The reproducibility of curet sampling of subgingival biofilms

Pursuing new periodontal pathogens with an improved RNA-oligonucleotide quantification technique (ROQT)

OBJECTIVE

The aim of this study was to optimize the sensitivity, specificity and cost-effectiveness of the RNA-Oligonucleotide Quantification Technique (ROQT) in order to identify periodontal pathogens that remain unrecognized or uncultured in the oral microbiome.

DESIGN

Total nucleic acids (TNA) were extracted from subgingival biofilm samples using an automated process. RNA, DNA and Locked Nucleic Acid (LNA) digoxigenin-labeled oligonucleotide probes targeting 5 cultivated/named species and 16 uncultivated or unnamed bacterial taxa were synthesized. Probe specificity was determined by targeting 96 oral bacterial species; sensitivity was assessed using serial dilutions of reference bacterial strains. Different stringency temperatures were compared and new standards were tested. The tested conditions were evaluated analyzing samples from periodontally healthy individuals, and patients with moderate or severe periodontitis.

RESULTS

The automated extraction method at 63⁰C along with LNA-oligunucleotides probes, and use of reverse RNA sequences for standards yielded stronger signals without cross-reactions. In the pilot clinical study, the most commonly detected uncultivated/unrecognized species were Selenomonas sp. HMT 134, Prevotella sp. HMT 306, Desulfobulbus sp. HMT 041, Synergistetes sp. HMT 360 and Bacteroidetes HMT 274. In the cultivated segment of the microbiota, the most abundant taxa were T. forsythia HMT 613 and Fretibacterium fastidiosum (formerly Synergistetes) HMT 363.

CONCLUSIONS

In general, samples from severe patients had the greatest levels of organisms. Classic (T. forsythia, P. gingivalis) and newly proposed (F. alocis and Desulfobulbus sp. HMT 041) pathogens were present in greater amounts in samples from severe periodontitis sites, followed by moderate periodontitis sites.

Toward Personalized Oral Diagnosis: Distinct Microbiome Clusters in Periodontitis Biofilms

Periodontitis is caused by pathogenic subgingival microbial biofilm development and dysbiotic interactions between host and hosted microbes. A thorough characterization of the subgingival biofilms by deep amplicon sequencing of 121 individual periodontitis pockets of nine patients and whole metagenomic analysis of the saliva microbial community of the same subjects were carried out. Two biofilm sampling methods yielded similar microbial compositions. Taxonomic mapping of all biofilms revealed three distinct microbial clusters. Two clinical diagnostic parameters, probing pocket depth (PPD) and clinical attachment level (CAL), correlated with the cluster mapping. The dysbiotic microbiomes were less diverse than the apparently healthy ones of the same subjects. The most abundant periodontal pathogens were also present in the saliva, although in different representations. The single abundant species Tannerella forsythia was found in the diseased pockets in about 16–17-fold in excess relative to the clinically healthy sulcus, making it suitable as an indicator of periodontitis biofilms. The discrete microbial communities indicate strong selection by the host immune system and allow the design of targeted antibiotic treatment selective against the main periodontal pathogen(s) in the individual patients.

Bacterial composition of subgingival plaque in crowded and noncrowded teeth

INTRODUCTION

Patients with dental crowding, even with good oral hygiene, may show increased bacterial presence in the crowded area. This study aimed to determine the microbial composition of subgingival plaque in crowded and noncrowded dental regions.

METHODS

Forty dental students with anterior dental crowding, who were aware of correct brushing techniques and oral hygiene, were enrolled in this study. After orthodontic records were taken and the periodontal examination was performed, subgingival plaque samples were collected from the crowded (experimental) and noncrowded regions (control) of each patient. Colony counting was performed for Aggregatibacter actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg), and streptococcus species.

RESULTS

The mean amount of Aa and Pg colonies was significantly higher in crowded areas (P <0.0001), but there was no significant difference between streptococcus species colonization and crowding. Aa and Pg colonization had a significant direct relation with the amount of crowding. (P <0.0001).

CONCLUSIONS

Crowded dental areas, even with good oral hygiene, are more suitable environments for Aa and Pg colonization.

