Checkerboard DNA-DNA hybridisation technology focused on the analysis of Gram-positive cariogenic bacteria

Microbial Analysis of Obturators During Maxillofacial Prosthodontic Treatment Over an 8-Year Period

The aim of the study was to investigate the microbial colonization (by Candida species, anaerobic and facultative anaerobic bacteria) of maxillary obturators used for the restoration of maxillary defects, including during radiotherapy.

Retrospective cohort study.

Fifteen patients requiring a maxillary obturator prosthesis had swabs of their obturators and adjacent tissues taken at different stages of their treatment over a period of 8 years.

Identification of microbial species from the swabs was carried out using randomly amplified polymorphic DNA polymerase chain reaction (RAPD PCR) analysis, checkerboard DNA-DNA hybridization, CHROMagar Candida chromogenic agar, and DNA sequencing.

Candida species were detected in all patients and all patients developed mucositis and candidiasis during radiotherapy which was associated with an increase in colonization of surfaces with Candida spp., particularly C albicans. Microbial colonization increased during radiotherapy and as an obturator aged, and decreased following a reline, delivery of a new prosthesis, or antifungal treatment during radiotherapy.

Microbial colonization of maxillary obturators was related to the stage of treatment, age of the obturator material, radiotherapy and antifungal medications, and antifungal treatment may be recommended if C albicans colonization of palatal tissues is greater than 105 colony-forming units per cm2 following the first week of radiotherapy.

Associations of sex, oral hygiene and smoking with oral species in distinct habitats at age 32 years

The oral microbiome is ecologically diverse, complex, dynamic, and little understood. We describe the microbiota of four oral habitats in a birth cohort at age 32 and examine differences by sex, oral hygiene, and current smoking status, dental caries, and periodontal health. Oral biofilm samples collected from anterior labial supragingival, posterior lingual supragingival, subgingival, and tongue sites of 841 Dunedin Multidisciplinary Health and Development Study members were analysed using checkerboard DNA-DNA hybridization; focusing on 30 ecologically important bacterial species. The four habitats exhibited distinct microbial profiles that differed by sex. Streptococcus gordonii was more dominant in supragingival and tongue biofilms of males; Porphyromonas gingivalis exhibited higher relative abundance in subgingival biofilm of females. Males had higher scores than females for periodontal pathogens at supragingival sites. The relative abundance of several putative caries and periodontal pathogens differed in smokers and non-smokers. With poor oral hygiene significantly higher proportions of Gram-negative facultative anaerobes were present in subgingival biofilm and there were higher scores for the principal components characterised by putative cariogenic and periodontal pathogens at each site. Distinctive microenvironments shape oral biofilms and systematic differences exist by sex, oral hygiene, and smoking status.

Effect of Lactobacillus brevis CD2 containing lozenges and plaque pH and cariogenic bacteria in diabetic children: a randomised clinical trial

Objective

The short-term effect (60 days) of Lactobacillus brevis CD2 lozenges vs placebo on variables related to caries and gingivitis in type 1 diabetic children was evaluated.

Material and methods

Eight diabetics (4–14 years old) were assigned to two groups (n = 34 subjects each), probiotic lozenges and placebo. Stimulated saliva for microbiological analysis and plaque pH were assessed at baseline (t₀), 30 days (t₁), 60 days (t₂) and in the follow-up period (90 days from baseline, t₃). Gingival status was assessed at t₀, t₂ and t₃. Two-way ANOVA assessed differences between groups.

Results

In the probiotic group, Streptococcus mutans bacterial density mean scores dropped from 3.11 ± 1.13 at baseline to 1.82 ± 0.72 (t₂) and to 2.06 ± 0.56 (t₃), while in the placebo group, the scores were 3.09 ± 0.8 (t₀), 2.82 ± 0.47 (t₂) and 3.11 ± 0.43 (t₃) (p < 0.01). Lowest and maximum pH fall increased in the probiotic group, from 5.37 ± 0.41 at baseline to 5.49 ± 0.24 at t₃ (p < 0.01) and from 1.20 ± 0.46 to 0.98 ± 0.29 (p = 0.02). Bleeding score decreased significantly in both groups, showing a statistically significant lower bleeding score at t₂ in the probiotic group (25.6%, 95% CI 21.5–32.7 vs 29.5%, 95% CI 25.2–34.9, p = 0.02).

Conclusions

Lactobacillus brevis CD2 has shown to improve caries-related risk factors and gingival health in diabetic children.

Clinical relevance

Lactobacillus brevis CD2 might contribute to improved oral health in type 1 diabetic children.

Electronic supplementary material

The online version of this article (10.1007/s00784-020-03342-0) contains supplementary material, which is available to authorized users.

