Detection of unculturable bacteria in periodontal health and disease by PCR

The Oral Microbiota in Health and Disease: An Overview of Molecular Findings

Culture-independent nucleic acid technologies have been extensively applied to the analysis of oral bacterial communities associated with healthy and diseased conditions. These methods have confirmed and substantially expanded the findings from culture studies to reveal the oral microbial inhabitants and candidate pathogens associated with the major oral diseases. Over 1000 bacterial distinct species-level taxa have been identified in the oral cavity and studies using next-generation DNA sequencing approaches indicate that the breadth of bacterial diversity is even much larger. Nucleic acid technologies have also been helpful in profiling bacterial communities and identifying disease-related patterns. This chapter provides an overview of the diversity and taxonomy of oral bacteria associated with health and disease.

Ultra-Sensitive and Specific Detection of S. aureus Bacterial Cultures Using an Oligonucleotide Probe Integrated in a Lateral Flow-Based Device

The identification of pathogens causing infectious diseases is still based on laborious and time-consuming techniques. Therefore, there is an urgent need for the development of novel methods and devices that can considerably reduce detection times, allowing the health professionals to administer the right treatment at the right time. Lateral flow-based systems provide fast, cheap and easy to use alternatives for diagnosis. Herein, we report on a lateral flow approach for specifically detecting S. aureus bacteria within 6 h.

Prevalence of unculturable bacteria in the periapical abscess: A systematic review and meta-analysis

OBJECTIVE

To assess the prevalence of unculturable bacteria in periapical abscess, radicular cyst, and periapical granuloma.

METHODS

PubMed, Scopus, Science Direct, and Ovid databases were systematically searched from January 1990 to May 2020. All the included studies were cross-sectional design. The risk of bias was assessed using Joanna Briggs Institute check-list. Heterogeneity was described using meta-regression and mixed-effects model for lesion, country, and sequence technique moderators. Funnel plot and unweighted Egger's regression test were used to estimate the publication bias. Microbiome data on diversity, abundance, and frequency of unculturable bacteria in the periapical lesions were reviewed, analysed, and the principal component analysis (PCA) was performed.

RESULTS

A total of 13 studies out of 14,780, were selected for the final analysis. These studies focused on the prevalence of unculturable bacteria in periapical abscesses and related lesions. Approximately 13% (95% CI: 7-23%) of the cumulative number of bacteria derived from periapical abscesses was unculturable. Country moderator significantly (P = 0.05) affects the diversity summary proportion. While the pooled frequency of unculturable bacteria was 8%; 95% CI: 5, 14%, the estimate of the pooled abundance of unculturable bacteria was 5%; 95% CI: 2, 12% with a significant (P = 0.05) country moderator that affects the abundance summary proportion. Of the 62 unculturable bacteria, 35 were subjected to PCA and Peptostreptococcus sp. oral clone CK035 was the most abundant species in periapical abscesses. Hybridization techniques were found to be the most reliable molecular methods in detecting the abundance and frequency of unculturable bacteria.

CONCLUSION

The significant prevalence of unculturable bacteria in the periapical abscess, suggests that they are likely to play, a yet unknown, critical role in the pathogenesis and progression of the disease. Further research remains to be done to confirm their specific contributions in the virulence and disease progression.

Exploring microbial communities, assessment methodologies and applications of animal's carcass decomposition: a review

Animals are an essential part of the ecosystem, and their carcasses are the nutrient patches or hotspots where nutrients accumulate for a long time. After death, the physical and chemical properties undergo alterations inside the carcass. The animal carcass is decomposed by many decomposers such as bacteria, fungi, microeukaryotes and insects. The role of microbial symbionts in living organisms is well explored and studied, but there is a scarcity of knowledge and research related to their role in decomposing animal carcasses. Microbes play an important role in carcass decomposition. The origins of microbial communities associated with a carcass, including the internal and external microbiome, are discussed in this review. The succession and methods used for the detection and exploration of decomposition-associated microbial communities have been briefly described. Also, the applications of carcass-associated microbial taxa have been outlined. This review is intended to understand the dynamics of microbial communities associated with the carcass and pave the way to estimate postmortem interval and its role in recycling nutrients.

Did Omics change periodontal therapy?

The starting point for defining effective treatment protocols is a clear understanding of the etiology and pathogenesis of a condition. In periodontal diseases, this understanding has been hindered by a number of factors, such as the difficulty in differentiating primary pathogens from nonpathogens in complex biofilm structures. The introduction of DNA sequencing technologies, including taxonomic and functional analyses, has allowed the oral microbiome to be investigated in much greater breadth and depth. This article aims to compile the results of studies, using next-generation sequencing techniques to evaluate the periodontal microbiome, in an attempt to determine how far the knowledge provided by these studies has brought us in terms of influencing the way we treat periodontitis. The taxonomic data provided, to date, by published association and elimination studies using next-generation sequencing confirm previous knowledge on the role of classic periodontal pathogens in the pathobiology of disease and include new species/genera. Conversely, species and genera already considered as host-compatible and others less explored were associated with periodontal health as their levels were elevated in healthy individuals and increased after therapy. Functional and transcriptomic analyses also demonstrated that periodontal biofilms are taxonomically diverse, functionally congruent, and highly cooperative. Very few interventional studies to date have examined the effects of treatment on the periodontal microbiome, and such studies are heterogeneous in terms of design, sample size, sampling method, treatment provided, and duration of follow-up. Hence, it is still difficult to draw meaningful conclusions from them. Thus, although OMICS knowledge has not yet changed the way we treat patients in daily practice, the information provided by these studies opens new avenues for future research in this field. As new pathogens and beneficial species become identified, future randomized clinical trials could monitor these species/genera more comprehensively. In addition, the metatranscriptomic data, although still embryonic, suggest that the interplay between the host and the oral microbiome may be our best opportunity to implement personalized periodontal treatments. Therapeutic schemes targeting particular bacterial protein products in subjects with specific genetic profiles, for example, may be the futuristic view of enhanced periodontal therapy.