Profiling of Aggregatibacter actinomycetemcomitans Serotypes B and C and the genotypes in periodontal health and disease

BACKGROUND

A. actinomycetemcomitans is prevalent in periodontitis but is found in some periodontally healthy individuals as well. Certain serotypes of the organism have shown to determine severity of the disease. The distribution of serotype and genotype is affected by geographic and ethnic variation. Therefore, the present study was aimed to detect serotypes b & c of A. actinomycetemcomitans and the genotypes and find its correlation with periodontal status.

MATERIALS AND METHODS

A total of 75 subjects (25 aggressive periodontitis, 25 chronic periodontitis and 25 periodontally healthy) in age range of 14-55 yrs were included. Subgingival plaque samples were collected and checked for the presence of A. actinomycetemcomitans. Following isolation of the organism, detection of the serotype b or c was done by multiplex PCR. Genotyping of A. actinomycetemcomitans was done by arbitrarily primed PCR(polymerase chain reaction).

RESULTS

Out of 75 plaque samples, 35(46.66%) tested positive for A. actinomycetemcomitans. Serotype c was detected in 19/35 (54.28%), whereas serotype b alone was not detected in any of the samples. Two samples were positive for both the serotypes (b and c) (5.71%) and 14 (40%) were untypeable. 14 different arbitrarily primed PCR genotypes were obtained among 35 A. actinomycetemcomitans isolates.

CONCLUSION

Serotype c was predominant in periodontally diseased as well as periodontally healthy individuals. An association could be present between genotype - serotype and genotype - periodontal status.

Molecular analyses of two bacterial sampling methods in ligature-induced periodontitis in rats

The prevalence profile of periodontal pathogens in dental plaque can vary as a function of the detection method; however, the sampling technique may also play a role in determining dental plaque microbial profiles. We sought to determine the bacterial composition comparing two sampling methods, one well stablished and a new one proposed here. In this study, a ligature-induced periodontitis model was used in 30 rats. Twenty-seven days later, ligatures were removed and microbiological samples were obtained directly from the ligatures as well as from the periodontal pockets using absorbent paper points. Microbial analysis was performed using DNA probes to a panel of 40 periodontal species in the checkerboard assay. The bacterial composition patterns were similar for both sampling methods. However, detection levels for all species were markedly higher for ligatures compared with paper points. Ligature samples provided more bacterial counts than paper points, suggesting that the technique for induction of periodontitis could also be applied for sampling in rats. Our findings may be helpful in designing studies of induced periodontal disease-associated microbiota.

Serotypes of Aggregatibacter actinomycetemcomitans in relation to periodontal status and assessment of leukotoxin in periodontal disease: A clinico-microbiological study

Context:

Aggregatibacter actinomycetemcomitans (A.a) serotypes may add some important information of the pathogenetic background of periodontal infections. A.a leukotoxin is an important virulence factor in the pathogenesis of periodontal disease and its rate of progression. When compared to minimally leukotoxic strains, variants of A.a highly leukotoxic strains produce 10–20 times more leukotoxin.

Aims:

The aim of the present study was to detect serotypes a, b, c, d, and e of A.a its leukotoxin and find its correlation with periodontal status.

Settings and Design:

Microbiological analysis and cross-sectional study.

Materials and Methods:

A total of 80 subjects (40 chronic periodontitis and 40 aggressive periodontitis) in the age range of 14–55 years were selected. Subgingival plaque samples were collected and checked for the presence of A.a. Following isolation of the organism, detection of the serotypes and leukotoxin assessment was done.

Statistical Analysis Used:

The proportions of A.a were calculated using descriptive statistics in terms of percentage. Chi-square test was used to find association between serotype, leukotoxin, and periodontal disease in individual group.

Results:

Out of 80 plaque samples, 45% tested positive for A.a. serotype b was detected in 33.33%, whereas serotype e in 8.33% samples and serotype c in 2.77% samples. Serotypes a and d were not detected in any of the samples. A combination of serotypes was seen in 47.22% of the sites. Of these 76.47% showed a combination of 2 serotypes, while 23.52%showed a combination of 3 serotypes. 8.33% showed untypable serotype. All samples had low-toxic variants of A.a.

