Microorganisms

Editorial

9 pages, 662 KiB

Open AccessEditorial

Oral Microorganisms and Biofilms: New Insights to Defeat the Main Etiologic Factor of Oral Diseases

by Martinna Bertolini, Raphael Cavalcante Costa, Valentim Adelino Ricardo Barão, Cristina Cunha Villar, Belen Retamal-Valdes, Magda Feres and João Gabriel Silva Souza

Microorganisms 2022, 10(12), 2413; https://doi.org/10.3390/microorganisms10122413 - 6 Dec 2022

Cited by 29 | Viewed by 9109

Abstract

The oral cavity presents a highly diverse community of microorganisms due to the unique environmental conditions for microbial adhesion and growth [...] Full article

(This article belongs to the Special Issue Oral Microorganisms and Biofilms)

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Research

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26 pages, 7075 KiB

Open AccessArticle

Investigation of the Antibacterial, Anti-Biofilm, and Antioxidative Effect of Piper betle Leaf Extract against Bacillus gaemokensis MW067143 Isolated from Dental Caries, an In Vitro-In Silico Approach

by Varda Jalil, Maryam Khan, Syed Zeeshan Haider and Saba Shamim

Microorganisms 2022, 10(12), 2485; https://doi.org/10.3390/microorganisms10122485 - 15 Dec 2022

Cited by 8 | Viewed by 3143

Abstract

Among oral diseases, dental caries is one of the most frequent to affect human health. The current research work aimed to ascertain the antibacterial, anti-biofilm, and antioxidative potential of Piper betle leaf extract against bacteria isolated from dental caries. Analysis for the presence [...] Read more.

Among oral diseases, dental caries is one of the most frequent to affect human health. The current research work aimed to ascertain the antibacterial, anti-biofilm, and antioxidative potential of Piper betle leaf extract against bacteria isolated from dental caries. Analysis for the presence of phytochemical compounds revealed compounds, such as tannins, steroids, phenolic compounds, and alkaloids, which were also confirmed by TLC and FTIR. GC-MS analysis elucidated the presence of 20 phytocompounds, among which were some well-reported bioactive compounds. The chloroform extract of P. betle demonstrated good antibacterial activity (7 mm) and minimum inhibitory concentration (MIC) (100 mg mL⁻¹) against Bacillus gaemokensis MW067143, which was the frequent biofilm producer among isolated bacterial strains. Fractions of the extract were isolated through column chromatography, after which the antibacterial activity was again evaluated. Spirost-8-en-11-one,3-hydroxy(3β,5α,14β,20β,22β,25R), an oxosteroid in nature, was observed to exhibit remarkable antibacterial potential (12 mm) against B. gaemokensis. Bacterial cells treated with P. betle extract had elevated SOD, APOX, POX, and GR activity, while its proteolytic activity against whole bacterial proteins was pronounced with the suppression of several proteins (50, 40, 15, and 10 kDa) in SDS-PAGE. Bacterial cells treated with P. betle extract demonstrated decreased growth, while the extract was also observed to exhibit inhibition of biofilm formation (70.11%) and demolition of established B. gaemokensis biofilms (57.98%). SEM analysis revealed significant changes to bacterial morphology post treatment with P. betle, with cellular disintegration being prominent. In silico network pharmacology analysis elucidated proteins like ESR1 and IL6 to be majorly involved in biological pathways of dental caries, which also interact with the protective ability of P. betle. Gene Ontology (GO) terms and KEGG pathways were also screened using enrichment analysis. Molecular docking demonstrated the highest binding affinity of Spirost-8-en-11-one,3-hydroxy-,(3β,5α,14β,20β,22β,25R) with bacterial proteins FabI (−12 kcal/mol), MurB (−17.1 kcal/mol), and FtsZ (−14.9 kcal/mol). Therefore, it is suggested that P. betle can serve a potentially therapeutic role and could be used in the preparation of herbal formulations for managing bacterial flora. Full article

(This article belongs to the Special Issue Oral Microorganisms and Biofilms)

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20 pages, 3056 KiB

Open AccessArticle

Effects of Preservation and Propagation Methodology on Microcosms Derived from the Oral Microbiome

by Baoqing Zhou, Jen Mobberley, Kelly Shi and Irene A. Chen

Microorganisms 2022, 10(11), 2146; https://doi.org/10.3390/microorganisms10112146 - 29 Oct 2022

Cited by 1 | Viewed by 2132

Abstract

The creation of oral microcosms with reproducible composition is important for developing model systems of the oral microbiome. However, oral microbiomes vary substantially across individuals. To derive a reproducible composition from inocula sourced from different individuals, we tested whether selective conditions from cold [...] Read more.

