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Li H, Li J, Hu J, Chen J, Zhou W. High-performing cross-dataset machine learning reveals robust microbiota alteration in secondary apical periodontitis. Front Cell Infect Microbiol 2024; 14:1393108. [PMID: 38975327 PMCID: PMC11224960 DOI: 10.3389/fcimb.2024.1393108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/22/2024] [Indexed: 07/09/2024] Open
Abstract
Multiple research groups have consistently underscored the intricate interplay between the microbiome and apical periodontitis. However, the presence of variability in experimental design and quantitative assessment have added a layer of complexity, making it challenging to comprehensively assess the relationship. Through an unbiased methodological refinement analysis, we re-analyzed 4 microbiota studies including 120 apical samples from infected teeth (with/without root canal treatment), healthy teeth, using meta-analysis and machine learning. With high-performing machine-learning models, we discover disease signatures of related species and enriched metabolic pathways, expanded understanding of apical periodontitis with potential therapeutic implications. Our approach employs uniform computational tools across datasets to leverage statistical power and define a reproducible signal potentially linked to the development of secondary apical periodontitis (SAP).
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Affiliation(s)
- Hao Li
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Jiehang Li
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Jiani Hu
- Research and Development Department, Beijing Xunzhu Biotechnology Co. Ltd., Beijing, China
- School of Chemistry Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jionglin Chen
- Research and Development Department, Beijing Xunzhu Biotechnology Co. Ltd., Beijing, China
| | - Wei Zhou
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
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Green SJ, Torok T, Allen JE, Eloe-Fadrosh E, Jackson SA, Jiang SC, Levine SS, Levy S, Schriml LM, Thomas WK, Wood JM, Tighe SW. Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report. ASTROBIOLOGY 2023; 23:897-907. [PMID: 37102710 PMCID: PMC10457625 DOI: 10.1089/ast.2022.0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 01/23/2023] [Indexed: 06/19/2023]
Abstract
Molecular biology methods and technologies have advanced substantially over the past decade. These new molecular methods should be incorporated among the standard tools of planetary protection (PP) and could be validated for incorporation by 2026. To address the feasibility of applying modern molecular techniques to such an application, NASA conducted a technology workshop with private industry partners, academics, and government agency stakeholders, along with NASA staff and contractors. The technical discussions and presentations of the Multi-Mission Metagenomics Technology Development Workshop focused on modernizing and supplementing the current PP assays. The goals of the workshop were to assess the state of metagenomics and other advanced molecular techniques in the context of providing a validated framework to supplement the bacterial endospore-based NASA Standard Assay and to identify knowledge and technology gaps. In particular, workshop participants were tasked with discussing metagenomics as a stand-alone technology to provide rapid and comprehensive analysis of total nucleic acids and viable microorganisms on spacecraft surfaces, thereby allowing for the development of tailored and cost-effective microbial reduction plans for each hardware item on a spacecraft. Workshop participants recommended metagenomics approaches as the only data source that can adequately feed into quantitative microbial risk assessment models for evaluating the risk of forward (exploring extraterrestrial planet) and back (Earth harmful biological) contamination. Participants were unanimous that a metagenomics workflow, in tandem with rapid targeted quantitative (digital) PCR, represents a revolutionary advance over existing methods for the assessment of microbial bioburden on spacecraft surfaces. The workshop highlighted low biomass sampling, reagent contamination, and inconsistent bioinformatics data analysis as key areas for technology development. Finally, it was concluded that implementing metagenomics as an additional workflow for addressing concerns of NASA's robotic mission will represent a dramatic improvement in technology advancement for PP and will benefit future missions where mission success is affected by backward and forward contamination.