Conclusions:

Serotype b and serotype e were predominant in chronic periodontitis, and serotype b was predominant in aggressive periodontitis. An association could be present between serotype and periodontal disease.

Simultaneous Detection of Oral Pathogens in Subgingival Plaque and Prostatic Fluid of Men With Periodontal and Prostatic Diseases

BACKGROUND

Chronic prostatitis (CPr) and benign prostatic hyperplasia (BPH) are complex inflammatory conditions for which etiologic determinants are still poorly defined. Periodontitis is caused by subgingival colonizing bacteria in the oral cavity. The causal effect of periodontal disease on prostatic inflammation has not been established. The purpose of this study is to isolate oral pathogens from expressed prostatic secretions of patients with periodontal disease and CPr or BPH.

METHODS

Twenty-four men diagnosed with CPr/BPH participated in the study. A complete periodontal examination consisting of probing depth, bleeding on probing, tooth mobility, gingival index, and plaque index was performed on the men, and prostatic secretion was collected for the study. Dental plaque and prostatic secretion samples were used for analysis of bacterial DNA for Porphyromonas gingivalis (Pg), Prevotella intermedia (Pi), Treponema denticola (Td), and Escherichia coli using reverse transcription-polymerase chain reaction.

RESULTS

Six patients were diagnosed with severe, seven with moderate, and four with mild chronic periodontitis. Seventeen of 24 (70.8%) of the prostatic secretion samples showed one or more of the studied oral pathogens. Nine of 10 BPH and eight of 14 patients with CPr had at least one oral pathogen in their prostatic secretions. Pg was found in both prostatic secretion and plaque samples in six of 17 (35.3%) patients, Td was found in both samples in seven of 15 (46.7%) patients, and E. coli was found in both samples in three of 15 (20%) patients. Pi was detected in all dental plaque samples but not in the prostatic secretion.

CONCLUSION

An association between chronic inflammatory prostate and periodontal diseases has been demonstrated by the presence of similar bacterial DNA in both prostatic secretion and subgingival dental plaque from the same individual.

Sampling Modification Effects in the Subgingival Microbiome Profile of Healthy Children

Background: Oral microbiota are considered major players in the development of periodontal diseases. Thorough knowledge of intact subgingival microbiomes is required to elucidate microbial shifts from health to disease.

Aims: This comparative study investigated the subgingival microbiome of healthy children, possible inter- and intra-individual effects of modified sampling, and basic comparability of subgingival microprints.

Methods: In five 10-year-old children, biofilm was collected from the upper first premolars and first molars using sterilized, UV-treated paper-points inserted into the subgingival sulcus at eight sites. After supragingival cleaning using an electric toothbrush and water, sampling was performed, firstly, excluding (Mode A) and, secondly, including (Mode B) cleansing with sterile cotton pellets. DNA was extracted from the pooled samples, and primers targeting 16S rRNA hypervariable regions V5 and V6 were used for 454-pyrosequencing. Wilcoxon signed rank test and t-test were applied to compare sampling modes. Principal coordinate analysis (PCoA) and average agglomerative hierarchical clustering were calculated with unweighted UniFrac distance matrices. Sample grouping was tested with permutational MANOVA (Adonis).

Results: Data filtering and quality control yielded 67,218 sequences with an average sequence length of 243bp (SD 6.52; range 231–255). Actinobacteria (2.8–24.6%), Bacteroidetes (9.2–25.1%), Proteobacteria (4.9–50.6%), Firmicutes (16.5–57.4%), and Fusobacteria (2.2–17.1%) were the five major phyla found in all samples. Differences in microbial abundances between sampling modes were not evident. High sampling numbers are needed to achieve significance for rare bacterial phyla. Samples taken from one individual using different sampling modes were more similar to each other than to other individuals' samples. PCoA and hierarchical clustering showed a grouping of the paired samples. Permutational MANOVA did not reveal sample grouping by sampling modes (p = 0.914 by R² = 0.09).

