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Bellato M, Cappellato M, Longhin F, Del Vecchio C, Brancaccio G, Cattelan AM, Brun P, Salaris C, Castagliuolo I, Di Camillo B. Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 + . Sci Rep 2023; 13:16867. [PMID: 37803040 PMCID: PMC10558486 DOI: 10.1038/s41598-023-43040-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023] Open
Abstract
The outbreak of Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, forced us to face a pandemic with unprecedented social, economic, and public health consequences. Several nations have launched campaigns to immunize millions of people using various vaccines to prevent infections. Meanwhile, therapeutic approaches and discoveries continuously arise; however, identifying infected patients that are going to experience the more severe outcomes of COVID-19 is still a major need, to focus therapeutic efforts, reducing hospitalization and mitigating drug adverse effects. Microbial communities colonizing the respiratory tract exert significant effects on host immune responses, influencing the susceptibility to infectious agents. Through 16S rDNAseq we characterized the upper airways' microbiota of 192 subjects with nasopharyngeal swab positive for SARS-CoV-2. Patients were divided into groups based on the presence of symptoms, pneumonia severity, and need for oxygen therapy or intubation. Indeed, unlike most of the literature, our study focuses on identifying microbial signatures predictive of disease progression rather than on the probability of infection itself, for which a consensus is lacking. Diversity, differential abundance, and network analysis at different taxonomic levels were synergistically adopted, in a robust bioinformatic pipeline, highlighting novel possible taxa correlated with patients' disease progression to intubation.
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Affiliation(s)
- Massimo Bellato
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| | - Marco Cappellato
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| | - Francesca Longhin
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| | - Claudia Del Vecchio
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Giuseppina Brancaccio
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
- Infectious Diseases Unit, University Hospital Padova, 35128, Padova, Italy
| | - Anna Maria Cattelan
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
- Infectious Diseases Unit, University Hospital Padova, 35128, Padova, Italy
| | - Paola Brun
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Claudio Salaris
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Ignazio Castagliuolo
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
- Microbiology and Virology Unit, University Hospital Padova, 35121, Padova, Italy
| | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, 35131, Padova, Italy.
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro (PD), Italy.
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Altaie AM, Saddik B, Alsaegh MA, Soliman SSM, Hamoudi R, Samaranayake LP. Prevalence of unculturable bacteria in the periapical abscess: A systematic review and meta-analysis. PLoS One 2021; 16:e0255485. [PMID: 34351963 PMCID: PMC8341601 DOI: 10.1371/journal.pone.0255485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 07/18/2021] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE To assess the prevalence of unculturable bacteria in periapical abscess, radicular cyst, and periapical granuloma. METHODS PubMed, Scopus, Science Direct, and Ovid databases were systematically searched from January 1990 to May 2020. All the included studies were cross-sectional design. The risk of bias was assessed using Joanna Briggs Institute check-list. Heterogeneity was described using meta-regression and mixed-effects model for lesion, country, and sequence technique moderators. Funnel plot and unweighted Egger's regression test were used to estimate the publication bias. Microbiome data on diversity, abundance, and frequency of unculturable bacteria in the periapical lesions were reviewed, analysed, and the principal component analysis (PCA) was performed. RESULTS A total of 13 studies out of 14,780, were selected for the final analysis. These studies focused on the prevalence of unculturable bacteria in periapical abscesses and related lesions. Approximately 13% (95% CI: 7-23%) of the cumulative number of bacteria derived from periapical abscesses was unculturable. Country moderator significantly (P = 0.05) affects the diversity summary proportion. While the pooled frequency of unculturable bacteria was 8%; 95% CI: 5, 14%, the estimate of the pooled abundance of unculturable bacteria was 5%; 95% CI: 2, 12% with a significant (P = 0.05) country moderator that affects the abundance summary proportion. Of the 62 unculturable bacteria, 35 were subjected to PCA and Peptostreptococcus sp. oral clone CK035 was the most abundant species in periapical abscesses. Hybridization techniques were found to be the most reliable molecular methods in detecting the abundance and frequency of unculturable bacteria. CONCLUSION The significant prevalence of unculturable bacteria in the periapical abscess, suggests that they are likely to play, a yet unknown, critical role in the pathogenesis and progression of the disease. Further research remains to be done to confirm their specific contributions in the virulence and disease progression.
