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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 December 2022) | Viewed by 21881

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Special Issue Editors

Dr. David R. Drake

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Guest Editor

Iowa Institute for Oral Health Research, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA
Interests: development of the oral microbiome and role in oral diseases
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Jeffrey A. Banas

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Guest Editor

Special Issue Information

Dear Colleagues,

The composition and activities of the oral microbiome play a foundational role in health and disease within the oral cavity and beyond. This Special Issue is dedicated to the breadth of research focusing on how variables such as microbial properties, host genetics, cell biology, and immunology interact with environmental influences to maintain or disrupt the healthy balance between the host and resident microflora in oral.

Dr. David R. Drake
Dr. Jeffrey A. Banas
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

oral microbiome
dental diseases
dental caries
periodontitis oral cancer
oral microbiology
oral pathogens
host genetics
immunology
nutrition dysbiosis
oral hygiene

Published Papers (10 papers)

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Research

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10 pages, 889 KiB

Open AccessArticle

Prevalence of Oral Pathogen Slackia exigua among Clinical Orthodontic and Non-Orthodontic Saliva Samples

by Ching Shen, Justin Simpson, James Brigham Clawson, Steven Lam and Karl Kingsley

Microorganisms 2023, 11(4), 867; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11040867 - 28 Mar 2023

Cited by 1 | Viewed by 1063

Abstract

Slackia exigua (SE) is a recently identified intestinal microbe, which recent oral surveys suggest may be associated with oral diseases including caries and periodontal disease. Based upon the lack of information regarding this organism, the primary objective of this study was to determine the oral prevalence of this microbe and any potential associations with patient characteristics such as age, sex, or the presence of orthodontic appliances. This retrospective study involved the screening of an existing saliva repository composed of previously collected unstimulated clinical saliva samples. More specifically, N = 266 were identified and screened using a spectrophotometer at absorbances of A260 and A280 nm to determine their DNA purity and concentration. qPCR screening of these samples revealed a higher prevalence of Slackia exigua positive samples among pediatric patients (63.1%) compared with adults (36.9%) in this clinic population, p = 0.0007. In addition, higher percentages of Slackia exigua were observed among orthodontic patients (71.2%) compared with non-orthodontic patients (28.8%), p = 0.0001. These results did not vary by sex with nearly equal percentages of Slackia exigua positive males and females among adult and pediatric patients, as well as orthodontic and non-orthodontic samples. These results suggest a strong potential for association between the prevalence of this organism with age as well as orthodontic status, given that younger patients and those with orthodontic brackets (regardless of age) were most likely to harbor this pathogen in sufficient levels to be detected in saliva. More research will be needed to determine any associations with specific outcomes, such as caries or periodontal disease, among Slackia exigua positive patients within these specific populations. Full article

(This article belongs to the Special Issue Microbiology of Oral Diseases)

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11 pages, 758 KiB

Open AccessArticle

In Vitro Assessment of Biofilm Production, Antibacterial Resistance of Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter spp. Obtained from Tonsillar Crypts of Healthy Adults

by Renata Viksne, Karlis Racenis, Renars Broks, Arta Olga Balode, Ligija Kise and Juta Kroica

Microorganisms 2023, 11(2), 258; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11020258 - 19 Jan 2023

Cited by 2 | Viewed by 1691

Abstract

Background and Objective: Tonsillar crypts can be considered a reservoir for a variety of bacterial species. Some bacterial species can be considered part of the normal oropharyngeal microbiota. The roles of other pathogens, for example, the so-called non-oral and respiratory pathogens Staphylococcus aureus, Klebsiella, Pseudomonas, and Acinetobacter spp., which have strong virulence factors, biofilm production capacity, and the ability to initiate infectious diseases, are unclear. The purpose of this study was to detect the presence of S. aureus, K. pneumoniae, P. aeruginosa, and Acinetobacter spp. within the tonsillar crypts of healthy individuals, and to analyze the pathogens’ biofilm production and antibacterial resistances. Results: Only common oropharyngeal microbiota were cultivated from 37 participant samples (40.7%). The most commonly isolated pathogenic bacterium was S. aureus, which was isolated in 41 (45%) participant samples. K. pneumoniae was isolated in seven (7.7%) samples, Acinetobacter spp. were isolated in five (5.5%) samples, and P. aeruginosa was isolated in two (2.2%) samples. Biofilm producers predominated among the pathogenic bacteria; 51 strains were biofilm producers, and among them, 31 strains were moderate or strong biofilm producers. The tested S. aureus, K. pneumoniae, P. aeruginosa, and Acinetobacter spp. strains were sensitive to commonly used antibiotics (amoxicillin–clavulanic acid, clindamycin, or ciprofloxacin). One of the isolated S. aureus strains was MRSA. Conclusions: Biofilm is a commonly observed feature that seems to be a naturally existing form of pathogenic bacteria colonizing human tissue. S. aureus, K. pneumoniae, P. aeruginosa, and Acinetobacter spp. occasionally occur in the tonsillar crypts of healthy individuals, and, therefore, it is most likely that S. aureus, K. pneumoniae, P. aeruginosa, and Acinetobacter spp. in opportunistic tonsillar infections originate from the tonsillar crypt microbiota. Full article