Conclusion: A slight modification of sampling mode has minor effects corresponding to a natural variability in the microbiome profiles of healthy children. The inter-individual variability in subgingival microprints is greater than intra-individual differences. Statistical analyses of microbial populations should consider this baseline variability and move beyond mere quantification with input from visual analytics. Comparative results are difficult to summarize as methods for studying huge datasets are still evolving. Advanced approaches are needed for sample size calculations in clinical settings.

Effects of azithromycin, metronidazole, amoxicillin, and metronidazole plus amoxicillin on an in vitro polymicrobial subgingival biofilm model

Chronic periodontitis is one of the most prevalent human diseases and is caused by dysbiosis of the subgingival microbiota. Treatment involves primarily mechanical disruption of subgingival biofilms and, in certain cases, adjunctive use of systemic antibiotic therapy. In vitro biofilm models have been developed to study antimicrobial agents targeting subgingival species. However, these models accommodate a limited number of taxa, lack reproducibility, and have low throughput. We aimed to develop an in vitro multispecies biofilm model that mimics subgingival plaque, to test antimicrobial agents. Biofilms were cultivated using the Calgary Biofilm Device and were exposed to amoxicillin (AMX), metronidazole (MTZ), azithromycin (AZM), and AMX-MTZ at four different concentrations for 12, 24, or 36 h. Chlorhexidine (CHX) (0.12%) was used as the positive control. The compositions of the biofilms were analyzed by checkerboard DNA-DNA hybridization, and the percent reduction in biofilm metabolic activity was determined using 2,3,5-triphenyltetrazolium chloride and spectrophotometry. Thirty-five of the 40 species used in the inoculum were consistently recovered from the resulting in vitro biofilms. After 36 h of exposure at the 1:27 dilution, AMX-MTZ reduced metabolic activity 11% less than CHX (q = 0.0207) but 54% more than AMX (q = 0.0031), 72% more than MTZ (q = 0.0031), and 67% more than AZM (q = 0.0008). Preliminary evidence of a synergistic interaction between AMX and MTZ was also observed. In summary, we developed reproducible biofilms with 35 subgingival bacterial species, and our results suggested that the combination of AMX and MTZ had greater antimicrobial effects on these in vitro multispecies biofilms than expected on the basis of the independent effects of the drugs.

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.

Reproducibility of subgingival bacterial samples from patients with peri-implant mucositis

OBJECTIVE

The aim of the present study was to investigate the reproducibility of bacterial enumeration from subsequent subgingival samples collected from patients with peri-implant mucositis.

MATERIAL AND METHODS

Duplicate microbial samples from 222 unique implant sites in 45 adult subjects were collected with paper points and analyzed using the checkerboard DNA-DNA hybridization technique. Whole genomic probes of 74 preselected bacterial species were used. Based on the bacterial scores, Cohen's kappa coefficient was used to calculate the inter-annotator agreement for categorical data. The percentage agreement was considered as "good" when the two samples showed the same score or differed by 1 to the power of 10.

RESULTS

Moderate to fair kappa values were displayed for all bacterial species in the test panel (range 0.21-0.58). There were no significant differences between Gram-positive and Gram-negative species. The percentage of good agreement between the first and second samples averaged 74.7 % (n = 74; range 56-83 %), while the proportion of poor agreement ranged from 1 to 19 % for the various strains.

CONCLUSION

While an acceptable clinical agreement was obtained in most cases, diverging bacterial scores may appear in subgingival samples collected at the same time point from patients with peri-implant mucositis.

CLINICAL RELEVANCE

The broad bulky base of implant crowns may present an obstacle for the collection of reproducible subgingival samples with paper points.

Age-dependent changes in Porphyromonas gingivalis and Prevotella species/phylotypes in healthy gingiva and inflamed/diseased sub-gingival sites

OBJECTIVES

Early colonisation of oral surfaces by periodontal pathogens presents a significant risk factor for subsequent development of destructive disease affecting tissues that support the dentition. The aims of the present study were to establish the age-dependent relationship between sub-gingival profiles of 22 Prevotella species/phylotypes in children, adolescents and adults from an isolated Aboriginal community and, further, to use this information to identify Prevotella species that could serve as microbial risk indicators.

MATERIALS AND METHODS

DNA isolated from sub-gingival plaque samples (three healthy sites and three inflamed/diseased sites) from adults, adolescents and children was screened for Porphyromonas gingivalis load and 22 Prevotella species/phylotypes by species-specific PCR.