Presence of Helicobacter pylori and Campylobacter ureolyticus in the oral cavity of a Northern Thailand population that experiences stomach pain

Objective: To investigate oral diseases and microbiological conditions, such as the presence of ureolytic bacteria in dental plaque, in relation to experience of stomach pain in a remote adult Asian population. Methods: Ninety-three adults, 40-60-years old, from the Karen Hill tribe in Northern Thailand with no regular access to dental care were examined. Clinical registrations were performed and interproximal gingival plaque samples were collected and analyzed with the checkerboard (CKB) method for the presence of 14 oral bacterial species. Results: A number of 61 subjects reported daily stomach pain while 32 subjects had no symptoms from the stomach. The subjects with stomach pain had fewer remaining teeth (p < 0.05), higher caries experience (p < 0.05) and less BoP (p < 0.01). Most of the bacterial species were clustered statistically in three factors in a factor analysis, which together explained 65% of the microbiological variance. Factor 1, explaining 43.0% of the variance, was statistically associated with stomach pain (p < 0.001). Conclusions: The interproximal plaque/biofilm in adults of the study population showed a common presence of two gastrointestinal pathogens H. pylori and C. ureolyticus. The study also indicates for the first time a potential association between C. ureolyticus and stomach pain.

Soluble urokinase-type plasminogen activator receptor is associated with signs of periodontitis in adolescents

Owing to its molecular stability in body fluids, soluble urokinase-type plasminogen activator receptor (suPAR) is used as a biomarker for the level of systemic inflammation. This study compares the suPAR levels in serum with those in the saliva of adolescents and evaluates their association with the periodontal conditions. Adolescents identified as screen positive (n = 87) or screen negative (n = 73) for periodontitis had saliva and serum samples taken, along with subgingival plaque samples. The concentrations of suPAR were determined in saliva and serum, and 18 microbial species and the immunoglobulin response to them was evaluated. Factor analyses were used to reduce the number of variables within each of the domains of clinical, microbiological, and immunological findings. The median salivary suPAR concentration was 13.18 [(interquartile range (IQR): 6.20-23.36] μg l^-1 and was not associated with the serum suPAR levels (median 2.05; IQR: 1.62-2.46 μg l^-1 ). Linear regression analysis showed that the log₁₀ (salivary suPAR concentration) was statistically significantly positively associated with the clinical phenotype 'Periodontitis Extent' (β = 0.28; 95% CI: 0.16-0.39) along with 'Putative periodontopathogens' (β = 0.65; 95% CI: 0.51-0.79). The study represents the first determination of salivary suPAR concentration in a larger well-defined adolescent population. Our results suggest the potential for clinical use of suPAR in saliva as an inflammatory risk indicator/biomarker of periodontitis.

Evaluation of the difference in caries experience in diabetic and non-diabetic children-A case control study

Aim

To evaluate the caries prevalence and related variables in Type 1 diabetic and non-diabetic children and among the diabetic children according to their metabolic status.

Methods

Sixty-eight diabetic and 136 non-diabetic children, matching by gender and age (4–14 years) were enrolled. The diabetic children were divided: a) 20 children in good metabolic control (Hb1ac≤7.5) and b) 48 children in bad metabolic control (Hb1ac>7.5). Dietary and oral hygiene habits were investigated. Caries status was registered using the International Caries Detection and Assessment System. Oral microflora was analysed using the checkerboard DNA-DNA hybridisation method. Plaque acidogenicity was recorded after a sucrose rinse.

Results

Sugared beverage and snack intake was higher in diabetic group compared to non-diabetic group (p = 0.03 and p = 0.04, respectively) and in subjects in bad metabolic control (p = 0.03 and p<0.01, respectively). Oral hygiene habits were similar, except for the use of fluoridated adjuvants, higher in non-diabetic children (p = 0.04). No statistically significant differences were observed regarding caries figures, but a higher number of caries free subjects was found in diabetic subjects in good metabolic control (p<0.01). Significant difference for the main cariogenic bacteria was found between diabetic and non-diabetic subjects (p<0.05). The pH values showed statistically significant differences between diabetic and non-diabetic subjects and between diabetic subjects in good and bad metabolic control (p<0.01).

Conclusions

Diabetic children in good metabolic control might even be considered at low caries risk, while those in bad metabolic control showed an oral environment prone to a high caries risk.

Studying the human oral microbiome: challenges and the evolution of solutions

Since the pioneering work of van Leeuwenhoek in 1684, subsequently built upon by other renowned microbiologists Robert Koch, Willoughby Miller and GV Black, oral microbiology has developed innovative techniques to study the oral microflora (now termed the 'oral microbiome'). The advent of molecular techniques such as DNA-DNA hybridization, polymerase chain reaction and DNA sequencing has created an array of opportunities to construct a comprehensive picture of the diversity and composition of the oral microbiome. Approximately 700 oral bacterial species have been identified, of which 50% have yet to be cultivated, and some of these are known only by their signature DNA sequences. The synergism of ever-evolving culture-based and state-of-the-art culture-independent molecular techniques has facilitated in-depth understanding of the dynamics, acquisition and transfer of oral bacteria, along with their role in oral and general health and disease. Further research is needed to not only analyse but also to make sense of the ever-increasing volumes of data which these molecular techniques (especially high-throughput DNA sequencing) are generating, as well as why particular bacteria are present and what they are 'actually doing' there. This review presents a comprehensive literature search of oral microbiology-related methods currently used to study the oral microbiome.

Oral microflora in preschool children attending a fluoride varnish program: a cross-sectional study

Background

To compare the oral microflora in preschool children attending a fluoride varnish program with a reference group receiving a standard oral health program without fluoride varnish applications. A second aim was to relate the microbial composition to the caries prevalence.

