Root canal microbiota of teeth with chronic apical periodontitis

Frequency and levels of candidate endodontic pathogens in acute apical abscesses as compared to asymptomatic apical periodontitis

Introduction

Acute apical abscess is caused by bacteria that leave the infected dental root canal to invade the periodontal tissues. Most species occurring in abscesses are also found in asymptomatic infections; therefore, the possibility exists that not only the presence of certain species but also their specific counts influence the appearance of symptoms. This molecular study compared the frequency and levels of several candidate endodontic pathogens in teeth with acute apical abscesses and asymptomatic apical periodontitis.

Methods

Samples were taken from the root canals of teeth with asymptomatic apical periodontitis (n = 73) and by aspiration of purulent exudate from acute abscesses (n = 55). DNA was extracted from samples and bacterial identifications were performed by a closed-ended semi-quantitative reverse-capture checkerboard approach targeting 40 bacterial species/phylotypes.

Results

Bacterial DNA was detected in all cases. In abscesses, the most prevalent taxa were Fusobacterium nucleatum (60%), Porphyromonas endodontalis (53%), Parvimonas micra (51%), and Streptococcus species (45%). The most frequently detected taxa in asymptomatic teeth were P. endodontalis (63%), Dialister invisus (58%), Olsenella uli (56%), and F. nucleatum (51%). None of the targeted taxa were significantly associated with abscesses when only mere presence was evaluated (p>0.05). However, semi-quantitative data demonstrated that P. endodontalis, Prevotella baroniae, Treponema denticola and Streptococcus species were significantly more frequent at levels >10⁵ in abscesses than in asymptomatic cases (p<0.05).

Conclusion

None of the target species/phylotypes were associated with abscesses in terms of frequency. However, some taxa were significantly found in higher levels in abscesses. Presence of a potentially virulent pathogen in high counts may increase the collective pathogenicity of the bacterial community and give rise to symptoms.

Discuss the role of microorganisms in the aetiology and pathogenesis of periapical disease

The literature indicates that microorganisms have a critical role in the aetiology and pathogenesis of apical periodontitis. The advancement in microbiological study methods has allowed for the identification of newer species associated with the disease process. At our current understanding, however, the exact roles of specific microorganisms in apical periodontitis are not fully understood but the poly-microbial aetiology of the disease appears to be supported by the literature. The endodontic microbiota is comprised of a subset of microbiota present in the oral cavity, consisting of predominantly anaerobic bacterial species, some fungal and viral species. The pathogenesis of apical periodontitis is essentially the result of a complex interplay between bacterial and host factors, giving rise to a range of presentations depending on the balance of the interaction. The role of endodontic microbiota in the initiation and persistence of apical periodontitis means that the mainstay of endodontic treatment is the elimination of such bacteria. A challenge to the resolution of apical periodontitis after treatment lies in the inadequacy of treatment protocol in completely eradicating the pathogenic species and the inherent ability of certain species to survive the treatment. This issue should be the focus of future research as we continually search for more predictable treatment methods of achieving the resolution of apical periodontitis.

Oxidative Stress in the Local and Systemic Events of Apical Periodontitis

Oxidative stress is involved in the pathogenesis of a variety of inflammatory disorders. Apical periodontitis (AP) usually results in the formation of an osteolytic apical lesion (AL) caused by the immune response to endodontic infection. Reactive oxygen species (ROS) produced by phagocytic cells in response to bacterial challenge represent an important host defense mechanism, but disturbed redox balance results in tissue injury. This mini review focuses on the role of oxidative stress in the local and associated systemic events in chronic apical periodontitis. During endodontic infection, ligation of Toll-like receptors (TLRs) on phagocytes' surface triggers activation, phagocytosis, synthesis of ROS, activation of humoral and cellular responses, and production of inflammatory mediators, such as, cytokines and matrix metalloproteinases (MMPs). The increment in ROS perturbs the normal redox balance and shifts cells into a state of oxidative stress. ROS induce molecular damage and disturbed redox signaling, that result in the loss of bone homeostasis, increased pro-inflammatory mediators, and MMP overexpression and activation, leading to apical tissue breakdown. On the other hand, oxidative stress has been strongly involved in the pathogenesis of atherosclerosis, where a chronic inflammatory process develops in the arterial wall. Chronic AP is associated with an increased risk of cardiovascular diseases (CVD) and especially atherogenesis. The potential mechanisms linking these diseases are also discussed.

Simplified Method of Detection of Dialister invisus and Olsenella uli in Oral Cavity Samples by Polymerase Chain Reaction

Aims and Objectives:

The oral microbial flora is highly complex and diverse with obligate anaerobic bacteria as the predominant component. Most of these are not yet cultivated/difficult to cultivate due to technical limitations. In this study, we aim to detect two novel oral bacterial species Dialister invisus and Olsenella uli by simplified and economical procedure of polymerase chain reaction (PCR) and study their association with primary and persistent endodontic infections.

Material and Methods:

The study involved 60 patients that included 30 patients of primary endodontic infections and 30 with persistent endodontic infections. The sample collection from the root canal was performed by universally accepted protocol by using sterile paper points. The deoxyribonucleic acid (DNA) extraction was done, followed by PCR with species specific primers. We made several changes to the protocol mentioned by original authors. We adopted a one-step protocol for amplification of bacterial DNA, omitting the 16SrDNA amplification step with universal primers.

Results:

It was seen that 7 (23.3 %) samples in primary endodontic infection group and 24 (80 %) samples in persistent endodontic infection group were positive for D. invisus. On the other hand, 11 (36.6 %) patients of primary endodontic infection showed positivity for O. uli in comparison to 9 (30 %) of persistent endodontic infection.

Conclusion:

The results from the present study showed efficient amplification of both O. uli and D. invisus in a single-step PCR. Hence, we conclude that the modified protocol used here with taq polymerase enzyme offers a faster and cheaper alternative to nested PCR without compromising the quality of amplification process.

Bactericidal Effect of Different Anti-Microbial Agents on Fusobacterium Nucleatum Biofilm

INTRODUCTION

The root canal anatomy of the teeth is very complex. Complete debridement of the root canals is a challenge and is very important for the success of the root canal treatment. Hence, this study was done to find an effective irrigant which can be used during root canal treatment.