The creation of oral microcosms with reproducible composition is important for developing model systems of the oral microbiome. However, oral microbiomes vary substantially across individuals. To derive a reproducible composition from inocula sourced from different individuals, we tested whether selective conditions from cold storage and culturing in defined media would generate a reproducible community composition despite individual variations. In this pilot study, we collected dental plaque scrapings from three individuals, inoculated media under anaerobic conditions, and characterized the bacterial community compositions after cold storage and subsequent propagation in liquid media. Harvested cultures were extracted and bacterial composition was determined by 16S rRNA gene amplicon sequencing and the mothur pipeline. Our results show that samples from two out of three individuals clustered into a specific compositional type (termed “attractor” here). In addition, the samples from the third individual could adopt this attractor compositional type after propagation in vitro, even though its original composition did not display this type. These results indicate that simple selective environments could help create reproducible microcosms despite variation among dental plaque samples sourced from different individuals. The findings illustrate important parameters to consider for creating reproducible microcosms from the human oral microbiome. Full article

(This article belongs to the Special Issue Oral Microorganisms and Biofilms)

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10 pages, 1338 KiB

Open AccessArticle

Extracellular Vesicle Subproteome Differences among Filifactor alocis Clinical Isolates

by Kai Bao, Rolf Claesson, Georgios N. Belibasakis and Jan Oscarsson

Microorganisms 2022, 10(9), 1826; https://doi.org/10.3390/microorganisms10091826 - 13 Sep 2022

Cited by 3 | Viewed by 1709

Abstract

Filifactor alocis is a Gram-positive asaccharolytic, obligate anaerobic rod of the Firmicutes phylum, which has recently been implicated in oral infections. Extracellular vesicles (EVs) are crucial conveyors of microbial virulence in bacteria and archaea. Previously, in highly purified EVs from the F. alocis [...] Read more.

Filifactor alocis is a Gram-positive asaccharolytic, obligate anaerobic rod of the Firmicutes phylum, which has recently been implicated in oral infections. Extracellular vesicles (EVs) are crucial conveyors of microbial virulence in bacteria and archaea. Previously, in highly purified EVs from the F. alocis reference strain ATCC 35896 (CCUG 47790), 28 proteins were identified. The present study aimed to use label-free quantification proteomics in order to chart these EV proteins, in the reference strain, and in nine less-well-characterized clinical F. alocis isolates. In total, 25 of the EV proteins were identified and 24 were quantified. Sixteen of those were differentially expressed between the ten strains and the novel FtxA RTX toxin and one lipoprotein were among them. Consistent expression was observed among ribosomal proteins and proteins involved in L-arginine biosynthesis and type IV pilin, demonstrating a degree of EV protein expression preservation among strains. In terms of protein–protein interaction analysis, 21 functional associations were revealed between 19 EV proteins. Interestingly, FtxA did not display predicted interactions with any other EV protein. In conclusion, the present study charted 25 EV proteins in ten F. alocis strains. While most EV proteins were consistently identified among the strains, several of them were also differentially expressed, which justifies that there may be potential variations in the virulence potential among EVs of different F. alocis strains. Full article

(This article belongs to the Special Issue Oral Microorganisms and Biofilms)

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14 pages, 1683 KiB

Open AccessArticle

Effect of Calcium Ion Supplementation on Oral Microbial Composition and Biofilm Formation In Vitro

by Bhumika Shokeen, Elaine Pham, Julia Esfandi, Takeru Kondo, Hiroko Okawa, Ichiro Nishimura and Renate Lux

Microorganisms 2022, 10(9), 1780; https://doi.org/10.3390/microorganisms10091780 - 3 Sep 2022

Cited by 8 | Viewed by 1851

Abstract

The oral cavity contains a variety of ecological niches with very different environmental conditions that shape biofilm structure and composition. The space between the periodontal tissue and the tooth surface supports a unique anaerobic microenvironment that is bathed in the nutrient-rich gingival crevicular [...] Read more.