Methods

Five hundred seven 3-year-old children were enrolled from a cohort of 3403 preschool children taking part in a community based oral health project. Two hundred sixty-three of them had attended caries-preventive program with semi-annual applications of a fluoride varnish since the age of 1 year (test group) while 237 had received standard preventive care (reference group). Oral samples were collected with a sterile swab and analysed with checkerboard DNA-DNA hybridization using 12 pre-determined bacterial probes. Caries and background data were collected from clinical examinations and questionnaires.

Results

Gram-positive streptococci (S. intermedius, S. salivarius, S. oralis) were most frequently detected and displayed the highest counts in both groups. There were no significant differences between the groups concerning prevalence of any of the selected bacterial strains except for S. oralis that occurred less frequently in the reference group. In children with caries, V. parvula were significantly more common (p < 0.05) while strains of Lactobacillus, Bifidobacterium and Neisseria were more prevalent among the caries-free children (p < 0.05).

Conclusions

A 2-year community program with semi-annual fluoride varnish applications did not seem to significantly influence the oral microflora in preschool children.

Trial registration

www.controlled-trials.com (ISRCTN35086887) 20131216 ‘retrospectively registered’.

Bacterial Diversity and Community Structure of Supragingival Plaques in Adults with Dental Health or Caries Revealed by 16S Pyrosequencing

Dental caries has a polymicrobial etiology within the complex oral microbial ecosystem. However, the overall diversity and structure of supragingival plaque microbiota in adult dental health and caries are not well understood. Here, 160 supragingival plaque samples from patients with dental health and different severities of dental caries were collected for bacterial genomic DNA extraction, pyrosequencing by amplification of the 16S rDNA V1–V3 hypervariable regions, and bioinformatic analysis. High-quality sequences (2,261,700) clustered into 10,365 operational taxonomic units (OTUs; 97% identity), representing 453 independent species belonging to 122 genera, 66 families, 34 orders, 21 classes, and 12 phyla. All groups shared 7522 OTUs, indicating the presence of a core plaque microbiome. α diversity analysis showed that the microbial diversity in healthy plaques exceeded that of dental caries, with the diversity decreasing gradually with the severity of caries. The dominant phyla of plaque microbiota included Bacteroidetes, Actinobacteria, Proteobacteria, Firmicutes, Fusobacteria, and TM7. The dominant genera included Capnocytophaga, Prevotella, Actinomyces, Corynebacterium, Neisseria, Streptococcus, Rothia, and Leptotrichia. β diversity analysis showed that the plaque microbial community structure was similar in all groups. Using LEfSe analysis, 25 differentially abundant taxa were identified as potential biomarkers. Key genera (27) that potentially contributed to the differential distributions of plaque microbiota between groups were identified by PLS-DA analysis. Finally, co-occurrence network analysis and function predictions were performed. Treatment strategies directed toward modulating microbial interactions and their functional output should be further developed.

Salivary microflora and mode of delivery: a prospective case control study

Background

Previous cross-sectional studies have suggested that the mode of delivery can influence the composition of oral microflora. The aim of this prospective study was to compare the salivary colonization in vaginally delivered children with children delivered by Caesarian section (C-section) during their first 6 months of life.

Methods

The study group consisted of 149 consecutively enrolled infants, delivered either vaginally (n = 96) or by C-section (n = 53) that volunteered after consent of their parents. Saliva samples were collected within 2 days after birth and then after 1, 3, and 6 months. A saliva sample from the mothers was obtained 6 months after delivery. The parents were asked to complete a questionnaire on socioeconomic factors, lifestyle, and hygiene at baseline and throughout the study period. All samples were analyzed with 13 pre-determined bacterial probes using checkerboard DNA-DNA hybridization.

Results

The groups were balanced at baseline concerning all relevant background factors. Gram-positive streptococci (S. mitis, S. salivarius) displayed the highest counts in both groups but a greater diversity was observed in the vaginally delivered group. A. naeslundi, A. odontolytics, F. nucleatum and L. salivarius were only detected among the vaginally delivered infants. The prevalence of S. sanguinis, S. gordoni, R. denticariosa, and B. dentinum increased by age in both groups but the prevalence was significantly lower in the C-section group (p < 0.05). There was a link between the mothers and their offspring’s concerning the salivary microbial profile.

Conclusion

The microbial composition in saliva differs by the mode of delivery during the first six months of life.

Methodological issues in the quantification of subgingival microorganisms using the checkerboard technique

The reproducibility and reliability of quantitative microbiological assessments using the DNA-DNA hybridization "checkerboard method" (CKB) were assessed. The data originated from 180 chronic periodontitis patients, who were enrolled in a clinical trial and sampled at baseline, and 3 and 12m post-therapy. The samples were divided into two portions allowing evaluation of reproducibility. In total, 531 samples were analyzed in a first run, using standard bacterial preparations of cells and 513 samples were accessible for analysis in the second, using standards based on purified DNA from the species. The microbial probe panel consisted of periodontitis marker bacteria as well as non-oral microorganisms. Three different ways of quantifying and presenting data; the visual scoring method, VSM, the standard curve method, SCM, and the percent method, PM, were compared. The second set of analyses based on the use of standard preparations of pure DNA was shown to be more consistent than the first set using standards based on cells, while the effect of storage time per se up to 2.5y seemed to be marginal. The best reproducibility was found for Tannerella forsythia, irrespective of quantification technique (Spearman's rho=0.587, Pearson's r≥0.540). The percent method (PM) based on percent of High Standard (10(6) cells) was more reliable than SCM based on a linear calibration of the High Standard and a Low Standard (10(5) cells). It was concluded that the reproducibility of the CBK method varied between different bacteria. High quality and pure specific DNA whole genomic probes and standards may have a stronger impact on the precision of the data than storage time and conditions.