Thanatomicrobiome composition profiling as a tool for forensic investigation

Thanatomicrobiome, or the postmortem microbiome, has been recognized as a useful microbial marker of the time and location of host death. In this mini-review, we compare the experimental methods commonly applied to thanatomicrobiome studies to the state-of-the-art methodologies in the microbiome field. Then, we review present findings in thanatomicrobiome studies, focusing on the diversity of the thanatomicrobiome composition and prediction models that have been proposed. Finally, we discuss potential improvements and future directions of the field.

Atomic Force Microscopy: A three-dimensional reconstructive tool of oral microbiota in gingivitis and periodontitis

Aim:

This study aims to ascertain the advantages of Atomic Force Microscopy (AFM) in the morphologic study of microorganisms and their interactions within the subgingival biofilm in patients with gingivitis and periodontitis.

Settings and Design:

Conducted a study on twenty patients, ten patients with severe periodontitis with probing the pocket depth of ≥8 mm, with a clinical attachment loss (CAL) of ≥6 mm CAL and ten patients with gingivitis: ≥5 mm pocket depth, and no attachment loss, was selected for the study.

Materials and Methods:

Bacterial biofilms were collected and slide preparation done. Morphological study was done using AFM. AFM consists of a cantilever-mounted tip, a piezoelectric scanner, a photodetector diode, a laser diode, and a feedback control. The laser beam is reflected from back of the cantilever into the quadrant of the photodetector. AFM works on the principle of interaction between the tip and the sample which causes the cantilever to deflect, thereby changing the position of laser onto the photodetector. Methodology used for studying the bacteria through AFM includes the following: (1) Probe type: Platinum coated silicon nitrate tip. (2) Probe force: 0.11 N/m. (3) Probe geometry: Triangular shaped tip. (4) Probe frequency: 22 KHz. (5) Probe immobilization: Used in Contact mode. AFM Solver Pro-M (NT-MDT) equipped with ETALON probe was used to take images in Nova software.

Results:

The investigation showed various morphological features, such as shape, size, and secretory product-like vesicles of the bacterial species involved in gingivitis and periodontitis. More bacterial surface details were studied by reproducing a three-dimensional reconstruction using AFM.

Conclusions:

The morphological variations of bacteria of different sizes, and shapes, cell wall structures, secretory product-like vesicles flagellated and filamentous microorganisms, polymorphonuclear leukocytes, and bacterial coaggregation analysis were done by AFM. Results of the present study conclude that AFM is a quite a reliable method for studying morphology of bacterial species involving periodontal diseases and is also used to study microbial interactions in biofilm.

Do different probing depths exhibit striking differences in microbial profiles?

AIM

To perform a thorough characterization of the subgingival microbiota of shallow, moderate and deep sites in subjects with chronic periodontitis (ChP).

MATERIAL AND METHODS

Subgingival samples were collected from subjects with ChP (n = 3/category of probing depth: ≤3, 4-6 and ≥7 mm) and periodontal health (PH). Individual samples were submitted to 16S rDNA high- throughput sequencing and the analysis was made using mothur and R packages.

RESULTS

Nine subjects with ChP and seven with PH were included and 101 samples were evaluated. Thirteen phyla, 118 genera and 211 OTUs were detected. Taxa from Chloroflexi and Spirochaetes phyla were associated with initial stages of disease. Fretibacterium, Eubacterium[XI][G-6], Desulfobulbus, Peptostreptococcaceae[XI][G-1] and [G-3], Bacteroidetes[G-3], Bacteroidaceae[G-1] genera and Filifactor alocis, Fretibacterium fastidiosum, Johnsonella spHOT166, Peptostreptococcaceae[XIII][G-1]HOT113, Porphyromonas endodontalis and Treponema sp. HOT258, which are not conventionally associated with disease, increased with the deepening of the pockets and/or were elevated in ChP; while Streptococcus, Corynebacterium and Bergeyella genera were associated with PH (p < .05).

CONCLUSION

Striking differences were observed between the microbiota of shallow and moderate/deep sites, but not between moderate and deep sites in ChP subjects. Differences between shallow sites in PH and ChP were also observed. The characterized microbiota included known oral microorganisms and newly identified periodontal taxa, some of them not-yet-cultured.

The Oral Microbiota in Health and Disease: An Overview of Molecular Findings

Culture-independent nucleic acid technologies have been extensively applied to the analysis of oral bacterial communities associated with healthy and diseased conditions. These methods have confirmed and substantially expanded the findings from culture studies to reveal the oral microbial inhabitants and candidate pathogens associated with the major oral diseases. Over 1000 bacterial distinct species-level taxa have been identified in the oral cavity and studies using next-generation DNA sequencing approaches indicate that the breadth of bacterial diversity may be even much larger. Nucleic acid technologies have also been helpful in profiling bacterial communities and identifying disease-related patterns. This chapter provides an overview of the diversity and taxonomy of oral bacteria associated with health and disease.

Newly identified pathogens associated with periodontitis: a systematic review

There is substantial evidence supporting the role of certain oral bacteria species in the onset and progression of periodontitis. Nevertheless, results of independent-culture diagnostic methods introduced about a decade ago have pointed to the existence of new periodontal pathogens. However, the data of these studies have not been evaluated together, which may generate some misunderstanding on the actual role of these microorganisms in the etiology of periodontitis. The aim of this systematic review was to determine the current weight of evidence for newly identified periodontal pathogens based on the results of "association" studies. This review was conducted and reported in accordance with the PRISMA statement. The MEDLINE, EMBASE, and Cochrane databases were searched up to September 2013 for studies (1) comparing microbial data of subgingival plaque samples collected from subjects with periodontitis and periodontal health and (2) evaluating at least 1 microorganism other than the already-known periodontal pathogens. From 1,450 papers identified, 41 studies were eligible. The data were extracted and registered in predefined piloted forms. The results suggested that there is moderate evidence in the literature to support the association of 17 species or phylotypes from the phyla Bacteroidetes, Candidatus Saccharibacteria, Firmicutes, Proteobacteria, Spirochaetes, and Synergistetes. The phylum Candidatus Saccharibacteria and the Archaea domain also seem to have an association with disease. These data point out the importance of previously unidentified species in the etiology of periodontitis and might guide future investigations on the actual role of these suspected new pathogens in the onset and progression of this infection.

