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Genome, Biofilm Forming Ability and Antibiotic Resistance of Oral Pathogenic Bacteria

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Medical Microbiology".

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 11230

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Special Issue Editors

Dr. Catalina-Suzana Stingu

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Guest Editor

Institut for Medical Microbiology and Virology, University Medical Center, Leipzig, Germany
Interests: anaerobic bacteria; antibiotic resistance; oral biofilm
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Sebastian Hahnel

E-Mail Website
Guest Editor

Clinic for Prosthetic Dentistry and Dental Materials Science, Leipzig University Medical Center, Leipzig, Germany
Interests: biofilms; interface; dental materials; saliva

Special Issue Information

Dear Colleagues,

Over the past few decades, increased understanding of oral biology and advances in technology have facilitated more accurate simulation of intraoral conditions and have allowed the development of in vitro biofilm model systems to quantify biofilm architecture and analyze microbial community composition. With the development of culture independent techniques, such as RT-PCR and NGS, the detection and identification of the non-cultivable bacteria have become possible. Investigations through metagenomics, genomics and proteomics have widened our view on oral bacteria and influenced the traditional patterns of oral infection therapy.

In recent years, many studies have reported the increased resistance of oral pathogens to several antibiotics. On the other hand, there are newly emerged oral pathogens whose antimicrobial susceptibility is still unknown. This underlines the necessity of reliable routine identification and susceptibility testing methods for oral pathogens and the implementation of antimicrobial surveillance all over the world.

In this Special Issue of Microorganisms, we invite you to send your contributions regarding any aspects of the ability of oral bacteria to form biofilms or concerning the impact of genome investigation on our understanding of oral pathogens. In addition, research on the antimicrobial susceptibility of oral pathogen-based studies is welcome for this Special Issue.

Dr. Catalina-Suzana Stingu
Prof. Dr. Sebastian Hahnel
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

genome
oral pathogen
biofilm
antimicrobial susceptibility

Published Papers (5 papers)

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Research

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19 pages, 2784 KiB

Open AccessArticle

Genomic Diversity among Actinomyces naeslundii Strains and Closely Related Species

by Sadaf Rasheed Mughal, Sadia Ambreen Niazi, Thuy Do, Steven C. Gilbert, Xavier Didelot, David R. Radford and David Beighton

Microorganisms 2023, 11(2), 254; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11020254 - 19 Jan 2023

Cited by 2 | Viewed by 1546

Abstract

The aim of this study was to investigate and clarify the ambiguous taxonomy of Actinomyces naeslundii and its closely related species using state-of-the-art high-throughput sequencing techniques, and, furthermore, to determine whether sub-clusters identified within Actinomyces oris and Actinomyces naeslundii in a previous study by multi locus sequence typing (MLST) using concatenation of seven housekeeping genes should either be classified as subspecies or distinct species. The strains in this study were broadly classified under Actinomyces naeslundii group as A. naeslundii genospecies I and genospecies II. Based on MLST data analysis, these were further classified as A. oris and A. naeslundii. The whole genome sequencing of selected strains of A. oris (n = 17) and A. naeslundii (n = 19) was carried out using Illumina Genome Analyzer IIxe and Roche 454 allowing paired-end and single-reads sequencing, respectively. The sequences obtained were aligned using CLC Genomic workbench version 5.1 and annotated using RAST (Rapid Annotation using Subsystem Technology) release version 59 accessible online. Additionally, genomes of seven publicly available strains of Actinomyces (k20, MG1, c505, OT175, OT171, OT170, and A. johnsonii) were also included. Comparative genomic analysis (CGA) using Mauve, Progressive Mauve, gene-by-gene, Core, and Pan Genome, and finally Digital DNA-DNA homology (DDH) analysis was carried out. DDH values were obtained using in silico genome–genome comparison. Evolutionary analysis using ClonalFrame was also undertaken. The mutation and recombination events were compared using chi-square test among A. oris and A. naeslundii isolates (analysis methods are not included in the study). CGA results were consistent with previous traditional classification using MLST. It was found that strains of Actinomyces k20, MG1, c505, and OT175 clustered in A. oris group of isolates, while OT171, OT170, and A. johnsonii appeared as separate branches. Similar clustering to MLST was observed for other isolates. The mutation and recombination events were significantly higher in A. oris than A. naeslundii, highlighting the diversity of A. oris strains in the oral cavity. These findings suggest that A. oris forms six distinct groups, whereas A. naeslundii forms three. The correct designation of isolates will help in the identification of clinical Actinomyces isolates found in dental plaque. Easily accessible online genomic sequence data will also accelerate the investigation of the biochemical characterisation and pathogenesis of this important group of micro-organisms. Full article

(This article belongs to the Special Issue Genome, Biofilm Forming Ability and Antibiotic Resistance of Oral Pathogenic Bacteria)

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11 pages, 2658 KiB

Open AccessArticle

Preclinical Testing of Boron-Doped Diamond Electrodes for Root Canal Disinfection—A Series of Preliminary Studies

by Maximilian Koch, Victor Palarie, Lisa Koch, Andreas Burkovski, Manuel Zulla, Stefan Rosiwal and Matthias Karl

Microorganisms 2022, 10(4), 782; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10040782 - 07 Apr 2022