Hydrogen sulfide production from subgingival plaque samples

Periodontitis is a polymicrobial anaerobe infection. Little is known about the dysbiotic microbiota and the role of bacterial metabolites in the disease process. It is suggested that the production of certain waste products in the proteolytic metabolism may work as markers for disease severity. Hydrogen sulfide (H2S) is a gas produced by degradation of proteins in the subgingival pocket. It is highly toxic and believed to have pro-inflammatory properties. We aimed to study H2S production from subgingival plaque samples in relation to disease severity in subjects with natural development of the disease, using a colorimetric method based on bismuth precipitation. In remote areas of northern Thailand, adults with poor oral hygiene habits and a natural development of periodontal disease were examined for their oral health status. H2S production was measured with the bismuth method and subgingival plaque samples were analyzed for the presence of 20 bacterial species with the checkerboard DNA-DNA hybridization technique. In total, 43 subjects were examined (age 40-60 years, mean PI 95 ± 6.6%). Fifty-six percent had moderate periodontal breakdown (CAL > 3 < 7 mm) and 35% had severe periodontal breakdown (CAL > 7 mm) on at least one site. Parvimonas micra, Filifactor alocis, Porphyromonas endodontalis and Fusobacterium nucleatum were frequently detected. H2S production could not be correlated to periodontal disease severity (PPD or CAL at sampled sites) or to a specific bacterial composition. Site 21 had statistically lower production of H2S (p = 0.02) compared to 16 and 46. Betel nut chewers had statistically significant lower H2S production (p = 0.01) than non-chewers. Rapid detection and estimation of subgingival H2S production capacity was easily and reliably tested by the colorimetric bismuth sulfide precipitation method. H2S may be a valuable clinical marker for degradation of proteins in the subgingival pocket.

Dental plaque pH and ureolytic activity in children and adults of a low caries population

OBJECTIVES

The aim of this study was to evaluate the plaque pH level and ureolytic activity among children and adults of Karen Hill tribes.

METHODS

Thirty-four children aged 6-10 years and 46 adults aged 20-38 years were interviewed regarding oral hygiene practices, sucrose intake and betel chewing. Caries experience (DMFT and DT), calculus, bleeding on probing (BoP) and Plaque index (PlI) were registered. Ureolytic activity in supragingival plaque was tested at two interproximal sites (11/12 and 41/42) with the rapid urease test (RUT). Registration of plaque pH was performed at two interproximal sites (15/16 and 31/41) before, during and 30 min after rinsing with an urea solution (0.25%). Four interproximal plaque samples (one from each quadrant) per individual were collected to test the bacterial composition using the checkerboard technique.

RESULTS

Children and adults had similarly low DMFT and DT values. Children had a higher baseline pH and a higher ureolytic activity in the maxilla (p < 0.05) compared with adults. A significant correlation (r (2) = 0.63) was found between baseline pH and urease activity in the mandibular anterior teeth. Caries-free individuals had a higher baseline pH compared with caries active individuals in the anterior mandibular region (p < 0.01). The microbiological composition was characterized by an anaerobic low acidiogenic microbiota.

CONCLUSIONS

Dental plaque pH is related to the ureolytic activity, which explains the low acidogenic plaque microflora and the low caries levels in the Karen population.

Supragingival plaque microbial analysis in reflection to caries experience

Background

Dental caries develops as a result of the metabolism of carbohydrates by cariogenic bacteria present in a complex biofilm. The present study aimed to examine if bacteria in pooled supragingival plaque samples quantified using a “checkerboard DNA-DNA hybridization” based panel of caries-related bacteria, could reflect the caries experience in a manner similar to saliva samples analysed using a chair-side method in a previous investigation.

Methods

A total of 86 mothers and their children aged 4–6 years and 12–16 years old participated. Caries experience (DMFT/dmft; Decayed, Missing and Filled Teeth for permanent and primary teeth) was registered clinically and radiographically. Caries was recorded at the D₃ level (caries into dentine). The D/d component was divided into three categories. A pooled supragingival plaque sample per participant was obtained from posterior approximal sites. Analyses of 15 bacterial species were performed using the checkerboard DNA-DNA hybridisation technique.

Results

No significant relationships were found between the bacterial scores and DMFT/dmft nor D/d groups.

Conclusions

Unlike the saliva samples and the chair-side method, interproximal pooled plaque samples analysed using the “checkerboard DNA-DNA hybridization technique” did not reveal any significant relations between the bacterial counts and the caries experience.

