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Anderson AC, Hellwig E, Vespermann R, Wittmer A, Schmid M, Karygianni L, Al-Ahmad A. Comprehensive analysis of secondary dental root canal infections: a combination of culture and culture-independent approaches reveals new insights. PLoS One 2012; 7:e49576. [PMID: 23152922 PMCID: PMC3495864 DOI: 10.1371/journal.pone.0049576] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/10/2012] [Indexed: 01/11/2023] Open
Abstract
Persistence of microorganisms or reinfections are the main reasons for failure of root canal therapy. Very few studies to date have included culture-independent methods to assess the microbiota, including non-cultivable microorganisms. The aim of this study was to combine culture methods with culture-independent cloning methods to analyze the microbial flora of root-filled teeth with periradicular lesions. Twenty-one samples from previously root-filled teeth were collected from patients with periradicular lesions. Microorganisms were cultivated, isolated and biochemically identified. In addition, ribosomal DNA of bacteria, fungi and archaea derived from the same samples was amplified and the PCR products were used to construct clone libraries. DNA of selected clones was sequenced and microbial species were identified, comparing the sequences with public databases. Microorganisms were found in 12 samples with culture-dependent and -independent methods combined. The number of bacterial species ranged from 1 to 12 in one sample. The majority of the 26 taxa belonged to the phylum Firmicutes (14 taxa), followed by Actinobacteria, Proteobacteria and Bacteroidetes. One sample was positive for fungi, and archaea could not be detected. The results obtained with both methods differed. The cloning technique detected several as-yet-uncultivated taxa. Using a combination of both methods 13 taxa were detected that had not been found in root-filled teeth so far. Enterococcus faecalis was only detected in two samples using culture methods. Combining the culture-dependent and –independent approaches revealed new candidate endodontic pathogens and a high diversity of the microbial flora in root-filled teeth with periradicular lesions. Both methods yielded differing results, emphasizing the benefit of combined methods for the detection of the actual microbial diversity in apical periodontitis.
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Affiliation(s)
- Annette Carola Anderson
- Department of Operative Dentistry and Periodontology, Albert-Ludwigs-University, Freiburg, Germany
| | - Elmar Hellwig
- Department of Operative Dentistry and Periodontology, Albert-Ludwigs-University, Freiburg, Germany
| | - Robin Vespermann
- Department of Operative Dentistry and Periodontology, Albert-Ludwigs-University, Freiburg, Germany
| | - Annette Wittmer
- Department of Hygiene and Microbiology, Albert-Ludwigs-University, Freiburg, Germany
| | - Michael Schmid
- Michael Schmid, Research Unit Microbe-Plant Interactions, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lamprini Karygianni
- Department of Operative Dentistry and Periodontology, Albert-Ludwigs-University, Freiburg, Germany
| | - Ali Al-Ahmad
- Department of Operative Dentistry and Periodontology, Albert-Ludwigs-University, Freiburg, Germany
- * E-mail:
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You M, Mo S, Watt RM, Leung WK. Prevalence and diversity of Synergistetes taxa in periodontal health and disease. J Periodontal Res 2012; 48:159-68. [PMID: 22881378 DOI: 10.1111/j.1600-0765.2012.01516.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2012] [Indexed: 11/28/2022]
Abstract
BACKGROUND AND OBJECTIVE Members of the phylum Synergistetes have previously been identified within periodontitis subgingival plaque and are considered putative periodontopathogens. This study compared the diversity of subginigval Synergistetes in a cohort of subjects with periodontitis (n = 10) vs. periodontitis-free controls (n = 10). MATERIAL AND METHODS Pooled subgingival plaque samples from all deep periodontal pockets or all sulci were collected from the periodontitis and periodontitis-free subjects, respectively. Bacterial 16S rRNA genes were PCR-amplified from purified subgingival plaque DNA using a Synergistetes 'selective' primer set. PCR products were cloned and sequenced to analyze the prevalence and diversity of Synergistetes operational taxonomic units (OTUs) present in plaque samples of both subject groups. RESULTS A total of 1030 non-chimeric 16S rRNA clones were obtained, of which 162 corresponded to members of the phylum Synergistetes. A significantly larger number of Synergistetes clones were obtained from periodontitis subgingival plaque than from periodontitis-free controls (25.4% vs. 5.9%, p < 0.001). All Synergistetes clones corresponded to cluster A oral Synergistetes, and fell into 31 OTUs (99% sequence identity cut-off). Twenty-nine Synergistetes OTUs were detected in the periodontitis group while eight were detected in the periodontitis-free group (p < 0.001). Five Synergistetes OTUs; including one OTU corresponding to the recently-characterized species Fretibacterium fastidiosum, were more prevalent in the periodontitis subjects (p < 0.05). CONCLUSION OTUs belonging to oral Synergistetes cluster A were more readily detectable and were more diverse in subgingival plaque from periodontitis subjects compared with periodontitis-free controls. Specific Synergistetes OTUs appear to be associated with periodontitis.