Pathogenic bacterial species associated with endodontic infection evade innate immune control by disabling neutrophils

Endodontic infections, in which oral bacteria access the tooth pulp chamber, are common and do not resolve once established. To investigate the effects of these infections on the innate immune response, we established a mouse subcutaneous chamber model, where a mixture of four oral pathogens commonly associated with these infections (endodontic pathogens [EP]), i.e., Fusobacterium nucleatum, Streptococcus intermedius, Parvimonas micra, and Prevotella intermedia, was inoculated into subcutaneously implanted titanium chambers. Cells that infiltrated the chamber after these infections were primarily neutrophils; however, these neutrophils were unable to control the infection. Infection with a nonpathogenic oral bacterial species, Streptococcus mitis, resulted in well-controlled infection, with bacterial numbers reduced by 4 to 5 log units after 7 days. Propidium iodide (PI) staining of the chamber neutrophils identified three distinct populations: neutrophils from EP-infected chambers were intermediate in PI staining, while cells in chambers from mice infected with S. mitis were PI positive (apoptotic) or negative (live). Strikingly, neutrophils from EP-infected chambers were severely impaired in their ability to phagocytose and to generate reactive oxygen species in vitro after removal from the chamber compared to cells from S. mitis-infected chambers. The mechanism of neutrophil impairment was necrotic cell death as determined by morphological analyses. P. intermedia alone could induce a similar neutrophil phenotype. We conclude that the endodontic pathogens, particularly P. intermedia, can efficiently disable and kill infiltrating neutrophils, allowing these infections to become established. These results can help explain the persistence of endodontic infections and demonstrate a new virulence mechanism associated with P. intermedia.

Cystic fibrosis transmembrane conductance regulator (CFTR) allelic variants relate to shifts in faecal microbiota of cystic fibrosis patients

Introduction

In this study we investigated the effects of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene variants on the composition of faecal microbiota, in patients affected by Cystic Fibrosis (CF). CFTR mutations (F508del is the most common) lead to a decreased secretion of chloride/water, and to mucus sticky secretions, in pancreas, respiratory and gastrointestinal tracts. Intestinal manifestations are underestimated in CF, leading to ileum meconium at birth, or small bowel bacterial overgrowth in adult age.

Methods

Thirty-six CF patients, fasting and under no-antibiotic treatment, were CFTR genotyped on both alleles. Faecal samples were subjected to molecular microbial profiling through Temporal Temperature Gradient Electrophoresis and species-specific PCR. Ecological parameters and multivariate algorithms were employed to find out if CFTR variants could be related to the microbiota structure.

Results

Patients were classified by two different criteria: 1) presence/absence of F508del mutation; 2) disease severity in heterozygous and homozygous F508del patients. We found that homozygous-F508del and severe CF patients exhibited an enhanced dysbiotic faecal microbiota composition, even within the CF cohort itself, with higher biodiversity and evenness. We also found, by species-specific PCR, that potentially harmful species (Escherichia coli and Eubacterium biforme) were abundant in homozygous-F508del and severe CF patients, while beneficial species (Faecalibacterium prausnitzii, Bifidobacterium spp., and Eubacterium limosum) were reduced.

Conclusions

This is the first report that establishes a link among CFTR variants and shifts in faecal microbiota, opening the way to studies that perceive CF as a ‘systemic disease’, linking the lung and the gut in a joined axis.

Role of topical antibiotic prophylaxis in prevention of bacterial translocation into upper trachea in nasally intubated patients undergoing tonsillectomies

INTRODUCTION

The human oropharynx and nasopharynx are home of different bacteria and fungi. The initial sterile endotracheal tube (ETT) transfers mechanically the bacteria from the nasopharynx and oropharynx to the sterile tracheobronchial tree. We investigated the efficacy of Neomycin-Bacitracin combination spray in the prevention of this bacterial translocation through its application over and inside the lumen of the endotracheal tubes preoperatively.

PATIENTS AND METHODS

Ninety patients aged (from 8 to 15 years) with ASA I and II were randomly assigned into 2 groups (45 patients for each): Group I; patients with naso-tracheal intubation which sprayed by placebo spray (Lidocaine) and group II; with naso-tracheal intubation that sprayed with antibiotic spray (combined Neomycin sulphate and Bacitracin) on the outside wall of the tube and inside its lumen. At the end of surgery and immediately after extubation, swabs were taken from the upper trachea using cotton tipped swab for bacterial growth. Inflammatory biomarkers were assessed preoperatively and postoperatively to detect any laboratory differences between both groups.

RESULTS

In the control group, all patients had heavy bacterial contamination and they were at either level 3 or 4 colony forming units. Thirty-two patients (71%) were at level 3 while 13 patients (29%) were at level 4. In the study group, there were 28 (62.2%) patients showed no bacterial growth, 15 (33.3%) patients were level 1, and 2 patients (4.4%) at level 2 colony forming units. There were no clinical differences between the 2 groups. Also, there was no significant difference between the 2 groups regarding to their postoperative body temperature although the inflammatory biomarkers were significantly higher in the control group.

CONCLUSION

Bacterial translocation by endotracheal intubation to the tracheobronchial tree could be prevented by local antibiotic spray application to outer and inner walls of the endotracheal tubes.