RESULTS

A noticeable feature in adolescents was the marked increase in colonisation by P. gingivalis across all test sites. The mean number of Prevotella species/phylotypes colonising inflamed/diseased sub-gingival sites increased with age. Progressive partitioning of selected Prevotella species/phylotypes to healthy or inflamed/diseased sites was evident. Prevalence of Prevotella intermedia, Prevotella oral clone P4PB_24 and Prevotella oris increased significantly with age in diseased sites. Similarly, significant age-dependent increase in colonisation of healthy as well as inflamed/diseased sub-gingival sites was apparent for Prevotella oralis, Prevotella multiformis, Prevotella denticola, Prevotella strain P4P_53 and Prevotella oral clone BR014.

CONCLUSION

Early colonisation of children by P. gingivalis, P. intermedia and Prevotella oral clone P4PB_24 provides indication of risk for subsequent development of periodontal disease.

CLINICAL RELEVANCE

In the present study, the complexity of Prevotella species within gingival sites is explored as a basis for evaluating contribution of Prevotella species to disease.

Lessons learned and unlearned in periodontal microbiology

Periodontal diseases are initiated by bacterial species living in polymicrobial biofilms at or below the gingival margin and progress largely as a result of the inflammation elicited by specific subgingival species. In the past few decades, efforts to understand the periodontal microbiota have led to an exponential increase in information about biofilms associated with periodontal health and disease. In fact, the oral microbiota is one of the best-characterized microbiomes that colonize the human body. Despite this increased knowledge, one has to ask if our fundamental concepts of the etiology and pathogenesis of periodontal diseases have really changed. In this article we will review how our comprehension of the structure and function of the subgingival microbiota has evolved over the years in search of lessons learned and unlearned in periodontal microbiology. More specifically, this review focuses on: (i) how the data obtained through molecular techniques have impacted our knowledge of the etiology of periodontal infections; (ii) the potential role of viruses in the etiopathogenesis of periodontal diseases; (iii) how concepts of microbial ecology have expanded our understanding of host-microbe interactions that might lead to periodontal diseases; (iv) the role of inflammation in the pathogenesis of periodontal diseases; and (v) the impact of these evolving concepts on therapeutic and preventive strategies to periodontal infections. We will conclude by reviewing how novel systems-biology approaches promise to unravel new details of the pathogenesis of periodontal diseases and hopefully lead to a better understanding of their mechanisms.

Pattern of distribution of Prevotella species/phylotypes associated with healthy gingiva and periodontal disease

The purpose of the present study was to obtain diverse profiles of Prevotella species associated with gingival sites in an isolated Aboriginal and an urban community by phylogenetic analysis and to establish patterns of association of identified Prevotella species in gingival sites. Species/phylotypes identified from the phylogenetic analysis of near full-length Bacteroidetes 16S rRNA gene sequences cloned from subgingival plaque samples obtained from an Aboriginal community were compared with those from an ethnically diverse urban metropolitan population suffering from periodontal disease. Specific primer sets were designed and validated for 22 distinct Prevotella species from the 24 species/phylotypes identified from both populations. Within the isolated Aboriginal community, gingival sites in adults were colonised by a mean of 15 different Prevotella species. Prevotella sp. oral clone P4PB24, Prevotella intermedia, Prevotella oralis, Prevotella denticola and Prevotella sp. strain P4P62 had the highest association with increasing probing depth in diseased sites (p < 0.05). P. intermedia and Prevotella sp. oral clone P4PB24, the Prevotella species significantly associated with increasing probing depth in diseased gingival sites and also strongly associated with P. gingivalis load (p < 0.05) in diseased gingival sites, showed significant correlation for co-colonisation (r = 0.6). Prevotella sp. oral clone B31FD, showing strong association with P. gingivalis load (p < 0.05) in diseased gingival sites, showed no significant correlation for co-colonisation with any other Prevotella species. This study provides a comprehensive analysis of Prevotella species associated with gingival sites for the informative evaluation of the epidemiology of infection by this genus.

