans in the SDF groups were significantly lower than the control group (p<0.001). Further, the lesion depth decreased by approximately 14.79±7.00% in the SDF groups, while it increased by 11.07±8.61% in the control (p<0.001), and the mineral density increased by 16.36±4.58% in the SDF group, as opposed to a 5.59±2.64% reduction in the control (p<0.001) implying their caries mitigating effect. These findings were corroborated by SEM images of the lesions.

CONCLUSION

SDF significantly mitigated dentin caries due to an assault by a polymicrobial plaque biofilm whilst arresting mineral loss and lesion growth. There was no difference in the caries-arresting efficacy of the compared SDF variants.

A cross-cohort analysis of dental plaque microbiome in early childhood caries

Early childhood caries (ECC) is a multifactorial disease with a microbiome playing a significant role in caries progression. Understanding changes at the microbiome level in ECC is required to develop diagnostic and preventive strategies. In our study, we combined data from small independent cohorts to compare microbiome composition using a unified pipeline and applied a batch correction to avoid the pitfalls of batch effects. Our meta-analysis identified common biomarker species between different studies. We identified the best machine learning method for the classification of ECC versus caries-free samples and compared the performance of this method using a leave-one-dataset-out approach. Our random forest model was found to be generalizable when used in combination with other studies. While our results highlight the potential microbial species involved in ECC and disease classification, we also mentioned the limitations that can serve as a guide for future researchers to design and use appropriate tools for such analyses.

Comparative analysis of microbiome in coronal and root caries

BACKGROUND

The global rise in the elderly population has increased the prevalence of root caries. Streptococcus mutans, Lactobacilli and Actinomyces are considered the primary pathogens of dental caries in culture-based studies. This study aimed to investigate bacterial profiles in coronal and root caries lesions and determine the association of specific bacterial genera at each site.

METHODS

Dentine samples from carious lesions were collected from 22 extracted teeth using an excavator. Microbial DNA was extracted from the samples using a protocol developed for this study. 16S rRNA gene amplicon sequencing was employed for microbial analysis. PCR amplification targeted the V3-V4 region of the bacterial 16S rRNA, and the amplicon sequencing used an Illumina MiSeq system (2 × 300 bp paired-end reads). Statistical analysis was performed by the Phyloseq and DESeq2 packages in R.

RESULTS

In coronal caries, Olsenella, Lactobacillus and Prevotella were the most prevalent genera, comprising approximately 70% of the microbiome community. In the root caries, however, although Olsenella, Prevotella and Lactobacillus remained the dominant genera, they accounted for only half of the microbiome community. This study identified significant differences in alpha diversity indices between the coronal and root caries. LEfSE analysis revealed several unique genera in each caries lesion.

CONCLUSION

The microbiome of root caries lesions was richer and more complex than the coronal caries microbiota. The results suggest that lesion-related variations in the oral microflora may be detected in carious dentine.

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

OBJECTIVES

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

DATA

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

SOURCES

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

STUDY SELECTION/RESULTS

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

CONCLUSION

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

CLINICAL SIGNIFICANCE

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

Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples

Obtaining complete, high-quality reference genomes is essential to the study of any organism. Recent advances in nanopore sequencing, as well as genome assembly and analysis methods, have made it possible to obtain complete bacterial genomes from metagenomic (i.e., multispecies) samples, including those from the human microbiome. In this study, methods are presented to obtain complete bacterial genomes from human saliva using complementary Oxford Nanopore (ONT) and Illumina sequencing. Applied to 3 human saliva samples, these methods resulted in 11 complete bacterial genomes: 3 Saccharibacteria clade G6 (also known as Ca. Nanogingivalaceae HMT-870), 1 Saccharibacteria clade G1 HMT-348, 2 Rothia mucilaginosa, 2 Actinomyces graevenitzii, 1 Mogibacterium diversum, 1 Lachnospiraceae HMT-096, and 1 Lancefieldella parvula; and one circular chromosome of Ruminococcaceae HMT-075 (which likely has at least 2 chromosomes). The 4 Saccharibacteria genomes, as well as the Actinomyces graeventizii genomes, represented the first complete genomes from their respective bacterial taxa. Aside from the complete genomes, the assemblies contained 147 contigs of over 500,000 bp each and thousands of smaller contigs, together representing a myriad of additional draft genomes including many which are likely nearly complete. The complete genomes enabled highly accurate pangenome analysis, which identified unique and missing features of each genome compared to its closest relatives with complete genomes available in public repositories. These features provide clues as to the lifestyle and ecological role of these bacteria within the human oral microbiota, which will be particularly useful in designing future studies of the taxa that have never been isolated or cultivated. IMPORTANCE Obtaining complete and accurate genomes is crucial to the study of any organism. Previously, obtaining complete genomes of bacteria, including those of the human microbiome, frequently required isolation of the organism, as well as low-throughput, manual sequencing methods to resolve repeat regions. Advancements in long-read sequencing technologies, including Oxford Nanopore (ONT), have made it possible to obtain complete, closed bacterial genomes from metagenomic samples. This study reports methods to obtain complete genomes from the human oral microbiome using complementary ONT and Illumina sequencing of saliva samples. Eleven complete genomes were obtained from 3 human saliva samples, with genomes of Saccharibacteria HMT-870, Saccharibacteria HMT-348, and Actinomyces graeventzii being the first complete genomes from their respective taxa. Obtaining complete bacterial genomes in a high-throughput manner will help illuminate the metabolic and ecological roles of important members of the human microbiota, particularly those that have remained recalcitrant to isolation and cultivation.

The diversity analysis and gene function prediction of intestinal bacteria in three equine species

The intestinal flora has a variety of physiological functions involved in the regulation of host metabolism, immunity and endocrinology, and plays an important role in maintaining the health of the host. In this study, we used high-throughput sequencing technology to analyze the intestinal bacterial diversity and their gene functions in three equine species of the genus Shetland Pony (SP), Mongolian Wild Ass (MA), and Plain Zebra (PZ) in captivity in two wildlife parks in Inner Mongolia Autonomous Region, China. The results showed that only the SP intestinal bacterial abundance index (Chao1) was significantly different (P < 0.05) between the same species in the two wildlife parks, but neither the intestinal bacterial diversity index (Shannon) nor the community composition were significantly different (P > 0.05). The bacterial abundance index (Chao1) was significantly higher in MA than SP (P < 0.05) and highly significantly higher than PZ (P < 0.01); the bacterial diversity index (Shannon) was higher in MA than PZ, but there was no significant difference, but both MA and PZ were significantly higher than SP (P < 0.05). Moreover, the intestinal bacterial community composition was significantly different among the three equine species (P = 0.001). The dominant bacterial phyla for SP, MA, and PZ were Firmicutes and Bacteroidota; among them, the bacterial family with the highest relative abundance was Lachnospiraceae and the bacterial genus was Rikenellaceae_RC9_gut_group. Analysis of the metabolic gene functions of intestinal bacteria revealed that the highest relative abundance at Pathway level 2 was for global and overview maps; at Pathway level 3, the highest relative abundance was for biosynthesis of secondary metabolites. In sum, the intestinal bacterial community composition and diversity of the above three equine species differed significantly, but their metabolic gene functions were similar. Moreover, the results of this manuscript fill the gap in the study of intestinal bacterial diversity in SP, MA, and PZ. It also provides a reference for the study of the dominant bacteria in the intestinal microorganisms of these three equine species and the discovery of novel functional genes.