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Microorganisms
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Advances in Oral Microorganisms and Biofilms
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Advances in Oral Microorganisms and Biofilms

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

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 15145

Special Issue Editor

Dr. Raluca Cosgarea

E-Mail Website
Guest Editor
Poliklinik für Parodontologie, Zahnerhaltung und Präventive Zahnheilkunde, Universitätklinikum Bonn, Welschnonnenstr. 17, 53111 Bonn, Germany
Interests: orial microbiome; oral biofilm; periodontal diseases

Special Issue Information

Dear Colleagues,

The oral microflora plays an important role in maintaining oral and systemic health. A large variety of bacteria, viruses, and fungi form complex biofilm communities interacting in a synergistic manner in various environments of the oral cavity. A dysbiosis in these biofilms plays a key role in the pathoetiology of several oral and systemic diseases. The emergence of advanced molecular methods with gene sequencing and various microscopy and DNA analyses has expanded our knowledge of the compositions and function of oral microorganisms and biofilms, as well as the role of the oral microbiome in health and disease. Studies focusing on oral microorganisms and the host-immune response are critical in understanding the etiopathology of several oral or systemic diseases and developing and channeling appropriate therapies.

This Special Issue focusses on publishing data related to oral microorganisms and biofilms in periodontal and peri-implant infections, in dental caries and endodontic infections, as well as other oral diseases. The aim is to present research outcomes related to the role and impact of oral microorganisms and biofilms, as well as therapeutical strategies and new developments in reestablishing dysbiotical microbial changes and resolution of inflammation.

We invite you to submit research articles, review articles, communications, and perspective related to oral microorganisms and biofilms.

Dr. Raluca Cosgarea
Guest Editor

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

  • oral microbiome
  • oral biofilm
  • oral pathogens
  • microorganisms
  • endodontic infections
  • dental caries
  • periodontal diseases
  • peri-implant disease
  • oral candidiasis
  • antimicrobial therapy

Published Papers (7 papers)