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Affiliation(s)
- M You
- Oral Diagnosis and Polyclinics, Prince Philip Dental Hospital, The University of Hong Kong, Hong Kong SAR, China
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Pushalkar S, Ji X, Li Y, Estilo C, Yegnanarayana R, Singh B, Li X, Saxena D. Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma. BMC Microbiol 2012; 12:144. [PMID: 22817758 PMCID: PMC3507910 DOI: 10.1186/1471-2180-12-144] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 07/20/2012] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Bacterial infections have been linked to malignancies due to their ability to induce chronic inflammation. We investigated the association of oral bacteria in oral squamous cell carcinoma (OSCC/tumor) tissues and compared with adjacent non-tumor mucosa sampled 5 cm distant from the same patient (n = 10). By using culture-independent 16S rRNA approaches, denaturing gradient gel electrophoresis (DGGE) and cloning and sequencing, we assessed the total bacterial diversity in these clinical samples. RESULTS DGGE fingerprints showed variations in the band intensity profiles within non-tumor and tumor tissues of the same patient and among the two groups. The clonal analysis indicated that from a total of 1200 sequences characterized, 80 bacterial species/phylotypes were detected representing six phyla, Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Actinobacteria and uncultivated TM7 in non-tumor and tumor libraries. In combined library, 12 classes, 16 order, 26 families and 40 genera were observed. Bacterial species, Streptococcus sp. oral taxon 058, Peptostreptococcus stomatis, Streptococcus salivarius, Streptococcus gordonii, Gemella haemolysans, Gemella morbillorum, Johnsonella ignava and Streptococcus parasanguinis I were highly associated with tumor site where as Granulicatella adiacens was prevalent at non-tumor site. Streptococcus intermedius was present in 70% of both non-tumor and tumor sites. CONCLUSIONS The underlying changes in the bacterial diversity in the oral mucosal tissues from non-tumor and tumor sites of OSCC subjects indicated a shift in bacterial colonization. These most prevalent or unique bacterial species/phylotypes present in tumor tissues may be associated with OSCC and needs to be further investigated with a larger sample size.
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Affiliation(s)
- Smruti Pushalkar
- Department of Basic Sciences and Craniofacial Biology, New York University College of Dentistry, 345 E, 24th Street, Room 921B, New York, NY, 10010, USA
| | - Xiaojie Ji
- Department of Basic Sciences and Craniofacial Biology, New York University College of Dentistry, 345 E, 24th Street, Room 921B, New York, NY, 10010, USA
- Department of Chemical and Biological Sciences, Polytechnic Institute of NYU, New York, NY, USA
| | - Yihong Li
- Department of Basic Sciences and Craniofacial Biology, New York University College of Dentistry, 345 E, 24th Street, Room 921B, New York, NY, 10010, USA
| | - Cherry Estilo
- Dental Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ramanathan Yegnanarayana
- Laboratory of Epithelial Cancer Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Bhuvanesh Singh
- Laboratory of Epithelial Cancer Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Xin Li
- Department of Basic Sciences and Craniofacial Biology, New York University College of Dentistry, 345 E, 24th Street, Room 921B, New York, NY, 10010, USA
| | - Deepak Saxena
- Department of Basic Sciences and Craniofacial Biology, New York University College of Dentistry, 345 E, 24th Street, Room 921B, New York, NY, 10010, USA
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Characterization of microbiota of root canal-treated teeth with posttreatment disease. J Clin Microbiol 2012; 50:1721-4. [PMID: 22403423 DOI: 10.1128/jcm.00531-12] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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.
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Analysis of Symptomatic and Asymptomatic Primary Root Canal Infections in Adult Norwegian Patients. J Endod 2011; 37:1206-12. [DOI: 10.1016/j.joen.2011.05.026] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 05/20/2011] [Accepted: 05/21/2011] [Indexed: 02/01/2023]
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Ito IY, Junior FM, Paula-Silva FWG, Da Silva LAB, Leonardo MR, Nelson-Filho P. Microbial culture and checkerboard DNA-DNA hybridization assessment of bacteria in root canals of primary teeth pre- and post-endodontic therapy with a calcium hydroxide/chlorhexidine paste. Int J Paediatr Dent 2011; 21:353-60. [PMID: 21481034 DOI: 10.1111/j.1365-263x.2011.01131.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIM To investigate the root canal microbiota of primary teeth with apical periodontitis and the in vivo antimicrobial effects of a calcium hydroxide/chlorhexidine paste used as root canal dressing. DESIGN Baseline samples were collected from 30 root canals of primary teeth with apical periodontitis. Then, the root canals were filled with a calcium hydroxide paste containing 1% chlorhexidine for 14 days and the second bacteriologic samples were taken prior to root canal filling. Samples were submitted to microbiologic culture procedure to detect root canal bacteria and processed for checkerboard DNA-DNA hybridization. RESULTS Baseline microbial culture revealed high prevalence and cfu number of anaerobic, black-pigmented bacteroides, Streptococcus, and aerobic microorganisms. Following root canal dressing, the overall number of cfu was dramatically diminished compared to initial contamination (P <0.05), although prevalence did not change (P > 0.05). Of 35 probes used for checkerboard DNA-DNA hybridization, 31 (88.57%) were present at baseline, and following root canal dressing, the number of positive probes reduced to 13 (37.14%). Similarly, the number of bacterial cells diminished folowing application of calcium hydroxide/chlorhexidine root canal dressing (P = 0.006). CONCLUSION Apical periodontitis is caused by a polymicrobial infection, and a calcium hydroxide/chlorhexidine paste is effective in reducing the number of bacteria inside root canals when applied as a root canal dressing.