Oral microflora in infants delivered vaginally and by caesarean section

BACKGROUND.  Early in life, vaginally delivered infants exhibit a different composition of the gut flora compared with infants delivered by caesarean section (C-section); however, it is unclear whether this also applies to the oral cavity. AIM.  To investigate and compare the oral microbial profile between infants delivered vaginally and by C-section. DESIGN.  This is a cross-sectional case-control study. Eighty-four infants delivered either vaginally (n = 42) or by C-section (n = 42) were randomly selected from the 2009 birth cohort at the County Hospital in Halmstad, Sweden. Medically compromised and premature children (<32 weeks) were excluded. The mean age was 8.25 months (range 6-10 months), and parents were asked to complete a questionnaire on socioeconomic factors, lifestyle, and hygiene habits. Saliva was collected and analysed using checkerboard DNA-DNA hybridization. RESULTS.  A higher prevalence of salivary Streptococcus salivarius, Lactobacillus curvata, Lactobacillus salivarius, and Lactobacuillus casei was detected in infants delivered vaginally (P < 0.05). The caries-associated bacteria Streptococcus mutans and Streptococcus sobrinus were detected in 63% and 59% of all children, respectively. CONCLUSION.  A significantly higher prevalence of certain strains of health-related streptococci and lactobacilli was found in vaginally delivered infants compared with infants delivered by C-section. The possible long-term effects on oral health need to be further investigated.

Perpetuation of subgingival biofilms in an in vitro model

This study evaluated the reproducibility of in-vitro-grown biofilms, initiated with subgingival plaque from patients with periodontal disease, and continued through several cycles by re-inoculating new biofilms from previously grown biofilms. Subgingival plaque samples from bleeding pockets along with saliva samples were collected from three patients with chronic periodontitis and perpetuated through seven cycles. Calcium hydroxyapatite disks were coated with sterilized saliva inoculated with dispersed subgingival plaque. The biofilms were grown anaerobically at 37 degrees C for 10 days, and at specific intervals total viable bacteria were enumerated and the species present were analysed by DNA-DNA checkerboard hybridization. All cycles of biofilm growth occurred at similar rates and reached steady-state at day 7. No statistically or microbially significant differences were found for viable counts or species present, at the same period of maturation, among the different cycles. This study demonstrated that growth of certain target subgingival periodontal species in this biofilm model was reproducible and could be perpetuated in vitro through several cycles. The model could be useful in future studies to characterize different periodontopathogenic properties and biofilm interactions, especially in recolonization studies.

Antifungal drug resistance of oral fungi

Fungi comprise a minor component of the oral microbiota but give rise to oral disease in a significant proportion of the population. The most common form of oral fungal disease is oral candidiasis, which has a number of presentations. The mainstay for the treatment of oral candidiasis is the use of polyenes, such as nystatin and amphotericin B, and azoles including miconazole, fluconazole, and itraconazole. Resistance of fungi to polyenes is rare, but some Candida species, such as Candida glabrata and C. krusei, are innately less susceptible to azoles, and C. albicans can acquire azole resistance. The main mechanism of high-level fungal azole resistance, measured in vitro, is energy-dependent drug efflux. Most fungi in the oral cavity, however, are present in multispecies biofilms that typically demonstrate an antifungal resistance phenotype. This resistance is the result of multiple factors including the expression of efflux pumps in the fungal cell membrane, biofilm matrix permeability, and a stress response in the fungal cell. Removal of dental biofilms, or treatments to prevent biofilm development in combination with antifungal drugs, may enable better treatment and prevention of oral fungal disease.

Use of the DNA Checkerboard hybridization method for detection and quantitation of Candida species in oral microbiota

The DNA Checkerboard method enables the simultaneous identification of distinct microorganisms in a large number of samples and employs up to 45 whole genomic DNA probes to gram-negative and gram-positive bacterial species present in subgingival biofilms. Collectively, they account for 55%-60% of the bacteria in subgingival biofilms. In this study, we present the DNA Checkerboard hybridization as an alternative method for the detection and quantitation of Candida species in oral cavities. Our results reveal that DNA Checkerboard is sensitive enough and constitutes a powerful and appropriate method for detecting and quantifying Candida species found in the oral cavity.

[Not Available]

Human saliva can be separated by centrifugation into cell pellet and cell-free supernatant, which are called cellular phase and liquid phase in this study. While it is well documented that the cellular phase of saliva contains hundreds of oral bacteria species, little is known whether the liquid phase of saliva contains any information related to oral microbiota. In this study, we analyzed the bacterial nucleic acid contents of the liquid phase of saliva. Using primers universal to most eubacterial 16S rDNA, we detected large amounts of bacterial 16S rRNA and rDNA in the cell-free phase of saliva. Random sequencing analysis of forty PCR amplicons from the cell-free phase of saliva led to 15 operational taxonomic unit (OTU) groups. Furthermore, using denaturing gradient gel electrophoresis (DGGE), we compared 16S rRNA/rDNA profiles derived from liquid phases and cellular phases of saliva samples, and found positive correlations (Pearson Correlation=0.822, P<0.001) between these sample groups. These findings indicate that the liquid phase of saliva contains numerous bacterial 16S rRNA/rDNA molecules that have correlations with bacteria existing in the cellular phase.