The oral cavity contains a variety of ecological niches with very different environmental conditions that shape biofilm structure and composition. The space between the periodontal tissue and the tooth surface supports a unique anaerobic microenvironment that is bathed in the nutrient-rich gingival crevicular fluid (GCF). During the development of periodontitis, this environment changes and clinical findings reported a sustained level of calcium ion concentration in the GCF collected from the periodontal pockets of periodontitis patients. Here, we report the effect of calcium ion supplementation on human oral microbial biofilm formation and community composition employing an established SHI medium-based in vitro model system. Saliva-derived human microbial biofilms cultured in calcium-supplemented SHI medium (SHICa) exhibited a significant dose-dependent increase in biomass and metabolic activity. The effect of SHICa medium on the microbial community composition was evaluated by 16S rRNA gene sequencing using saliva-derived microbial biofilms from healthy donors and periodontitis subjects. In this study, intracellular microbial genomic DNA (iDNA) and extracellular DNA (eDNA) were analyzed separately at the genus level. Calcium supplementation of SHI medium had a differential impact on iDNA and eDNA in the biofilms derived from healthy individuals compared to those from periodontitis subjects. In particular, the genus-level composition of the eDNA portion was distinct between the different biofilms. This study demonstrated the effect of calcium in a unique microenvironment on oral microbial complex supporting the dynamic transformation and biofilm formation. Full article

(This article belongs to the Special Issue Oral Microorganisms and Biofilms)

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24 pages, 4581 KiB

Open AccessArticle

Effect of a Stannous Fluoride Dentifrice on Biofilm Composition, Gene Expression and Biomechanical Properties

by Hardeep Kaur Gumber, Artemis S. Louyakis, Tulika Sarma, Kristina Ivana Fabijanic, Reeba Paul, Kristen Mellenbruch and Latonya Kilpatrick-Liverman

Microorganisms 2022, 10(9), 1691; https://doi.org/10.3390/microorganisms10091691 - 23 Aug 2022

Cited by 8 | Viewed by 3341

Abstract

An in situ study was conducted to examine the mode of action of a 0.454% stannous fluoride (SnF₂)-containing dentifrice in controlling the composition and properties of oral biofilm. Thirteen generally healthy individuals participated in the study. Each participant wore an intra-oral [...] Read more.

An in situ study was conducted to examine the mode of action of a 0.454% stannous fluoride (SnF₂)-containing dentifrice in controlling the composition and properties of oral biofilm. Thirteen generally healthy individuals participated in the study. Each participant wore an intra-oral appliance over a 48-h period to measure differences in the resulting biofilm’s architecture, mechanical properties, and bacterial composition after using two different toothpaste products. In addition, metatranscriptomics analysis of supragingival plaque was conducted to identify the gene pathways influenced. The thickness and volume of the microcolonies formed when brushing with the SnF₂ dentifrice were dramatically reduced compared to the control 0.76% sodium monofluorophosphate (MFP)-containing toothpaste. Similarly, the biophysical and nanomechanical properties measured by atomic force microscopy (AFM) demonstrated a significant reduction in biofilm adhesive properties. Metatranscriptomic analysis identified pathways associated with biofilm formation, cell adhesion, quorum sensing, and N-glycosylation that are significantly downregulated with SnF₂. This study provides a clinically relevant snapshot of how the use of a stabilized, SnF₂ toothpaste formulation can change the spatial organization, nanomechanical, and gene expression properties of bacterial communities. Full article

(This article belongs to the Special Issue Oral Microorganisms and Biofilms)

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17 pages, 3572 KiB

Open AccessArticle

Nisin and Nisin Probiotic Disrupt Oral Pathogenic Biofilms and Restore Their Microbiome Composition towards Healthy Control Levels in a Peri-Implantitis Setting

by Allan Radaic, Hanna Brody, Fernando Contreras, Maryam Hajfathalian, Luke Lucido, Pachiyappan Kamarajan and Yvonne L. Kapila

Microorganisms 2022, 10(7), 1336; https://doi.org/10.3390/microorganisms10071336 - 1 Jul 2022

Cited by 14 | Viewed by 2682

Abstract

Peri-implantitis is characterized by chronic inflammation of the peri-implant supporting tissues that progressively and irreversibly leads to bone loss and, consequently, implant loss. Similar to periodontal disease, oral dysbiosis is thought to be a driver of peri-implantitis. However, managing peri-implantitis with traditional treatment [...] Read more.