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Affiliation(s)
- Izabel Yoko Ito
- Department of Clinical Analysis, Toxicology and Bromatology, School of Pharmaceutical Sciences of Ribeirão Preto, Ribeirão Preto, SP, Brazil
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Chugal N, Wang JK, Wang R, He X, Kang M, Li J, Zhou X, Shi W, Lux R. Molecular characterization of the microbial flora residing at the apical portion of infected root canals of human teeth. J Endod 2011; 37:1359-64. [PMID: 21924182 DOI: 10.1016/j.joen.2011.06.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 06/07/2011] [Accepted: 06/23/2011] [Indexed: 11/18/2022]
Abstract
INTRODUCTION This study investigated the bacterial communities residing in the apical portion of human teeth with apical periodontitis in primary and secondary infections by using a culture-independent molecular biology approach. METHODS Root canal samples from the apical root segments of extracted teeth were collected from 18 teeth with necrotic pulp and 8 teeth with previous endodontic treatment. Samples were processed for amplification via polymerase chain reaction and separated with denaturing gradient gel electrophoresis. Selected bands were excised from the gel and sequenced for identification. RESULTS Comparable to previous studies of entire root canals, the apical bacterial communities in primary infections were significantly more diverse than in secondary infections (P = .0003). Interpatient and intrapatient comparisons exhibited similar variations in profiles. Different roots of the same teeth with secondary infections displayed low similarity in bacterial composition, whereas an equivalent sample collected from primary infection contained almost identical populations. Sequencing revealed a high prevalence of Fusobacteria, Actinomyces species, and oral Anaeroglobus geminatus in both types of infection. Many secondary infections contained Burkholderiales or Pseudomonas species, both of which represent opportunistic environmental pathogens. CONCLUSIONS Certain microorganisms exhibit similar prevalence in primary and secondary infection, indicating that they are likely not eradicated during endodontic treatment. The presence of Burkholderiales and Pseudomonas species underscores the problem of environmental contamination. Treatment appears to affect the various root canals of multirooted teeth differently, resulting in local changes of the microbiota.
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Affiliation(s)
- Nadia Chugal
- Section of Endodontics, UCLA School of Dentistry, UCLA School of Medicine, Los Angeles, California 90095-1668, USA
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60
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Ferreira DC, Rôças IN, Paiva SS, Carmo FL, Cavalcante FS, Rosado AS, Santos KR, Siqueira JF. Viral-bacterial associations in acute apical abscesses. ACTA ACUST UNITED AC 2011; 112:264-71. [DOI: 10.1016/j.tripleo.2011.01.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 01/21/2011] [Accepted: 01/22/2011] [Indexed: 01/30/2023]
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Rôças IN, Siqueira JF. In Vivo Antimicrobial Effects of Endodontic Treatment Procedures as Assessed by Molecular Microbiologic Techniques. J Endod 2011; 37:304-10. [DOI: 10.1016/j.joen.2010.11.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 11/06/2010] [Accepted: 11/06/2010] [Indexed: 01/28/2023]
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Comparison of the In Vivo Antimicrobial Effectiveness of Sodium Hypochlorite and Chlorhexidine Used as Root Canal Irrigants: A Molecular Microbiology Study. J Endod 2011; 37:143-50. [DOI: 10.1016/j.joen.2010.11.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2010] [Revised: 11/06/2010] [Accepted: 11/06/2010] [Indexed: 02/06/2023]
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Rôças IN, Alves FRF, Santos AL, Rosado AS, Siqueira JF. Apical root canal microbiota as determined by reverse-capture checkerboard analysis of cryogenically ground root samples from teeth with apical periodontitis. J Endod 2010; 36:1617-21. [PMID: 20850664 DOI: 10.1016/j.joen.2010.07.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 07/04/2010] [Accepted: 07/05/2010] [Indexed: 02/06/2023]
Abstract
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.
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Affiliation(s)
- Isabela N Rôças
- Department of Endodontics and Molecular Microbiology Laboratory, Estácio de Sá University, Rio de Janeiro, RJ, Brazil
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64
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Göker M, Held B, Lucas S, Nolan M, Yasawong M, Glavina Del Rio T, Tice H, Cheng JF, Bruce D, Detter JC, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Sikorski J, Pukall R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Olsenella uli type strain (VPI D76D-27C). Stand Genomic Sci 2010; 3:76-84. [PMID: 21304694 PMCID: PMC3035265 DOI: 10.4056/sigs.1082860] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Olsenella uli (Olsen et al. 1991) Dewhirst et al. 2001 is the type species of the genus Olsenella, which belongs to the actinobacterial family Coriobacteriaceae. The species is of interest because it is frequently isolated from dental plaque in periodontitis patients and can cause primary endodontic infection. The species is a Gram-positive, non-motile and non-sporulating bacterium. The strain described in this study was isolated from human gingival crevices. This is the first completed sequence of the genus Olsenella and the fifth sequence from a member of the family Coriobacteriaceae. The 2,051,896 bp long genome with its 1,795 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Yek EC, Cintan S, Topcuoglu N, Kulekci G, Halim İssever, Kantarci A. Efficacy of Amoxicillin and Metronidazole Combination for the Management of Generalized Aggressive Periodontitis. J Periodontol 2010; 81:964-74. [DOI: 10.1902/jop.2010.090522] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Abstract
Although fungi, archaea, and viruses contribute to the microbial diversity in endodontic infections, bacteria are the most common micro-organisms occurring in these infections. Datasets from culture and molecular studies, integrated here for the first time, showed that over 460 unique bacterial taxa belonging to 100 genera and 9 phyla have been identified in different types of endodontic infections. The phyla with the highest species richness were Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Diversity varies significantly according to the type of infection. Overall, more taxa have been disclosed by molecular studies than by culture. Many cultivable and as-yet-uncultivated phylotypes have emerged as candidate pathogens based on detection in several studies and/or high prevalence. Now that a comprehensive inventory of the endodontic microbial taxa has been established, future research should focus on the association with different disease conditions, functional roles in the community, and susceptibility to antimicrobial treatment procedures.