The use of fluorescein for labeling genomic probes in the checkerboard DNA–DNA hybridization method

Molecular methods that permit the simultaneous detection and quantification of a large number of microbial species are currently employed in the evaluation of complex ecosystems. The checkerboard DNA-DNA hybridization technique enables the simultaneous identification of distinct bacterial species in a large number of dental samples. The original technique employed digoxigenin-labeled whole genomic DNA probes which were detected by chemiluminescence. In this study, we present an alternative protocol for labeling and detecting whole genomic DNA probes in the Checkerboard DNA-DNA hybridization method. Whole genomic DNA was extracted from five bacterial species and labeled with fluorescein. The fluorescein labeled whole genomic DNA probes were hybridized against whole genomic DNA or subgingival plaque samples in a checkerboard hybridization format, followed by chemiluminescent detection. Our results reveal that fluorescein is a viable and adequate alternative labeling reagent to be employed in the checkerboard DNA-DNA hybridization technique.

An in vitro biofilm model of subgingival plaque

INTRODUCTION

Numerous biofilm models have been described for the study of bacteria associated with the supragingival plaque. However, there are fewer models available for the study of subgingival plaque. The purpose of this study was to develop and validate a model that closely mimicked the composition of the subgingival flora.

METHODS

The model was developed as follows: calcium hydroxyapatite disks were coated overnight with 10% sterile saliva, placed in flat-bottomed tissue culture plates containing trypticase-soy broth, directly inoculated with a small aliquot of dispersed subgingival plaque, incubated anaerobically, and transferred to fresh medium at 48-h intervals until climax (steady-state) biofilms were formed ( approximately 10 days).

RESULTS

The model, based on samples from eight periodontitis patients and eight healthy subjects, yielded a multi-species, heterogeneous biofilm, consisting of both gram-positive and gram-negative species, and comprising 15-20 cultivable species associated with the subgingival flora. The species present and their proportions were reflective of the initial cultivable subgingival flora. Comparisons of the initial plaque samples from healthy subjects and the mature biofilms showed 81% similarity in species and 70% similarity in the proportions present. Biofilms formed from samples obtained from periodontally diseased subjects were 69% similar in species and 57% similar in the proportions present.

CONCLUSIONS

The biofilm model described here closely reproduces the composition of the cultivable subgingival plaque both in the species present and in their relative proportions. Differences existed between biofilms grown from diseased and non-diseased sites with the former being characterized by the presence of periodontal pathogens at microbially significant levels.

Candida albicans does not invade carious human dentine

AIM

Candida albicans has been proposed to be a caries pathogen, but the evidence for its specific role is lacking. To be considered significant in caries progression, a marked amount of yeasts should be present in a lesion. The aim of the study was to investigate the presence of C. albicans in dentinal caries lesions.

MATERIALS AND METHODS

To demonstrate the extension of caries and to identify the bacteria in a lesion, sections of 10 carious human teeth were stained with Gram and Giemsa stains. C. albicans was detected with periodic acid-Schiff (PAS) staining and by immunohistochemistry using a C. albicans-specific antibody 3H8. Thirty sections were used for each staining (in total 120 sections).

RESULTS

Extensive bacterial invasion and intensive staining by PAS occurred in all samples. However, with the C. albicans-specific antibody, only 30 (3.3%) sections stained weakly positive, with a few stained cells on the lesion surface. However, the positive identification of C. albicans, based on the morphology of the cells, was not possible.

CONCLUSIONS

The results do not support the previous suggestion that C. albicans is important in the dentine caries pathology. In addition, because of its unspecific nature, PAS turned out to be an unsuitable method for detecting yeasts in carious tooth samples.

Caries-related plaque microcosm biofilms developed in microplates

In vivo dental plaque biofilms consist of complex communities of oral bacteria that are a challenge to replicate in vitro. The aim of this investigation was to establish human dental plaque microcosms in microplates to reflect conditions that are relevant to dental caries. Microcosm plaque biofilms were initiated from the saliva of two different donors, grown for up to 10 days in 24-welled microplates on Thermanox coverslips in various types of artificial saliva with and without sucrose, which were replaced daily. Microbiota composition of 40 species associated with oral health and dental caries was monitored in the plaques using Checkerboard DNA-DNA hybridization analysis. pH was measured as an indicator of cariogenic potential. The composition of the saliva inocula was different, and yielded plaque microcosms with different composition and growth responses to sucrose. Artificial saliva type and presence of sucrose, and the resulting growth and pH conditions, modified the growth of individual species and hence the ecological profile of the microplate plaques during development. Complex population shifts were observed during development, and older plaques comprised predominantly facultative anaerobic species. Sucrose supplementation limited the decline of Streptococci over time but did not increase the abundance of mutans Streptococci. Sucrose at 0.15% increased levels of caries-associated species including Lactobacillus fermentum, Lactobacillus acidophilus and Actinomyces gerensceriae; these were further increased with sucrose at 0.5%, in addition to Actinomyces israelii, Rothia dentocariosa and Capnocytophaga gingivalis. The microplate plaques demonstrated complex community dynamics that appeared to reflect the maturation of natural plaques, and sucrose induced a cariogenic plaque composition and pH.

Microbiology in toothbrush samples from children exposed to lead in southern Thailand

OBJECTIVE

The purpose of this study was to evaluate the prevalence and level of selected oral bacterial species in association with dental caries in low versus high blood lead (PbB) children.