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Research

Jump to: Review

27 pages, 2173 KiB  
Article
Phenotypic Analysis, Molecular Characterization, and Antibiogram of Caries-Causing Bacteria Isolated from Dental Patients
by Khushbu Farva, Huma Sattar, Hayat Ullah, Abdur Raziq, Muhammad Danish Mehmood, Afrasiab Khan Tareen, Imrana Niaz Sultan, Quratulaain Zohra and Muhammad Waseem Khan
Microorganisms 2023, 11(8), 1952; https://doi.org/10.3390/microorganisms11081952 - 31 Jul 2023
Cited by 3 | Viewed by 1830
Abstract
Dental caries is a biofilm-mediated, sugar-driven, multifactorial, dynamic disease that results in the phasic demineralization and remineralization of dental hard tissues. Despite scientific advances in cariology, dental caries remains a severe global concern. The aim of this study was to determine the optimization [...] Read more.
Dental caries is a biofilm-mediated, sugar-driven, multifactorial, dynamic disease that results in the phasic demineralization and remineralization of dental hard tissues. Despite scientific advances in cariology, dental caries remains a severe global concern. The aim of this study was to determine the optimization of microbial and molecular techniques for the detection of cariogenic pathogens in dental caries patients, the prevalence of cariogenic bacteria on the basis of socioeconomic, climatological, and hygienic factors, and in vitro evaluation of the antimicrobial activity of selected synthetic antibiotics and herbal extracts. In this study, oral samples were collected from 900 patients for bacterial strain screening on a biochemical and molecular basis. Plant extracts, such as ginger, garlic, neem, tulsi, amla, and aloe vera, were used to check the antimicrobial activity against the isolated strains. Synthetic antimicrobial agents, such as penicillin, amoxicillin, erythromycin, clindamycin, metronidazole, doxycycline, ceftazidime, levofloxacin, and ciprofloxacin, were also used to access the antimicrobial activity. Among 900 patients, 63% were males and 37% were females, patients aged between 36 and 58 (45.7%) years were prone to disease, and the most common symptom was toothache (61%). For oral diseases, 21% used herbs, 36% used antibiotics, and 48% were self-medicated, owing to sweets consumption (60.66%) and fizzy drinks and fast food (51.56%). Staphylococcus mutans (29.11%) and Streptococcus sobrinus (28.11%) were found as the most abundant strains. Seven bacterial strains were successfully screened and predicted to be closely related to genera S. sobrinus, S. mutans, Actinomyces naeslundii, Lactobacillus acidophilus, Eubacterium nodatum, Propionibacterium acidifaciens, and Treponema Pallidum. Among plant extracts, the maximum zone of inhibition was recorded by ginger (22.36 mm) and amla (20.01 mm), while among synthetic antibiotics, ciprofloxacin and levofloxacin were most effective against all microbes. This study concluded that phyto extracts of ginger and amla were considered suitable alternatives to synthetic antibiotics to treat dental diseases. Full article
(This article belongs to the Special Issue Advances in Oral Microorganisms and Biofilms)
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15 pages, 3334 KiB  
Article
A Transcriptional Analysis Showing the Effects of GH12 Combined with Fluoride for Suppressing the Acidogenicity of Streptococcus mutans Biofilms
by Yuhao Zeng, Yu Chen, Chengchen Duan, Xuelian Jiang, Yufei Wang and Linglin Zhang
Microorganisms 2023, 11(7), 1796; https://doi.org/10.3390/microorganisms11071796 - 13 Jul 2023
Cited by 1 | Viewed by 1164
Abstract
The acidogenicity of Streptococcus mutans is important for caries development. The antimicrobial peptide GH12 can affect the integrity of cellular membranes and the virulence factors of S. mutans. Combining GH12 and NaF (GF) efficiently controlled the development of caries, but its mechanisms [...] Read more.
The acidogenicity of Streptococcus mutans is important for caries development. The antimicrobial peptide GH12 can affect the integrity of cellular membranes and the virulence factors of S. mutans. Combining GH12 and NaF (GF) efficiently controlled the development of caries, but its mechanisms remained unrevealed. This research intended to verify the effects of GF on the acidogenicity of S. mutans biofilms and to reveal the mechanisms. Lactic acid production assays and pH monitoring assays were conducted to investigate the regulatory effects of the GF treatment on the acidogenicity of S. mutans biofilms. RNA sequencing and bioinformatics analyses were conducted to screen the transcriptional profile affected by the GF treatment. The results demonstrated the GF group had significantly less lactic acid and maintained the broth’s pH values above 5.0 for longer times. Thereafter, GO/KEGG enrichment analyses and RT-qPCR validation revealed that the GF treatment mainly restrained the expression of genes related to the carbohydrates’ internalization and metabolism. Compared with NaF, the GF treatment further downregulated the carbohydrates transportation genes. Moreover, compared with GH12, the GF treatment affected the membrane’s integrity more significantly. Generally, GF treatment could arrest the acidogenicity of S. mutans biofilms, mainly through suppressing carbohydrates transportation and inhibiting overall metabolism. Full article
(This article belongs to the Special Issue Advances in Oral Microorganisms and Biofilms)
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11 pages, 2258 KiB  
Article
Effects of Bacterial Metabolites on the Wnt4 Protein in Dental-Pulp-Stem-Cells-Based Endodontic Pulpitis Treatment
by Ayman M. Abulhamael, Shilpa Bhandi, Nasreen H. Albar, Amal S. Shaiban, Shashit Shetty Bavabeedu, Khalid J. Alzahrani, Fuad M. Alzahrani, Ibrahim F. Halawani and Shankargouda Patil
Microorganisms 2023, 11(7), 1764; https://doi.org/10.3390/microorganisms11071764 - 6 Jul 2023
Viewed by 1145
Abstract