(This article belongs to the Special Issue Microbiology of Oral Diseases)

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12 pages, 804 KiB

Open AccessArticle

Oral Prevalence of Akkermansia muciniphila Differs among Pediatric and Adult Orthodontic and Non-Orthodontic Patients

by Ching Shen, James Brigham Clawson, Justin Simpson and Karl Kingsley

Microorganisms 2023, 11(1), 112; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11010112 - 01 Jan 2023

Cited by 2 | Viewed by 2136

Abstract

Akkermansia muciniphila (AM) is one of many highly abundant intestinal microbes that influences homeostasis and metabolic disorders and may also play a role in oral disorders. However, there is little evidence regarding the oral prevalence of this organism. Based upon this lack of evidence, the primary goal of this project is to survey an existing saliva repository to determine the overall prevalence of this organism and any associations with demographic or patient characteristics (age, sex, body mass index, race/ethnicity, orthodontic therapy). Using an approved protocol,, a total n = 141 pediatric samples from an existing saliva repository were screened using qPCR revealing 29.8% harbored AM with nearly equal distribution among males and females, p = 0.8347. Significantly higher percentages of pediatric, non-orthodontic patients were positive for AM (42.3%) compared with age-matched orthodontic patients (14.3%)—which were equally distributed among non-orthodontic males (42.1%) and non-orthodontic females (42.5%). In addition, analysis of the adult samples revealed that nearly equal percentages of males (18.2%) and females (16.7%) harbored detectable levels of salivary AM, p = 0.2035. However, a higher proportion of non-orthodontic adult samples harbored AM (21.3%) compared to orthodontic samples (12.8%, p = 0.0001), which was equally distributed among males and females. These results suggest that both age and the presence of orthodontic brackets may influence microbial composition and, more specifically, are associated with reduction in AM among both pediatric and adult populations from their baseline levels. Full article

(This article belongs to the Special Issue Microbiology of Oral Diseases)

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10 pages, 1716 KiB

Open AccessArticle

Maternal Gut Microbiome Decelerates Fetal Endochondral Bone Formation by Inducing Inflammatory Reaction

by Yoko Uchida-Fukuhara, Takako Hattori, Shanqi Fu, Sei Kondo, Miho Kuwahara, Daiki Fukuhara, Md Monirul Islam, Kota Kataoka, Daisuke Ekuni, Satoshi Kubota, Manabu Morita, Mika Iikegame and Hirohiko Okamura

Microorganisms 2022, 10(5), 1000; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10051000 - 10 May 2022

Cited by 1 | Viewed by 1895

Abstract

To investigate the effect of the maternal gut microbiome on fetal endochondral bone formation, fetuses at embryonic day 18 were obtained from germ-free (GF) and specific-pathogen-free (SPF) pregnant mothers. Skeletal preparation of the fetuses’ whole bodies did not show significant morphological alterations; however, micro-CT analysis of the tibiae showed a lower bone volume fraction in the SPF tibia. Primary cultured chondrocytes from fetal SPF rib cages showed a lower cell proliferation and lower accumulation of the extracellular matrix. RNA-sequencing analysis showed the induction of inflammation-associated genes such as the interleukin (IL) 17 receptor, IL 6, and immune-response genes in SPF chondrocytes. These data indicate that the maternal gut microbiome in SPF mice affects fetal embryonic endochondral ossification, possibly by changing the expression of genes related to inflammation and the immune response in fetal cartilage. The gut microbiome may modify endochondral ossification in the fetal chondrocytes passing through the placenta. Full article

(This article belongs to the Special Issue Microbiology of Oral Diseases)

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6 pages, 686 KiB

Open AccessCommunication

Reverse Genomics: Design of Universal Epitope Sets to Isolate All Saccharibacteria Members from the Human Oral Cavity

by Ahmad Ibrahim, Mohamad Maatouk, Didier Raoult and Fadi Bittar

Microorganisms 2022, 10(3), 602; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10030602 - 11 Mar 2022