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Affiliation(s)
- Stefan J. Green
- Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, Illinois, USA
| | - Tamas Torok
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Emiley Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Scott A. Jackson
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Sunny C. Jiang
- Department of Civil and Environmental Engineering, University of California, Irvine, California, USA
| | - Stuart S. Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Lynn M. Schriml
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - W. Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Jason M. Wood
- Research Informatics Core, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Scott W. Tighe
- Vermont Integrative Genomics, University of Vermont, Burlington, Vermont, USA
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The impact of an enhanced infection control protocol on the microbial community profile in molar root canal treatment-an in vivo NGS molecular study. J Endod 2022; 48:1352-1360.e3. [PMID: 36087763 DOI: 10.1016/j.joen.2022.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Recent findings demonstrated that one-year CBCT-based outcomes of molar root canal treatment were improved through an Enhanced infection protocol (EnP), when compared to a current best-practice standard infection control protocol (StP). The EnP comprised measures to reduce iatrogenic contamination from direct and indirect contact surfaces, including the replacement of the rubber dams, gloves, files, all instruments, and surface barriers before root canal obturation. The aim of this study was to investigate the effect of such an enhanced infection control protocol on resident microbiome present after chemomechanical instrumentation and the protocol ability in reducing iatrogenic contamination in molar teeth during root canal treatment. METHODS Molar teeth were block-randomized to receive either treatment under EnP or StP. To compare the differential effect of the protocol on the identity of bacteria present, one hundred and fifty, matched DNA extracts from 75 molar teeth samples (StP, n=39; EnP, n=36), were evaluated. Samples were taken before (S1) and after (S2) chemomechanical preparation and were subjected to next-generation sequencing of the V3-V4 region of the 16S rRNA gene, prior to bioinformatical identification using the HOMD oral microbiome database and downstream taxonomic processing, providing measures of richness and diversity of bacteria and significant bacterial taxa during chemomechanical instrumentation and the effect of the two treatment groups. RESULTS 88 microbial taxa were significantly more abundant in StP S2 samples, including endodontically relevant contaminants taxa as Actinomyces, Cutibacterium, and Haemophilus. The S2 samples demonstrated fewer residual bacterial species in the EnP group, with 26.8 observed species compared to 38.3 in the StP. Reduced diversity and richness measures were noted in the EnP pre-obturation samples compared to the StP in OTU, Chao1 and ACE indices (p≤0.05). Differential microbial identities between S1 and S2 samples and protocols demonstrated that the previously observed increased effectiveness of the EnP protocol was likely to prevent recontamination or de novo contamination of the root canal space during treatment. CONCLUSIONS The implemented enhanced infection control protocol resulted in a specific reduction of microbial taxa often associated with recontamination or iatrogenic contamination, suggesting the basis for improved infection control measures during root canal treatment.
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Nardello LCL, Pinheiro ET, Gavini G, Prado LC, Romero RX, Gomes BPFA, Skelton-Macedo MC. Nature and Prevalence of Bacterial Taxa Persisting after Root Canal Chemomechanical Preparation in Permanent Teeth: A Systematic Review and Meta-analysis. J Endod 2022; 48:572-596. [PMID: 35114271 DOI: 10.1016/j.joen.2022.01.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 01/15/2022] [Accepted: 01/21/2022] [Indexed: 01/05/2023]
Abstract
INTRODUCTION Culture-independent molecular studies have shown a broad spectrum of bacterial taxa that persist after chemomechanical procedures (CMP). Therefore, this study systematically reviewed these reports to explore the prevalence of bacteria in post-instrumentation samples of root canals from permanent teeth, especially of as-yet-uncultivated/difficult-to-culture bacteria. METHODS Electronic databases were searched from 2007 to January 2021. Clinical studies using culture-independent molecular methods to identify species-level taxa before and after CMP were included. Studies were critically appraised using the Joanna Briggs Institute Prevalence Critical Appraisal Checklist and the funnel plot analysis. The meta-analysis was performed on the prevalence of as-yet-uncultivated/difficult-to-culture bacterial taxa using RStudio. RESULTS A total of 3781 titles were screened, but only 20 studies were included. The most frequent species in post-instrumentation samples were Streptococcus spp., Leptotrichia buccalis, Fusobacterium nucleatum, and Capnocytophaga ochracea. The detection frequency of some species increased after CMP, including mainly Firmicutes members such as streptococci, Enterococcus faecium, Selenomonas noxia, and Solobacterium moorei. The prevalence (confidence interval) of difficult-to-culture species was as follows: Dialister invisus, 17% (7%-29%); Solobacterium moorei, 14% (8%-23%); Bacteroidaceae [G-1] bacterium HMT 272, 13% (5%-23%); and Filifactor alocis, 11% (3%-23%). CONCLUSIONS The prevalence of as-yet-uncultivated/difficult-to-culture bacterial taxa in post-instrumentation samples was low. The persistent species belonged mainly to the phylum Firmicutes, and streptococci were the major members. Future larger clinical studies on the composition of the whole bacterial community that persist after CMP are still necessary for a better understanding of bacterial interactions and their clinical significance in the treatment outcome.