Porphyromonas gingivalis is associated with endodontic pulpitis, causing damage to the dental pulp, leading to severe pain and a decline in quality of life. Regenerative pulp treatments using dental pulp stem cells (DPSCs) can be hindered by interactions between DPSCs and the infecting [...] Read more.
Porphyromonas gingivalis is associated with endodontic pulpitis, causing damage to the dental pulp, leading to severe pain and a decline in quality of life. Regenerative pulp treatments using dental pulp stem cells (DPSCs) can be hindered by interactions between DPSCs and the infecting bacteria. The protein WNT family member 4 (Wnt4) plays a critical role in the differentiation of DPSCs and the regeneration of odontogenic tissue. However, the specific influence of P. gingivalis on Wnt4 remains unclear. In this study, we employed a computational approach to investigate the underlying mechanisms through which P. gingivalis-produced metabolites inhibit the Wnt4 protein, thereby diminishing the regenerative potential and therapeutic efficacy of odontogenic tissue. Among the metabolites examined, C29H46N7O18P3S−4 exhibited the strongest inhibitory effect on the Wnt4 protein, as evidenced by the lowest binding energy score of −6782 kcal/mol. Molecular dynamic simulation trajectories revealed that the binding of C29H46N7O18P3S−4 significantly altered the structural dynamics and stability of the Wnt4 protein. These alterations in protein trajectories may have implications for the molecular function of Wnt4 and its associated pathways. Overall, our findings shed light on the inhibitory impact of P. gingivalis-produced metabolites on the Wnt4 protein. Further in vitro, in vivo, and clinical studies are necessary to validate and expand upon our findings. Full article
(This article belongs to the Special Issue Advances in Oral Microorganisms and Biofilms)
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11 pages, 1226 KiB  
Communication
Used Nasogastric Feeding Tubes from Neonates Contain Infant-Specific Bacterial Profiles
by Sandra Meinich Juhl, Karen Angeliki Krogfelt, Witold Kot, Dennis Sandris Nielsen and Lukasz Krych
Microorganisms 2023, 11(6), 1365; https://doi.org/10.3390/microorganisms11061365 - 23 May 2023
Cited by 2 | Viewed by 1470
Abstract
Nasogastric feeding tubes (NG-tubes) from neonates contain potentially pathogenic bacteria. Using culture-based techniques, we have previously determined that the usage duration of NG-tubes did not impact the colonization of the nasogastric tubes. In the present study, we performed 16S rRNA gene amplicon sequencing [...] Read more.
Nasogastric feeding tubes (NG-tubes) from neonates contain potentially pathogenic bacteria. Using culture-based techniques, we have previously determined that the usage duration of NG-tubes did not impact the colonization of the nasogastric tubes. In the present study, we performed 16S rRNA gene amplicon sequencing to evaluate the microbial profile of 94 used nasogastric tubes collected from a single neonatal intensive care unit. Using culture-based whole genome sequencing, we as-sessed whether the same strain persisted in NG-tubes collected from the same neonate across different time-points. We found that the most commonly occurring Gram-negative bacteria were Enterobacteriaceae, Klebsiella and Serratia, while the most common Gram-positive bacteria were staphylococci and streptococci. The microbiota of the NG-feeding tube was overall infant-specific, rather than dependent on the duration of use. Furthermore, we determined that reoccurring species from the individual infant represented the same strain and that several strains were common for more than one infant. Our findings indicate that bacterial profiles found in NG-tubes of neonates are host-specific, not dependent on the duration of use and strongly influenced by the environment. Full article
(This article belongs to the Special Issue Advances in Oral Microorganisms and Biofilms)
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12 pages, 659 KiB  
Article
Pilot Study on the Prevalence of Entamoeba gingivalis in Austria—Detection of a New Genetic Variant
by Martina Köhsler, Edwin Kniha, Angelika Wagner and Julia Walochnik
Microorganisms 2023, 11(5), 1094; https://doi.org/10.3390/microorganisms11051094 - 22 Apr 2023
Viewed by 1519
Abstract
Entamoeba gingivalis is a parasitic protist that resides in the oral cavity. Although E. gingivalis has been frequently detected in individuals with periodontitis, its precise role in this context remains to be established, since E. gingivalis is also regularly found in healthy individuals. [...] Read more.
Entamoeba gingivalis is a parasitic protist that resides in the oral cavity. Although E. gingivalis has been frequently detected in individuals with periodontitis, its precise role in this context remains to be established, since E. gingivalis is also regularly found in healthy individuals. Sequence data on E. gingivalis are still scarce, with only a limited number of sequences available in public databases. In this study, a diagnostic PCR protocol was established in order to obtain a first impression on the prevalence of E. gingivalis in Austria and enable a differentiation of isolates by targeting the variable internal transcribed spacer regions. In total, 59 voluntary participants were screened for E. gingivalis and almost 50% of the participants were positive, with a significantly higher prevalence of participants with self-reported gingivitis. Moreover, in addition to the established subtypes ST1 and ST2, a potentially new subtype was found, designated ST3. 18S DNA sequencing and phylogenetic analyses clearly supported a separate position of ST3. Interestingly, subtype-specific PCRs revealed that, in contrast to ST2, ST3 only occurred in association with ST1. ST2 and ST1/ST3 were more often associated with gingivitis; however, more data will be necessary to corroborate this observation. Full article
(This article belongs to the Special Issue Advances in Oral Microorganisms and Biofilms)
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Review

