OBJECTIVES: This study aimed to analyze the bacteria in dental caries and establish an optimized dental-ca-ries diagnosis model based on 16S ribosomal RNA (rRNA) data of oral flora. METHODS: We searched the public databa-ses of microbiomes including NCBI, MG-RAST, EMBL-EBI, and QIITA and collected data involved in the relevant research on human oral microbiomes worldwide. The samples in the caries dataset (1 703) were compared with healthy ones (20 540) by using the microbial search engine (MSE) to obtain the microbiome novelty score (MNS) and construct a caries diagnosis model based on this index. Nonparametric multivariate ANOVA was used to analyze and compare the impact of different host factors on the oral flora MNS, and the model was optimized by controlling related factors. Finally, the effect of the model was evaluated by receiver operating characteristic (ROC) curve analysis. RESULTS: 1) The oral microbiota distribution obviously differed among people with various oral-health statuses, and the species richness and species diversity index decreased. 2) ROC curve was used to evaluate the caries data set, and the area under ROC curve was AUC=0.67. 3) Among the five hosts' factors including caries status, country, age, decayed missing filled tooth (DMFT) indices, and sampling site displayed the strongest effect on MNS of samples (P=0.001). 4) The AUC of the model was 0.87, 0.74, 0.74, and 0.75 in high caries, medium caries, low caries samples in Chinese children, and mixed dental plaque samples after controlling host factors, respectively. CONCLUSIONS The model based on the analysis of 16S rRNA data of oral flora had good diagnostic efficiency.
Humans ; Child ; Bacteria/genetics* ; Dental Caries/microbiology* ; Dental Caries Susceptibility ; Microbiota/genetics* ; RNA, Ribosomal, 16S

Objective: To detect and analyze the characteristics of oral microbiota in species composition, function and metabolism among caries, periodontitis and oral healthy individuals, hunting for the microbiome-derived biomarkers with specificity and sensitivity to estimate the occurrence of these two diseases. Methods: Saliva samples were collected from 10 patients with high caries risk [decayed-missing-filled teeth (DMFT)≥6, HC group] in Department of Endodontics, 10 patients with periodontitis of grade Ⅱ A-Ⅲ C (PG group) in Department of Periodontology and 10 oral healthy individuals (HH group) from School of Stomatology, The Fourth Military Medical University during from March 2022 to June 2022. A baseline examination was conducted on all participants, including their oral conditions of caries and periodontal health. Metagenomic sequencing (Illumina PE150 platform) and liquid chromatography-mass spectrometry were used to detect microorganisms and their metabolites in the samples respectively. The sequencing data were analyzed to obtain the information of microbial taxonomic composition, functional genes and metabolites in each group of samples. The basic oral conditions and saliva samples of subjects in each group were evaluated and collected by the same professional endodontist. Results: There were no significant difference in baseline characteristics such as age and sex among the subjects in each group (P>0.05). DMFT in HC group (9.0±1.7) was significantly higher than that in HH group (0) and PG group (0) (F=243.00, P<0.001). Sequencing data analysis showed that the taxonomic compositions of salivary microbiota in each group were mainly Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria at the phylum level, and Streptococcus, Neisseria, Rothia, Prevotella at the genus level. Differential analysis showed that, compared with the HH group, HC group and PG group had significant differences in taxonomic composition (P<0.05), and the most significant among them was Prevotella. At the species level, Prevotella pallens was the most significant change in HC group, and Porphyromonas gingivalis in PG group. Metabolite analysis showed that there were significant differences in metabolites between HC group and PG group. The results showed that, compared with the HH group, the most significant metabolite change was 3-hydroxy-1, 5-diphenylpentan-1-one in HC group (P=0.001) and N1 acetylspermine in PG group (P=0.002) respectively. Compared with the PG group, the metabolite of HC group with the most significant difference is D-glucosamine 6-phosphate (P=0.006). The metabolism gene function analysis showed that, the enrichment of carbohydrate metabolism related genes was highest in HC group, followed with HH group, and it was lowest in PG group. In addition, compared with the HH group, the abundance of functional genes related to glucose metabolism, such as ABC transporter and phosphotransferase system, were significantly decreased in PG group (P<0.05), but significantly increased in HC group (P<0.05). Conclusions: There is a significant correlation between the alternation of carbohydrate metabolism of salivary microbiota with the occurrence of caries and periodontitis. In the future, Prevotella pallens and 3-hydroxy-1, 5-diphenylpentan-1-one may be the potential biomarkers of caries; while Porphyromonas gingivalis and N1 acetylspermine work in the predictions of periodontitis.
Humans ; Saliva/microbiology* ; Dental Caries Susceptibility ; Periodontitis/microbiology* ; Microbiota/genetics* ; Porphyromonas gingivalis/genetics* ; RNA, Ribosomal, 16S/genetics*