OBJECTIVE

The bactericidal effect of a potential root canal irrigant was compared with two commonly used root canal irrigants against monoculture biofilm of a commercially available isolate of Fusobacterium nucleatum.

METHODS

A monoculture biofilm of Fusobacterium nucleatum was grown on glass slides. The glass slides containing the biofilm were immersed in centrifuge tubes containing 5% sodium hypochlorite, 2% Chlorhexidine, 6% turmeric solution, 9% turmeric solution and distilled water for a time span of one minute. A wire loop was used to scrape off the biofilms onto sterile brain heart infusion agar plates. This was further subjected to an incubation period of 96 hours at 37° C. Colony forming units were quantified by statistical analysis and results were obtained.

RESULTS

The anti-bacterial activity of 6% and 9% turmeric solution was statistically significant against Fusobacterium nucleatum when compared to 2% Chlorhexidine and 5% sodium hypochlorite.

CONCLUSION

In endodontic treatment, turmeric solution may be considered as an effective irrigant.

Evaluation of Bacteriological Profile in the Apical Root Segment of the Patients with Primary Apical Periodontitis

INTRODUCTION

Apical periodontitis usually results from bacterial accumulation and contamination occurring in the root-canal system, and extending beyond the apical foramen to involve the periapical tissues. Literature has a paucity of the studies that stress on the division and analysis of the pulp canal segments. The reason for this disparity might be the technique used for collecting the samples from the pulp canals. Hence, we carried out the present study to evaluate the microbial flora in the apical part of the roots with necrotic pulp canals.

MATERIALS AND METHODS

The present study included the assessment of 40 freshly extracted teeth that had necrotized pulpal tissue along with the presence of periapical periodontal lesions. Removal of the soft tissue lesions attached to the root portion of the teeth along with apical periodontal lesions was done with the help of scalpel blade, after rinsing them with a sterile solution of saline. Thorough cleaning of the root surfaces was done with hydrogen peroxide followed by rapid disinfection with the help of sodium hypochlorite at varying concentrations. Sectioning of the root portion of all the specimens with the help of a disk was done perpendicular to the long axis of the teeth at a distance of roughly 5 to 6 mm from the teeth's apicalmost point. Cryotubes were used for transferring the specimens of apical portions containing 1 mL of buffer and were subjected to immediate frozen processing at a temperature of -20°C. A 10 K-type file was used for the initial collection of the samples followed by subsequent incubation of the files and paper pints in the incubation cabinet. Subsequent deoxyribonucleic acid (DNA) extraction from the samples was done following the procedure described by Siqueira et al. Paster et al's modification of the reverse-capture checkerboard assay was used in the present study. Semiquantitative data were used for overcoming the difficulties arising due to obtaining the counts of the polymerase chain reaction (PCR)-based analysis of specimens.

RESULTS

A positive result for the 16S ribosomal ribonucleic acid (rRNA) gene primer was observed only in two examined specimens of all the samples of the apical portion of the root canals in the present study. Negative result was shown by all the control group specimens, which were sterile samples. Presence of bacteria was confirmed by PCR in 38 out of 40 examined specimens. Amount of bacterial taxa, out of these 24 samples, ranged up to 6. Pseudoramibacter alactolyticus, Porphyromonas endodontalis, Dialister oral species, Bacteroidetes species, Streptococcus species, Olsenella uli, Synergistes species, Fusobacterium nucleatum, Parvimonas micra, Treponema denticola, and Filifactor alocis were the specific species detected. Bacteroidetes species was the only species that were detected at levels at or above 10⁵. Heavy bacterial infections were noticed in more than 45% of the cases at the periradicular part of the root canals.

CONCLUSION

Microbial flora of the apical segment of the root with necrotized pulp tissue comprises a vast variety of pathogenic bacteria.

CLINICAL SIGNIFICANCE

For better prognosis of the treatment of such cases, adequate knowledge of the microbial flora of the root, especially the apical portion is necessary.

Effects of inactivated Enterococcus faecalis on the proliferation and osteogenic induction of osteoblasts

The present study aimed to evaluate the effects of Enterococcus faecalis, inactivated by the common intracanal irrigants sodium hypochlorite (NaOCl) and chlorhexidine (CHX), on osteoblasts. E. faecalis was inactivated with 2% CHX or 5.25% NaOCl. Subsequently, the Cell Counting kit-8 assay was used to examine the effects of CHX- and NaOCl-inactivated E. faecalis on MC3T3-E1 osteoblast cell proliferation. Alizarin red staining was used to determine osteoblast mineralization, and osteogenic induction was quantified by determining the optical density of the dye solution. The relative expression levels of osteogenic genes were detected after 1, 4, 7 and 14 days of stimulation with CHX- and NaOCl-inactivated E. faecalis by reverse transcription-quantitative polymerase chain reaction. The results indicated that CHX-inactivated E. faecalis inhibited osteoblast proliferation, whereas NaOCl-inactivated E. faecalis did not suppress cell proliferation. Various concentrations of CHX- and NaOCl-inactivated E. faecalis induced different degrees of osteoblast mineralization. The expression levels of osteocalcin, alkaline phosphatase, runt-related transcription factor 2, osteopontin and osterix were upregulated in cells following stimulation with 10⁷ and 10⁵ colony-forming units/ml E. faecalis inactivated by CHX and NaOCl; the upregulation of these osteogenic genes occurred at various time points. In conclusion, the present study demonstrated that CHX-inactivated E. faecalis exerted more of an effect on osteoblast proliferation compared with NaOCl-inactivated E. faecalis. In addition, CHX- and NaOCl-inactivated E. faecalis was able to induce mineralization and relevant osteogenic gene expression in osteoblast cells.

Bacteria in the apical root canals of teeth with apical periodontitis

BACKGROUND/PURPOSE

Bacteria in the tooth root canal may cause apical periodontitis. This study examined the bacterial species present in the apical root canal of teeth with apical periodontitis. Antibiotic sensitivity tests were performed to evaluate whether these identified bacterial species were susceptible to specific kinds of antibiotics.