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17 pages, 1932 KiB  
Review
Antimicrobial Activity of Honey against Oral Microorganisms: Current Reality, Methodological Challenges and Solutions
by Diego Romário-Silva, Severino Matias Alencar, Bruno Bueno-Silva, Janaína de Cássia Orlandi Sardi, Marcelo Franchin, Rafaela Durrer Parolina de Carvalho, Thayná Ellen de Sousa Alves Ferreira and Pedro Luiz Rosalen
Microorganisms 2022, 10(12), 2325; https://doi.org/10.3390/microorganisms10122325 - 24 Nov 2022
Cited by 7 | Viewed by 4226
Abstract
Honey has been shown to have antimicrobial activity against different microorganisms, but its effects on oral biofilms are largely unknown. In this review, we analyzed the currently available literature on the antimicrobial activity of honey against oral biofilms in order to determine its [...] Read more.
Honey has been shown to have antimicrobial activity against different microorganisms, but its effects on oral biofilms are largely unknown. In this review, we analyzed the currently available literature on the antimicrobial activity of honey against oral biofilms in order to determine its potential as a functional food in the treatment and/or prevention of oral diseases. Here, we compare studies reporting on the antimicrobial activity of honey against systemic and oral bacteria, discuss methodological strategies, and point out current gaps in the literature. To date, there are no consistent studies supporting the use of honey as a therapy for oral diseases of bacterial origin, but current evidence in the field is promising. The lack of studies examining the antibiofilm activity of honey against oral microorganisms reveals a need for additional research to better define aspects such as chemical composition, the mechanism(s) of action, and antimicrobial action. Full article
(This article belongs to the Special Issue Advances in Oral Microorganisms and Biofilms)
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20 pages, 980 KiB  
Review
Propolis, Aloe Vera, Green Tea, Cranberry, Calendula, Myrrha and Salvia Properties against Periodontal Microorganisms
by Luciene Cristina Figueiredo, Nathalia Freitas Figueiredo, Daniele Ferreira da Cruz, Gustavo Titonele Baccelli, Gabriela Espinoza Sarachini, Manuela Rocha Bueno, Magda Feres and Bruno Bueno-Silva
Microorganisms 2022, 10(11), 2172; https://doi.org/10.3390/microorganisms10112172 - 31 Oct 2022
Cited by 10 | Viewed by 3031
Abstract
The oral cavity harbors hundreds of microorganisms that may be uncontrolled and provoke several diseases. In this sense, periodontitis is a complex multifactorial disease with an essential microbial component in its etiology. Periodontal treatment involves mechanical control of the supra- and subgingival biofilm, [...] Read more.
The oral cavity harbors hundreds of microorganisms that may be uncontrolled and provoke several diseases. In this sense, periodontitis is a complex multifactorial disease with an essential microbial component in its etiology. Periodontal treatment involves mechanical control of the supra- and subgingival biofilm, but not all patients respond predictably to treatment. In this way, the biofilm chemical control helps in the reduction of periodontal pathogens during treatment or in the delay of bacterial re-colonization after scaling and root planning. Several products have been studied as adjunctive therapy and have shown promising results. Therefore, the present article reviews the biological effects of propolis, aloe vera, green tea, cranberry, calendula, myrrha and salvia that may support their use in the control of subgingival biofilm in patients with periodontitis. All the natural products cited above showed exciting results against microorganisms related to oral diseases, mainly periodontitis. These substances also have anti-inflammatory and antioxidant activities. The natural agents propolis, aloe vera, green tea, cranberry, calendula, myrrha and salvia demonstrated potential to be used as oral hygiene products, based on their antimicrobial and anti-inflammatory actions. Full article
(This article belongs to the Special Issue Advances in Oral Microorganisms and Biofilms)
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