A universal method for the identification of bacteria based on general PCR primers

The Universal Method (UM) described here will allow the detection of any bacterial rDNA leading to the identification of that bacterium. The method should allow prompt and accurate identification of bacteria. The principle of the method is simple; when a pure PCR product of the 16S gene is obtained, sequenced, and aligned against bacterial DNA data base, then the bacterium can be identified. Confirmation of identity may follow. In this work, several general 16S primers were designed, mixed and applied successfully against 101 different bacterial isolates. One mixture, the Golden mixture7 (G7) detected all tested isolates (67/67). Other golden mixtures; G11, G10, G12, and G5 were useful as well. The overall sensitivity of the UM was 100% since all 101 isolates were detected yielding intended PCR amplicons. A selected PCR band from each of 40 isolates was sequenced and the bacterium identified to species or genus level using BLAST. The results of the UM were consistent with bacterial identities as validated with other identification methods; cultural, API 20E, API 20NE, or genera and species specific PCR primers. Bacteria identified in the study, covered 34 species distributed among 24 genera. The UM should allow the identification of species, genus, novel species or genera, variations within species, and detection of bacterial DNA in otherwise sterile samples such as blood, cerebrospinal fluid, manufactured products, medical supplies, cosmetics, and other samples. Applicability of the method to identifying members of bacterial communities is discussed. The approach itself can be applied to other taxa such as protists and nematodes.

The oral microbiota: general overview, taxonomy, and nucleic acid techniques

Application of nucleic acid technology to the analysis of the bacterial diversity in the oral cavity in conditions of health and disease has not only confirmed the findings from early culture studies but also significantly expanded the list of oral inhabitants and candidate pathogens associated with the major oral diseases. Over 800 bacterial distinct species-level taxa have been detected in the oral cavity and recent studies using high-throughput technology suggest that the breadth of bacterial diversity can be much larger. This chapter provides an overview of the diversity and taxonomy of oral bacteria. Emphasis is also given on nucleic acid technologies that have been widely used for the study of the oral microbiota.

Total bacterial counts on oral mucosa after using a commercial saliva substitute in patients undergoing hematopoietic cell transplantation

PURPOSE

The commercial saliva substitute Oralbalance has been reported to alleviate symptoms of postradiotherapy xerostomia in head and neck cancer patients. Oralbalance may also be effective for xerostomia in patients undergoing hematopoietic cell transplantation (HCT) with high-dose chemotherapy and total-body irradiation. However, HCT patients are in a severely compromised condition, and saliva substitute must not promote infection. We reported previously that Oralbalance has antimicrobial effects against microbial species detected during HCT in vitro. This study was performed to determine the in vivo effects of Oralbalance on oral mucosal total bacterial counts in patients undergoing HCT.

METHODS

A total of 18 neutropenic patients undergoing HCT were enrolled in this study. Before and after 1 week of Oralbalance use, bacterial samples were obtained from patients by wiping an area of varphi1 cm on the buccal mucosa with sterilized cotton swabs. Total bacterial counts of the obtained samples were examined by quantitative polymerase chain reaction amplification of the bacterial 16S ribosomal RNA gene. As controls, bacterial samples were also obtained from ten healthy subjects, and total bacterial counts were examined.

RESULTS

No significant increase in bacterial count was observed with use of Oralbalance. None of the patients showed bacterial counts above the range found in healthy controls after using Oralbalance.

CONCLUSIONS

In neutropenic patients undergoing HCT, Oralbalance did not increase the total counts of oral mucosal bacteria beyond the range found in healthy controls. Oral care using Oralbalance may alleviate the symptoms induced by hyposalivation without promoting infection.

Bacterial diversity in persistent periapical lesions on root-filled teeth

BACKGROUND

The purpose of this study was to analyze the bacterial diversity in persistent apical lesions on root-filled teeth by using culture-independent molecular methods.

DESIGN

Twenty surgically removed apical lesions from therapy-resistant teeth were examined for the presence of bacterial DNA using PCR targeting the 16s ribosomal RNA gene, followed by cloning and sequencing.

RESULTS

Bacterial DNA was detected in 17 of the 20 samples (85%). A total of 236 clones were analyzed. Seven different bacterial phyla were represented and a total of 75 different bacterial taxa were identified; 36% of the species have not yet been cultivated. Commonly detected bacterial species included Fusobacterium spp., Prevotella spp., Tannerella forsythia, Porphyromonas endodontalis, Treponema denticola, Bacteroidetes spp., Peptostreptococcus spp., and Streptococcus spp.

CONCLUSIONS

A wide range of bacteria was identified in periapical lesions on therapy-resistant teeth. These bacteria may contribute in the etiology of periapical infection and impede healing of these lesions.

Rapid and simple detection of eight major periodontal pathogens by the loop-mediated isothermal amplification method

Loop-mediated isothermal amplification (LAMP) was applied to develop a rapid and simple detection system for eight periodontal pathogens: Aggregatibacter (Actinobacillus) actinomycetemcomitans, Campylobacter rectus, Eikenella corrodens, Fusobacterium nucleatum, Porphyromonas gingivalis, Prevotella intermedia, Treponema denticola and Tannerella forsythia. Primers were designed from the 16S ribosomal RNA gene for each pathogen, and the LAMP amplified the targets specifically and efficiently under isothermal condition at 64 degrees C. To simplify the manipulation of LAMP examination, boiled cells and intact cells suspended in phosphate-buffered saline (PBS) were tested as templates besides extracted DNA template. The detection limits were 1-10 cells per tube using extracted DNA template. However, LAMP methods using boiled cells and intact cells required 10-100 and 100-1000 cells per tube, respectively. LAMPs for A. actinomycetemcomitans, P. gingivalis and P. intermedia were then applied to clinical plaque samples, and the method demonstrated equal or higher sensitivity compared with the conventional real-time PCR method. These findings suggest the usefulness of the LAMP method for the rapid and simple microbiological diagnosis of periodontitis, and the possibility of LAMP examination without the DNA extraction step.