METHODS

Selective media plating and biochemical tests were used first to detect the bacterial species in samples taken from the apical portion of root canals of 62 teeth with apical periodontitis. The isolated bacterial species were further confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

RESULTS

We found concomitant presence of two (32 teeth) or three species (18 teeth) of bacteria in 50 (80.6%) out of 62 tested teeth. However, only 34 bacterial species were identified. Of a total of 118 bacterial isolates (83 anaerobes and 35 aerobes), Prophyromonas endodontalis was detected in 10; Bacteroides, Dialister invisus or Fusobacterium nucleatum in 9; Treponema denticola or Enterococcus faecalis in 8; Peptostreptococcus or Olsenella uli in 6; and Veillonella in 5 teeth. The other 25 bacterial species were detected in fewer than five teeth. Approximately 80-95% of bacterial isolates of anaerobes were sensitive to ampicillin/sulbactam (Unasyn), amoxicillin/clavulanate (Augmentin), cefoxitin, and clindamycin. For E. faecalis, 85-90% of bacterial isolates were sensitive to gentamicin and linezolid.

CONCLUSION

Root canal infections are usually caused by a mixture of two or three species of bacteria. Specific kinds of antibiotic can be selected to control these bacterial infections after antibiotic sensitivity testing.

Bacterial invasion into radicular dentine-an in vitro study

OBJECTIVES

We wanted to investigate differences in invasiveness into radicular dentinal tubules by monocultured and co-cultured bacteria frequently found in infected root canals.

METHODS

Fifty-one human roots were incubated for 8 weeks with monocultured Streptococcus gordonii ATCC 10558, Streptococcus sanguinis ATCC 10556, and with five capnophiles/anaerobes as well as with capnophiles/anaerobes co-cultured with a streptococcal species. Thereafter, bacterial samples were cultured from the inner, middle, and outer third of the root dentine of longitudinally broken teeth (n = 5). In addition, scanning electron microscopy (SEM) images were obtained.

RESULTS

Single gram-positive species were able to penetrate into the middle and outer third of the root dentine. Fusobacterium nucleatum ATCC 25586 was not found in any of the dentine specimens. Prevotella intermedia ATCC 25611 and Porphyromonas gingivalis ATCC 33277 were found in the inner and middle third. The bacterial load of streptococci was higher in all thirds in co-cultures compared to single infections. In co-cultures with streptococci, Actinomyces oris ATCC 43146 was found in the outer third in 9/10 samples, whereas P. intermedia ATCC 25611 was not detectable inside dentine. Co-culture with S. sanguinis ATCC 10556 enabled F. nucleatum ATCC 25586 to invade dentine; SEM images showed that F. nucleatum ATCC 25586 had a swollen shape.

CONCLUSIONS

Invasiveness of bacteria into dentinal tubules is species-specific and may change depending on culturing as a single species or co-culturing with other bacteria.

CLINICAL RELEVANCE

Oral streptococci may promote or inhibit invasion of capnophiles/anaerobes into radicular dentine.

Antibacterial Efficacy of Neem (Azadirachta indica) Extract against Enterococcus faecalis: An in vitro Study

INTRODUCTION

Debridement and disinfection of the root canal is a crucial step in the success of endodontic treatment. Several antimicrobial agents alone or in combination are used to achieve this. The objective of this in vitro study was to assess the antimicrobial efficacy of neem (Azadirachta indica) extract against Enterococcus faecalis.

MATERIALS AND METHODS

Neem leaf extract, 2% chlorhexidine, 3% sodium hypochlorite were used to assess the antimicrobial efficiency. Agar well diffusion test was used to study the antimicrobial efficacy with saline as control. The zone of inhibition was recorded, tabulated, and analyzed statistically with the help of IBM Statistical Package for the Social Sciences statistics version 20 using analysis of variance test.

RESULTS

All the three medicaments showed well-defined and comparable zones of inhibition around their respective wells. All values were significantly higher than the control group. Analysis of variance showed significant difference between zone diameters of chlorhexidine, neem leaf extract, and 3% sodium hypochlorite against E. faecalis (p < 0.05).

CONCLUSION

From the present study, it can be concluded that neem leaf extract shows comparable zones of inhibition with that of chlorhexidine and sodium hypochlorite.

CLINICAL SIGNIFICANCE

Neem leaf extract has significant antimicrobial activity against E. faecalis and thus opens the perspectives for the use of neem extract as an intracanal medication.

Microbiome in the Apical Root Canal System of Teeth with Post-Treatment Apical Periodontitis

INTRODUCTION

Bacteria present in the apical root canal system are directly involved with the pathogenesis of post-treatment apical periodontitis. This study used a next-generation sequencing approach to identify the bacterial taxa occurring in cryopulverized apical root samples from root canal-treated teeth with post-treatment disease.

METHODS

Apical root specimens obtained during periradicular surgery of ten adequately treated teeth with persistent apical periodontitis were cryogenically ground. DNA was extracted from the powder and the microbiome was characterized on the basis of the V4 hypervariable region of the 16S rRNA gene by using paired-end sequencing on Illumina MiSeq device.

RESULTS

All samples were positive for the presence of bacterial DNA. Bacterial taxa were mapped to 11 phyla and 103 genera composed by 538 distinct operational taxonomic units (OTUs) at 3% of dissimilarity. Over 85% of the sequences belonged to 4 phyla: Proteobacteria, Firmicutes, Fusobacteria and Actinobacteria. In general, these 4 phyla accounted for approximately 80% of the distinct OTUs found in the apical root samples. Proteobacteria was the most abundant phylum in 6/10 samples. Fourteen genera had representatives identified in all cases. Overall, the genera Fusobacterium and Pseudomonas were the most dominant. Enterococcus was found in 4 cases, always in relatively low abundance.

CONCLUSIONS

This study showed a highly complex bacterial community in the apical root canal system of adequately treated teeth with persistent apical periodontitis. This suggests that this disease is characterized by multispecies bacterial communities and has a heterogeneous etiology, because the community composition largely varied from case to case.

