Comparison of Oral Microbial Profiles between Children with Severe Early Childhood Caries and Caries-Free Children Using the Human Oral Microbe Identification Microarray

Objective

Early childhood caries (ECC) has become a prevalent public health problem among Chinese preschool children. The bacterial microflora is considered to be an important factor in the formation and progress of dental caries. However, high-throughput and large-scale studies of the primary dentition are lacking. The present study aimed to compare oral microbial profiles between children with severe ECC (SECC) and caries-free children.

Methods

Both saliva and supragingival plaque samples were obtained from children with SECC (n = 20) and caries-free children (n = 20) aged 3 to 4 years. The samples were assayed using the Human Oral Microbe Identification Microarray (HOMIM).

Results

A total of 379 bacterial species were detected in both the saliva and supragingival plaque samples from all children. Thirteen (including Streptococcus) and two (Streptococcus and Actinomyces) bacterial species in supragingival plaque and saliva, respectively, showed significant differences in prevalence between the two groups. Of these, the frequency of Streptococcus mutans detection was significantly higher in both saliva (p = 0.026) and plaque (p = 0.006) samples from the SECC group than in those from the caries-free group.

Conclusions

The findings of our study revealed differences in the oral microbiota between the SECC and caries-free groups Several genera, including Streptococcus, Porphyromonas, and Actinomyces, are strongly associated with SECC and can be potential biomarkers of dental caries in the primary dentition.     

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 Same Microbiota and a Potentially Discriminant Metabolome in the Saliva of Omnivore,Ovo-Lacto-Vegetarian and Vegan Individuals

The salivary microbiota has been linked to both oral and non-oral diseases. Scant knowledge is available on the effect of environmental factors such as long-term dietary choices on the salivary microbiota and metabolome. This study analyzed the microbial diversity and metabolomic profiles of the saliva of 161 healthy individuals who followed an omnivore or ovo-lacto-vegetarian or vegan diet. A large core microbiota was identified, including 12 bacterial genera, found in >98% of the individuals. The subjects could be stratified into three “salivary types” that differed on the basis of the relative abundance of the core genera Prevotella, Streptococcus/Gemella and Fusobacterium/Neisseria. Statistical analysis indicated no effect of dietary habit on the salivary microbiota. Phylogenetic beta-diversity analysis consistently showed no differences between omnivore, ovo-lacto-vegetarian and vegan individuals. Metabolomic profiling of saliva using ¹H-NMR and GC-MS/SPME identified diet-related biomarkers that enabled a significant discrimination between the 3 groups of individuals on the basis of their diet. Formate, urea, uridine and 5-methyl-3-hexanone could discriminate samples from omnivores, whereas 1-propanol, hexanoic acid and proline were characteristic of non-omnivore diets. Although the salivary metabolome can be discriminating for diet, the microbiota has a remarkable inter-individual stability and did not vary with dietary habits. Microbial homeostasis might be perturbed with sub-standard oral hygiene or other environmental factors, but there is no current indication that a choice of an omnivore, ovo-lacto-vegetarian or vegan diet can lead to a specific composition of the oral microbiota with consequences on the oral homeostasis.     

Oral microbiota of children in a school-based dental clinic

ObjectivesDental caries disproportionately affects disadvantaged subjects. This study hypothesized that there were greater caries extent and higher levels of caries-associated and anaerobic subgingival bacterial species in oral samples of Hispanic and immigrant children compared with non-Hispanic and US born children.MethodsChildren from a school-based dental clinic serving a community with a large Hispanic component were examined, and the extent of caries was recorded. Microbial samples were taken from teeth and the tongues of children. Samples were analyzed using DNA probes to 18 oral bacterial species.ResultsSeventy five children were examined. Extent of caries increased with child age in immigrant, but not in US born or Hispanic children. There were no differences in the microbiota based on ethnicity or whether the child was born in US or not. There was a higher species detection frequency from teeth than tongue samples. Levels of Streptococcus mutans and other Streptococcus spp increased with caries extent. Prevotella intermedia, Tannerella forsythia and Selenomonas spp were detected at low levels in these children.ConclusionsWe conclude that, while there was a high rate of dental caries in disadvantaged school children, there were no differences in the caries-associated microbiota, including S. mutans, based on ethnicity or immigration status. Furthermore, while anaerobic subgingival, periodontal pathogens were also detected in children, there was no difference in species detection based on ethnicity or immigration status. Increased levels of streptococci, including S. mutans, however, were detected with high caries levels. This suggested that while it is beneficial to target preventive and treatment programs to disadvantaged populations, there is likely no additional benefit to focus on subgroups within a population already at high risk for dental disease.     