Indigenous Microflora and Innate Immunity of the Head and Neck

The normal flora of the head and neck exists in a delicate balance within tightly regulated ecologic niches, counterbalanced by a highly efficient innate immune system of the host. Invasion by the normal oral flora is rare when mucosal defenses remain intact. An understanding of the indigenous microflora and the innate mucosal defense mechanisms is necessary for an appropriate evaluation of infections and therapies in this area.

Toluidine blue-mediated photoinactivation of periodontal pathogens from supragingival plaques

This study aimed to assess the effect of toluidine blue (TB)-mediated photodynamic inactivation of periodontal pathogens (PP) from periodontopathic patients. Photodynamic therapy (PDT) was carried out using TB and 635 nm laser light irradiation. The bactericidal effect was evaluated, and important PDT parameters including light intensity, energy dose, and TB concentration were determined. Our findings suggest that TB-mediated lethal photosensitization of PP in vivo is possible. However, to obtain ideal bactericidal effect, higher doses of light and photosensitizer should be required in treatment in vivo than their planktonic counterparts. The best therapeutic effect was observed in treatment by 1 mg/ml TB combined with 12 J/cm(2) at 159 mW/cm(2) light irradiation. Moreover, because of the considerable interindividual differences of bacterial populations, TB-mediated PDT might not be equally effective among periodontopathic patients, and further studies on improvement of this therapeutic modality is needed.

Septicemia due to Solobacterium moorei in a patient with multiple myeloma

We report a case of bacteremia caused by Solobacterium moorei, an anaerobic, non-sporulated Gram-positive bacillus in a patient with a multiple myeloma. The source of infection was presumably related to multiple dento-alveolar abscesses. This is the first recovery of S. moorei from blood cultures.

Detection of novel oral species and phylotypes in symptomatic endodontic infections including abscesses

This study was undertaken to investigate the occurrence of several uncultivated phylotypes and newly named bacterial species in symptomatic endodontic infections. Samples taken from cases clinically diagnosed as acute periradicular abscesses or acute periradicular periodontitis were surveyed for the presence of 12 taxa by means of a 16S rRNA-gene-based nested or hemi-nested PCR assay. The most prevalent of the target taxa were Dialister invisus, Olsenella uli, Granulicatella adiacens, and Synergistes clones BA121 and E3_33. Findings revealed that novel phylotypes and newly named species can take part in the microbiota associated with symptomatic endodontic infections and a pathogenetic role is suspected.

Uncultivated phylotypes and newly named species associated with primary and persistent endodontic infections

Endodontic infections have been traditionally studied by culture methods, but recent reports showing that over 50% of the oral microbiota is still uncultivable (B. J. Paster et al., J. Bacteriol. 183:3770-3783, 2001) raise the possibility that many endodontic pathogens remain unknown. This study intended to investigate the prevalence of several uncultivated oral phylotypes, as well as newly named species in primary or persistent endodontic infections associated with chronic periradicular diseases. Samples were taken from the root canals of 21 untreated teeth and 22 root-filled teeth, all of them with radiographic evidence of periradicular bone destruction. Genomic DNA was isolated directly from each sample, and 16S rRNA gene-based nested or heminested PCR assays were used to determine the presence of 13 species or phylotypes of bacteria. Species-specific primers had already been validated in the literature or were developed by aligning closely related 16S rRNA gene sequences. Species specificity for each primer pair was confirmed by running PCRs against a panel of several oral bacteria and by sequencing DNA from representative positive samples. All species or phylotypes were detected in at least one case of primary infections. The most prevalent species or phylotypes found in primary infections were Dialister invisus (81%), Synergistes oral clone BA121 (33%), and Olsenella uli (33%). Of the target bacteria, only these three species were detected in persistent infections. Detection of uncultivated phylotypes and newly named species in infected root canals suggests that there are previously unrecognized bacteria that may play a role in the pathogenesis of periradicular diseases.

Bacterial diversity in necrotizing ulcerative periodontitis in HIV-positive subjects

BACKGROUND

Necrotizing ulcerative periodontitis (NUP) is a painful and potentially debilitating affliction that affects about 2% to 6% of HIV-positive subjects. NUP may be caused by specific microorganisms that are presently unknown or by microbial species not usually thought to cause periodontal infections. The purpose of this study was to define the bacterial species associated with NUP in HIV-positive patients.

METHODS

16S rRNA bacterial genes of DNA isolated from subgingival plaque of 8 HIV-positive subjects with NUP were amplified by polymerase chain reaction (PCR) and cloned into Escherichia coli. The sequences of cloned inserts were used to determine species identity or closest relatives by comparison with known sequences. The microbial profiles in subgingival plaque of subjects with NUP, chronic periodontitis, and periodontal health were compared using a battery of over 200 oligonucleotide probes in a PCR-based, reverse-capture, checkerboard DNA-DNA hybridization assay.

RESULTS

Sequence analysis of over 400 clones revealed 108 species; 65 were "uncultivable" phylotypes, of which 26 were novel to NUP subjects. Species or phylotypes most commonly detected were Bulleidia extructa, Dialister, Fusobacterium, Selenomonas, Peptostreptococcus, Veillonella, and the phylum TM7. Based on sequence analysis and checkerboard analysis, NUP did not possess the classical periodontal pathogens such as Porphyromonas gingivalis. Otherwise, the microbial profiles of NUP and periodontitis had many similarities. The microbial profiles of subgingival plaque from periodontally healthy subjects were different and less complex in comparison to the profiles of both disease groups.

CONCLUSIONS

Certain species appear to be associated with health and periodontal diseases. The putative pathogens associated with periodontal disease in HIV-negative subjects are not associated with NUP in HIV-positive subjects.

Direct detection of Nocardia spp. in clinical samples by a rapid molecular method

We developed a 16S PCR-based assay for the rapid detection of Nocardia spp. directly from human clinical samples. The applicability of the assay was confirmed by using 18 samples from patients with nocardiosis as diagnosed by conventional cultures and 20 clinical samples from patients with confirmed tuberculosis used as negative controls.