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Affiliation(s)
- Alaa Muayad Altaie
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Oral and Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, UAE
| | - Basema Saddik
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Family and Community Medicine, College of Medicine, University of Sharjah, Sharjah, UAE
| | - Mohammed Amjed Alsaegh
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Oral and Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, UAE
| | - Sameh S. M. Soliman
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, UAE
| | - Rifat Hamoudi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, UAE
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
- * E-mail: (RH); (LPS)
| | - Lakshman P. Samaranayake
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Oral and Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, UAE
- * E-mail: (RH); (LPS)
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McCracken BA, Nathalia Garcia M. Phylum Synergistetes in the oral cavity: A possible contributor to periodontal disease. Anaerobe 2020; 68:102250. [PMID: 32791127 DOI: 10.1016/j.anaerobe.2020.102250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/13/2022]
Abstract
Microbial contributions to periodontal disease have been under renewed scrutiny with the advent of newer technologies to identify their presence and gene expression at the molecular level. Members of the phylum Synergistetes are some of the more recent bacteria to be associated with periodontal disease. Bacteria classified in this phylum can be found in a wide variety of habitats including both inside and outside of a mammalian host. Members of this phylum have been identified as part of the human microbiome. Indeed, many of the identified phylotypes have yet to be cultivated. Here we consider contributions of three named and formally described species to the oral microbial community and to pathogenesis of periodontal disease.
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Affiliation(s)
- Barbara Anne McCracken
- Section of Microbiology, Department of Growth, Development And Structure, 2800 College Ave., Alton, IL, 62002, USA.
| | - M Nathalia Garcia
- Southern Illinois University School of Dental Medicine, Alton, IL, 62002, USA
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Manoil D, Al‐Manei K, Belibasakis GN. A Systematic Review of the Root Canal Microbiota Associated with Apical Periodontitis: Lessons from Next‐Generation Sequencing. Proteomics Clin Appl 2020; 14:e1900060. [DOI: 10.1002/prca.201900060] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/14/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Daniel Manoil
- Division of Oral DiseasesDepartment of Dental MedicineKarolinska Institute Huddinge 14152 Sweden
| | - Khaled Al‐Manei
- Division of Oral DiseasesDepartment of Dental MedicineKarolinska Institute Huddinge 14152 Sweden
- Division of EndodonticsDepartment of Restorative Dental ScienceCollege of DentistryKing Saud University Riyadh 11545 Saudi Arabia
| | - Georgios N. Belibasakis
- Division of Oral DiseasesDepartment of Dental MedicineKarolinska Institute Huddinge 14152 Sweden
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5
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Brzezińska-Błaszczyk E, Pawłowska E, Płoszaj T, Witas H, Godzik U, Agier J. Presence of archaea and selected bacteria in infected root canal systems. Can J Microbiol 2018; 64:317-326. [DOI: 10.1139/cjm-2017-0531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Infections of the root canal have polymicrobial etiology. The main group of microflora in the infected pulp is bacteria. There is limited data that archaea may be present in infected pulp tissue. The aim of this study was to check the prevalence of archaea in necrotic root canal samples obtained from patients with primary or post-treatment infection. The prevalence of selected bacteria species (Prevotella intermedia, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Synergistes sp.) in necrotic samples was evaluated as well. Sixty-four samples from root canal were collected for DNA and RNA extraction. A PCR assay based on the 16S rRNA gene was used to determine the presence of archaea and selected bacteria. Of the 64 samples, 6 were analyzed by semiquantitative reverse transcription PCR to estimate expression profiles of 16S rRNA, and another 9 were selected for direct sequencing. Archaea were detected in 48.4% samples. Statistical analysis indicated a negative association in coexistence between archaea and Treponema denticola (P < 0.05; Pearson’s χ2 test). The main representative of the Archaea domain found in infected pulp tissue was Methanobrevibacter oralis. Archaea 16S rRNA gene expression was significantly lower than Synergistes sp., Porphyromonas gingivalis, and Tannerella forsythia (P < 0.05; Student’s t test). Thus, it can be hypothesized that archaea may participate in the endodontic microbial community.