Culture-based identification of pigmented Porphyromonas and Prevotella species in primary endodontic infections

Background. The most common species isolated from primary endodontic infections are black-pigmented bacteria. These species are implicated in apical abscess formation due to their proteolytic activity and are fastidious in nature. Therefore, the present study was carried out to evaluate the presence and identification of various pigmented Porphyromonas and Prevotella species in the infected root canal through culture-based techniques.

Methods. Thirty-one patients with primary endodontic infections were selected. Using sterile paper points, samples were collected from the root canals after access opening and prior to obturation, which were cultured using blood and kanamycin blood agar. Subsequently, biochemical test was used to identify the species and the results were analyzed using percentage comparison analysis, McNemar and chi-squared tests, Wilcoxon match pair test and paired t-test.

Results. Out of 31 samples 26 were positive for black-pigmented organisms; the predominantly isolated species were Prevotella followed by Porphyromonas. In Porphyromonas only P. gingivalis was isolated. One of the interesting features was isolation of P. gingivalis through culture, which is otherwise very difficult to isolate through culture.

Conclusion. The presence of Prevotella and Porphyromonas species suggests that a significant role is played by these organisms in the pathogenesis of endodontic infections.

Microorganisms in periradicular tissues: Do they exist? A perennial controversy

There is no greater association between the basic science and the practice of endodontics than that of microbiology. One of the strongest factors contributing to the controversies often encountered in the endodontic field is the lack of understanding that the disease processes of the pulp and periradicular tissues generally have a microbiological etiology. The vast majority of diseases of dental pulp and periradicular tissues are associated with microorganisms. After the microbial invasion of these tissues, the host responds with both nonspecific inflammatory responses and with specific immunologic responses to encounter such infections. The aim of this study is to fill the gaps in our knowledge regarding the role of microorganisms in endodontics and to discuss in depth whether their presence in periradicular lesions is a myth or a reality. An electronic search was carried out on PubMed database (custom range of almost 50 years) and Google using specific keywords and phrases. Inclusion and exclusion criteria were specified and around 50 articles were found suitable for inclusion. Full text of all the articles was retrieved and studied. Appropriate data were extracted and pooled and finally synthesized. It is important to understand the close relationship between the presence of microorganisms and endodontic disease process to develop an effective rationale for treatment.

Short-chain Fatty Acids in Infected Root Canals of Teeth with Apical Periodontitis before and after Treatment

INTRODUCTION

Short-chain fatty acids (SCFAs) are bacterial metabolic end products that may function as virulence factors. This study evaluated the occurrence of SCFAs in infected root canals before and after treatment.

METHODS

Samples were taken from root canals of teeth with apical periodontitis before (S1) and after (S2) chemomechanical preparation with either NaOCl or chlorhexidine as the irrigant and then after interappointment medication with calcium hydroxide (S3). High-performance liquid chromatography was used for detection of SCFAs. Selected bacterial taxa that are recognized producers of the target SCFAs were identified by real-time polymerase chain reaction.

RESULTS

Butyric acid was the most common fatty acid in S1, followed by propionic acid. Both molecules were also found in S2 and S3 from both NaOCl and chlorhexidine groups. Lactic acid was not present in detectable levels in S1, but it occurred in 1 postinstrumentation sample and in 9 samples taken after calcium hydroxide medication. Of the target taxa, Fusobacterium nucleatum was the most prevalent in S1 (76%), followed by members of the Actinobacteria phylum (71%), Streptococcus species (59%), and Parvimonas micra (53%). Gram-positive taxa, especially streptococci, were the most prevalent bacteria in S2 and S3. SCFA detection was matched with the respective potential producer species in most cases.

CONCLUSIONS

This first report of SCFAs in infected root canals suggests that these molecules may play a role in the pathogenesis of apical periodontitis. Significance of persistence of SCFAs after treatment and its effects on the long-term outcome await elucidation.

The oral microbiome diversity and its relation to human diseases

As one of the most clinically relevant human habitats, the human mouth is colonized by a set of microorganisms, including bacteria, archaea, fungi, and viruses. Increasing evidence has supported that these microbiota contribute to the two commonest oral diseases of man (dental caries and periodontal diseases), presenting significant risk factors to human health conditions, such as tumor, diabetes mellitus, cardiovascular diseases, bacteremia, preterm birth, and low birth weight in infants. It is widely accepted that oral microorganisms cause diseases mainly by a synergistic or cooperative way, and the interspecies interactions within the oral community play a crucial role in determining whether oral microbiota elicit diseases or not. Since a comprehensive understanding of the complex interspecies interactions within a community needs the knowledge of its endogenous residents, a plenty of research have been carried out to explore the oral microbial diversity. In this review, we focus on the recent progress in this field, including the oral microbiome composition and its association with human diseases.

Host-derived biomarkers in gingival crevicular fluid for complementary diagnosis of apical periodontitis

Apical periodontitis (AP) develops as a result of the host’s immune inflammatory response to pulpal infection of the dental root canals that leads to the generation of an apical lesion of endodontic origin (ALEO) and potentially to systemic metabolic alterations. Misdiagnosed ALEO is not infrequent due to the lack of diagnostic tools to differentiate apical lesions of different natures. Despite the conservative endodontic treatment shows a high success rate, there are refractory cases that can not be identified early enough during follow up. This evidences the need to develop complementary diagnostic tools, such as oral fluid biomarker analysis. Gingival crevicular fluid (GCF) is a serum transudate that becomes an exudate under inflammatory conditions, carrying molecules from local periodontal tissues and general circulation than can be harvested non-invasively. We aimed to review the available literature analyzing GCF composition in AP patients to evaluate whether GCF has any potential for complementary diagnosis. To the date, only few studies addressing changes of GCF components in AP are available. Most studies support GCF modifications in specific components in AP-affected teeth, suggesting that it might reflect periapical inflammation. GCF has potential for diagnostic tool, treatment follow-up and eventually to assess systemic comprise.