RNA-oligonucleotide quantification technique (ROQT) for the enumeration of uncultivated bacterial species in subgingival biofilms

Approximately 35% of the species present in subgingival biofilms are as yet uncultivated, so their role in periodontal pathogenesis is unknown. The aim of the present study was to develop a high throughput method to quantify a wide range of cultivated and uncultivated taxa in subgingival biofilm samples associated with periodontal disease or health. Oligonucleotides targeting the 16S ribosomal DNA gene were designed, synthesized and labeled with digoxigenin. These probes were hybridized with the total nucleic acids of pure cultures or subgingival biofilm samples. Target species included cultivated taxa associated with periodontal health and disease, as well as uncultivated species, such as TM7 sp. OT 346, Mitsuokella sp. OT 131 and Desulfobulbus sp. OT 041. Sensitivity and specificity of the probes were determined. A Universal probe was used to assess total bacterial load. Sequences complementary to the probes were used as standards for quantification. Chemiluminescent signals were visualized after film exposure or using a CCD camera. In a pilot clinical study, 266 subgingival plaque samples from eight periodontally healthy people and 11 patients with periodontitis were examined. Probes were specific and sensitivity reached 10(4) cells. Fusobacterium nucleatum ss. polymorphum and Actinomyces gerencseriae were the most abundant cultivated taxa in clinical samples. Among uncultivated/unrecognized species, Mitsuokella sp. OT 131 and Prevotella sp. OT 306 were the most numerous. Porphyromonas gingivalis and Desulfobulbus sp. OT 041 were only detected in patients with periodontitis. Direct hybridization of total nucleic acids using oligonucleotide probes permitted the quantification of multiple cultivated and uncultivated taxa in mixed species biofilm samples.

Microbiota of deciduous endodontic infections analysed by MDA and Checkerboard DNA-DNA hybridization

AIMS

To evaluate the microbiota of endodontic infections in deciduous teeth by Checkerboard DNA-DNA hybridization after uniform amplification of DNA in samples by multiple displacement amplification (MDA).

METHODOLOGY

Forty samples from the root canal system of deciduous teeth exhibiting pulp necrosis with or without radiographically detectable periradicular/interradicular bone resorption were collected and 32 were analysed, with three individuals contributing two samples; these were MDA-amplified and analysed by Checkerboard DNA-DNA hybridization for levels of 83 bacterial taxa. Two outcome measures were used: the percentage of teeth colonized by each species and the mean proportion of each bacterial taxon present across all samples.

RESULTS

The mean amount of DNA in the samples prior to amplification was 5.2 (±4.7) ng and 6.1 (±2.3) μg after MDA. The mean number of species detected per sample was 19 (±4) (range: 3-66) to the nearest whole number. The most prevalent taxa were Prevotella intermedia (96.9%), Neisseria mucosa (65.6%), Prevotella nigrescens (56.2%) and Tannerella forsythia (56.2%). Aggregatibacter (Haemophilus) aphrophilus and Helicobacter pylori were not detected. P. intermedia (10%), Prevotella tannerae (7%) and Prevotella nigrescens (4.3%) presented the highest mean proportions of the target species averaged across the positive samples.

CONCLUSION

Root canals of infected deciduous teeth had a diverse bacterial population. Prevotella sp. were commonly found with P. intermedia, Prevotella tannerae and Prevotella nigrescens amongst the most prominent species detected.

Using DGGE profiling to develop a novel culture medium suitable for oral microbial communities

More than 700 bacterial species have been detected in the human oral cavity. They form highly organized microbial communities and are responsible for many oral infectious diseases, such as dental caries and periodontal disease. The prevention and treatment of these diseases require a comprehensive knowledge of oral microbial communities, which largely relies on culture-dependent methods to provide detailed phenotypic and physiological analysis of these communities. However, most of the currently available laboratory media can only selectively support the growth of a limited number of bacterial species within these communities, and fail to sustain the original oral microbial diversity. In this study, using denaturing gradient gel electrophoresis (DGGE) as an index to systematically survey and analyse the selectivity of commonly used laboratory media, we developed a new medium (SHI medium) by combining the ingredients of several selected media that can support different subpopulations within the original oral microbial community derived from pooled saliva. DGGE and 454 pyrosequencing analysis showed that SHI medium was capable of supporting a more diversified community with a microbial profile closer to that of the original oral microbiota. Furthermore, 454 pyrosequencing revealed that SHI medium supported the growth of many oral species that have not before been cultured. Crystal violet assay and the confocal laser scanning microscope analysis indicated that, compared with other media, SHI medium is able to support a more complex saliva-derived biofilm with higher biomass yield and more diverse species. This DGGE-guided method could also be used to develop novel media for other complex microbial communities.