Molecular analysis of human oral microbiota

OBJECTIVES

The application of molecular, mainly 16S ribosomal RNA (rRNA)-based approaches enables researchers to bypass the cultivation step and has proven its usefulness in studying the microbial composition in a variety of ecosystems, including the human oral cavity. In this mini-review, we describe the impact of these culture-independent approaches on our knowledge of the ecology of the human oral cavity and provide directions for future studies that should emphasize the role of specific strains, species and groups of microbes in periodontal disease.

MATERIALS AND METHODS

Recent findings are summarized to elucidate the relationship between periodontal disease and human oral microbiota, including as-yet-to-be-cultured organisms.

RESULTS

The real-time polymerase chain reaction (PCR) method was developed to detect and quantify periodontopathic bacteria, such as Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythensis (formerly Bacteroides forsythus) and Treponema denticola. The checkerboard DNA-DNA hybridization technique allowed enumeration of large numbers of species in very large numbers of samples. 16S rRNA gene clone library analysis revealed the diversity of human oral microbiota and the existence of as-yet-to-be-cultured organisms that are presumed periodontal pathogens. In addition, terminal restriction fragment length polymorphism (T-RFLP) analysis was applied for assessment of diversity of human oral microbiota.

CONCLUSION

Culture-independent approaches are useful for studying the microbial ecology in the human oral cavity and should be useful in the future to elucidate the etiology of periodontal disease.

Detection of periodontal pathogenPorphyromonas gingivalisby loop-mediated isothermal amplification method

A method for nucleic acid amplification, loop-mediated isothermal amplification (LAMP) was employed to develop a rapid and simple detection system for periodontal pathogen, Porphyromonas gingivalis. A set of six primers was designed by targeting the 16S ribosomal RNA gene. By the detection system, target DNA was amplified and visualized on agarose gel within 30 min under isothermal condition at 64 degrees C with a detection limit of 20 cells of P. gingivalis. Without gel electrophoresis, the LAMP amplicon was directly visualized in the reaction tube by addition of SYBR Green I for a naked-eye inspection. The LAMP reaction was also assessed by white turbidity of magnesium pyrophosphate (a by-product of LAMP) in the tube. Detection limits of these naked-eye inspections were 20 cells and 200 cells, respectively. Although false-positive DNA amplification was observed from more than 10(7) cells of Porphyromonas endodontalis, no amplification was observed in other five related oral pathogens. Further, quantitative detection of P. gingivalis was accomplished by a real-time monitoring of the LAMP reaction using SYBR Green I with linearity over a range of 10(2)-10(6) cells. The real-time LAMP was then applied to clinical samples of dental plaque and demonstrated almost identical results to the conventional real-time PCR with an advantage of rapidity. These findings indicate the potential usefulness of LAMP for detecting and quantifying P. gingivalis, especially in its rapidity and simplicity.

Quantitative real-time PCR using TaqMan and SYBR Green for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, tetQ gene and total bacteria

Accurate quantification of bacterial species in dental plaque is needed for microbiological diagnosis of periodontal diseases. The present study was designed to assess the sensitivity, specificity and quantitativity of the real-time PCR using the GeneAmp Sequence Detection System with two fluorescence chemistries. TaqMan probe with reporter and quencher dye, and SYBR Green dye were used for sources of the fluorescence. Primers and probes were designed for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia and total bacteria based on the nucleotide sequences of the respective 16S ribosomal RNA genes. Since spread of antibiotic resistance genes is one of the crucial problems in periodontal therapy, quantitative detection of tetQ gene, which confers resistance to tetracycline, was included in the examination. The detection of P. gingivalis, P. intermedia and A. actinomycetemcomitans was linear over a range of 10-10(7) cells (10-10(7) copies for tetQ gene), while the quantitative range for total bacteria was 10(2)-10(7) cells. Species-specific amplifications were observed for the three periodontal bacteria, and there was no significant difference between the TaqMan and SYBR Green chemistry in their specificity, quantitativity and sensitivity. The SYBR Green assay, which was simpler than TaqMan assay in its manipulations, was applied to the clinical plaque samples. The plaque samples were obtained from eight patients (eight periodontal pockets) before and 1 week after the local drug delivery of minocycline. Although the number of P. gingivalis, P. intermedia and A. actinomycetemcomitans markedly decreased after the antibiotic therapy in most cases, higher copy numbers of the tetQ gene were detectable. The real-time PCR demonstrated sufficient sensitivity, specificity and quantitativity to be a powerful tool for microbiological examination in periodontal disease, and the quantitative monitoring of antibiotic resistance gene accompanied with the antibiotic therapy should be included in the examination.

Diagnostic testing as a supportive measure of treatment strategy

The bacteriological tests in periodontology have been available to clinicians since the end of the 1980s. Despite the vast and varied information that they contribute to the literature on this topic, some controversy has arisen with regard to the use of these tests. Clinicians faced with a multitude of clinical forms of periodontal disease in their patients can count on laboratory examinations to help them in the therapeutic process. These biological examinations can offer help in five areas of application: support in diagnosis and prognosis, verification of the efficiency of the treatment, indication of the correct antibiotic therapy and choice of the most appropriate molecules. The clinician's needs determine the type of bacteriological technical analysis used: bacterial culture or genetic identification using the molecular techniques. Each technique has its advantages and disadvantages. Knowing these limits allows the most appropriate choice to be made, depending on the clinical situation. The richness of information provided by culture in the anti-microbial susceptibility test and the non-targeted aspect of this test make this technique very interesting for the diagnosis of periodontitis. However, the targeted aspect of molecular techniques (PCR), their excellent sensibility and their rapidity make them prevail, particularly in the control and maintenance phases. Furthermore, despite the constant development of bacterial identification techniques, these examinations are little used by dental surgeons as these examinations are little known. They are also difficult to interpret and generate heavy additional costs.

Application of denaturing gradient gel electrophoresis (DGGE) to the analysis of microbial communities of subgingival plaque

OBJECTIVES

Denaturing gradient gel electrophoresis (DGGE) was applied to the microbiologic examination of subgingival plaque.