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Affiliation(s)
- J F Siqueira
- Department of Endodontics and Molecular Microbiology, Faculty of Dentistry, Estácio de Sá University, Av. Alfredo Baltazar da Silveira, 580/cobertura, Recreio, Rio de Janeiro, RJ, Brazil.
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Siqueira JF, Rôças IN. Distinctive features of the microbiota associated with different forms of apical periodontitis. J Oral Microbiol 2009; 1. [PMID: 21523208 PMCID: PMC3077003 DOI: 10.3402/jom.v1i0.2009] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/08/2009] [Accepted: 07/09/2009] [Indexed: 12/17/2022] Open
Abstract
Microorganisms infecting the dental root canal system play an unequivocal role as causative agents of apical periodontitis. Although fungi, archaea, and viruses have been found in association with some forms of apical periodontitis, bacteria are the main microbial etiologic agents of this disease. Bacteria colonizing the root canal are usually organized in communities similar to biofilm structures. Culture and molecular biology technologies have demonstrated that the endodontic bacterial communities vary in species richness and abundance depending on the different types of infection and different forms of apical periodontitis. This review paper highlights the distinctive features of the endodontic microbiota associated with diverse clinical conditions.
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Affiliation(s)
- José F Siqueira
- Department of Endodontics and Molecular Microbiology Laboratory, School of Dentistry, Estácio de Sá University, Rio de Janeiro, RJ, Brazil
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68
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Parahitiyawa NB, Scully C, Leung WK, Yam WC, Jin LJ, Samaranayake LP. Exploring the oral bacterial flora: current status and future directions. Oral Dis 2009; 16:136-45. [PMID: 19627515 DOI: 10.1111/j.1601-0825.2009.01607.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE The oral cavity forms an indispensable part of the human microbiome, for its unique and diverse microflora distributed within various niches. While majority of these organisms exhibit commensalism, shifts in bacterial community dynamics cause pathological changes within oral cavity and distant sites. The aim of this review was to appraise the current and emerging methods of detecting bacteria of the oral cavity paying particular attention to the cultivation independent methods. DESIGN Literature pertaining to cultivation based and cultivation independent methods of oral bacterial identification was reviewed. METHODS The specific advantages and disadvantages of cultivation based, microscopic, immunological and metagenomic identification methods were appraised. RESULTS Because of their fastidious and exacting growth requirements, cultivation based studies grossly underestimate the extent of bacterial diversity in these polymicrobial infections. Culture independent methods deemed more sensitive in identifying difficult to culture and novel bacterial species. CONCLUSION Apart from characterizing potentially novel bacterial species, the nucleic acid sequence data analyzed using various bioinformatics protocols have revealed that there are in excess of 700 bacterial species inhabiting the mouth. Moreover, the latest pyrosequencing based methods have further broadened the extent of bacterial diversity in oral niches.
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Affiliation(s)
- N B Parahitiyawa
- Oral Biosciences, Faculty of Dentistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
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Olsen I, Preza D, Aas JA, Paster BJ. Cultivated and not-yet-cultivated bacteria in oral biofilms. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2009. [DOI: 10.1080/08910600902907509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Ingar Olsen
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Dorita Preza
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Jørn A. Aas
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Bruce J. Paster
- Forsyth Institute, Boston, MA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
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Downes J, Vartoukian SR, Dewhirst FE, Izard J, Chen T, Yu WH, Sutcliffe IC, Wade WG. Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum 'Synergistetes' isolated from the human oral cavity. Int J Syst Evol Microbiol 2009; 59:972-80. [PMID: 19406777 DOI: 10.1099/ijs.0.000364-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Four strains of anaerobic, Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group distinct from any species with validly published names. 16S rRNA and 23S rRNA gene sequence analyses and DNA-DNA reassociation data revealed that the strains constituted a novel group within the phylum 'Synergistetes' and were most closely related to Jonquetella anthropi. Two libraries of randomly cloned DNA were prepared from strain W5455(T) and were sequenced to provide a genome survey as a resource for metagenomic studies. A new genus and novel species, Pyramidobacter piscolens gen. nov., sp. nov., is proposed to accommodate these strains. The genus Pyramidobacter comprises strains that are anaerobic, non-motile, asaccharolytic bacilli that produce acetic and isovaleric acids and minor to trace amounts of propionic, isobutyric, succinic and phenylacetic acids as end products of metabolism. P. piscolens gen. nov., sp. nov. produced hydrogen sulphide but was otherwise largely biochemically unreactive. Growth was stimulated by the addition of glycine to broth media. The G+C content of the DNA of the type strain was 59 mol%. The type strain of Pyramidobacter piscolens sp. nov. is W5455(T) (=DSM 21147(T)=CCUG 55836(T)).
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Affiliation(s)
- Julia Downes
- King's College London Dental Institute, Infection Research Group, London SE1 9RT, UK
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Handal T, Caugant DA, Olsen I, Sunde PT. Bacterial diversity in persistent periapical lesions on root-filled teeth. J Oral Microbiol 2009; 1. [PMID: 21523213 PMCID: PMC3077005 DOI: 10.3402/jom.v1i0.1946] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 03/19/2009] [Accepted: 05/05/2009] [Indexed: 11/14/2022] Open
Abstract
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.
