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Applied Microbiology and Biotechnology May 2024Shotgun metagenomics sequencing experiments are finding a wide range of applications. Nonetheless, there are still limited guidelines regarding the number of sequences...
Shotgun metagenomics sequencing experiments are finding a wide range of applications. Nonetheless, there are still limited guidelines regarding the number of sequences needed to acquire meaningful information for taxonomic profiling and antimicrobial resistance gene (ARG) identification. In this study, we explored this issue in the context of oral microbiota by sequencing with a very high number of sequences (~ 100 million), four human plaque samples, and one microbial community standard and by evaluating the performance of microbial identification and ARGs detection through a downsampling procedure. When investigating the impact of a decreasing number of sequences on quantitative taxonomic profiling in the microbial community standard datasets, we found some discrepancies in the identified microbial species and their abundances when compared to the expected ones. Such differences were consistent throughout downsampling, suggesting their link to taxonomic profiling methods limitations. Overall, results showed that the number of sequences has a great impact on metagenomic samples at the qualitative (i.e., presence/absence) level in terms of loss of information, especially in experiments having less than 40 million reads, whereas abundance estimation was minimally affected, with only slight variations observed in low-abundance species. The presence of ARGs was also assessed: a total of 133 ARGs were identified. Notably, 23% of them inconsistently resulted as present or absent across downsampling datasets of the same sample. Moreover, over half of ARGs were lost in datasets having less than 20 million reads. This study highlights the importance of carefully considering sequencing aspects and suggests some guidelines for designing shotgun metagenomics experiments with the final goal of maximizing oral microbiome analyses. Our findings suggest varying optimized sequence numbers according to different study aims: 40 million for microbiota profiling, 50 million for low-abundance species detection, and 20 million for ARG identification. KEY POINTS: • Forty million sequences are a cost-efficient solution for microbiota profiling • Fifty million sequences allow low-abundance species detection • Twenty million sequences are recommended for ARG identification.
Topics: Humans; Metagenomics; Dental Plaque; Microbiota; Bacteria; Drug Resistance, Bacterial; Sequence Analysis, DNA; Metagenome
PubMed: 38709303
DOI: 10.1007/s00253-024-13152-z -
BMC Oral Health May 2024To evaluate the antibacterial effectiveness of a combination of ε-poly-L-lysine (ε-PL), funme peptide (FP) as well as domiphen against oral pathogens, and assess the... (Randomized Controlled Trial)
Randomized Controlled Trial
OBJECTIVE
To evaluate the antibacterial effectiveness of a combination of ε-poly-L-lysine (ε-PL), funme peptide (FP) as well as domiphen against oral pathogens, and assess the efficacy of a BOP® mouthwash supplemented with this combination in reducing halitosis and supragingival plaque in a clinical trial.
MATERIALS AND METHODS
The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of the compound against Fusobacterium nucleatum, Porphyromonas gingivalis, Streptococcus mutans, and Aggregatibacter actinomycetemcomitans were determined by the gradient dilution method. Subsequently, the CCK-8 assay was used to detect the toxicity of mouthwash on human gingival fibroblastst, and the effectiveness in reducing halitosis and supragingival plaque of the mouthwash supplemented with the combination was analyzed by a randomized, double-blind, parallel-controlled clinical trial.
RESULTS
The combination exhibited significant inhibitory effects on tested oral pathogens with the MIC < 1.56% (v/v) and the MBC < 3.13% (v/v), and the mouthwash containing this combination did not inhibit the viability of human gingival fibroblasts at the test concentrations. The clinical trial showed that the test group displayed notably lower volatile sulfur compounds (VSCs) at 0, 10, 24 h, and 7 d post-mouthwash (P < 0.05), compared with the baseline. After 7 days, the VSC levels of the and control groups were reduced by 50.27% and 32.12%, respectively, and notably cutting severe halitosis by 57.03% in the test group. Additionally, the Plaque Index (PLI) of the test and control group decreased by 54.55% and 8.38%, respectively, and there was a significant difference in PLI between the two groups after 7 days (P < 0.01).
CONCLUSIONS
The combination of ε-PL, FP and domiphen demonstrated potent inhibitory and bactericidal effects against the tested oral pathogens, and the newly formulated mouthwash added with the combination exhibited anti-dental plaque and anti-halitosis properties in a clinical trial and was safe.