MATERIALS AND METHODS

The PCR primers were designed from conserved nucleotide sequences on 16S ribosomal RNA gene (16SrDNA) with GC rich clamp at the 5'-end. Polymerase chain reaction (PCR) was performed using the primers and genomic DNAs of typical periodontal bacteria. The generated 16SrDNA fragments were separated by denaturing gel.

RESULTS

Although the sizes of the amplified DNA fragments were almost the same among the species, 16SrDNAs of the periodontal bacteria were distinguished according to their specific sequences. The microflora of clinical plaque samples were profiled by the PCR-DGGE method, and the dominant 16SrDNA bands were cloned and sequenced. Simultaneously, Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis and Prevotella intermedia were detected by an ordinary PCR method. In the deep periodontal pockets, the bacterial community structures were complicated and P. gingivalis was the most dominant species, whereas the DGGE profiles were simple and Streptococcus or Neisseria species were dominant in the shallow pockets. The species-specific PCR method revealed the presence of A. actinomycetemcomitans, P. gingivalis and P. intermedia in the clinical samples. However, corresponding bands were not always observed in the DGGE profiles, indicating a lower sensitivity of the DGGE method.

CONCLUSION

Although the DGGE method may have a lower sensitivity than the ordinary PCR methods, it could visualize the bacterial qualitative compositions and reveal the major species of the plaque. The DGGE analysis and following sequencing may have the potential to be a promising bacterial examination procedure in periodontal diseases.

Genetic relatedness and phenotypic characteristics of Treponema associated with human periodontal tissues and ruminant foot disease

Treponema have been implicated recently in the pathogenesis of digital dermatitis (DD) and contagious ovine digital dermatitis (CODD) that are infectious diseases of bovine and ovine foot tissues, respectively. Previous analyses of treponemal 16S rDNA sequences, PCR-amplified directly from DD or CODD lesions, have suggested relatedness of animal Treponema to some human oral Treponema species isolated from periodontal tissues. In this study a range of adhesion and virulence-related properties of three animal Treponema isolates have been compared with representative human oral strains of Treponema denticola and Treponema vincentii. In adhesion assays using biotinylated treponemal cells, T. denticola cells bound in consistently higher numbers to fibronectin, laminin, collagen type I, gelatin, keratin and lactoferrin than did T. vincentii or animal Treponema isolates. However, animal DD strains adhered to fibrinogen at equivalent or greater levels than T. denticola. All Treponema strains bound to the amino-terminal heparin I/fibrin I domain of fibronectin. 16S rDNA sequence analyses placed ovine strain UB1090 and bovine strain UB1467 within a cluster that was phylogenetically related to T. vincentii, while ovine strain UB1466 appeared more closely related to T. denticola. These observations correlated with phenotypic properties. Thus, T. denticola ATCC 35405, GM-1, and Treponema UB1466 had similar outer-membrane protein profiles, produced chymotrypsin-like protease (CTLP), trypsin-like protease and high levels of proline iminopeptidase, and co-aggregated with human oral bacteria Porphyromonas gingivalis and Streptococcus crista. Conversely, T. vincentii ATCC 35580, D2A-2, and animal strains UB1090 and UB1467 did not express CTLP or trypsin-like protease and did not co-aggregate with P. gingivalis or S. crista. Taken collectively, these results suggest that human oral-related Treponema have broad host specificity and that similar control or preventive strategies might be developed for human and animal Treponema-associated infections.

Anaerobic cocci populating the deep tissues of chronic wounds impair cellular wound healing responses in vitro

BACKGROUND

Anaerobic cocci are estimated to be present in the deep tissues of over 50% of chronic skin wounds. While the part they play in the chronicity of these wounds is uninvestigated, anaerobic cocci have previously been shown to be involved in other chronic inflammatory human conditions.

METHODS

In this study the anaerobic microflora of the deep tissues of 18 patients with refractory chronic venous leg ulcers (mean age 80.3 years; mean duration > 24 months) was characterized using strict anaerobic culture conditions. The effect of the anaerobic organisms isolated from these tissues on extracellular matrix (ECM) proteolysis and cellular wound healing responses was studied using in vitro models.

RESULTS

Anaerobic organisms were present in the deep tissues of 14 of 18 wounds and were principally Peptostreptococcus spp. The effects of three Peptostreptococcus spp. isolated from these wounds (P. magnus, P. vaginalis and P. asaccharolyticus) on cellular wound healing responses were compared with those of two pathogenic organisms also isolated from these wounds (Pseudomonas aeruginosa and Citrobacter diversus). While the direct ECM proteolytic activity exhibited by the Peptostreptococcus spp. was limited, they did significantly inhibit both fibroblast and keratinocyte proliferation, but only at high concentrations. However, at lower concentrations peptostreptococcal supernatants profoundly inhibited keratinocyte wound repopulation and endothelial tubule formation. The magnitude of these effects varied between strains and they were distinct from those demonstrated by Pseudomonas aeruginosa and Citrobacter diversus.

CONCLUSIONS

These studies confirm the importance of anaerobic organisms in chronic wounds and demonstrate an indirect, strain-specific mechanism by which these microorganisms may play a part in mediating the chronicity of these wounds.

Detection of novel oral phylotypes associated with periodontitis

A phylogenetic approach based on 16S rRNA (rDNA) has been recently applied to investigate the diversity of cultivable and uncultivable species in the human oral cavity without cultivation. In a previous study [Sakamoto et al. (2000) Microbiol. Immunol. 44, 643-652], we identified a number of novel oral phylotypes, representing as yet uncultured organisms. The purpose of this study was to design specific PCR primers for five phylotypes AP12, AP21, AP24, AP50, and RP58, which are deeply branched particularly in the phylogenetic tree, and determine the prevalence of these phylotypes in 45 patients with periodontitis and 18 healthy subjects. The specificity of each primer was validated by the sequence analysis of PCR products obtained from saliva and subgingival plaque samples. Among phylotypes tested, phylotype AP24, which is closely related to oral clone DA014 reported previously [Paster et al. (2001) J. Bacteriol. 183, 3770-3783], was significantly associated with saliva and subgingival plaque samples from patients with periodontitis (P<0.01), but the difference was not statistically significant in the presence of other phylotypes. These data suggest that phylotype AP24 may play an important role in periodontal disease.