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Affiliation(s)
- Trude Handal
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
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72
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Bacteria in the apical root canal of teeth with primary apical periodontitis. ACTA ACUST UNITED AC 2009; 107:721-6. [DOI: 10.1016/j.tripleo.2009.01.042] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2008] [Revised: 01/20/2009] [Accepted: 01/25/2009] [Indexed: 11/24/2022]
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73
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Diversity and morphology of members of the phylum "synergistetes" in periodontal health and disease. Appl Environ Microbiol 2009; 75:3777-86. [PMID: 19346352 DOI: 10.1128/aem.02763-08] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of the phylum "Synergistetes" have frequently been detected in the human oral cavity at sites of dental disease, but they have rarely been detected in studies of oral health. Only two oral "Synergistetes" taxa are cultivable. The aims of this study were to investigate the diversity of "Synergistetes" in the oral cavity, to establish whether "Synergistetes" taxa are more strongly associated with periodontitis than with oral health, and to visualize unculturable "Synergistetes" in situ. Sixty samples (saliva, dental plaque, and mucosal swabs) were collected from five subjects with periodontitis and five periodontally healthy controls. Using phylum-specific 16S rRNA gene primers, "Synergistetes" were identified by PCR, cloning, and sequencing of 48 clones per PCR-positive sample. Subgingival plaque samples were labeled with probes targeting rRNA of unculturable oral "Synergistetes" using fluorescent in situ hybridization (FISH). Analysis of 1,664 clones revealed 12 "Synergistetes" operational taxonomic units (OTUs) at the 99% sequence identity level, 5 of which were novel. "Synergistetes" OTU 4.2 was found in significantly more subjects with periodontitis than controls (P = 0.048) and was more abundant in subgingival plaque at diseased sites than at healthy sites in subjects with periodontitis (P = 0.019) or controls (P = 0.019). FISH analysis revealed that unculturable oral "Synergistetes" cells were large curved bacilli. The human oral cavity harbors a diverse population of "Synergistetes." "Synergistetes" OTU 4.2 is associated with periodontitis and may have a pathogenic role.
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74
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Abstract
The acute dental abscess is frequently underestimated in terms of its morbidity and mortality. The risk of potential serious consequences arising from the spread of a dental abscess is still relevant today with many hospital admissions for dental sepsis. The acute dental abscess is usually polymicrobial comprising facultative anaerobes, such as viridans group streptococci and the Streptococcus anginosus group, with predominantly strict anaerobes, such as anaerobic cocci, Prevotella and Fusobacterium species. The use of non-culture techniques has expanded our insight into the microbial diversity of the causative agents, identifying such organisms as Treponema species and anaerobic Gram-positive rods such as Bulleidia extructa, Cryptobacterium curtum and Mogibacterium timidum. Despite some reports of increasing antimicrobial resistance in isolates from acute dental infection, the vast majority of localized dental abscesses respond to surgical treatment, with antimicrobials limited to spreading and severe infections. The microbiology and treatment of the acute localized abscess and severe spreading odontogenic infections are reviewed.
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Affiliation(s)
- D. Robertson
- Department of Restorative Dentistry, University of Glasgow, Medical Faculty, Glasgow Dental Hospital and School, 378 Sauchiehall Street, Glasgow G2 3JZ, UK
| | - A. J. Smith
- Infection and Immunity Section, University of Glasgow, Medical Faculty, Glasgow Dental Hospital and School, 378 Sauchiehall Street, Glasgow G2 3JZ, UK
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75
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Schirrmeister JF, Liebenow AL, Pelz K, Wittmer A, Serr A, Hellwig E, Al-Ahmad A. New Bacterial Compositions in Root-filled Teeth with Periradicular Lesions. J Endod 2009; 35:169-74. [DOI: 10.1016/j.joen.2008.10.024] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Revised: 10/23/2008] [Accepted: 10/23/2008] [Indexed: 01/12/2023]
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76
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Abstract
Samples from infected root canals of 43 teeth with chronic apical periodontitis were analyzed for the presence and relative levels of 83 oral bacterial species and/or phylotypes using a reverse-capture checkerboard hybridization assay. Associations between the most frequently detected taxa were also recorded. The most prevalent taxa were Olsenella uli (74%), Eikenella corrodens (63%), Porphyromonas endodontalis (56%), Peptostreptococcus anaerobius (54%), and Bacteroidetes oral clone X083 (51%). When prevalence was considered only for bacteria present at levels >10(5), Bacteroidetes clone X083 was the most frequently isolated bacterium (37%), followed by Parvimonas micra (28%), E. corrodens (23%), and Tannerella forsythia (19%). The number of target taxa per canal was directly proportional to the size of the apical periodontitis lesion, with lesions >10 mm in diameter harboring a mean number of approximately 20 taxa. Several positive associations for the most prevalent taxa were disclosed for the first time and may have important ecological and pathogenic implications. In addition to strengthening the association of several cultivable named species with chronic apical periodontitis, the present findings using a large-scale analysis allowed the inclusion of some newly named species and as-yet-uncultivated phylotypes in the set of candidate pathogens associated with this disease.