Streptococcus mutans (S. mutans) is generally regarded as a major contributor to dental caries because of its ability to synthesize extracellular polysaccharides (EPS) that aid in the formation of plaque biofilm. The VicRKX system of S. mutans plays an important role in biofilm formation. The aim of this study was to investigate the effects of vicK gene on specific characteristics of EPS in S. mutans biofilm. We constructed single-species biofilms formed by different mutants of vicK gene. Production and distribution of EPS were detected through atomic force microscopy, scanning electron microscopy and confocal laser scanning microscopy. Microcosmic structures of EPS were analyzed by gel permeation chromatography and gas chromatography-mass spectrometry. Cariogenicity of the vicK mutant was assessed in a specific pathogen-free rat model. Transcriptional levels of cariogenicity-associated genes were confirmed by quantitative real-time polymerase chain reaction. The results showed that deletion of vicK gene suppressed biofilm formation as well as EPS production, and EPS were synthesized mostly around the cells. Molecular weight and monosaccharide components underwent evident alterations. Biofilms formed in vivo were sparse and contributed a decreased degree of caries. Moreover, expressional levels of genes related to EPS synthesis were down-regulated, except for gtfB. Our report demonstrates that vicK gene enhances biofilm formation and subsequent caries development. And this may due to its regulations on EPS metabolism, like synthesis or microcosmic features of EPS. This study suggests that vicK gene and EPS can be considered as promising targets to modulate dental caries.
Animals ; Biofilms ; Dental Caries ; Dental Plaque ; Rats ; Streptococcus mutans/genetics*

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), 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.
Adolescent ; Child ; DMF Index ; Dental Caries ; microbiology ; Dental Caries Susceptibility ; genetics ; Galactokinase ; Genome-Wide Association Study ; Humans ; Streptococcus mutans ; genetics ; isolation & purification ; Tooth, Deciduous

OBJECTIVE: This study aims to investigate the association between human leucocyte antigen (HLA)-DQB1 allele polymorphisms and the presence dental caries among the Uygur and Han children in Xinjiang. METHODS: HLA-DQB1 allele in the Uygur and Han children with dental caries and healthy control in Xinjiang was tested (n=40) using the polymerase chain reaction-sequence specific primer (PCR-SSP) DNA parting technology. RESULTS: A total of five specific loci were detected in the HLA-DQB1 locus among the Uygur and Han children. The frequency of the HLA-DQB1*02 allele in the Han group with severe caries (12.5%) was significantly lower than in the control group (32.5%) (P<0.05, OR=0.297). Moreover, the frequency of the HLA-DQB1*05 allele in the Uygur group with severe caries (37.5%) was significantly higher than in the control group (17.5%) (P<0.05, OR=2.829). CONCLUSIONS Caries susceptibility among the Uygur and Han children in Xinjiang is related to the HLA-DQB1 allele. The HLA-DQB1*02 allele may protect against caries among the Han children, whereas the HLA-DQB1*05 allele may be responsible for the susceptibility of the Uygur children to caries.
Alleles ; Asian Continental Ancestry Group ; Child ; China ; Dental Caries ; ethnology ; genetics ; Gene Frequency ; Genetic Predisposition to Disease ; HLA-DQ beta-Chains ; genetics ; Humans ; Polymerase Chain Reaction ; Polymorphism, Genetic

OBJECTIVETo analyze the whole microbial structure in a case of rampant caries to provide evidence for its prevention and treatment.