Cited by 3 | Viewed by 2058

Abstract

Microorganisms not yet cultured represent a large proportion of the microbes described to date. Progress in sequencing and metagenomic tools continues to increase microbial diversity without providing information on their physiological and pathophysiological characteristics, such as the recent discovery of enigmatic microbes belonging to Candidate Phyla Radiation (CPR). Reverse genomics is a recent technique allowing co-cultivation of a few CPR members, affiliated to the Saccharibacteria phylum, based on the analysis of their already-available genomes. Here, our aim is to designate a common system capable of cultivating any given taxon of this phylum from human samples. We managed to design, in silico, 11 common epitopes for all Saccharibacteria species recovered from the human oral cavity and which can serve as antigens via bioinformatics analyses. These sequences allow the synthesis of target antibodies, sorting Saccharibacteria spp. by flow cytometry and co-culturing them afterwards with adapted hosts. This epitope set can facilitate the cultivation of CPR in general, which in recent years has been considered a challenge for microbiologists, and subsequently contributes to better studying this new branch on the tree of life. Full article

(This article belongs to the Special Issue Microbiology of Oral Diseases)

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18 pages, 9127 KiB

Open AccessArticle

The Use of a Diode Laser for Removal of Microorganisms from the Surfaces of Zirconia and Porcelain Applied to Superstructure Dental Implants

by Anna Wawrzyk, Michał Łobacz, Agnieszka Adamczuk, Weronika Sofińska-Chmiel, Sławomir Wilczyński and Mansur Rahnama

Microorganisms 2021, 9(11), 2359; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112359 - 15 Nov 2021

Cited by 5 | Viewed by 1683

Abstract

The aim of this paper was to study the effectiveness of a diode laser (LD) for removal of microorganisms isolated from porcelain and zirconia crown surfaces used in implantoprosthetics in order to minimize infections around dental implants. In order to optimize biocidal efficacy of the process (at the same time, avoiding increasing the surface roughness during decontamination) the effects of diode laser doses were investigated. The irradiation was performed with a diode laser at the wavelength of λ = 810 nm in three variants with a different number of repetitions (1 × 15 s, 2 × 15 s, 3 × 15 s). The quantitative microbial contamination of the surface of teeth, porcelain and zirconia crowns assessment was made using the culture-dependent method. The identification of microorganisms took place using the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and next-generation sequencing (NGS) methods. The studies of the surface morphology and roughness were carried out by means of the optical profilometry, scanning electron microscopy (SEM) and optical microscopy with the C1 confocal attachment. The most important conclusion from the research is the fact that the laser operation, regardless of the exposure time, effectively eliminates the microorganisms from the surfaces used for dental implant rebuilding and does not have a destructive effect on the tested material. Full article

(This article belongs to the Special Issue Microbiology of Oral Diseases)

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Review

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13 pages, 3920 KiB

Open AccessReview

An Outlook on Dental Practices to Avoid the Oral Transmission of COVID-19

by Manal Alsulami, Waad Kattan, Lama Alsamadani, Ghadah Alahmari, Wasan Al Juhani and Maha Almabadi

Microorganisms 2023, 11(1), 146; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11010146 - 06 Jan 2023

Cited by 1 | Viewed by 2056

Abstract

The oral microbiome plays an important role in the maintenance of immune homeostasis, whereas its association with SARS-CoV-2 infection remains under investigation. Since the oral path is one of the transmission routes for COVID-19, we attempt to show the relationship between the oral microbiome, COVID-19 infection, and oral hygiene. We highlight the importance of oral hygiene to control the infection, especially for ICU cases with COVID-19. Moreover, we present the current strategies adapted by in-person dental clinics to overcome the spread of COVID-19. New emerging policies and protocols suggested during the pandemic and their future implementation to minimize virus transmission are also summarized in this review. Full article

(This article belongs to the Special Issue Microbiology of Oral Diseases)

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18 pages, 1186 KiB

Open AccessReview

Another Look at the Contribution of Oral Microbiota to the Pathogenesis of Rheumatoid Arthritis: A Narrative Review

by Jean-Marie Berthelot, Octave Nadile Bandiaky, Benoit Le Goff, Gilles Amador, Anne-Gaelle Chaux, Assem Soueidan and Frederic Denis

Microorganisms 2022, 10(1), 59; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10010059 - 28 Dec 2021