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77
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Rôças IN, Hülsmann M, Siqueira JF. Microorganisms in Root Canal–treated Teeth from a German Population. J Endod 2008; 34:926-31. [DOI: 10.1016/j.joen.2008.05.008] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 05/19/2008] [Accepted: 05/22/2008] [Indexed: 11/25/2022]
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78
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Sakamoto M, Siqueira Jr JF, Rôças IN, Benno Y. Molecular analysis of the root canal microbiota associated with endodontic treatment failures. ACTA ACUST UNITED AC 2008; 23:275-81. [DOI: 10.1111/j.1399-302x.2007.00423.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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79
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Jumas-Bilak E, Carlier JP, Jean-Pierre H, Citron D, Bernard K, Damay A, Gay B, Teyssier C, Campos J, Marchandin H. Jonquetella anthropi gen. nov., sp. nov., the first member of the candidate phylum 'Synergistetes' isolated from man. Int J Syst Evol Microbiol 2008; 57:2743-2748. [PMID: 18048718 DOI: 10.1099/ijs.0.65213-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six clinical isolates of a hitherto unknown, strictly anaerobic, Gram-negative rod showing fastidious growth were subjected to a polyphasic taxonomic study, including phenotypic, genomic and phylogenetic feature analyses. 16S rRNA gene sequenced-based phylogeny revealed that the novel strains represent a homogeneous group distant from any recognized species in the candidate phylum 'Synergistetes'. The novel isolates were most closely related to species of the genus Dethiosulfovibrio, with 88.2-88.7 % 16S rRNA gene sequence similarity. Large-scale chromosome structure and DNA G+C content also differentiated the novel strains from members of the genus Dethiosulfovibrio. The novel strains were asaccharolytic. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic, lactic, succinic and isovaleric acids and the major cellular fatty acids iso-C(15 : 0) and C(16 : 0). Based on the data presented here, a new genus, Jonquetella gen. nov., is proposed with one novel species, Jonquetella anthropi sp. nov. J. anthropi is the first characterized species of the candidate phylum 'Synergistetes' that includes human isolates. The G+C content of the DNA of the type strain of J. anthropi ADV 126(T) (=AIP 136.05(T)=CIP 109408(T)=CCUG 53819(T)) is 59.4 mol%.
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Affiliation(s)
- Estelle Jumas-Bilak
- Université Montpellier 1, EA 3755, Faculté de Pharmacie, Laboratoire de Bactériologie-Virologie, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France
| | - Jean-Philippe Carlier
- Institut Pasteur, Centre National de Référence des Bactéries Anaérobies et du Botulisme, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Hélène Jean-Pierre
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Diane Citron
- R. M. Alden Research Laboratory, Santa Monica Blvd, Santa Monica, CA 90404, USA
| | - Kathryn Bernard
- National Microbiology Laboratory - Public Health Agency of Canada, 1015 Arlington St., Suite H5040, Winnipeg, MB R3E 3R2, Canada
| | - Audrey Damay
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Bernard Gay
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Corinne Teyssier
- Université Montpellier 1, EA 3755, Faculté de Pharmacie, Laboratoire de Bactériologie-Virologie, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France
| | - Josiane Campos
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Hélène Marchandin
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,Université Montpellier 1, EA 3755, Faculté de Pharmacie, Laboratoire de Bactériologie-Virologie, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France
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80
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Siqueira JF. On the issue of uncultivated bacteria and dead cell detection by molecular methods: Reply to Dr. Nair’s commentary. ACTA ACUST UNITED AC 2008; 105:5-8; author reply 8-10. [DOI: 10.1016/j.tripleo.2007.07.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Accepted: 07/17/2007] [Indexed: 11/24/2022]
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81
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Antimicrobial susceptibilities and clinical sources of Dialister species. Antimicrob Agents Chemother 2007; 51:4498-501. [PMID: 17923492 DOI: 10.1128/aac.00538-07] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Seventy-four strains representing the four species of the genus Dialister were isolated from various clinical samples. Dialister pneumosintes and Dialister micraerophilus were the two mainly encountered species. Fifty-five isolates were tested against 14 antimicrobial agents. Decreased susceptibilities to piperacillin, metronidazole, macrolides, fluoroquinolones, and rifampin were demonstrated. The clinical impact of these decreased susceptibilities remains to be investigated but should prompt microbiologists to perform antimicrobial susceptibility testing for clinically important Dialister spp.
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82
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Siqueira JF, Rôças IN, Paiva SSM, Magalhães KM, Guimarães-Pinto T. Cultivable bacteria in infected root canals as identified by 16S rRNA gene sequencing. ACTA ACUST UNITED AC 2007; 22:266-71. [PMID: 17600539 DOI: 10.1111/j.1399-302x.2007.00355.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Traditionally, cultivable bacteria isolated from infected root canals have been identified by phenotype-based methods. Because 16S ribosomal RNA (rRNA) gene sequencing has emerged as a more accurate and reliable tool for bacterial identification, the present study applied this approach to identify bacterial isolates recovered from the root canals of teeth with chronic apical periodontitis. METHODS Anaerobic techniques were used for culturing; identification of the isolates was carried out by polymerase chain reaction amplification and sequencing of the V5-V8 region of the 16S rRNA gene. Bacteria were found in all samples. The mean number of taxa per canal was 3.1, ranging from 2 to 8. The median number of cultivable bacterial cells in the root canals was 4.2 x 10(5), ranging from 2.8 x 10(3) to 3.3 x 10(7). Eighty-seven strains belonging to 52 bacterial taxa were identified. The most prevalent taxa were Fusobacterium nucleatum, Porphyromonas gingivalis, Pseudoramibacter alactolyticus, Micromonas micros and streptococci. The following bacterial phyla were represented in this study: Firmicutes (22 taxa, 46% of the identified isolates), Actinobacteria (14 taxa, 25.3% of the isolates), Bacteroidetes (eight taxa, 13.8% of the isolates), Fusobacteria (three taxa, 9.2% of the isolates) and Proteobacteria (five taxa, 5.7% of the isolates). Some of the isolates represented unnamed species not previously cultivated and characterized. In conclusion, our findings using a combined anaerobic culture-molecular identification approach confirmed the polymicrobial nature of primary endodontic infections with dominance of anaerobic bacteria. Notably several bacteria that are difficult or impossible to identify by phenotypic means were identified, including previously uncultivated taxa, cultivated-but-not-yet-characterized taxa and newly named species.