In vitro regulation of CCL3 and CXCL12 by bacterial by-products is dependent on site of origin of human oral fibroblasts

INTRODUCTION

Production of chemokines by tissue resident cells is one of the main mechanisms involved in the inflammatory infiltrate formation during inflammation. The specific ability of fibroblasts from different oral tissues such as gingiva, periodontal ligament, and dental pulp from permanent and deciduous teeth in producing the chemokines CCL3 and CXCL12 under stimulation by bacterial products commonly found in endodontic infections was investigated.

METHODS

Cultures of fibroblasts from gingiva and periodontal ligament as well as from dental pulp from permanent and deciduous teeth were established by using an explant technique and stimulated with increasing concentrations of Escherichia coli lipopolysaccharide (EcLPS) and Enterococcus faecalis lipoteichoic acid (EfLTA) for 1, 6, and 24 hours. Supernatants were tested for CCL3 and CXCL12 by enzyme-linked immunosorbent assay.

RESULTS

In general, CCL3 production was induced by EcLPS in the 4 fibroblast subtypes and by EfLTA in fibroblasts from gingiva and periodontal ligament. Constitutive CXCL12 synthesis decreased in all fibroblast subtypes especially under stimulation with EcLPS. Fibroblast from permanent deciduous teeth was the cell type presenting the most expressive reduction in CXCL12 release by both stimuli. On the basis of computational matching of CXCL12 mRNA with the microRNAs miR-141 and miR-200a, their expression was also investigated. Although detected in the fibroblasts, these molecules remained unaltered by bacterial by-product stimulation.

CONCLUSIONS

EcLPS and EfLTA induced the production of CCL3 and unbalanced the synthesis of CXCL12 in a manner dependent on the specific tissue origin of fibroblasts.

Microarray analysis of microbiota of gingival lesions in noma patients

Noma (cancrum oris) is a gangrenous disease of unknown etiology affecting the maxillo-facial region of young children in extremely limited resource countries. In an attempt to better understand the microbiological events occurring during this disease, we used phylogenetic and low-density microarrays targeting the 16S rRNA gene to characterize the gingival flora of acute noma and acute necrotizing gingivitis (ANG) lesions, and compared them to healthy control subjects of the same geographical and social background. Our observations raise doubts about Fusobacterium necrophorum, a previously suspected causative agent of noma, as this species was not associated with noma lesions. Various oral pathogens were more abundant in noma lesions, notably Atopobium spp., Prevotella intermedia, Peptostreptococcus spp., Streptococcus pyogenes and Streptococcus anginosus. On the other hand, pathogens associated with periodontal diseases such as Aggregatibacter actinomycetemcomitans, Capnocytophaga spp., Porphyromonas spp. and Fusobacteriales were more abundant in healthy controls. Importantly, the overall loss of bacterial diversity observed in noma samples as well as its homology to that of ANG microbiota supports the hypothesis that ANG might be the immediate step preceding noma.

Microbiology and treatment of acute apical abscesses

Acute apical abscess is the most common form of dental abscess and is caused by infection of the root canal of the tooth. It is usually localized intraorally, but in some cases the apical abscess may spread and result in severe complications or even mortality. The reasons why dental root canal infections can become symptomatic and evolve to severe spreading and sometimes life-threatening abscesses remain elusive. Studies using culture and advanced molecular microbiology methods for microbial identification in apical abscesses have demonstrated a multispecies community conspicuously dominated by anaerobic bacteria. Species/phylotypes commonly found in these infections belong to the genera Fusobacterium, Parvimonas, Prevotella, Porphyromonas, Dialister, Streptococcus, and Treponema. Advances in DNA sequencing technologies and computational biology have substantially enhanced the knowledge of the microbiota associated with acute apical abscesses and shed some light on the etiopathogeny of this disease. Species richness and abundance and the resulting network of interactions among community members may affect the collective pathogenicity and contribute to the development of acute infections. Disease modifiers, including transient or permanent host-related factors, may also influence the development and severity of acute abscesses. This review focuses on the current evidence about the etiology and treatment of acute apical abscesses and how the process is influenced by host-related factors and proposes future directions in research, diagnosis, and therapeutic approaches to deal with this disease.

Susceptibility of as-yet-uncultivated and difficult-to-culture bacteria to chemomechanical procedures

INTRODUCTION

A significant portion of the bacteria taking part of the microbiome associated with apical periodontitis still remain to be cultivated and phenotypically characterized. This molecular study evaluated the prevalence of selected as-yet-uncultivated and difficult-to-culture bacterial taxa in infected root canals and their susceptibility to chemomechanical procedures.

METHODS

Root canals of single-rooted teeth with apical periodontitis were prepared using rotary nickel-titanium instruments and 2.5% sodium hypochlorite as the irrigant. DNA extracts from samples taken before (S1) and after (S2) chemomechanical preparation were surveyed for the presence of 7 as-yet-uncultivated phylotypes and 1 difficult-to-culture species using end-point polymerase chain reaction. Samples were also subjected to quantitative analysis of total bacteria and levels of the 2 most prevalent taxa.

RESULTS

Bacteroidaceae sp. HOT-272 (24%) and Fretibacterium fastidiosum (20%) were the most prevalent taxa in S1. Their mean counts in S1 were 8.25 × 10(3) and 2.13 × 10(3) rRNA gene copies, corresponding to 0.18% and 0.55% of the total bacteria. Chemomechanical debridement promoted a highly statistically significant reduction in total bacterial counts (P < .001), but 64% of the canals were still positive for bacterial presence. Of the target taxa, only Bacteroidaceae sp. HOT-272 and F. fastidiosum were detected in S2 (each one in 1 sample). The reduction in counts of both taxa was also highly significant (P < .001).

CONCLUSIONS

Findings confirmed that several as-yet-uncultivated and difficult-to-grow bacterial taxa can participate in the microbiome associated with apical periodontitis. Two of them were found in relatively high prevalence but rarely as a dominant species. Chemomechanical procedures were highly effective in completely eliminating these taxa or at least substantially reducing their numbers.