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Affiliation(s)
- Laura C L Nardello
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
| | - Ericka T Pinheiro
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil.
| | - Giulio Gavini
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
| | - Laís C Prado
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
| | - Roberto X Romero
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
| | - Brenda P F A Gomes
- Department of Restorative Dentistry, Piracicaba Dental School, State University of Campinas, Piracicaba, SP, Brazil
| | - Mary C Skelton-Macedo
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
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de Castro Kruly P, Alenezi HEM, Manogue M, Devine DA, Teixeira ND, Pimentel Garcia FC, Do T. Residual bacteriome after chemomechanical preparation of root canals in primary and secondary infections. J Endod 2022; 48:855-863. [DOI: 10.1016/j.joen.2022.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 02/13/2022] [Accepted: 03/27/2022] [Indexed: 12/27/2022]
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Selvakumar DR, Krishnamoorthy S, Venkatesan K, Ramanathan A, Abbott PV, Angambakkam Rajasekaran P. Active Bacteria in Carious Dentin of Mandibular Molars with Different Pulp Conditions: An In Vivo Study. J Endod 2021; 47:1883-1889. [PMID: 34534554 DOI: 10.1016/j.joen.2021.08.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION This study evaluated the relative abundance and ribosomal activity of selected bacteria in carious dentin of teeth with different pulp conditions. METHODS Thirty healthy patients with class I occlusal caries in molars were categorized into 3 groups based on the pulp diagnosis: normal pulp (NP, n = 10) with caries extending less than half the thickness of dentin (as assessed radiographically), reversible pulpitis (n = 10), and symptomatic irreversible pulpitis (n = 10) with caries extending more than two thirds of the thickness of dentin. Carious dentin samples were collected from the deepest part of the cavity and stored in RNAlater solution (Ambion Inc, Austin, TX). Eight bacterial taxa were evaluated from the samples: Streptococcus mutans, Lactobacillus fermentum, Veillonella, Actinomyces, Rothia dentocariosa, Olsenella profusa, Prevotella intermedia, and Bifidobacterium dentium. The 16S ribosomal RNA (rRNA) gene and 16S rRNA were quantified by real-time polymerase chain reaction and used to calculate the relative genome abundance and relative ribosomal abundance. The Fisher exact test was used to compare proportions between groups. The mean rank difference between the various groups was assessed using the Kruskal-Wallis test with the Bonferroni-Holm correction. RESULTS The reversible pulpitis group had significantly higher 16S rRNA gene and rRNA counts of Actinomyces (P < .001 and P = .002) and B. dentium (P = .005 and P = .007) relative to the NP group. The symptomatic irreversible pulpitis group had significantly higher 16S rRNA gene and rRNA counts of L. fermentum (P < .001 and P < .001), Actinomyces (P < .001 and P < .001), O. profusa (P < .001 and P < .001), P. intermedia (P = .001 and P = .002), and Bifidobacterium (P < .001 and P < .001) relative to the NP group. CONCLUSIONS Specific bacterial activity varies in carious dentin of teeth with different pulp conditions.