TRIAL REGISTRATION
The randomized controlled clinical trial was registered on Chinese Clinical Trial Registry (No. ChiCTR2300073816, Date: 21/07/2023).
Topics: Humans; Halitosis; Mouthwashes; Dental Plaque; Double-Blind Method; Male; Female; Polylysine; Adult; Microbial Sensitivity Tests; Young Adult; Anti-Bacterial Agents; Porphyromonas gingivalis; Fusobacterium nucleatum; Fibroblasts; Peptides; Aggregatibacter actinomycetemcomitans; Streptococcus mutans
PubMed: 38702623
DOI: 10.1186/s12903-024-04255-0 -
Archives of Oral Biology Aug 2024The effectiveness of supragingival dental biofilm control during orthodontic treatment and changes in the bacterial profile were analyzed. (Randomized Controlled Trial)
Randomized Controlled Trial
OBJECTIVE
The effectiveness of supragingival dental biofilm control during orthodontic treatment and changes in the bacterial profile were analyzed.
DESIGN
Sixty-four participants aged 12-22 years (57% female) were included in the study. Participants underwent orthodontic treatment with fixed appliances and were randomly assigned to one of the three groups, which during a period of one month: (I) used chlorhexidine digluconate (CHX), (II) used high concentration of fluoride (F) gel and (III) performed standard oral hygiene. The plaque and gingivitis index, pH of biofilm and white spot lesions (WSL) were assessed. Changes of the bacteria in the biofilm were analyzed by the quantitative polymerase chain reaction RESULTS: Increase in the plaque index, pH of biofilm, and WSL was observed during orthodontic treatment with standard oral hygiene. Large interindividual variability was present, and the effects of one-month use of fluorides and CHX on clinical parameters were not significant. Despite standard hygiene the abundance of studied biofilm bacteria increased - the most Streptoccocus mutans (14.2x) and S. salivarius (3.3x), moderate Veillonella parvula (3x) and the least S. sobrinus (2.3x) and Agregatibacter actinomycetemcomitans (1.9x). The use of CHX reduced S. sobrinus (2.2x) and A. actinomycetemcomitans (1.9x). Fluoride use reduced A. actinomycetemcomitans (1.3x) and S. sobrinus (1.2x). Fluorides better controlled S. mutans than CHX.
CONCLUSION
Bacterial biomass in supragingival biofilm increased during treatment with metal orthodontic appliances, with greater increase in cariogenic bacteria than periopathogens. Fluoride controlled S. mutans, while CHX S. sobrinus and A. actinomycetemcomitans.
Topics: Humans; Biofilms; Female; Adolescent; Chlorhexidine; Child; Male; Orthodontic Appliances, Fixed; Young Adult; Fluorides; Dental Plaque Index; Oral Hygiene; Dental Plaque; Hydrogen-Ion Concentration; Streptococcus mutans; Gingivitis; Anti-Infective Agents, Local; Polymerase Chain Reaction; Dental Caries
PubMed: 38701663
DOI: 10.1016/j.archoralbio.2024.105984 -
Bone Aug 2024This review examines the possible role of mitochondria in maintaining calcium and phosphate ion homeostasis and participating in the mineralization of bone, cartilage... (Review)
Review
This review examines the possible role of mitochondria in maintaining calcium and phosphate ion homeostasis and participating in the mineralization of bone, cartilage and other vertebrate hard tissues. The paper builds on the known structural features of mitochondria and the documented observations in these tissues that the organelles contain calcium phosphate granules. Such deposits in mitochondria putatively form to buffer excessively high cytosolic calcium ion concentrations and prevent metabolic deficits and even cell death. While mitochondria protect cytosolic enzyme systems through this buffering capacity, the accumulation of calcium ions by mitochondria promotes the activity of enzymes of the tricarboxylic acid (TCA/Krebs) cycle, increases oxidative phosphorylation and ATP synthesis, and leads to changes in intramitochondrial pH. These pH alterations influence ion solubility and possibly the transitions and composition in the mineral phase structure of the granules. Based on these considerations, mitochondria are proposed to support the mineralization process by providing a mobile store of calcium and phosphate ions, in smaller cluster or larger granule form, while maintaining critical cellular activities. The rise in the mitochondrial calcium level also increases the generation of citrate and other TCA cycle intermediates that contribute to cell function and the development of extracellular mineral. This paper suggests that another key role of the mitochondrion, along with the effects just noted, is to supply phosphate ions, derived from the breakdown of ATP, to endolysosomes and autophagic vesicles originating in the endoplasmic reticulum and Golgi and at the plasma membrane. These many separate but interdependent mitochondrial functions emphasize the critical importance of this organelle in the cellular control of vertebrate mineralization.