As-yet-uncultivated oral bacteria: breadth and association with oral and extra-oral diseases

It has been shown that 40–60% of the bacteria found in different healthy and diseased oral sites still remain to be grown in vitro, phenotypically characterized, and formally named as species. The possibility exists that these as-yet-uncultivated bacteria play important ecological roles in oral bacterial communities and may participate in the pathogenesis of several oral infectious diseases. There is also a potential for these as-yet-uncultivated oral bacteria to take part in extra-oral infections. For a comprehensive characterization of physiological and pathogenic properties as well as antimicrobial susceptibility of individual bacterial species, strains need to be grown in pure culture. Advances in culturing techniques have allowed the cultivation of several oral bacterial taxa only previously known by a 16S rRNA gene sequence signature, and novel species have been proposed. There is a growing need for developing improved methods to cultivate and characterize the as-yet-uncultivated portion of the oral microbiome so as to unravel its role in health and disease.

Gram-positive anaerobic cocci--commensals and opportunistic pathogens

Among the Gram-positive anaerobic bacteria associated with clinical infections, the Gram-positive anaerobic cocci (GPAC) are the most prominent and account for approximately 25-30% of all isolated anaerobic bacteria from clinical specimens. Still, routine culture and identification of these slowly growing anaerobes to the species level has been limited in the diagnostic laboratory, mainly due to the requirement of prolonged incubation times and time-consuming phenotypic identification. In addition, GPAC are mostly isolated from polymicrobial infections with known pathogens and therefore their relevance has often been overlooked. However, through improvements in diagnostic and in particular molecular techniques, the isolation and identification of individual genera and species of GPAC associated with specific infections have been enhanced. Furthermore, the taxonomy of GPAC has undergone considerable changes over the years, mainly due to the development of molecular identification methods. Existing species have been renamed and novel species have been added, resulting in changes of the nomenclature. As the abundance and significance of GPAC in clinical infections grow, knowledge of virulence factors and antibiotic resistance patterns of different species becomes more important. The present review describes recent advances of GPAC and what is known of the biology and pathogenic effects of Anaerococcus, Finegoldia, Parvimonas, Peptoniphilus and Peptostreptococcus, the most important GPAC genera isolated from human infections.

Efficacy of Er,Cr:YSGG laser with endodontical radial firing tips on the outcome of endodontic treatment: blind randomized controlled clinical trial with six-month evaluation

Clinical reports stating the efficacy of novel root canal disinfection protocols are an important focus in endodontic research. This blind randomized clinical trial assessed the clinical efficacy of the erbium, chromium:yttrium-scandium-gallium-garnet (Er,Cr:YSGG) laser radial firing tips (RFT) versus the concomitant use of 3 % sodium hypochlorite and interim calcium hydroxide paste in necrotic teeth with chronic apical periodontitis. We hypothesized to find similar or improved bone healing in the laser-assisted endodontic treatment. Thirty-six anterior and premolar teeth were randomly assigned. In group 1, teeth were prepared with 3 % sodium hypochlorite for irrigation and calcium hydroxide as inter-appointment dressing; in group 2, teeth were prepared with saline solution and irradiated with Er,Cr:YSGG laser using RFT2 (140 μs, 37.5 mJ, 20 Hz) and RFT3 (140 μs, 62.5 mJ, 20 Hz) in the first and second appointment, respectively, four times each, moving at 2 mm s(-1) from apical to coronal. The primary outcome measure was changed in apical bone density at 6 months, using the periapical index (PAI) for blind radiographic evaluation. Twenty-nine patients were examined and subjected to statistical analysis, 12 in group 1 and 17 in group 2. There was one treatment failure in group 1. Both groups gave similar outcomes exhibiting statistically significant decreases in PAI scores.

Characterization of microbiota of root canal-treated teeth with posttreatment disease

This study evaluated the microbiota of root canals undergoing retreatment. The most prevalent taxa detected by checkerboard included Propionibacterium species, Fusobacterium nucleatum, streptococci, and Pseudoramibacter alactolyticus. Quantitative real-time PCR detected Enterococcus faecalis and streptococci in 38% and 41% of the cases, comprising 9.76% and 65.78% of the total bacterial counts, respectively. The findings call into question the status of E. faecalis as the main pathogen and suggest that other species can be candidate pathogens associated with persistent/secondary endodontic infections.

Microflora profiling of infected root canal before and after treatment using culture-independent methods

This study aimed to profile the microflora in infected root canals before and after root canal treatment using culture-independent methods. Six infected root canals in single-rooted teeth with periapical lesions from five subjects were included. Quantification of total bacteria was performed by real-time PCR with primers targeting 16S rRNA genes. PCR products with universal 16S rRNA gene primers were cloned and partially sequenced, and bacterial identification at the species level was performed by comparative analysis with the GenBank database. The concentration of extracted DNA before treatment was higher than that after root canal treatment, although the difference was not statistically significant. Sequence analysis revealed that oral bacteria such as Fusobacterium, Streptococcus, Olsenella, and Pseudoramibacter detected in cases before root canal treatment disappeared after treatment. These results suggest that the root canal microflora are distinct before and after root canal treatment, and that treatment changes the microflora in both quantity and quality.

Antibiotic effects on bacterial profile in osteonecrosis of the jaw

OBJECTIVE

Oral infection is considered to play a critical role in the pathogenesis of bisphosphonate-related osteonecrosis of the jaw (BRONJ), and antibiotic therapy has become a mainstay of BRONJ therapy. This study was aimed to investigate the effect of antibiotics on bacterial diversity in BRONJ tissues.

MATERIALS AND METHODS

The bacterial profile from soft tissues associated with the BRONJ lesion was determined using 16S rRNA-based denaturing gradient gel electrophoresis (DGGE) and sequencing. Twenty BRONJ subjects classified as stage 0-2 were enrolled in this study, and patient groups were divided into an antibiotic cohort (n=10) treated with systemic antibiotic and a non-antibiotic cohort (n=10) with no prior antibiotic therapy.

RESULTS

The DGGE fingerprints indicated no significant differences in bacterial diversity of BRONJ tissue samples. Patients on antibiotics had higher relative abundance of phylum Firmicutes with bacterial species, Streptococcus intermedius, Lactobacillus gasseri, Mogibacterium timidum, and Solobacterium moorei, whereas patients without antibiotics had greater amounts of Parvimonas micra and Streptococcus anginosus. Thirty percent of bacterial populations were uncultured (yet-to be cultured) phylotypes.