新疆博州地区三民族儿童口腔优势菌群结构

目的研究新疆博州地区汉族、维吾尔族和蒙古族3～5岁儿童的口腔唾液细菌优势菌群结构多样性的差异,并探讨与低龄儿童龋发生的相关性。方法从本课题组在新疆博州地区3～5岁儿童口腔流行病学调查时建立的资料样本库中选取唾液样本120例(汉族40例,维吾尔族40例,蒙古族40例)作为研究对象,其中每个民族中高龋组(ECC)各20例,无龋组(CF)各20例,取非刺激性唾液,提取细菌DNA后进行聚合酶链反应(PCR)扩增和变性梯度凝胶电泳(DGGE)分析,采用Quantity One软件对PCR-DGGE指纹图谱进行数据分析。结果 DGGE总体图谱表明:口腔微生物菌群结构具有民族差异性和个体差异性;维吾尔族总的条带数和多样性指数(条带数:87.00±10.40,多样性指数:5.99±1.12)大于汉族(条带数:63.00±8.07,多样性指数:3.29±0.74)和蒙古族(条带数:71.60±5.79,多样性指数:4.98±0.50)(P0.05),高龋儿童组的细菌菌群结构多样性小于无龋儿童组(P0.05),无龋儿童组的细菌菌群结构多样性存在民族差异(P0.05);聚类分析发现:每个民族组内大部分样本均表现出明显的聚类群。结论博州地区儿童口腔唾液细优势菌群结构多样性在民族之间差异明显,在低龄儿童龋病进展中,细菌多样性逐渐减少。     

Pyrosequencing Analysis of Oral Microbiota in Children with Severe Early Childhood Dental Caries

Severe early childhood caries are a prevalent public health problem among preschool children throughout the world. However, little is known about the microbiota found in association with severe early childhood caries. Our study aimed to explore the bacterial microbiota of dental plaques to study the etiology of severe early childhood caries through pyrosequencing analysis based on 16S rRNA gene V1–V3 hypervariable regions. Forty participants were enrolled in the study, and we obtained twenty samples of supragingival plaque from caries-free subjects and twenty samples from subjects with severe early childhood caries. A total of 175,918 reads met the quality control standards, and the bacteria found belonged to fourteen phyla and sixty-three genera. Our results show the overall structure and microbial composition of oral bacterial communities, and they suggest that these bacteria may present a core microbiome in the dental plaque microbiota. Three genera, Streptococcus, Granulicatella, and Actinomyces, were increased significantly in children with severe dental cavities. These data may facilitate improvements in the prevention and treatment of severe early childhood caries.     

Temporal Stability of the Salivary Microbiota in Oral Health

Objectives

Saliva is a biological fluid suitable for biomarker analysis, and differences in the salivary microbiota in oral health and disease have been reported. For such comparative analyses, time of sampling is critical since the bacterial composition may vary throughout the day, i.e., diurnal variation. The purpose of this study is to compare the salivary microbiome over time to determine the optimal time for sampling.

Design

Stimulated saliva samples were collected from 5 orally healthy individuals in 4 h intervals for 24 h, and collection was repeated 7 days later (number of samples per person, n = 12, total number of samples, n = 60). Salivary microbiota was analyzed using the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS), and statistical analysis was performed using the Kruskal-Wallis test with Benjamini-Hochberg’s correction for multiple comparisons, cluster analysis, principal component analysis and correspondence analysis.

Results

From a total of 60 saliva samples, 477 probe targets were collectively identified with a mean number of probes per sample of 207 (range: 153–307). Little or no variation in microbial profiles within subjects was observed over time.

Conclusions

Although there was considerable variation between subjects, microbial profiles within subjects were stable throughout a 24 hour period and after 1 week. Since there is little or no evidence of diurnal variation of the salivary microbiome, time of sampling of saliva is not critical for perturbation or other microbial studies.     