Topics: Animals; Mitochondria; Humans; Calcification, Physiologic; Vertebrates; Calcium; Phosphates
PubMed: 38697384
DOI: 10.1016/j.bone.2024.117112 -
Journal of Oral Pathology & Medicine :... May 2024To evaluate the presence of myofibroblasts (MFs) in the development of lip carcinogenesis, through the correlation of clinical, histomorphometric and immunohistochemical...
Assessment of the association of myofibroblasts and structural components of the extracellular matrix with histopathological parameters of actinic cheilitis and lower lip squamous cell carcinoma.
BACKGROUND
To evaluate the presence of myofibroblasts (MFs) in the development of lip carcinogenesis, through the correlation of clinical, histomorphometric and immunohistochemical parameters, in actinic cheilitis (ACs) and lower lip squamous cell carcinomas (LLSCCs).
METHODS
Samples of ACs, LLSCCs, and control group (CG) were prepared by tissue microarray (TMA) for immunohistochemical TGF-β, α-SMA, and Ki-67 and histochemical hematoxylin and eosin, picrosirius red, and verhoeff van gieson reactions. Clinical and microscopic data were associated using the Mann-Whitney, Kruskal-Wallis/Dunn, and Spearman correlation tests (SPSS, p < 0.05).
RESULTS
ACs showed higher number of α-SMA MFs when compared to CG (p = 0.034), and these cells were associated with the vertical expansion of solar elastosis (SE) itself (p = 0.027). Areas of SE had lower deposits of collagen (p < 0.001), immunostaining for TGF-β (p < 0.001), and higher density of elastic fibers (p < 0.05) when compared to areas without SE. A positive correlation was observed between high-risk epithelial dysplasia (ED) and the proximity of SE to the dysplastic epithelium (p = 0.027). LLSCCs showed a higher number of α-SMA MFs about CG (p = 0.034), as well as a reduction in the deposition of total collagen (p = 0.009) in relation to ACs and CG. There was also a negative correlation between the amount of α-SMA cells and the accumulation of total collagen (p = 0.041). Collagen and elastic density loss was higher in larger tumors (p = 0.045) with nodal invasion (p = 0.047).
CONCLUSIONS
Our findings show the possible role of MFs, collagen fibers, and elastosis areas in the lip carcinogenesis process.
Topics: Humans; Cheilitis; Lip Neoplasms; Myofibroblasts; Carcinoma, Squamous Cell; Male; Female; Middle Aged; Extracellular Matrix; Aged; Transforming Growth Factor beta; Adult; Actins; Immunohistochemistry; Ki-67 Antigen; Collagen; Elastic Tissue
PubMed: 38693618
DOI: 10.1111/jop.13541 -
Oral Health & Preventive Dentistry Apr 2024To investigate the microbiological outcomes obtained with either subgingival debridement (SD) in conjunction with a gel containing sodium hypochlorite and amino acids... (Randomized Controlled Trial)
Randomized Controlled Trial Comparative Study
PURPOSE
To investigate the microbiological outcomes obtained with either subgingival debridement (SD) in conjunction with a gel containing sodium hypochlorite and amino acids followed by subsequent application of a cross-linked hyaluronic acid gel (xHyA) gel, or with SD alone.
MATERIALS AND METHODS
Forty-eight patients diagnosed with stages II-III (grades A/B) generalised periodontitis were randomly treated with either SD (control) or SD plus adjunctive sodium hypochlorite/amino acids and xHyA gel (test). Subgingival plaque samples were collected from the deepest site per quadrant in each patient at baseline and after 3 and 6 months. Pooled sample analysis was performed using a multiplex polymerase chain reaction (PCR)-based method for the identification of detection frequencies and changes in numbers of the following bacteria: Aggregatibacter actinomycetemcomitans (A.a), Porphyromonas gingivalis (P.g), Tannerella forsythia (T.f), Treponema denticola (T.d), and Prevotella intermedia (P.i).