Cited by 3 | Viewed by 1900

Abstract

While numerous approaches have meanwhile been described, sufficient disinfection of root canals is still challenging, mostly due to limited access and the porous structure of dentin. Instead of using different rinsing solutions and activated irrigation, the electrolysis of saline using boron-doped diamond (BDD) electrodes thereby producing reactive oxygen species may be an alternative approach. In a first step, experiments using extracted human teeth incubated with multispecies bacterial biofilm were conducted. The charge quantities required for electrochemical disinfection of root canals were determined, which were subsequently applied in an animal trial using an intraoral canine model. It could be shown that also under realistic clinical conditions, predictable disinfection of root canals could be achieved using BDD electrodes. The parameters required are in the range of 5.5 to 7.0 V and 9 to 38 mA, applied for 2.5 to 6.0 min with approximately 5 to 8 mL of saline. The direct generation of disinfective agents inside the root canal seems to be advantageous especially in situations with compromised access and limited canal sizes. The biologic effect with respect to the host reaction on BDD-mediated disinfection is yet to be examined. Full article

(This article belongs to the Special Issue Genome, Biofilm Forming Ability and Antibiotic Resistance of Oral Pathogenic Bacteria)

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14 pages, 1224 KiB

Open AccessArticle

Transcriptomic Stress Response in Streptococcus mutans following Treatment with a Sublethal Concentration of Chlorhexidine Digluconate

by Denise Muehler, Xiaojun Mao, Stefan Czemmel, Janina Geißert, Christina Engesser, Karl-Anton Hiller, Matthias Widbiller, Tim Maisch, Wolfgang Buchalla, Ali Al-Ahmad and Fabian Cieplik

Microorganisms 2022, 10(3), 561; https://doi.org/10.3390/microorganisms10030561 - 04 Mar 2022

Cited by 8 | Viewed by 2133

Abstract

Despite the widespread use of antiseptics such as chlorhexidine digluconate (CHX) in dental practice and oral care, the risks of potential resistance toward these antimicrobial compounds in oral bacteria have only been highlighted very recently. Since the molecular mechanisms behind antiseptic resistance or adaptation are not entirely clear and the bacterial stress response has not been investigated systematically so far, the aim of the present study was to investigate the transcriptomic stress response in Streptococcus mutans after treatment with CHX using RNA sequencing (RNA-seq). Planktonic cultures of stationary-phase S. mutans were treated with a sublethal dose of CHX (125 µg/mL) for 5 min. After treatment, RNA was extracted, and RNA-seq was performed on an Illumina NextSeq 500. Differentially expressed genes were analyzed and validated by qRT-PCR. Analysis of differential gene expression following pathway analysis revealed a considerable number of genes and pathways significantly up- or downregulated in S. mutans after sublethal treatment with CHX. In summary, the expression of 404 genes was upregulated, and that of 271 genes was downregulated after sublethal CHX treatment. Analysis of differentially expressed genes and significantly regulated pathways showed regulation of genes involved in purine nucleotide synthesis, biofilm formation, transport systems and stress responses. In conclusion, the results show a transcriptomic stress response in S. mutans upon exposure to CHX and offer insight into potential mechanisms that may result in development of resistances. Full article

(This article belongs to the Special Issue Genome, Biofilm Forming Ability and Antibiotic Resistance of Oral Pathogenic Bacteria)

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11 pages, 257 KiB

Open AccessArticle

Antimicrobial Susceptibility of Clinical Oral Isolates of Actinomyces spp.

by Alexandra Wolff, Arne C. Rodloff, Paul Vielkind, Toralf Borgmann and Catalina-Suzana Stingu

Microorganisms 2022, 10(1), 125; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10010125 - 07 Jan 2022

Cited by 5 | Viewed by 2625

Abstract

Actinomyces species play an important role in the pathogenesis of oral diseases and infections. Susceptibility testing is not always routinely performed, and one may oversee a shift in resistance patterns. The aim of the study was to analyze the antimicrobial susceptibility of 100 well-identified clinical oral isolates of Actinomyces spp. against eight selected antimicrobial agents using the agar dilution (AD) and E-Test (ET) methods. We observed no to low resistance against penicillin, ampicillin-sulbactam, meropenem, clindamycin, linezolid and tigecycline (0–2% ET, 0% AD) but high levels of resistance to moxifloxacin (93% ET, 87% AD) and daptomycin (83% ET, 95% AD). The essential agreement of the two methods was very good for benzylpenicillin (EA 95%) and meropenem (EA 92%). The ET method was reliable for correctly categorizing susceptibility, in comparison with the reference method agar dilution, except for daptomycin (categorical agreement 87%). Penicillin is still the first-choice antibiotic for therapy of diseases caused by Actinomyces spp. Full article

(This article belongs to the Special Issue Genome, Biofilm Forming Ability and Antibiotic Resistance of Oral Pathogenic Bacteria)

Review

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17 pages, 1289 KiB

Open AccessReview

Culturing the Human Oral Microbiota, Updating Methodologies and Cultivation Techniques

by Saber Khelaifia, Pilliol Virginie, Souad Belkacemi, Herve Tassery, Elodie Terrer and Gérard Aboudharam

Microorganisms 2023, 11(4), 836; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11040836 - 24 Mar 2023

Cited by 1 | Viewed by 2255

Abstract

Recent years have been marked by a paradigm shift in the study of the human microbiota, with a re-emergence of culture-dependent approaches. Numerous studies have been devoted to the human microbiota, while studies on the oral microbiota still remain limited. Indeed, various techniques described in the literature may enable an exhaustive study of the microbial composition of a complex ecosystem. In this article, we report different methodologies and culture media described in the literature that can be applied to study the oral microbiota by culture. We report on specific methodologies for targeted culture and specific culture techniques and selection methodologies for cultivating members of the three kingdoms of life commonly found in the human oral cavity, namely, eukaryota, bacteria and archaea. This bibliographic review aims to bring together the various techniques described in the literature, enabling a comprehensive study of the oral microbiota in order to demonstrate its involvement in oral health and diseases. Full article

(This article belongs to the Special Issue Genome, Biofilm Forming Ability and Antibiotic Resistance of Oral Pathogenic Bacteria)

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