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Affiliation(s)
| | | | - Tomasz Płoszaj
- Department of Molecular Biology, Medical University of Lodz, Lodz, Poland
| | - Henryk Witas
- Department of Molecular Biology, Medical University of Lodz, Lodz, Poland
| | - Urszula Godzik
- Department of Experimental Immunology, Medical University of Lodz, Lodz, Poland
| | - Justyna Agier
- Department of Experimental Immunology, Medical University of Lodz, Lodz, Poland
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Hiranmayi KV, Sirisha K, Ramoji Rao MV, Sudhakar P. Novel Pathogens in Periodontal Microbiology. J Pharm Bioallied Sci 2017; 9:155-163. [PMID: 28979069 PMCID: PMC5621177 DOI: 10.4103/jpbs.jpbs_288_16] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Periodontitis is a polymicrobial disease caused by complex interactions between distinct pathogens in a biofilm resulting in the destruction of periodontal tissues. It seems evident that unknown microorganisms might be involved in onset or progression of periodontitis. For many decades, research in the field of oral microbiology failed to identify certain subgingival microbiota due to technical limitations but, over a period of 12 years using molecular approaches and sequencing techniques, it became feasible to reveal the existence of new periodontal pathogens. Therefore, it is evident that in addition to conventional periodontal pathogens, other microbes might be involved in onset and progression of periodontitis. The novel pathogens enlisted under periodontal phylogeny include Cryptobacterium curtum, Dialister pneumosintes, Filifactor alocis, Mitsuokella dentalis, Slackia exigua, Selenomonas sputigena, Solobacterium moorei, Treponema lecithinolyticum, and Synergistes. The polymicrobial etiology of periodontitis has been elucidated by comprehensive techniques, and studies throwing light on the possible virulence mechanisms possessed by these novel periodontal pathogens are enlisted.
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Affiliation(s)
- K Vidya Hiranmayi
- Post Graduate Student, Department of Periodontics and Implantology, Drs S and NR Siddhartha Institute of Dental Sciences, Krishna District, Andhra Pradesh, India
| | - K Sirisha
- Reader, Department of Periodontics and Implantology, Drs S and NR Siddhartha Institute of Dental Sciences, Krishna District, Andhra Pradesh, India
| | - M V Ramoji Rao
- HOD, Department of Periodontics and Implantology, Drs S and NR Siddhartha Institute of Dental Sciences, Krishna District, Andhra Pradesh, India
| | - P Sudhakar
- Post Graduate Student, Department of Periodontics and Implantology, Drs S and NR Siddhartha Institute of Dental Sciences, Krishna District, Andhra Pradesh, India
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Zehnder M, Belibasakis GN. On the dynamics of root canal infections-what we understand and what we don't. Virulence 2016; 6:216-22. [PMID: 25654162 DOI: 10.4161/21505594.2014.984567] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Infections of the root canal space and their sequelae can be extremely painful and potentially dangerous, yet they do not necessarily have to be. Chronic, asymptomatic inflammatory lesions around the apex of a tooth with a necrotic dental pulp or an insufficient root canal treatment can develop unnoticed by the patient, and remain so for years. The course of disease is modulated by both the virulence of the microbiota established in the root canal space and the capacity of the immune system to curb the infection. To both ends, highly convincing investigations to help us understand when and why the tissues around an endodontically involved tooth become acutely inflamed are missing. We will discuss how recent advances in molecular identification of microorganisms have altered our understanding of root canal infections, and which information is currently missing to link clinical experience with observations from experimental research.
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Affiliation(s)
- Matthias Zehnder
- a Department of Preventive Dentistry, Periodontology, and Cariology, University of Zürich Center of Dental Medicine , Switzerland
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8
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Identification of Synergistetes in endodontic infections. Microb Pathog 2014; 73:1-6. [DOI: 10.1016/j.micpath.2014.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/24/2014] [Accepted: 05/05/2014] [Indexed: 11/24/2022]
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9
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Rôças IN, Neves MAS, Provenzano JC, Siqueira JF. Susceptibility of as-yet-uncultivated and difficult-to-culture bacteria to chemomechanical procedures. J Endod 2013; 40:33-7. [PMID: 24331987 DOI: 10.1016/j.joen.2013.07.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/28/2013] [Accepted: 07/30/2013] [Indexed: 02/04/2023]
Abstract
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.