RESULTS
In terms of detection frequency, in the test group, statistically significant reductions were found for P.g, T.f, T.d and P.i (p < 0.05) after 6 months. In the control group, the detection frequencies of all investigated bacterial species at 6 months were comparable to the baseline values (p > 0.05). The comparison of the test and control groups revealed statistically significant differences in detection frequency for P.g (p = 0.034), T.d (p < 0.01) and P.i (p = 0.02) after 6 months, favouring the test group. Regarding reduction in detection frequency scores, at 6 months, statistically significant differences in favour of the test group were observed for all investigated bacterial species: A.a (p = 0.028), P.g (p = 0.028), T.f (p = 0.004), T.d (p <0.001), and P.i (p = 0.003).
CONCLUSIONS
The present microbiological results, which are related to short-term outcomes up to 6 months post-treatment, support the adjunctive subgingival application of sodium hypochlorite/amino acids and xHyA to subgingival debridement in the treatment of periodontitis.
Topics: Humans; Hyaluronic Acid; Sodium Hypochlorite; Aggregatibacter actinomycetemcomitans; Porphyromonas gingivalis; Female; Middle Aged; Male; Prevotella intermedia; Tannerella forsythia; Treponema denticola; Adult; Dental Plaque; Amino Acids; Periodontal Debridement; Bacterial Load; Gels; Combined Modality Therapy; Follow-Up Studies; Cross-Linking Reagents; Periodontal Pocket; Periodontitis
PubMed: 38687029
DOI: 10.3290/j.ohpd.b5281925 -
BMC Oral Health Apr 2024Orthodontic treatment presents challenges with plaque accumulation around brackets, archwires, and elastics, leading to retained plaque and gingival inflammation.... (Randomized Controlled Trial)
Randomized Controlled Trial
BACKGROUND
Orthodontic treatment presents challenges with plaque accumulation around brackets, archwires, and elastics, leading to retained plaque and gingival inflammation. Conventional toothbrushing may not be enough, requiring additional oral hygiene aids like interproximal brushes, dental flosses, and water flossers. Limited research exists on comparing water flossing and interdental flossing in orthodontic patients. Therefore, this study aims to assess their effectiveness in maintaining oral hygiene during active orthodontic treatment.
METHODS
A single-blind, randomized, parallel clinical study recruited orthodontic patients with full-mouth brackets and archwires. Thirty participants were randomly assigned to either water jet flossing or interdental flossing groups. All participants were instructed to brush twice daily with a provided toothbrush and toothpaste and use the assigned intervention once daily at night. Clinical measures, including the Gingival Bleeding Index (BI), Plaque Index (PI), and Gingival Index (GI), were recorded at baseline and day 14. Descriptive statistics and statistical tests were performed using SPSS software.
RESULTS
The water jet flossing group demonstrated a slightly higher, albeit non-significant, benefit in plaque removal (median difference of 6.79%%, P = 0.279) and bleeding reduction (median difference of 5.21%%, P = 0.172) compared to the interdental flossing group after two weeks. Both groups showed significant reductions in gingival bleeding index and plaque index from baseline to the 2-week follow-up. The interdental flossing group had median mean percentage differences of 16.13%% (plaque index) and 23.57% (gingival bleeding index), while the water jet flossing group had median percentage differences of 21.87% (plaque index) and 32.29% (gingival bleeding index). No significant changes in gingival index grades were observed in either group.
CONCLUSION
Both water jet flossing and interdental flossing were effective in reducing plaque accumulation and gingival bleeding among orthodontic patients. While no significant differences were found between the two methods, water jet flossing showed a potential advantage. Further research is needed to validate its effectiveness, assess long-term impact, and understand its benefits for orthodontic patients.
Topics: Humans; Dental Devices, Home Care; Female; Single-Blind Method; Oral Hygiene; Male; Periodontal Index; Dental Plaque Index; Adolescent; Orthodontic Appliances, Fixed; Dental Plaque; Young Adult; Toothbrushing; Water; Adult
PubMed: 38678246
DOI: 10.1186/s12903-024-04166-0 -
British Dental Journal Apr 2024Understanding that dental carious lesions occur as a result of the action of micro-organisms in the dental plaque biofilm, where demineralisation on the tooth surface is... (Review)
Review
Understanding that dental carious lesions occur as a result of the action of micro-organisms in the dental plaque biofilm, where demineralisation on the tooth surface is the first sign of the disease, such incipient lesions can be treated using preventive, non-operative and minimally invasive operative dentistry. If the caries process is left unmanaged, the lesions progress towards cavitation, leading to more invasive treatments. This article discusses the principles of preventive, non-invasive and micro-invasive treatments of early carious lesions, outlining the clinical situations where these therapies can be applied.