MATERIAL AND METHODS

With an observational cross-sectional design, a sample of 292 children aged 6-11 years from two primary schools around a shipyard, known to be an area contaminated with lead, were examined. The number of decayed and filled surfaces on deciduous teeth (dfs) and the number of decayed, missing, and filled surfaces on permanent teeth (DMFS) were recorded. Microbiological plaque samples were taken from each child with a toothbrush. Enumeration of 17 bacterial species was carried out using the checkerboard DNA-DNA hybridization technique.

RESULTS

Overall means (SD) of dfs and DMFS were 13.2 (9.5) and 1.3 (2.3), respectively. Prevalence of excessive count (>or=10(6) cells/sample) was 100% for 4 known cariogenic bacteria and over 95% in another 2 species. With Bonferroni correction for type I error adjustment, there was no significant association between the count of each bacterial species and PbB and caries experience. The checkerboard method is sensitive in bacteria detection, but may not be suitable for differentiating caries risk in the endemic population.

Microbiota of plaque microcosm biofilms: effect of three times daily sucrose pulses in different simulated oral environments

AIM

To explore the Ecological Plaque Hypothesis for dental caries. To test modification of the microbiota of dental plaque microcosm biofilms by sucrose pulsing during growth in two different simulated oral fluids, and with a urea-induced plaque pH elevation.

METHODS

Plaque microcosm biofilms were cultured in an 'artificial mouth' with and without 6-min 5% w/v sucrose pulses every 8 h in an environment of continuously supplied saliva-like defined medium with mucin (DMM), or basal medium mucin (BMM, a high-peptone-yeast extract oral fluid analogue), and also in DMM + 10 mmol/l urea, with sucrose pulsing. Forty plaque species were quantified by checkerboard DNA:DNA hybridization analysis.

RESULTS

Sucrose pulsing extended rapid plaque growth in DMM and BMM, inducing major microbiota changes in DMM but not in BMM. In DMM, some streptococci and lactobacilli were unaffected while others implicated in caries, together with Candida albicans and Capnocytophaga gingivalis, increased. Aerobic, microaerophilic and major anaerobic species decreased. Elevation of the pH(max) from 6.4 to 7.0 had almost no effect on the microbiota. BMM plaques were distinct from DMM plaques with particularly low levels of Candida albicans and Actinomyces.

CONCLUSIONS

Modest sucrose exposure in a saliva-like environment causes profound changes in the developmental self-organization of plaque microcosms, supporting the Ecological Plaque Hypothesis. Nevertheless, there is significant stability in microbial composition with varying pH near neutrality. Increases in levels of specific bacteria in response to sucrose could be characteristic of organisms particularly important in caries.

Individual microflora beget unique oral microcosms

AIMS

To examine the efficacy of the multiple Sorbarod device (MSD) for the reproduction of inter-individual variations in oral microbiotas. The MSD supports sessile growth on parallel cellulose filters, perfused with artificial saliva. This enables biofilms (BF) to be grown and sampled, together with released cells in eluted medium (perfusates, PAs).

METHODS AND RESULTS

Two sets of triplicate MSDs were established. One set was inoculated using fresh saliva from three separate volunteers; the second set was inoculated from one saliva donor. Both were incubated in an anaerobic cabinet. BF and PA were analysed at 24-h intervals by PCR-denaturing gradient gel electrophoresis (DGGE) of 16S rDNA. Hierarchical dendrograms were constructed in order to sort community fingerprints over time, based on community relatedness. The MSD supported complex oral communities, as evidenced by DGGE (>20 distinct DGGE bands) and confocal scanning laser microscopy. DGGE band sequencing revealed bacteriological diversity and a high incidence of anaerobic species, including Prevotella sp. Dendrograms demonstrated marked inter-individual variation in the relative species abundance within salivary inocula from different volunteers (DV) and each associated MSD (all >45%, majority c. 85% concordance). Less variation was shown between triplicate models established using saliva from a single volunteer (SV) (all >58%; majority c. 95% concordance). PAs clustered together with the associated biofilms and inocula in the majority of cases for the DV MSDs whilst SV MSD community profiles clustered between replicate MSDs.

CONCLUSIONS

Data indicate that marked inter-individual variations in human salivary composition can be partially replicated in individualized MSD microcosms.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates the in vitro reproduction of individual oral microbiotas and suggests that taking inter-individual variability into account will increase the relevance of microcosm studies.

Variation in bacterial DGGE patterns from human saliva: over time, between individuals and in corresponding dental plaque microcosms

OBJECTIVE

Eubacterial 16S rDNA fingerprints of human saliva and dental plaque microcosm biofilms grown in the multi-plaque artificial mouth (MAM) were characterised using denaturing gradient gel electrophoresis (DGGE).

DESIGN

The stability of the bacterial community in the saliva of one individual collected over 7 years was assessed and compared with bacterial patterns in the saliva of 10 different individuals. DGGE was also used to assess changes in bacterial composition between saliva and mature plaque microcosms developed in the MAM from these 10 individual saliva samples.