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Affiliation(s)
- Isabela N Rôças
- Department of Endodontics and Molecular Microbiology Laboratory, Faculty of Dentistry, Estácio de Sá University, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mônica A S Neves
- Department of Endodontics and Molecular Microbiology Laboratory, Faculty of Dentistry, Estácio de Sá University, Rio de Janeiro, Rio de Janeiro, Brazil
| | - José C Provenzano
- Department of Endodontics and Molecular Microbiology Laboratory, Faculty of Dentistry, Estácio de Sá University, Rio de Janeiro, Rio de Janeiro, Brazil
| | - José F Siqueira
- Department of Endodontics and Molecular Microbiology Laboratory, Faculty of Dentistry, Estácio de Sá University, Rio de Janeiro, Rio de Janeiro, Brazil.
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Siqueira JF, Rôças IN. As-yet-uncultivated oral bacteria: breadth and association with oral and extra-oral diseases. J Oral Microbiol 2013; 5:21077. [PMID: 23717756 PMCID: PMC3664057 DOI: 10.3402/jom.v5i0.21077] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 05/01/2013] [Accepted: 05/02/2013] [Indexed: 12/19/2022] Open
Abstract
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.
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Affiliation(s)
- José F Siqueira
- Department of Endodontics and Molecular Microbiology Laboratory, Estácio de Sá University, Rio de Janeiro, Brazil
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11
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Belibasakis GN, Öztürk VÖ, Emingil G, Bostanci N. Synergistetes
cluster A in saliva is associated with periodontitis. J Periodontal Res 2013; 48:727-32. [DOI: 10.1111/jre.12061] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2013] [Indexed: 10/27/2022]
Affiliation(s)
- G. N. Belibasakis
- Oral Microbiology and Immunology; Institute of Oral Biology; Center of Dental Medicine; University of Zürich; Zürich Switzerland
| | - V.-Ö. Öztürk
- Oral Translational Research; Institute of Oral Biology; Center of Dental Medicine; University of Zürich; Zürich Switzerland
- Department of Periodontology; School of Dentistry; Ege University; İzmir Turkey
| | - G. Emingil
- Department of Periodontology; School of Dentistry; Ege University; İzmir Turkey
| | - N. Bostanci
- Oral Translational Research; Institute of Oral Biology; Center of Dental Medicine; University of Zürich; Zürich Switzerland
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12
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Baumgartner A, Thurnheer T, Lüthi-Schaller H, Gmür R, Belibasakis GN. The phylum Synergistetes in gingivitis and necrotizing ulcerative gingivitis. J Med Microbiol 2012; 61:1600-1609. [PMID: 22878253 DOI: 10.1099/jmm.0.047456-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The clinical manifestation of necrotizing ulcerative gingivitis (NUG) is distinct from that of common gingivitis in that it is characterized by local necrosis of the gingival tissues, rapid onset, pain and extensive bleeding. The phylum Synergistetes is a novel bacterial phylum consisting of Gram-negative anaerobes, with evidence of presence in biofilms associated with periodontal and endodontic infections. To date, the involvement of members of this phylum in NUG has not been investigated. This study aimed to evaluate the presence and levels of known human oral Synergistetes bacterial clusters in dental plaque from patients with NUG and compare them with those found in gingivitis. Marginal dental plaque samples from 21 NUG and 21 gingivitis patients were analysed quantitatively by fluorescent in situ hybridization and microscopy for members of two oral Synergistetes clusters (A and B) and for Jonquetella anthropi. Synergistetes cluster A bacteria were detected in all samples but at higher levels (9.4-fold) and proportions (2.5-fold) in NUG patients than in gingivitis patients. However, with regard to Synergistetes cluster B bacteria, there were no differences between NUG and gingivitis patients. J. anthropi was detected in only half of the samples and at lower levels than the other taxa. In conclusion, these data demonstrate that Synergistetes cluster A bacteria, but not cluster B bacteria or J. anthropi, are more strongly associated with NUG than with gingivitis.