Analysis of the Microbiota of Black Stain in the Primary Dentition

Black tooth stain is a characteristic extrinsic discoloration commonly seen on the cervical enamel following the contour of the gingiva. To investigate the relationship between black tooth stain and the oral microbiota, we used 16S rRNA gene sequencing to compare the microbial composition of dental plaque and saliva among caries-free children with and without black stain. Dental plaque and saliva, as well as black stain, were sampled from 10 children with and 15 children without black stain. Data were analyzed using the pipeline tool MOTHUR. Student’s t-test was used to compare alpha diversities and the Mann-Whitney U test to compare the relative abundances of the microbial taxa. A total of 10 phyla, 19 classes, 32 orders, 61 families and 102 genera were detected in these samples. Shannon and Simpson diversity were found to be significantly lower in saliva samples of children with black stain. Microbial diversity was reduced in the black stain compared to the plaque samples. Actinomyces, Cardiobacterium, Haemophilus, Corynebacterium, Tannerella and Treponema were more abundant and Campylobacter less abundant in plaque samples of children with black stain. Principal component analysis demonstrated clustering among the dental plaque samples from the control group, while the plaque samples from the black stain group were not and appeared to cluster into two subgroups. Alterations in oral microbiota may be associated with the formation of black stain.     

Salivary calculi microbiota: new insights into microbial networks and pathogens reservoir

Sialolithiasis represents the most common disorders of salivary glands in middle-aged patients. It has been hypothesized that the retrograde migration of bacteria from the oral cavity to gland ducts may facilitate the formation of stones. Thus, in the present study, a microbiome characterization of salivary calculi was performed to evaluate the abundance and the potential correlations between microorganisms constituting the salivary calculi microbiota. Our data supported the presence of a core microbiota of sialoliths constituted principally by Streptococcus spp., Fusobacterium spp. and Eikenella spp., along with the presence of important pathogens commonly involved in infective sialoadenitis.     

Plaques from different individuals yield different microbiota responses to oral-antiseptic treatment

Dental caries is a polymicrobial disease and complicated to treat. Understanding the microbiota responses to treatment from different individuals is a key factor in developing effective treatments. The aim of this study was to investigate the 24-h posttreatment effect of two oral antiseptics (chlorhexidine and Listerine) on species composition of microplate plaque biofilms that had been initiated from the saliva of five different donors and grown in both 0.15% and 0.5% sucrose. Plaque composition was analyzed using checkerboard DNA : DNA hybridization analysis, which comprised of a panel of 40 species associated with oral health and disease. The supernatant pH of the plaques grown in 0.15% sucrose ranged from 4.3 to 6 and in 0.5% sucrose, it ranged from 3.8 to 4. Plaque biomass was largely unaffected by either antiseptic. Each donor had a different salivary microbial profile, differentiating according to the prevalence of either caries or periodontal/anaerobic pathogens. Despite similar plaque microbiota compositions being elicited through the sucrose growth conditions, microbiota responses to chlorhexidine and Listerine differentiated according to the donor. These findings indicate that efficacious caries treatments would depend on the responses of an individual's microbiota, which may differ from person to person.     

Meta-omics analysis indicates the saliva microbiome and its proteins associated with the prognosis of oral cancer patients

Saliva is a biofluid that maintains the health of oral tissues and the homeostasis of oral microbiota. Studies have demonstrated that Oral squamous cell carcinoma (OSCC) patients have different salivary microbiota than healthy individuals. However, the relationship between these microbial differences and clinicopathological outcomes is still far from conclusive. Herein, we investigate the capability of using metagenomic and metaproteomic saliva profiles to distinguish between Control (C), OSCC without active lesion (L0), and OSCC with active lesion (L1) patients. The results show that there are significantly distinct taxonomies and functional changes in L1 patients compared to C and L0 patients, suggesting compositional modulation of the oral microbiome, as the relative abundances of Centipeda, Veillonella, and Gemella suggested by metagenomics are correlated with tumor size, clinical stage, and active lesion. Metagenomics results also demonstrated that poor overall patient survival is associated with a higher relative abundance of Stenophotromonas, Staphylococcus, Centipeda, Selenomonas, Alloscordovia, and Acitenobacter. Finally, compositional and functional differences in the saliva content by metaproteomics analysis can distinguish healthy individuals from OSCC patients. In summary, our study suggests that oral microbiota and their protein abundance have potential diagnosis and prognosis value for oral cancer patients. Further studies are necessary to understand the role of uniquely detected metaproteins in the microbiota of healthy and OSCC patients as well as the crosstalk between saliva host proteins and the oral microbiome present in OSCC.     