Cited by 12 | Viewed by 2509

Abstract

Although autoimmunity contributes to rheumatoid arthritis (RA), several lines of evidence challenge the dogma that it is mainly an autoimmune disorder. As RA-associated human leukocyte antigens shape microbiomes and increase the risk of dysbiosis in mucosae, RA might rather be induced by epigenetic changes in long-lived synovial presenting cells, stressed by excessive translocations into joints of bacteria from the poorly cultivable gut, lung, or oral microbiota (in the same way as more pathogenic bacteria can lead to “reactive arthritis”). This narrative review (i) lists evidence supporting this scenario, including the identification of DNA from oral and gut microbiota in the RA synovium (but in also healthy synovia), and the possibility of translocation through blood, from mucosae to joints, of microbiota, either directly from the oral cavity or from the gut, following an increase of gut permeability worsened by migration within the gut of oral bacteria such as Porphyromonas gingivalis; (ii) suggests other methodologies for future works other than cross-sectional studies of periodontal microbiota in cohorts of patients with RA versus controls, namely, longitudinal studies of oral, gut, blood, and synovial microbiota combined with transcriptomic analyses of immune cells in individual patients at risk of RA, and in overt RA, before, during, and following flares of RA. Full article

(This article belongs to the Special Issue Microbiology of Oral Diseases)

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12 pages, 881 KiB

Open AccessReview

Assessment of Oral Microbiome Changes in Healthy and COVID-19-Affected Pregnant Women: A Narrative Review

by Andrea Butera, Carolina Maiorani, Annalaura Morandini, Manuela Simonini, Arianna Colnaghi, Stefania Morittu, Stefania Barbieri, Maria Ricci, Gaetano Guerrisi, Daniela Piloni, Roberta Cimarossa, Barbara Fusaro, Antonia Sinesi, Ambra Bruni and Andrea Scribante

Microorganisms 2021, 9(11), 2385; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112385 - 19 Nov 2021

Cited by 8 | Viewed by 3296

Abstract

During pregnancy, there are several metabolic changes and an alteration in the composition of microorganisms that inhabit the oral cavity, with an increase in pathogenic bacteria that promote the onset of gingival diseases. This review is based on research in reference to the PICO model (Problem/Intervention/Comparison/Outcome), related to changes in the oral microbiome of pregnant women and possible oral consequences in patients with COVID-19. The results showed a growth of some pathogenic bacteria in pregnant women, including Aggregatibacter actinomycetemcomitans and Fusobacterium nucleatum, and the selective growth of the Prevotella intermedia, Porphyromonas gingivalis and Tannerella species, probably due to the fact that these bacteria use progesterone as a source of nutrition. These same bacteria are implicated in the development of periodontal disease. Periodontal pockets have bidirectional interactions between the oral cavity and the systemic circulatory system through the peripheral gingival blood vessels. The affinity of the SARS-CoV-2 virus to specific membrane receptors is now clear, and could involve the internal and external epithelial lining or the fibroblasts of the periodontal ligament. According to the results of the present review, the control of oral microbiome changes during pregnancy would be welcomed. The use of probiotics could help clinicians manage pregnant patients, reducing inflammatory indexes. Future studies should focus not only on changes in the level of the oral microbiome in pregnancy or the correlation between periodontal disease and COVID-19, but also on oral changes induced by both clinical situations. Full article

(This article belongs to the Special Issue Microbiology of Oral Diseases)

Other

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4 pages, 858 KiB

Open AccessCase Report

Isolated Epiglottic Manifestations of HIV Infection: Two Cases Reports

by Yi-Chieh Lee, Hsueh-Yu Li and Wan-Ni Lin

Microorganisms 2022, 10(12), 2404; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10122404 - 05 Dec 2022

Cited by 1 | Viewed by 2162

Abstract

Diagnosis of the Human Immunodeficiency Virus (HIV) remains challenging due to non-specific clinical presentations and mostly flu-like symptoms, e.g., fever, headache, sore throat, and general weakness. Oral lesions, such as oral candidiasis and Kaposi sarcoma, are also frequently associated with HIV infection, whereas laryngeal manifestations are rare. We report two cases of newly diagnosed HIV patients with clinical presentations of sore throat, and endoscopy revealed an epiglottic ulcerative tumor-like lesion. A laryngomicrosurgical biopsy of the lesions was performed for persistent symptoms and suspicion of malignancy. The result revealed acute and chronic inflammation without a conclusive pathology diagnosis. Further laboratory analysis was arranged in consideration of autoimmune diseases, Epstein–Barr virus (EBV), and HIV infection due to their persistent and atypical symptoms. The results were positive for HIV infection. These patients were treated successfully with antiviral treatment and the laryngeal symptoms improved within weeks. In patients with idiopathic and persistent epiglottitis or an epiglottic ulcer after medical treatment, HIV infection needs to be considered as a potential etiology in order to institute proper treatment. Full article

(This article belongs to the Special Issue Microbiology of Oral Diseases)

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