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Affiliation(s)
- J F Siqueira
- Department of Endodontics, Estácio de Sá University, Rio de Janeiro, RJ, Brazil
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83
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Vianna ME, Conrads G, Gomes BPFA, Horz HP. Quantification and characterization of Synergistes in endodontic infections. ACTA ACUST UNITED AC 2007; 22:260-5. [PMID: 17600538 DOI: 10.1111/j.1399-302x.2007.00353.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
INTRODUCTION Bacterial species belonging to the poorly characterized division Synergistes have recently been reported in endodontic infections, and therefore may be part of the etiology of periradicular diseases. The objective of this study was to characterize and quantify the predominant Synergistes phylotypes in infected root canals. METHODS We analyzed 32 necrotic teeth, each from a different patient, with radiographic evidence of apical periodontitis and with primary endodontic infections. RESULTS Using real-time quantitative polymerase chain reaction based on Synergistes-specific primers, seven of the 32 cases were found to be positive. Comparative sequence analysis showed that each of the seven samples was infected by one numerically dominant phylotype. Diversity among phylotypes was such that they could be grouped into three major evolutionary branches within the Synergistes division. The size of the total Synergistes population ranged from 4.5 x 10(4) to 1.5 x 10(6) 16S rRNA gene copies, and the median proportion accounted for 0.79% of the total bacterial community. For comparison, we also quantified such recognized endodontic pathogens as Prevotella intermedia, Porphyromonas gingivalis, and Treponema. The first two species were found in five and nine cases, respectively, with a median proportion below 0.01%, while Treponema was found in 18 cases with a median proportion of 1.48%. CONCLUSION Thus, the prevalence and quantity of Synergistes was clearly within the range of the other analyzed pathogens, suggesting their clinical relevance in endodontic infections. Furthermore, the diversity of Synergistes found at the diseased sites designates infected root canals as an important human ecosystem providing several unique micro-niches for this novel group of bacteria.
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Affiliation(s)
- M E Vianna
- Endodontic Unit, Dental School of Piracicaba, State University of Campinas, Piracicaba, Sao Paulo, Brazil
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84
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Siqueira JF, Rôças IN. Molecular detection and identification of Synergistes phylotypes in primary endodontic infections. Oral Dis 2007; 13:398-401. [PMID: 17577326 DOI: 10.1111/j.1601-0825.2006.01301.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIM Uncultivated phylotypes from the Synergistes group have recently emerged as suspected endodontic pathogens. This study aimed to investigate the presence and identity of these bacteria in primary endodontic infections using a 16S rRNA gene-based group-specific heminested polymerase chain reaction (PCR) protocol. MATERIALS AND METHODS Genomic DNA was isolated directly from clinical samples and used as templates for PCR. Amplicons from positive specimens were sequenced and phylogenetically analyzed to determine species identity. RESULTS Overall, about one-third of the samples harbored Synergistes bacteria. The following phylotypes were disclosed: oral clones W028, BA121/P4G_18 P1, W090, BH017 and E3_33. CONCLUSIONS These results demonstrated that as-yet uncultivated Synergistes phylotypes are present in the endodontic microbiota and a role in causation of apical periodontitis is suggested though remains unproven.
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Affiliation(s)
- J F Siqueira
- Department of Endodontics, Estácio de Sá University, Rio de Janeiro, Brazil.
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85
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Abstract
The "Synergistes" group of organisms are a phylogenetic cluster of Gram-negative anaerobes related to Synergistes jonesii, sufficiently distinct from all other phyla to be considered a distinct phylum or Division. They are widely distributed in nature although normally only a minor constituent of the bacterial community in each habitat. They have evolved to adapt to each habitat, and therefore exhibit a wide range of physiological and biochemical characteristics, although all cultivable taxa so far studied have the ability to degrade amino acids. They are found in the human mouth where they appear to be more numerous in tooth and gum disease than health. They have also been found in the human gut and soft tissue infections. Their role in human disease has yet to be established but improved knowledge of the characteristics that enable their identification should increase the likelihood of their recognition when present at diseased sites.
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Affiliation(s)
- Sonia R Vartoukian
- King's College London Dental Institute at Guy's, King's College and St Thomas' Hospitals, Infection Research Group, London, SE1 9RT, UK
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86
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Machado de Oliveira JC, Gama TGV, Siqueira JF, Rôças IN, Peixoto RS, Rosado AS. On the use of denaturing gradient gel electrophoresis approach for bacterial identification in endodontic infections. Clin Oral Investig 2006; 11:127-32. [PMID: 17115203 DOI: 10.1007/s00784-006-0085-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Accepted: 10/02/2006] [Indexed: 10/23/2022]
Abstract
Bacteria in infected root canals of teeth evincing chronic apical periodontitis lesions were identified by a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach. DNA was extracted from root canal samples, and part of the 16S rRNA gene of all bacteria was amplified by PCR and separated by DGGE, generating banding patterns representative of the community structure. Twenty visible bands were cut out of the gel, re-amplified, and sequenced to provide identification. Sequencing analysis revealed the presence of both cultivable and as-yet-uncultivated species in the samples analyzed, including representatives of the genera Fusobacterium, Bacteroides, Dialister, Synergistes, Prevotella, Eubacterium and Peptostreptococcus. Unambiguous identification was not always possible and the method's limitations are discussed. In general, the findings showed that PCR-DGGE can be useful for the identification of both cultivable and as-yet-uncultivated bacteria in endodontic infections.