Hydrophobic interaction chromatography and capillary zone electrophoresis to explore the correlation between the isoenzymes of salivary α-amylase and dental caries

High-performance hydrophobic interaction chromatography (HIC) and capillary zone electrophoresis (CZE) were utilized in an effort to find the correlation between the composition of some isoenzymes of human salivary α-amylase (HSA) and dental caries. The mixture of more than three isoenzymes of HSA, fractionated from human parotid saliva with HIC, was further separated by CZE at the optimum pH 6.50. The composition and relative quantity of these isoenzymes were compared between two groups of individuals with different caries-susceptibility. It is found that the present frequency of peak II on CZE in the caries-free group was higher than that in the caries-active group and the relative quantities of peak III and peak IV showed remarkable differences (p<0.05) between the two groups. These results may indicate that the composition of HSA isoenzymes is related to the occurrence of dental caries. However, more work should be done to further affirm this correlation between the isoenzymes of salivary α-amylase and dental caries.     

Novel antibody assessment method for microbial compositional alteration in the oral cavity

Recently, it has been demonstrated that dysbiosis, an alteration in commensal microflora composition, is intimately involved in the onset of a variety of diseases. It is becoming increasingly evident that the composition of commensal microflora in the oral cavity is closely connected to oral diseases, such as periodontal disease, and systemic diseases, such as inflammatory bowel disease. Next-generation sequencing techniques are used as a method to examine changes in bacterial flora, but additional analytical methods to assess bacterial flora are needed to understand bacterial activity in more detail. In addition, the oral environment is unique because of the role of secretory antibodies contained in saliva in the formation of bacterial flora. The present study aimed to develop a new method for evaluating the compositional change of microbiota using flow cytometry (FCM) with specific antibodies against the bacterial surface antigen, as well as salivary antibodies. Using specific antibodies against Streptococcus mutans, a causative agent of dental caries, and human IgA, bacterial samples from human saliva were analyzed via FCM. The results showed that different profiles could be obtained depending on the oral hygiene status of the subjects. These results suggest that changes in the amount and type of antibodies that bind to oral bacteria may be an indicator for evaluating abnormalities in the oral flora. Therefore, the protocol established in this report could be applied as an evaluation method for alterations in the oral microbiota.     

Terminal RFLP analysis to determine the oral microbiota with hyposalivation

Previous studies of oral microbiota by culture-dependent or targeted DNA approaches demonstrated that hyposalivation, a reduction in salivary secretions, might increase the amount of certain oral pathogens. However, the relationship between hyposalivation and the balance of oral microbiota, especially uncultivable bacteria, remains still unclear. The aim of this study was to elucidate the relationship between hyposalivation and oral microbiota by analyzing terminal restriction fragment length polymorphism (T-RFLP) of 16S rDNA. The 61 subjects were divided into two groups, hyposalivation group and normo-salivation group. The microbiota of tongue-coating samples was analyzed by T-RFLP. The amount of saliva, the number of Candida albicans, and also the dental status including plaque index, gingival index, bleeding on probing, probing pocket depth and decayed, missing, and filled teeth (DMFT) were assessed. Regarding the dental status, none of the evaluated factors were significantly different between the groups except the number of DMFT. According to the T-RFLP profiles, the patterns of microbiota in the tongue coating were classified into two groups, Clusters I and II. Cluster I is made up 76 % of subjects with hyposalivation, while Cluster II is made up 61 % of subjects with normo-salivation (p < 0.001). Compared with the microbiota found in Cluster II, that in Cluster I had higher proportions of T-RFs corresponding to genera Veillonella, Dialister, Prevotella, Fusobacterium, and Streptococcus. T-RFLP analysis showed a significant role of salivary volume in determining the composition of the microbial community, regardless of the cultivability of the bacteria.     

Role of amylase, mucin, IgA and albumin on salivary protein buffering capacity: A pilot study

It has been suggested that proteins serve as major salivary buffers below pH?5. It remains unclear, however, which salivary proteins are responsible for these buffering properties. The aim of this pilot study was to evaluate the correlation between salivary concentration of total protein, amylase, mucin, immunoglobulin A (IgA), albumin and total salivary protein buffering capacity at a pH range of 4–5. In addition, the buffering capacity and the number of carboxylic acid moieties of single proteins were assessed. Stimulated saliva samples were collected at 9:00, 13:00 and 17:00 from 4 healthy volunteers on 3 successive days. The buffering capacities were measured for total salivary protein or for specific proteins. Also, the concentration of total protein, amylase, mucin, IgA and albumin were analysed. Within the limits of the current study, it was found that salivary protein buffering capacity was highly positively correlated with total protein, amylase and IgA concentrations. A weak correlation was observed for both albumin and mucin individually. Furthermore, the results suggest that amylase contributed to 35% of the salivary protein buffering capacity in the pH range of 4–5.     