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Affiliation(s)
- Angelica Baumgartner
- Oral Microbiology and Immunology, Institute of Oral Biology, Center of Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland
| | - Thomas Thurnheer
- Oral Microbiology and Immunology, Institute of Oral Biology, Center of Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland
| | - Helga Lüthi-Schaller
- Oral Microbiology and Immunology, Institute of Oral Biology, Center of Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland
| | - Rudolf Gmür
- Oral Microbiology and Immunology, Institute of Oral Biology, Center of Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland
| | - Georgios N Belibasakis
- Oral Microbiology and Immunology, Institute of Oral Biology, Center of Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland
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13
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Ribeiro AC, Matarazzo F, Faveri M, Zezell DM, Mayer MPA. Exploring bacterial diversity of endodontic microbiota by cloning and sequencing 16S rRNA. J Endod 2011; 37:922-6. [PMID: 21689545 DOI: 10.1016/j.joen.2011.04.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 04/08/2011] [Accepted: 04/10/2011] [Indexed: 11/27/2022]
Abstract
INTRODUCTION The characterization of microbial communities infecting the endodontic system in each clinical condition may help on the establishment of a correct prognosis and distinct strategies of treatment. The purpose of this study was to determine the bacterial diversity in primary endodontic infections by 16S ribosomal-RNA (rRNA) sequence analysis. METHODS Samples from root canals of untreated asymptomatic teeth (n = 12) exhibiting periapical lesions were obtained, 16S rRNA bacterial genomic libraries were constructed and sequenced, and bacterial diversity was estimated. RESULTS A total of 489 clones were analyzed (mean, 40.7 ± 8.0 clones per sample). Seventy phylotypes were identified of which six were novel phylotypes belonging to the family Ruminococcaceae. The mean number of taxa per canal was 10.0, ranging from 3 to 21 per sample; 65.7% of the cloned sequences represented phylotypes for which no cultivated isolates have been reported. The most prevalent taxa were Atopobium rimae (50.0%), Dialister invisus, Prevotella oris, Pseudoramibacter alactolyticus, and Tannerella forsythia (33.3%). CONCLUSIONS Although several key species predominate in endodontic samples of asymptomatic cases with periapical lesions, the primary endodontic infection is characterized by a wide bacterial diversity, which is mostly represented by members of the phylum Firmicutes belonging to the class Clostridia followed by the phylum Bacteroidetes.
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Affiliation(s)
- Adriana C Ribeiro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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14
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Li L, Hsiao WWL, Nandakumar R, Barbuto SM, Mongodin EF, Paster BJ, Fraser-Liggett CM, Fouad AF. Analyzing endodontic infections by deep coverage pyrosequencing. J Dent Res 2010; 89:980-4. [PMID: 20519493 DOI: 10.1177/0022034510370026] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
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.
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Affiliation(s)
- L Li
- Department of Endodontics, Prosthodontics and Operative Dentistry, Dental School, University of Maryland, 650 W. Baltimore St., Baltimore, MD 21201, USA
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15
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Marchandin H, Damay A, Roudière L, Teyssier C, Zorgniotti I, Dechaud H, Jean-Pierre H, Jumas-Bilak E. Phylogeny, diversity and host specialization in the phylum Synergistetes with emphasis on strains and clones of human origin. Res Microbiol 2010; 161:91-100. [PMID: 20079831 DOI: 10.1016/j.resmic.2009.12.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Revised: 10/25/2009] [Accepted: 12/02/2009] [Indexed: 11/19/2022]
Abstract
Members of the phylum Synergistetes have been demonstrated in several environmental ecosystems and mammalian microflorae by culture-independent methods. In the past few years, the clinical relevance of some uncultivated phylotypes has been demonstrated in endodontic infections, and uncultured Synergistetes have been demonstrated in human mouth, gut and skin microbiota. However, Synergistetes are rarely cultured from human samples, and only 17 isolates are currently reported. Twelve members of Synergistetes isolated in the course of various infectious processes, including 3 Jonquetella anthropi, 2 Cloacibacillus evryensis, 2 Pyramidobacter piscolens and 5 unidentified strains, as well as 56 clones obtained by specific PCR from the normal vaginal microflora, were studied. 16S rRNA gene-based phylogeny showed that the clones were grouped into 3 clusters, corresponding to the genus Jonquetella, P. piscolens and one novel Synergistetes taxon. The presence and diversity of Synergistetes were reported for the first time in the vaginal microflora. Synergistetes were found in healthy patients, suggesting that they could play a functional role in human microflorae, but may also act as opportunistic pathogens. Studying the phylogenetic relationships between environmental and mammalian strains and clones revealed clearly delineated independent lineages according to the origin of the sequences.
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Affiliation(s)
- Hélène Marchandin
- Université Montpellier 1, EA 3755, Laboratoire de Bactériologie-Virologie, Faculté de Pharmacie, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France.
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16
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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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17
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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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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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