CONCLUSION

This study using limited sample size indicated that oral antibiotic therapy may have a limited efficacy on the bacterial population associated with BRONJ lesions.

Comparing the bacterial diversity of acute and chronic dental root canal infections

This study performed barcoded multiplex pyrosequencing with a 454 FLX instrument to compare the microbiota of dental root canal infections associated with acute (symptomatic) or chronic (asymptomatic) apical periodontitis. Analysis of samples from 9 acute abscesses and 8 chronic infections yielded partial 16S rRNA gene sequences that were taxonomically classified into 916 bacterial species-level operational taxonomic units (OTUs) (at 3% divergence) belonging to 67 genera and 13 phyla. The most abundant phyla in acute infections were Firmicutes (52%), Fusobacteria (17%) and Bacteroidetes (13%), while in chronic infections the dominant were Firmicutes (59%), Bacteroidetes (14%) and Actinobacteria (10%). Members of Fusobacteria were much more prevalent in acute (89%) than in chronic cases (50%). The most abundant/prevalent genera in acute infections were Fusobacterium and Parvimonas. Twenty genera were exclusively detected in acute infections and 18 in chronic infections. Only 18% (n = 165) of the OTUs at 3% divergence were shared by acute and chronic infections. Diversity and richness estimators revealed that acute infections were significantly more diverse than chronic infections. Although a high interindividual variation in bacterial communities was observed, many samples tended to group together according to the type of infection (acute or chronic). This study is one of the most comprehensive in-deep comparisons of the microbiota associated with acute and chronic dental root canal infections and highlights the role of diverse polymicrobial communities as the unit of pathogenicity in acute infections. The overall diversity of endodontic infections as revealed by the pyrosequencing technique was much higher than previously reported for endodontic infections.

Novel model for multispecies biofilms that uses rigid gas-permeable lenses

Oral biofilms comprise complex multispecies consortia aided by specific inter- and intraspecies interactions occurring among commensals and pathogenic bacterial species. Oral biofilms are primary initiating factors of periodontal disease, although complex multifactorial biological influences, including host cell responses, contribute to the individual outcome of the disease. To provide a system to study initial stages of interaction between oral biofilms and the host cells that contribute to the disease process, we developed a novel in vitro model system to grow biofilms on rigid gas-permeable contact lenses (RGPLs), which enable oxygen to permeate through the lens material. Bacterial species belonging to early- and late-colonizing groups were successfully established as single- or three-species biofilms, with each group comprising Streptococcus gordonii, Streptococcus oralis, and Streptococcus sanguinis; S. gordonii, Actinomyces naeslundii, and Fusobacterium nucleatum; or S. gordonii, F. nucleatum, and Porphyromonas gingivalis. Quantification of biofilm numbers by quantitative PCR (qPCR) revealed substantial differences in the magnitude of bacterial numbers in single-species and multispecies biofilms. We evaluated cell-permeable conventional nucleic acid stains acridine orange, hexidium iodide, and Hoechst 33258 and novel SYTO red, blue, and green fluorochromes for their effect on bacterial viability and fluorescence yield to allow visualization of the aggregates of individual bacterial species by confocal laser scanning microscopy (CLSM). Substantial differences in the quantity and distribution of the species in the multispecies biofilms were identified. The specific features of these biofilms may help us better understand the role of various bacteria in local challenge of oral tissues.

Metagenomic analysis of the uterine bacterial microbiota in healthy and metritic postpartum dairy cows

At present, many bacterial species are validly known as etiological agents of dairy cattle metritis, yet the vast uncultured fraction has received no attention so far. The purpose of this study was to use culture-independent methods to describe and compare the uterine bacterial composition in healthy and metritic postpartum Holstein dairy cows. Both group-specific 16S ribosomal DNA PCR-denaturing gradient gel electrophoresis (DGGE) and clone library sequencing of broad-range 16S ribosomal DNA PCR revealed differences in the bacterial communities comparing healthy and metritic cows. Bacterial diversity in healthy and metritic uteri was greater and more complex than described previously by traditional culture methods. Sequences were assigned to 5 major groups (Gammaproteobacteria, Firmicutes, Fusobacteria, Bacteroidetes, and Tenericutes) and to uncultured bacteria. Additionally, DGGE suggested the presence of Actinobacteria. Most clone sequences in the metritic status libraries were affiliated with the phylum Fusobacteria. Many components, especially from other phyla, have not previously been isolated from cases of metritis. In the clone libraries from the healthy status dairy cows, Gammaproteobacteria was the most prominent group and most sequences showed high identity with Mannheimia varigena, Pasteurella hemolytica, and members of the phylum Tenericutes. Our data showed that the uterine bacterial community in postpartum dairy cows differed considerably between healthy and metritic cows and described the occurrence of a previously unrecognized extent of this diversity in the bovine intrauterine microbiota.

Apical root canal microbiota as determined by reverse-capture checkerboard analysis of cryogenically ground root samples from teeth with apical periodontitis

INTRODUCTION

Bacteria located in the apical root canal system potentially participate in the pathogenesis of apical periodontitis. Detection and identification of apical bacteria can be compromised because of limitations in conventional sampling and identification procedures. This study identified several bacterial taxa in the apical and middle/coronal segments of primarily infected root canal system by using pulverized root segments and a culture-independent molecular method.

METHODS

Seventeen extracted teeth with attached apical periodontitis lesions were sectioned to obtain 2 root fragments (apical and middle/coronal segments). Root fragments were cryogenically ground, and DNA was extracted from samples. After multiple displacement amplification, DNA from samples was used as template in a reverse-capture checkerboard hybridization assay targeting 28 bacterial taxa.

RESULTS

Bacterial DNA was detected in all samples. The most prevalent taxa in the apical root canal system were Olsenella uli (76.5%), Prevotella baroniae (71%), Porphyromonas endodontalis (65%), Fusobacterium nucleatum (53%), and Tannerella forsythia (47%). O. uli, P. endodontalis, and Propionibacterium acnes were as frequently detected in apical samples as they were in middle/coronal samples. P. baroniae, T. forsythia, and F. nucleatum were found more frequently in the apical part of the canal as compared with matched coronal segments. Streptococcus species were more prevalent in middle/coronal samples. The median and mean of shared bacterial taxa between matched apical and middle/coronal segments were 27% and 41%, respectively.