Salivary metabolite signatures of children with and without dental caries lesions

A metabolomic approach was used to analyze endogenous metabolites and to correlate with a specific biological state. The analysis of salivary metabolites is a growing area of investigation with potential for basic and clinical applications. Analyses of children’s saliva in different dentitions and with or without caries could potentially reveal a specific profile related to oral disease risk. Nuclear Magnetic Resonance (NMR) is well suited for mixture analysis followed by Principal Component Analysis combined with Linear Regression (PCA-LR) statistics and was used to identify differences in the salivary metabolites. The classificatory analysis was performed using PCA-LR based on 1,000 cross-validation bootstrap runs from both classifiers in order to increase the data information from a small sample size. The PCA-LR presented a statistically good classificatory performance for children with and without caries with an accuracy of 90.11 % (P < 0.001), 89.61 % sensitivity (P < 0.001), and 90.82 % specificity (P < 0.001). Children with caries lesions presented higher levels of several metabolites, including lactate, fatty acid, acetate and n-butyrate. Saliva from subjects with different dentition stages was also analyzed. Although the salivary samples were poorly classified, permanent dentition presented increased levels of acetate, saccharides and propionate. The NMR data and PCA-LR were able to classify saliva from children with or without caries, with performance indexes comparable to the partial least-squares regression discriminant analysis (PLS-DA) results also performed. Our data also showed similar salivary metabolite profiles for healthy subjects despite the differences in their oral hygiene habits, socioeconomic status and food intake.     

Effect of LGG yoghurt on Streptococcus mutans and Lactobacillus spp. salivary counts in children

The aim of this study was to establish effect of 14 day consumption of commercially available yoghurt containing Lactobacillus rhamnosus ATCC53103 - LGG (Bioaktiv LGG, Dukat, Croatia) on Streptococcus mutans and Lactobacillus spp. salivary counts in children. Twenty five patients, 6-10 yr old participated in the study. At the inclusion in the study caries risk for every patient was evaluated. The saliva samples were tested with chair side kits for saliva buffer capacity (CRT buffer, Vivadent, Schaan, Liechtenstein), S. Mutans and Lactobacillus counts (CRT bacteria test, Vivadent, Schaan, Liechtenstein). Seven, 14 and 30d after yoghurt consumption saliva samples were tested again with CRT buffer and CRT bacteria tests. Obtained data were analyzed using chi2 and Kruskal-Wallis tests. Results showed significant increase in saliva buffer capacity 30d after yoghurt consumption. S. Mutans salivary counts were significantly decreased after 30d. Significant differences in Lactobacillus counts were not observed. It could be concluded that daily consumption of yoghurt containing LGG have an inhibitory effect on oral pathogenic bacteria and may be beneficial in caries prevention.     

Analysis of Oral Microbiota in Children with Dental Caries by PCR-DGGE and Barcoded Pyrosequencing

Oral microbiota plays a vital role in maintaining the homeostasis of oral cavity. Dental caries are among the most common oral diseases in children and pathogenic bacteria contribute to the development of the disease. However, the overall structure of bacterial communities in the oral cavity from children with dental caries has not been explored deeply heretofore. We used high-throughput barcoded pyrosequencing and PCR-denaturing gradient gel electrophoresis (DGGE) to examine bacterial diversity of oral microbiota in saliva and supragingival plaques from 60 children aged 3 to 6 years old with and without dental caries from China. The multiplex barcoded pyrosequencing was performed in a single run, with multiple samples tagged uniquely by multiplex identifiers. As PCR-DGGE analysis is a conventional molecular ecological approach, this analysis was also performed on the same samples and the results of both approaches were compared. A total of 186,787 high-quality sequences were obtained for evaluating bacterial diversity and 41,905 unique sequences represented all phylotypes. We found that the oral microbiota in children was far more diverse than previous studies reported, and more than 200 genera belonging to ten phyla were found in the oral cavity. The phylotypes in saliva and supragingival plaques were significantly different and could be divided into two distinct clusters (p < 0.05). The bacterial diversity in oral microbiome analyzed by PCR-DGGE and barcoded pyrosequencing was employed to cross validate the data sets. The genera of Streptococcus, Veillonella, Actinomyces, Granulicatella, Leptotrichia, and Thiomonas in plaques were significantly associated with dental caries (p < 0.05). The results showed that there was no one specific pathogen but rather pathogenic populations in plaque that significantly correlated with dental caries. The enormous diversity of oral microbiota allowed for a better understanding of oral microecosystem, and these pathogenic populations in plaque provide new insights into the etiology of dental caries and suggest new targets for interventions of the disease.