PCR-ELISA I: Application to simultaneous analysis of mixed bacterial samples composed of intestinal species

Sixteen oligonucleotide identification probes, designed in this study or adapted from literature, were tested for a PCR-ELISA application to simultaneously detect under standardised conditions selected intestinal bacteria, lactobacilli and bifidobacteria. The level of specificity obtained with most of the probes fulfilled the set criteria. The lack of efficiency of PCR performed with the primers, proposed to be specific for the entire eubacteria domain, and compromises made in hybridisation conditions due to simultaneous usage of multiple probes reduced the sensitivity of the PCR-ELISA test. The method was, however, found to be suitable for detecting predominant members of the intestinal flora. Applicability of the PCR-ELISA test could be further widened using primers with a more restricted specificity in the PCR step, as was demonstrated for the detection of Bifidobacterium with genus-specific primers. Advantages of the PCR-ELISA method include convenient performance and the possibility to test rapidly large amounts of samples with a multitude of probes.

Sulfate-reducing bacteria in relation with other potential periodontal pathogens

BACKGROUND, AIMS

Oral sulfate-reducing bacteria are involved in several clinical categories of periodontitis. The aim of this cross-sectional study was to compare the presence of sulfate-reducing bacteria (SRB) with other putative pathogens including spirochetes, Actinobacillus actinomycetemcomitans, Bacteroides forsythus, Porphyromonas gingivalis, and Treponema denticola in periodontal lesions.

METHOD

Periodontal SRB were detected by enrichment culture and compared with a microscopic spirochete count (n=168). Species-specific oligonucleotide probes directed against the 16S rRNA were employed to determine the presence of A. actinomycetemcomitans, P. gingivalis, B. forsythus, and T. denticola (n=55).

RESULTS

A significant positive correlation was observed between the presence of SRB and the proportions of spirochetes in subgingival plaque, although the 2 bacterial groups also occurred separately. SRB tended to be negatively correlated with the presence of A. actinomycetemcomitans. In contrast, all pockets with SRB harbored either T. denticola, or both T. denticola and B. forsythus (12/14) before therapy. Interestingly, the combination of SRB with P. gingivalis occurred in 32% of the periodontal pockets before treatment. After initial periodontal therapy, the prevalence of this combination was reduced to 2% of the sites, and to 25% of the sites in recall patients.

CONCLUSION

The presence of SRB was positively correlated with T. denticola, B. forsythus, and P. gingivalis in periodontal lesions. These suspected pathogens form a complex strongly associated with destructive periodontitis.

Use of molecular techniques to study microbial diversity in the skin: chronic wounds reevaluated

The skin is colonized by an array of microorganisms which form its natural microflora. Disruption to the normal barrier function of the skin (due to trauma or disease) may result in invasion of the dermis by opportunistic bacteria. To date, these organisms, which may contribute to the chronicity of skin wounds, have been analyzed solely by culture methods. It is increasingly realized that standard culture methods of analysis do not accurately reflect the full diversity of complex microflora. This review discusses the limitations of traditional culture approaches and reviews recent advances in molecular microbiological techniques which facilitate a more comprehensive characterization of the microflora within clinical samples. The currently available technologies and techniques are described, as is their use in clinical practice and their potential for diagnostic screening. Chronic venous ulceration of the lower limbs is an important skin disorder in which the microflora invading the dermal tissues contribute to the observed delayed healing. Using chronic leg ulcers as a working example, we show how strict culture and molecular microbiological techniques may be employed, for the first time in combination, to definitively characterize the invading microbial community of the dermis.

Bacterial diversity in human subgingival plaque

The purpose of this study was to determine the bacterial diversity in the human subgingival plaque by using culture-independent molecular methods as part of an ongoing effort to obtain full 16S rRNA sequences for all cultivable and not-yet-cultivated species of human oral bacteria. Subgingival plaque was analyzed from healthy subjects and subjects with refractory periodontitis, adult periodontitis, human immunodeficiency virus periodontitis, and acute necrotizing ulcerative gingivitis. 16S ribosomal DNA (rDNA) bacterial genes from DNA isolated from subgingival plaque samples were PCR amplified with all-bacterial or selective primers and cloned into Escherichia coli. The sequences of cloned 16S rDNA inserts were used to determine species identity or closest relatives by comparison with sequences of known species. A total of 2,522 clones were analyzed. Nearly complete sequences of approximately 1,500 bases were obtained for putative new species. About 60% of the clones fell into 132 known species, 70 of which were identified from multiple subjects. About 40% of the clones were novel phylotypes. Of the 215 novel phylotypes, 75 were identified from multiple subjects. Known putative periodontal pathogens such as Porphyromonas gingivalis, Bacteroides forsythus, and Treponema denticola were identified from multiple subjects, but typically as a minor component of the plaque as seen in cultivable studies. Several phylotypes fell into two recently described phyla previously associated with extreme natural environments, for which there are no cultivable species. A number of species or phylotypes were found only in subjects with disease, and a few were found only in healthy subjects. The organisms identified only from diseased sites deserve further study as potential pathogens. Based on the sequence data in this study, the predominant subgingival microbial community consisted of 347 species or phylotypes that fall into 9 bacterial phyla. Based on the 347 species seen in our sample of 2,522 clones, we estimate that there are 68 additional unseen species, for a total estimate of 415 species in the subgingival plaque. When organisms found on other oral surfaces such as the cheek, tongue, and teeth are added to this number, the best estimate of the total species diversity in the oral cavity is approximately 500 species, as previously proposed.