Topics: Humans; Dental Caries; Biofilms; Cariostatic Agents; Dental Plaque; Dental Restoration, Permanent
PubMed: 38671111
DOI: 10.1038/s41415-024-7292-0 -
Clinical Oral Investigations Apr 2024Chewing gums containing antiseptics or other antimicrobial substances may be effective in reducing plaque and gingivitis. Therefore, the aim of this randomized... (Randomized Controlled Trial)
Randomized Controlled Trial
OBJECTIVES
Chewing gums containing antiseptics or other antimicrobial substances may be effective in reducing plaque and gingivitis. Therefore, the aim of this randomized placebo-controlled clinical trial was to investigate the efficacy of a novel antimicrobial chewing gum containing essential oils (cinnamon, lemon, peppermint) and extracts on reduction of dental plaque and gingivitis as well as on oral health-related quality of life (OHRQoL) in adolescent orthodontic patients.
MATERIALS
52 patients (11-22 years of age) were randomly assigned to use a test chewing gum (COVIDGUM, Clevergum) or a commercially available control chewing gum over a period of 10 days. Approximal plaque index (API), papillary bleeding index (PBI) and an OHRQoL questionnaire for children (COHIP-G19) were assessed at baseline (BL), after 10 days (10d) and 30 days (30d). In addition, oral health and oral hygiene related questions of the COHIP-G19 questionnaire were evaluated separately in subscales at each timepoint. Data were analyzed using non-parametrical statistical procedures (α = 0.05).
RESULTS
API and PBI decreased significantly over time from BL to 10d and from BL to 30d in both groups, without significant differences between the groups. In both groups, the COHIP-G19 score, oral health subscale and oral hygiene subscale decreased significantly over time. Regarding the oral hygiene subscale, the test group showed significantly better scores at 30d (p = 0.011).
CONCLUSION
Both chewing gums performed similarly effective in terms of reducing plaque accumulation and gingival inflammation and improving OHRQoL.
CLINICAL RELEVANCE
Chewing gums without antimicrobial ingredients may be sufficient to decrease plaque accumulation and gingival inflammation.
Topics: Humans; Gingivitis; Adolescent; Chewing Gum; Female; Male; Dental Plaque; Quality of Life; Child; Young Adult; Surveys and Questionnaires; Anti-Infective Agents; Treatment Outcome; Oils, Volatile; Dental Plaque Index; Periodontal Index
PubMed: 38664261
DOI: 10.1007/s00784-024-05669-4 -
Oral Health & Preventive Dentistry Apr 2024To investigate the effect of full-mouth disinfection on the sizes of the periodontal wound and periodontal inflammatory burden and whether it leads to a decrease in...
PURPOSE
To investigate the effect of full-mouth disinfection on the sizes of the periodontal wound and periodontal inflammatory burden and whether it leads to a decrease in C-reactive protein (CRP) levels.
MATERIALS AND METHODS
The study included 20 systemically healthy subjects (11 women and 9 men) 30 to 68 years old with localised or generalised periodontitis (stage III, grade C). The sizes of the periodontal wound and periodontal inflammatory burden were measured with the web application "Periodontalwound", which is based on measurements of average tooth cervices, as well as probing depths and bleeding on probing assessed at six sites around each tooth present in the oral cavity. The levels of hsCRP (high-sensitivity CRP) were measured with an immunochemical method. All three parameters were measured before initial treatment and 3 months after therapy. Full-mouth disinfection included removal of plaque and calculus with ultrasonic and hand instruments in one session.
RESULTS
The results showed a statistically significant decrease in the size of the periodontal wound (p < 0.001), a statistically significant decrease in the size of periodontal inflammatory burden (p < 0.001), and a decrease in hsCRP levels 3 months after therapy.
CONCLUSION
Full-mouth disinfection leads to a decrease in the periodontal wound and periodontal inflammatory burden size, as well as a decrease in the levels of hsCRP in patients with localised or generalised periodontitis (stage III, grade C).
Topics: Humans; Male; Female; C-Reactive Protein; Middle Aged; Adult; Aged; Disinfection; Periodontitis; Periodontal Index; Dental Plaque; Dental Calculus; Periodontal Pocket; Ultrasonic Therapy
PubMed: 38652288
DOI: 10.3290/j.ohpd.b5245853