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Affiliation(s)
- Deepan Raj Selvakumar
- Department of Conservative Dentistry and Endodontics, Thai Moogambigai Dental College and Hospital, Dr. MGR Educational and Research Institute, Chennai, Tamilnadu, India
| | - Sridevi Krishnamoorthy
- Department of Conservative Dentistry and Endodontics, Thai Moogambigai Dental College and Hospital, Dr. MGR Educational and Research Institute, Chennai, Tamilnadu, India
| | - Keerthi Venkatesan
- Department of Conservative Dentistry and Endodontics, Thai Moogambigai Dental College and Hospital, Dr. MGR Educational and Research Institute, Chennai, Tamilnadu, India
| | | | - Paul Vincent Abbott
- UWA Dental School, The University of Western Australia, Nedlands, Western Australia, Australia
| | - PradeepKumar Angambakkam Rajasekaran
- Department of Conservative Dentistry and Endodontics, Thai Moogambigai Dental College and Hospital, Dr. MGR Educational and Research Institute, Chennai, Tamilnadu, India.
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Zahran S, Patel S, Koller G, Mannocci F. The impact of an enhanced infection control protocol on molar root canal treatment outcome - a randomized clinical trial. Int Endod J 2021; 54:1993-2005. [PMID: 34352123 DOI: 10.1111/iej.13605] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022]
Abstract
AIM To evaluate the effect of an enhanced infection control protocol on root canal treatment outcomes and on microbial load within root canals after chemomechanical preparation. METHODOLOGY A total of 144 molar teeth from 139 healthy patients receiving primary root canal treatment were block randomized to a standard protocol (StP) or an enhanced infection control protocol (EnP). Both treatment arms adhered to current best practice recommendations, while the EnP comprised additional steps that included replacing rubber dams, gloves, files, all instruments and surface barriers at the time of canal filling to reduce the chances of iatrogenic contamination. Patients and radiographic examiners were blinded to the protocol used. Intracanal microbial samples were taken at baseline (S1) and after completion of chemomechanical preparation (S2). Microbial 16S rDNA copy numbers were enumerated by quantitative polymerase chain reaction (qPCR). Cone beam computed tomography (CBCT) scans were taken before treatment and at one-year follow-up. The outcome was assessed clinically and radiographically using CBCT by logistic regression modelling. RESULTS At one-year follow-up, 115 teeth were analysed (54 in StP and 61 in EnP). The percentage of favourable outcomes assessed by CBCT was 85.2% in the EnP and 66.7% in the StP. The odds of 12-month success was three times higher in the EnP group compared with the StP group (OR=2.89; p=0.022, CI: 1.17 - 7.15). The median bacterial reads were reduced from 8.1×103 in S1 samples to 3.5×103 in the StP group and from 8.6×103 to 1.3×103 in the EnP group. The enhanced protocol significantly reduced bacterial counts in pre-canal filling samples when compared to the standard protocol (p=0.009). CONCLUSIONS The implementation of a facile, enhanced infection control protocol in primary root canal treatment resulted in less detectable bacterial DNA before canal filling and significantly more successful outcomes at one year.
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Affiliation(s)
- Shatha Zahran
- Department of Endodontics, Centre for Oral, Clinical and Translational Sciences, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK.,Department of Endodontics, Faculty of Dentistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shanon Patel
- Department of Endodontics, Centre for Oral, Clinical and Translational Sciences, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Garrit Koller
- Department of Endodontics, Centre for Oral, Clinical and Translational Sciences, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK.,Centre for Host Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK.,LCN - London Centre for Nanotechnology, Bloomsbury, London, UK
| | - Francesco Mannocci
- Department of Endodontics, Centre for Oral, Clinical and Translational Sciences, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
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