Lysine gingipain (kgp) biovars of Porphyromonas gingivalis exhibit differential distribution on oral mucosal sites

A predominant kgp biovar colonized subgingival sites and buccal and tongue mucosa in 45 of 56 adults in an isolated community. The presence of biovars 381, W83, and W83v, but not HG66, correlated with the Porphyromonas gingivalis load at diseased sites. Biovars W83 and W83v poorly colonized tongue and buccal mucosa.

Comparison between polymerase chain reaction-based and checkerboard DNA hybridization techniques for microbial assessment of subgingival plaque samples

AIM

To compare polymerase chain reaction (PCR) with subsequent reverse hybridization (micro-IDent test) and checkerboard DNA-DNA hybridization for the identification of 13 bacterial species in subgingival plaque samples.

MATERIAL AND METHODS

Subgingival plaque samples were taken using paper points and curettes from two sites each with pocket depth <4, 4-6 and >6 mm at baseline and 3 months in 25 periodontitis subjects and two sites in 25 periodontally healthy subjects. Samples were analysed for their content of 13 bacterial species using both assays. Similarities for each species between techniques were determined using regression analysis. Differences between health and periodontitis were determined using the Mann-Whitney test.

RESULTS

Three hundred and fifty samples were evaluated using both techniques. Regression analysis indicated that 10/13 test species showed significant positive correlations between the counts determined by checkerboard analysis and levels determined by the PCR-based test after adjusting for 13 comparisons. The highest rank correlations of 0.58, 0.49 and 0.46 were seen for Treponema denticola, Fusobacterium nucleatum and Eubacterium nodatum, respectively (p<0.0001). Both tests could distinguish samples from healthy and periodontitis subjects.

CONCLUSION

Detection patterns of 10/13 test species in subgingival plaque samples from periodontitis and healthy subjects were similar using the two molecular techniques.

In Vitro evaluation of Enterococcus faecalis adhesion on various endodontic medicaments

E. faecalis in endodontic infection represents a biofilm type of disease, which explains the bacteria's resistance to various antimicrobial compounds and the subsequent failure after endodontic treatment. The purpose of this study was to compare antimicrobial activities and bacteria kinetic adhesion in vitro for three endodontic medicaments with a clinical isolate of E. faecalis. We devised a shake culture which contained the following intracanalar preparations: CPD, Endoidrox (EIX), PulpCanalSealer (PCS); these were immersed in a liquid culture medium inoculated with the microorganism. The shake system velocity was able to prevent non-specific bacteria adhesion and simulated the salivary flow. Specimens were collected daily (from both the medium and medicaments) for 10 days; the viable cells were counted by plate count, while the adhesion index AI ° [E. faecalis fg DNA] /mm² was evaluated in the pastes after DNA extraction, by quantitative real time PCR for the 16S rRNA gene. A partial growth inhibition, during the first 24 hours, was observed in the liquid medium and on the medicaments for EIX and subsequently for CPD (six logs). EIX showed the lowest adhesion coefficient (5*10² [fg DNA]/mm²) for nine days and was similar to the control. PCS showed no antimicrobial/antibiofilm properties. This showed that "calcium oxide" base compounds could be active against biofilm progression and at least in the short term (2-4 days) on E. faecalis cells growing in planktonic cultures.

Detection of multiple pathogenic species in saliva is associated with periodontal infection in adults

We investigated whether certain bacterial species and their combinations in saliva can be used as markers for periodontitis. In 1,198 subjects, the detection of multiple species, rather than the presence of a certain pathogen, in saliva was associated with periodontitis as determined by the number of teeth with deepened periodontal pockets.