RESULTS

A relatively stable bacterial community (>87% concordance) was maintained within the individual oral environment of the standard donor over 7 years of monitoring. By comparison, DGGE fingerprint patterns of saliva from 10 different donors displayed greater variability (66% concordance). Variability between individual DGGE profiles increased further in mature plaque microcosms grown from the saliva of the 10 donors (52% concordance) with an increase in detected species diversity and evidence for conserved similarity and hence the maintenance of organisation during community development.

CONCLUSIONS

These results suggest that stable ecological conditions were maintained long-term within the oral environment of the individual saliva donor but that transient fluctuations also occurred. The ecology and predominating microbiota in different individuals was host-specific and these differences were maintained to a degree during development into mature plaque microcosms. These findings also demonstrate the potential usefulness of applying DGGE to monitor temporal and developmental changes and possibly pathogenic patterns in oral bacterial communities from saliva and plaque.

Development and characterization of a simple perfused oral microcosm

AIMS

To validate perfused, inline, filter-based fermentation systems (multiple Sorbarod devices, MSD) for their ability to maintain stable oral bacterial communities. MSD enable replicate (n=5) microcosm biofilms (BF) to be established and sampled, together with their perfusates (PA, cells in eluted medium).

METHODS AND RESULTS

Fresh saliva from human volunteers was used to inoculate MSD, incubated in an anaerobic cabinet and perfused with artificial saliva at 7 ml h(-1). BF within Sorbarod filters and cells eluted in the PA were analysed at 24-h intervals by differential bacteriological culture and checkerboard DNA-DNA hybridization (CKB, 40 oral species). Dynamic stability was apparent after 2-3 days within both BF and PA as evidenced by culture, CKB data and pH measurements. BF harboured large numbers of anaerobic species and facultative anaerobes [ca 10-11 log10 colony-forming units (CFU)/filter] comprising considerable numbers of streptococci and Gram-negative species. PA contained ca 9-10 log(10) CFU ml(-1) suggesting an apparent mean growth rate of 0.1 h(-1) for the BF, as a whole corresponding to a mean generation time of 10 h. CKB analysis revealed considerable bacterial diversity within the respective MSD. Inter-individual variations in the relative species abundance of inocula was broadly reproduced in the MSD (BF and PA), although considerable variation was apparent between triplicate models established using saliva from one saliva donor or from three individual donors. The dominance of Gram-negative species, indicated by culture was supported by CKB analysis (major species, Prevotella melaninogenica and Fusobacterium nucleatum).

CONCLUSIONS

Data obtained from the various analytical approaches showed a high degree of congruence. The MSD enables the maintenance of complex, stable salivary microcosms and represents a simple, reproducible tool for modelling individual oral bacterial ecosystems.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates the utility of the MSD for studying the micro-ecology of the oral cavity.

Effect of khat chewing on 14 selected periodontal bacteria in sub- and supragingival plaque of a young male population

BACKGROUND/AIMS

The habit of chewing khat (Catha edulis) for its amphetamine-like effects is highly prevalent in Yemen and east Africa, and has expanded to Western countries. The purpose of this study was to estimate and compare the prevalence and levels of 14 periodontal bacteria in gingival plaque of khat chewers and khat nonchewers, as well as of khat chewing sides and khat nonchewing sides.

METHODS

A total of 408 sub- and supragingival plaque samples were collected from 51 young males (29 khat chewers and 22 khat nonchewers; age range 19-28 years) and analyzed using whole genomic DNA probes and checkerboard DNA-DNA hybridization. Clinical parameters were recorded for all teeth at six sites per tooth.

RESULTS

Streptococcus intermedius and Veillonella parvula were significantly more prevalent in the subgingival plaque of chewers, which also showed significantly higher levels of V. parvula and Eikenella corrodens. Similar results were found for the subgingival plaque of the chewing sides compared to the nonchewing sides. However, there was a significantly higher prevalence and higher levels of Tannerella forsythia in the subgingival plaque of the nonchewing sides. No significant differences were observed for the supragingival plaque between the two study groups. There was a significantly lower prevalence of Capnocytophaga gingivalis and Fusobacterium nucleatum in the khat chewing sides, and higher levels of V. parvula and Actinomyces israelii.

CONCLUSION

The data suggest that khat chewing induces a microbial profile that is not incompatible with gingival health.

Minimizing prion risk without compromising the microbial composition of biofilms grown in vivo in a human plaque model

AIMS

To determine whether the stringency of sterilization procedures for biological components of in vivo dental plaque-generating devices based on enamel can be increased to minimize prion risk without compromising natural biofilm composition.

METHODS AND RESULTS

The composition of in vitro biofilms, grown on hypochlorite-treated and untreated autoclaved enamel surfaces, was determined using culture-based methods and checkerboard DNA: DNA hybridization analysis. No differences were found between biofilms recovered from either substrate.

SIGNIFICANCE

Several in situ models allow generation of plaque in the oral cavity, followed by recovery of intact biofilms for experimentation. Approaches allowing plaque formation on natural tooth surfaces are most valuable, but present a possible infection risk to volunteers wearing plaque-collecting devices, particularly with respect to prions. Hypochlorite treatment of biological material, as an adjunct to autoclaving, reduces infection risk without compromising biofilm composition and should be adopted in all future studies using plaque-generating devices incorporating enamel, where there is a potential prion threat, and further investigated in other biological hard tissues.