METHODSClinical samples including blood, supragingival plaque, plaque in the caries cavity, saliva, and mucosal swabs were collected with the patient's consent. The blood sample was sent for routine immune test, and the others samples were stained using Gram method and cultured for identifying colonies and 16S rRNA sequencing. DNA was extracted from the samples and tested for the main cariogenic bacterium (Streptococcus mutans) with qPCR, and the whole microbial structure was analyzed using DGGE.

RESULTSThe patient had a high levels of IgE and segmented neutrophils in his blood. Streptococci with extremely long chains were found in the saliva samples under microscope. Culture of the samples revealed the highest bacterial concentration in the saliva. The relative content of hemolytic bacterium was detected in the samples, the highest in the caries cavity; C. albicans was the highest in the dental plaque. In addition, 33 bacterial colonies were identified by VITEK system and 16S rDNA sequence phylogenetic analysis, and among them streptococci and Leptotrichia wade were enriched in the dental plaque sample, Streptococcus mutans, Fusobacterium nucleatum, and Streptococcus tigurinus in the caries cavity, and Lactobacillus in the saliva. S. mutans was significantly abundant in the mucosal swabs, saliva and plaque samples of the caries cavity as shown by qPCR. Compared to samples collected from a healthy individual and another two patients with rampant caries, the samples from this case showed a decreased bacterial diversity and increased bacterial abundance shown by PCR-DGGE profiling, and multiple Leptotrichia sp. were detected by gel sequencing.

CONCLUSIONThe outgrowth of such pathogenic microorganisms as S. mutans and Leptotrichia sp., and dysbiosis of oral microbial community might contribute to the pathogenesis of rampant caries in this case.

Abnormalities, Multiple ; Dental Caries ; microbiology ; Dental Plaque ; microbiology ; Fusobacterium ; isolation & purification ; Humans ; Immunoglobulin E ; blood ; Lactobacillus ; isolation & purification ; Leptotrichia ; isolation & purification ; Limb Deformities, Congenital ; Microbiota ; Mouth Mucosa ; microbiology ; Neutrophils ; cytology ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; genetics ; Saliva ; microbiology ; Streptococcus ; isolation & purification ; Tooth Abnormalities

OBJECTIVETo observe the dynamic changes of membrane-bound proton-translocating ATPase (F-ATPase) in the development of dental caries, the expression of Streptococcus mutans F-ATPase under different pH concentrations and during the development of dental caries is analyzed.

METHODSStreptococcus mutans cultured under different pH (pH4.0-7.0) concentrations and containing 5% glucose and no glucose containing BHI were collected. RNA was extracted. Subsequently, F-ATPase gene was detected using real-time polymerase chain reaction. Male Wistar rats were divided randomly into caries group and control group. The rats in the caries group were fed caries feed and 5% glucose water, whereas those of control group were fed normal feed. Total RNA was extracted from plaque samples, which were collected from rats' oral cavity every two weeks. F-ATPase gene was detected by real-time PCR. In the 11th week, the upper and lower jaw bone specimens of rats were taken, and molar caries damage assessed.

RESULTSThe expression of F-ATPase in the caries group was higher than that in the control group (P<0.05). In addition, the gene was expressed highest in pH5.0 and the lowest in pH4.0 (P<0.05). 2) The expression of F-ATPase progressively increased during the caries development in both groups; expression in the caries group was higher than that in control group (P<0.05).

CONCLUSIONAcid-resisting viru-lence factor F-ATPase is related closely with the incidence and development of dental caries.

Adenosine Triphosphatases ; metabolism ; Animals ; Dental Caries ; metabolism ; microbiology ; Dental Plaque ; microbiology ; Male ; Protons ; Random Allocation ; Rats ; Rats, Wistar ; Real-Time Polymerase Chain Reaction ; Streptococcus mutans ; drug effects ; genetics ; Virulence Factors

OBJECTIVETo compare the protein profiles between decapeptide-treated and untreated planktonic cells of Streptococcus mutans (S. mutans) by differential proteomic analysis to determine and identify the key proteins.

METHODSIn our previous study, we investigated decapeptide (KKVVFKVKFK-NH2), which was a novel adenosine monophosphate. Compared with other oral pathogens tested, decapeptide had a preferential antibacterial activity against S. mutans. It also inhibited S. mutans biofilm formation and reduced the one-day developed biofilm. In the present study, we first synthesized decapeptide, and then compared the protein profiles between decapeptide-treated and untreated planktonic cells of S. mutans by two-dimensional gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. We also verified different expressions of key protein enolase in the protein level.