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87
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Horz HP, Citron DM, Warren YA, Goldstein EJC, Conrads G. Synergistes group organisms of human origin. J Clin Microbiol 2006; 44:2914-20. [PMID: 16891512 PMCID: PMC1594628 DOI: 10.1128/jcm.00568-06] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial division Synergistes represents a poorly characterized phylotype of which only a few isolates have been cultured, primarily from natural environments. Recent detection of Synergistes-like sequence types in periodontal pockets and caries lesions of humans prompted us to search the R. M. Alden culture collection (Santa Monica, Calif.) for biochemically unidentifiable, slow-growing, obligately anaerobic gram-negative bacilli. Here we report on five clinical isolates cultured from peritoneal fluid and two isolates from soft-tissue infections that together constitute three separate evolutionary lineages within the phylogenetic radiation of the division Synergistes. One of these clusters was formed by the peritoneal isolates and had an 85% similarity to Synergistes jonesii, the first described Synergistes species, which was isolated from the rumen of a goat. The isolates from soft-tissue infections, on the other hand, formed two distinct lineages moderately related to each other with a similarity of approximately 78%. In addition, by using a newly designed 16S rRNA gene-based PCR assay with intended target specificity for Synergistes, we found that the dominant phylotype from a fecal sample was nearly identical to that of the strains obtained from peritonitis. Conversely, sequence types detected in periodontal pockets formed a separate cluster that shared a similarity of only 80% with the soft-tissue isolates. These findings suggest a high diversity of medically important Synergistes clades that apparently are unique to individual ecological niches in the human body. In conclusion, we now have available the first characterized human isolates of the division Synergistes which are colonizing, and probably infecting, several sites in the human body.
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Affiliation(s)
- Hans-Peter Horz
- Division of Oral Microbiology and Immunology, Department of Operative and Preventive Dentistry and Periodontology, University Hospital (RWTH), Pauwelsstrasse 30, D-52057 Aachen, Germany.
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88
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Zoletti GO, Siqueira JF, Santos KRN. Identification of Enterococcus faecalis in Root-filled Teeth With or Without Periradicular Lesions by Culture-dependent and—Independent Approaches. J Endod 2006; 32:722-6. [PMID: 16861069 DOI: 10.1016/j.joen.2006.02.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2005] [Revised: 01/31/2006] [Accepted: 02/01/2006] [Indexed: 11/26/2022]
Abstract
Enterococcus faecalis is the most commonly found species in root-filled teeth evincing recalcitrant periradicular lesions and as a consequence, a role in causation of endodontic treatment failure has been suggested. The purpose of this study was to evaluate the prevalence of this bacterial species in root-filled teeth with or without periradicular lesions. Identification of E. faecalis was carried out by polymerase chain reaction (PCR) or conventional culture procedures. Overall, E. faecalis was detected by species-specific 16S rRNA gene-based PCR in 40/50 teeth (80%), while culture revealed the occurrence of this species in 8/50 teeth (16%). PCR was significantly more effective than culture in detecting this bacterial species (p < 0.001). Of 27 root-filled teeth with no periradicular lesions, E. faecalis was found in 22 cases (81.5%) by PCR and in five cases (18.5%) by culture. Of 23 root-filled teeth with periradicular lesions, E. faecalis was identified in 18 cases (78%) by PCR and in three cases (13%) by culture. Regardless of the identification technique used, no significant difference was observed when comparing the occurrence of E. faecalis in root-filled teeth with and without periradicular lesions (p > 0.05). Although these findings apparently put into question the status of E. faecalis as the main species causing endodontic treatment failure, other related factors still need to be clarified before this assumption turns into certainty.
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Affiliation(s)
- G O Zoletti
- Department of Microbiology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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89
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Rôças IN, Siqueira JF. Characterization of Dialister species in infected root canals. J Endod 2006; 32:1057-61. [PMID: 17055906 DOI: 10.1016/j.joen.2006.04.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Revised: 04/17/2006] [Accepted: 04/20/2006] [Indexed: 11/23/2022]
Abstract
Members of the Dialister genus are asaccharolytic obligately anaerobic gram-negative coccobacilli that are culture-difficult or remain uncultivated. Their participation in endodontic infections has been only consistently demonstrated after advent of molecular biology approaches. This study was undertaken to characterize Dialister species in samples from primary endodontic infections using a devised 16S rRNA gene-based group-specific heminested PCR assay followed by sequencing of PCR products. Genomic DNA was isolated directly from clinical samples and used as template for PCR. Amplicons from positive specimens were sequenced and phylogenetically analyzed to determine species identity. Ten of 21 clinical samples yielded sequences with the highest percent similarities to oral Dialister species/phylotypes. Seven sequences were from Dialister invisus, and the other three sequences belonged to Dialister pneumosintes, Dialister oral clone BS095 and Dialister sp. clone IS013B24. Findings demonstrated that different Dialister species can take part in the microbiota associated with apical periodontitis lesions.
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Affiliation(s)
- Isabela N Rôças
- Department of Endodontics, Faculty of Dentistry, Estácio de Sá University, Rio de Janeiro, RJ, Brazil
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90
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Rôças IN, Siqueira JF. Detection of novel oral species and phylotypes in symptomatic endodontic infections including abscesses. FEMS Microbiol Lett 2005; 250:279-85. [PMID: 16099112 DOI: 10.1016/j.femsle.2005.07.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2005] [Revised: 07/04/2005] [Accepted: 07/15/2005] [Indexed: 11/23/2022] Open
Abstract
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.
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Affiliation(s)
- Isabela N Rôças
- Department of Endodontics, Estácio de Sá University, Av. Almte Ary Parreiras 311/1001, Icaraí, Niterói, RJ 24230-322, Brazil
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