Peri-implantitis is characterized by chronic inflammation of the peri-implant supporting tissues that progressively and irreversibly leads to bone loss and, consequently, implant loss. Similar to periodontal disease, oral dysbiosis is thought to be a driver of peri-implantitis. However, managing peri-implantitis with traditional treatment methods, such as nonsurgical debridement or surgery, is not always successful. Thus, novel strategies have been proposed to address these shortcomings. One strategy is the use of probiotics as antimicrobial agents since they are considered safe for humans and the environment. Specifically, the probiotic Lactococcus lactis produces nisin, which has been used worldwide for food preservation. The objective of this study was to determine whether nisin and the wild-type (WT) nisin-producing L. lactis probiotic can disrupt oral pathogenic biofilms and promote a healthier oral microbiome within these oral biofilms on titanium discs. Using confocal imaging and 16S rRNA sequencing, this study revealed that nisin and WT L. lactis probiotic disrupt oral pathogenic biofilms in a peri-implantitis setting in vitro. More specifically, nisin decreased the viability of the pathogen-spiked biofilms dose-dependently from 62.53 ± 3.69% to 54.26 ± 3.35% and 44.88 ± 2.98%, respectively. Similarly, 10⁵ CFU/mL of WT L. lactis significantly decreased biofilm viability to 52.45 ± 3.41%. Further, both treatments shift the composition, relative abundance, and diversity levels of these biofilms towards healthy control levels. A total of 1 µg/mL of nisin and 10³ CFU/mL of WT L. lactis were able to revert the pathogen-mediated changes in the Proteobacteria (from 80.5 ± 2.9% to 75.6 ± 2.0%, 78.0 ± 2.8%, and 75.1 ± 5.3%, respectively) and Firmicutes (from 11.6 ± 1.6% to 15.4 ± 1.3%, 13.8 ± 1.8%, and 13.7 ± 2.6%, respectively) phyla back towards control levels. Thus, nisin and its nisin-producing L. lactis probiotic may be useful in treating peri-implantitis by promoting healthier oral biofilms, which may be useful for improving patient oral health. Full article

(This article belongs to the Special Issue Oral Microorganisms and Biofilms)

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18 pages, 2901 KiB

Open AccessArticle

Engineered Salivary Peptides Reduce Enamel Demineralization Provoked by Cariogenic S. mutans Biofilm

by Lina Maria Marin, Yizhi Xiao, Jaime Aparecido Cury and Walter Luiz Siqueira

Microorganisms 2022, 10(4), 742; https://doi.org/10.3390/microorganisms10040742 - 30 Mar 2022

Cited by 6 | Viewed by 2228

Abstract

Engineering of the acquired enamel pellicle using salivary peptides has been shown to be a promising anticaries strategy. However, the mechanisms by which these peptides protect teeth against tooth decay are not fully understood. In this study, we evaluated the effect of the [...] Read more.

Engineering of the acquired enamel pellicle using salivary peptides has been shown to be a promising anticaries strategy. However, the mechanisms by which these peptides protect teeth against tooth decay are not fully understood. In this study, we evaluated the effect of the engineered salivary peptides DR9-DR9 and DR9-RR14 on enamel demineralization in two experimental conditions: (1) adsorbed onto the enamel surface forming the AEP, and (2) forming the AEP combined with their use to treat the biofilms 2×/day, using a validated cariogenic Streptococcus mutans in vitro biofilm model. Biofilms were grown for 144 h on enamel slabs and then collected to determine the bacterial viability (CFU/biofilm) and biofilm mass (mg protein/biofilm), and to extract cellular/extracellular proteins, which were characterized by mass spectrometry. The culture medium was changed 2×/day to fresh medium, and pH (indicator of biofilm acidogenicity) and calcium concentration (indicator of demineralization) was determined in used medium. DR9-RR14 peptide significantly reduced enamel demineralization (p < 0.0001) in both experimental conditions. However, this peptide did not have a significant effect on biofilm biomass (p > 0.05) nor did it modulate the expression of cellular and extracellular bacterial proteins involved in biofilm cariogenicity. These findings suggest that DR9-RR14 may control caries development mainly by a physicochemical mechanism. Full article

(This article belongs to the Special Issue Oral Microorganisms and Biofilms)

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