CONCLUSIONS

Several candidate endodontic pathogens were very prevalent in the apical root canal system. The apical microbiota was usually complex and differed in species composition when compared with the microbiota of middle/coronal samples from the same tooth.

Analyzing endodontic infections by deep coverage pyrosequencing

Bacterial diversity in endodontic infections has not been sufficiently studied. The use of modern pyrosequencing technology should allow for more comprehensive analysis than traditional Sanger sequencing. This study investigated bacterial diversity in endodontic infections through taxonomic classification based on 16S rRNA gene sequences generated by 454 GS-FLX pyrosequencing and conventional Sanger capillary sequencing technologies. Sequencings were performed on 7 specimens from endodontic infections. On average, 47 vs. 28,590 sequences were obtained per sample for Sanger sequencing vs. pyrosequencing, representing a 600-fold difference in "depth-of-coverage". Based on Ribosomal Database Project (RDP II) Classifier analysis, pyrosequencing identified 179 bacterial genera in 13 phyla, which was significantly more than Sanger sequencing. The phylum Bacteroidetes was the most prevalent bacterial phylum. These results indicate that bacterial communities in endodontic infections are more diverse than previously demonstrated. In addition, deep-coverage pyrosequencing of the 16S rRNA gene revealed low-abundance micro-organisms with potential clinical implications.

Response of subgingival bacteria to smoking cessation

It has been demonstrated that smoking cessation alters the subgingival microbial profile; however, the response of individual bacteria within this ecosystem has not been well studied. The aim of this investigation, therefore, was to longitudinally examine the effect of smoking cessation on the prevalence and levels of selected subgingival bacteria using molecular approaches for bacterial identification and enumeration. Subgingival plaque was collected from 22 smokers at the baseline and 12 months following periodontal nonsurgical management and smoking cessation counseling. The prevalence and abundance of selected organisms were examined using nested PCR and multiplexed bead-based flow cytometry. Eleven subjects successfully quit smoking over 12 months (quitters), while 11 continued to smoke throughout (smokers). Smoking cessation led to a decrease in the prevalence of Porphyromonas endodontalis and Dialister pneumosintes at 12 months and in the levels of Parvimonas micra, Filifactor alocis, and Treponema denticola. Smoking cessation also led to an increase in the levels of Veillonella parvula. Following nonsurgical periodontal therapy and smoking cessation, the subgingival microbiome is recolonized by a greater number of health-associated species and there are a significantly lower prevalence and abundance of putative periodontal pathogens. The results indicate a critical role for smoking cessation counseling in periodontal therapy for smokers in order to effectively alter the subgingival microbiome.

Identification of bacteria enduring endodontic treatment procedures by a combined reverse transcriptase-polymerase chain reaction and reverse-capture checkerboard approach

INTRODUCTION

This study identified the bacterial taxa enduring endodontic treatment procedures by using a combined 16S ribosomal RNA-based reverse-transcriptase polymerase chain reaction (RT-PCR) and reverse-capture checkerboard hybridization approach.

METHODS

Samples were taken from infected canals of 15 teeth with apical periodontitis before treatment (S1), after chemomechanical preparation with NaOCl as the irrigant (S2), and after interappointment medication with a calcium hydroxide paste (S3). Bacterial presence was first screened by a DNA-based single PCR assay. RNA extracts were subjected to RT-PCR, and the resulting products were surveyed for the presence of 28 targeted taxa by using the checkerboard method.

RESULTS

Bacteria were found in all S1 samples. Detectable levels of bacterial ribosomal RNA, used as an indicator of viability, were observed in 60% of the cases after chemomechanical preparation and 53% after intracanal medication. The most prevalent taxa in S1 were Olsenella uli (67%), Pyramidobacter piscolens (60%), Streptococcus species (53%), and Bacteroidetes clone X083 (53%). Streptococcus species (47%), Fusobacterium nucleatum (40%), and O. uli (33%) prevailed in S2, whereas Streptococcus species (47%), Propionibacterium acnes (27%), and O. uli (27%) were the most frequent taxa in S3.

CONCLUSIONS

The present study with a combined molecular approach revealed that bacterial diversity was overall markedly reduced by treatment procedures. Although bacterial taxa more frequently identified in post-treatment samples emerge as potential risk factors for persistent disease, this remains to be determined by longitudinal studies.

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.

Prevalence of new candidate pathogens Prevotella baroniae, Prevotella multisaccharivorax and as-yet-uncultivated Bacteroidetes clone X083 in primary endodontic infections

INTRODUCTION

Culture-independent studies have revealed a broad spectrum of oral bacterial taxa that may be associated with disease. This study investigated the prevalence of three new candidate oral pathogens: Prevotella baroniae, Prevotella multisaccharivorax, and as-yet-uncultivated Bacteroidetes oral clone X083 in primary endodontic infections using a devised culture-independent approach.

METHODS

Genomic DNA was isolated from samples taken from 52 teeth with different forms of apical periodontitis and used as template in a taxon-specific 16S rRNA gene-based nested polymerase chain reaction assay to determine the prevalence of the 3 target taxa.

RESULTS

Bacteroidetes clone X083, P. baroniae, and P. multisaccharivorax were respectively detected in 81%, 43%, and 38% of the root canals of teeth associated with chronic apical periodontitis, in 60%, 40% and 40% of the canals of teeth with acute apical periodontitis, and in 14%, 24%, and 5% of the pus aspirates from acute apical abscesses. No targeted taxon was positively associated with abscesses or clinical symptoms. Overall, Bacteroidetes clone X083, P. baroniae, and P. multisaccharivorax were found in 50%, 35%, and 25% of the samples taken from primary endodontic infections, respectively.

CONCLUSIONS

Findings confirmed that the two newly named species and the uncultivated phylotype targeted in this study are associated with different forms of apical periodontitis, and a pathogenetic or at least an ecologic role is suspected.