RESULTSThe results showed that decapeptide altered the protein expression of planktonic S. mutans. These proteins were functionally involved in carbohydrate degradation by glycolysis, protein folding, conjunction, transport, translation, adenosine triphosphate binding, protein binding, sequence-specific DNA binding, transcription factor activity, and two-component response regulator activity. Western blot results showed that enolase protein expression decreased obviously in decapeptide-treated cells of S. mutans.

CONCLUSIONThe protein expression of S. mutans significantly changed after synthetic antimicrobial decapeptide treatment, suggesting that decapeptide may present a preferential effect on oral caries by changing the expression of certain key proteins, such as enolase protein.

Anti-Bacterial Agents ; Anti-Infective Agents ; Biofilms ; Dental Caries ; Depsipeptides ; genetics ; Electrophoresis, Gel, Two-Dimensional ; Oligopeptides ; genetics ; Proteomics ; Streptococcus mutans ; metabolism

OBJECTIVETo establish a systematic method for isolation and identification of aerobic and facultative anaerobic bacteria in the oral cavity.

METHODSSamples of the saliva, dental plaque and periapical granulation tissue were collected from 20 subjects with healthy oral condition and from 8 patients with different oral diseases. The bacteria in the samples were identified by morphological identification, VITEK automatic microorganism identification and 16s rRNA gene sequencing.

RESULTSVITEK automatic microorganism identification and 16s rRNA gene sequencing showed an agreement rate of 22.39% in identifying the bacteria in the samples. We identified altogether 63 bacterial genus (175 species), among which Streptococcus, Actinomyces and Staphylococcus were the most common bacterial genus, and Streptococcus anginosus, Actinomyces oris, Streptococcus mutans and Streptococcus mitis were the most common species. Streptococcus anginosus was commonly found in patients with chronic periapical periodontitis. Streptococcus intermedius and Staphylococcus aureus were common in patients with radiation caries, and in patients with rampant caries, Streptococcus mutans was found at considerably higher rate than other species.

CONCLUSIONAerobic and facultative anaerobic bacteria are commonly found in the oral cavity, and most of them are gram-positive. 16s rRNA gene sequencing is more accurate than VITEK automatic microorganism identification in identifying the bacteria.

Actinomyces ; isolation & purification ; Dental Caries ; Dental Plaque ; microbiology ; Humans ; Mouth ; microbiology ; RNA, Ribosomal, 16S ; genetics ; Saliva ; microbiology ; Staphylococcus aureus ; isolation & purification ; Streptococcus ; isolation & purification

OBJECTIVETo select and identify ssDNA aptamers specific to Streptococcus mutans strains with different cariogenicity isolated from clinical specimens.

METHODSSubtractive SELEX technology targeting the whole intact cells was used to screen for ssDNA aptamers specific to the clinical isolates Streptococcus mutans strains with different cariogenicity. Radioactive isotope, flow cytometry, gene cloning and sequencing, MEME online software and RNA structure analysis software were employed to analyze the first and secondary structures of the aptamers and identify the screened aptamers.

RESULTSDetection by radioactive isotope showed sufficient pool enrichment after 9 rounds of subtractive SELEX. Flow cytometry showed that the selected aptamers H1, H16, H4, L1, L10 and H19 were capable of binding specifically with highly cariogenic Streptococcus mutans strains but not with strains with a low cariogenicity. The aptamer H19 had the strongest binding capacity to highly cariogenic Streptococcus mutans strains, with a dissociation constant of 69.45∓38.53 nmol/L.

CONCLUSIONWe have obtained the ssDNA aptamers specific to the clinical isolates of highly cariogenic Streptococcus mutans strains.

Aptamers, Nucleotide ; genetics ; Cloning, Molecular ; DNA Primers ; Dental Caries ; microbiology ; Gene Library ; Humans ; Nucleic Acid Conformation ; SELEX Aptamer Technique ; Species Specificity ; Streptococcus mutans ; classification ; genetics ; isolation & purification