• Genomics & Informatics
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• v.21 no.2
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• pp.21.1-21.14
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• 2023

Fusobacterium nucleatum is a gram-negative bacteria associated with diverse infections like appendicitis and colorectal cancer. It mainly attacks the epithelial cells in the oral cavity and throat of the infected individual. It has a single circular genome of 2.7 Mb. Many proteins in F. nucleatum genome are listed as "Uncharacterized." Annotation of these proteins is crucial for obtaining new facts about the pathogen and deciphering the gene regulation, functions, and pathways along with discovery of novel target proteins. In the light of new genomic information, an armoury of bioinformatic tools were used for predicting the physicochemical parameters, domain and motif search, pattern search, and localization of the uncharacterized proteins. The programs such as receiver operating characteristics determine the efficacy of the databases that have been employed for prediction of different parameters at 83.6%. Functions were successfully assigned to 46 uncharacterized proteins which included enzymes, transporter proteins, membrane proteins, binding proteins, etc. Apart from the function prediction, the proteins were also subjected to string analysis to reveal the interacting partners. The annotated proteins were also put through homology-based structure prediction and modeling using Swiss PDB and Phyre2 servers. Two probable virulent factors were also identified which could be investigated further for potential drug-related studies. The assigning of functions to uncharacterized proteins has shown that some of these proteins are important for cell survival inside the host and can act as effective drug targets.

• Journal of Periodontal and Implant Science
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• v.29 no.2
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• pp.325-333
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• 1999

The antibacterial efficacy of a mouthrinse(Denta Gargle) containing CPC(cetylpyridinium chloride), NaF and UDCA(ursodeoxycholic acid), on major periodontopathogens, was in vitro examined and compared with that of Listerine by a broth dilution method. The bacteria tested were Actinobacillus actinomycetemcomitans, Bacteroides forsythus, Fusobacterium nucleatum subsp. vincentii, Prevotella intermedia, Porphyromonas gingivalis and Treponema denticola. The growth of all the bacteria were completely inhibited by a 1-min exposure to the both mouthrinses. When diluted at 1:5 or more, all bacteria analyzed but P. intermedia were not inhibited by Listerine. In contrast, Denta Gargle showed highly increased maximum inhibitory dilutions(MID) against all periodontopathogens included in this study, with MIDs ranging from 5-fold(F. nucleatum) to 160-fold dilutions(P. intermedia). The MIDs against A. actinomycetemcomitans, B. forsythus, P. gingivalis and T. denticola. were 1:40, 1:80, 1:80 and 1:80, respectively.

• Journal of Periodontal and Implant Science
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• v.45 no.5
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• pp.178-183
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• 2015

Purpose: Elderly people are thought to be more susceptible to periodontal disease due to reduced immune function associated with aging. However, little information is available on the nature of immune responses against putative periodontal pathogens in geriatric patients. The purpose of this study was to evaluate the serum IgG antibody responses to six periodontal pathogens in geriatric subjects. Methods: The study population consisted of 85 geriatric patients and was divided into three groups: 29 mild (MCP), 27 moderate (MoCP), and 29 severe (SCP) chronic periodontitis patients. Serum levels of IgG antibody to Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum, and Prevotella intermedia were measured by enzyme-linked immunosorbent assay (ELISA) and compared among the groups. Results: All three groups showed levels of serum IgG in response to P. gingivalis, A. actinomycetemcomitans, and P. intermedia that were three to four times higher than levels of IgG to T. forsythia, T. denticola, and F. nucleatum. There were no significant differences among all three groups in IgG response to P. gingivalis (P=0.065), T. forsythia (P=0.057), T. denticola (P=0.1), and P. intermedia (P=0.167), although the IgG levels tended to be higher in patients with SCP than in those with MCP or MoCP (with the exception of those for P. intermedia). In contrast, there were significant differences among the groups in IgG levels in response to F. nucleatum (P=0.001) and A. actinomycetemcomitans (P=0.003). IgG levels to A. actinomycetemcomitans were higher in patients with MCP than in those with MoCP or SCP. Conclusions: When IgG levels were compared among three periodontal disease groups, only IgG levels to F. nucleatum significantly increased with the severity of disease. On the contrary, IgG levels to A. actinomycetemcomitans decreased significantly in patients with SCP compared to those with MCP. There were no significant differences in the IgG levels for P. gingivalis, T. forsythia, T. denticola, and P. intermedia among geriatric patients with chronic periodontitis.

• Journal of Periodontal and Implant Science
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• v.51 no.1
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• pp.53-62
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• 2021

Purpose: This study aimed to evaluate the clinical and microbiological efficacy of adjunctive local delivery of minocycline (Periocline^®) in patients receiving supportive periodontal therapy (SPT) after initial treatment. Methods: The participants were 16 men and 8 women (age, 20-65 years) who had at least 15 natural teeth, underwent SPT for more than 1 year due to chronic periodontitis, had 4 or more periodontal pocket sites deeper than 5 mm, and showed >25% gingival bleeding on probing (BoP). They were randomly assigned to the test and control groups. In the test group, mechanical debridement and local antibiotic delivery were performed for all periodontal sulci/pockets; in the control group, mechanical debridement and saline irrigation were performed. In patients who underwent SPT for more than 1 year, clinical and microbiological examinations were performed at baseline and 1 and 3 months after SPT. The clinical examination included an assessment of the periodontal pocket depth, clinical attachment level, plaque index, and BoP. Microbial tests were performed using real-time polymerase chain reaction; the relative ratios of Porphyromonas gingivalis and Fusobacterium nucleatum were determined. Results: Both groups showed significant improvements in clinical parameters at 1 and 3 months from baseline; there were no significant changes between months 1 and 3. Intergroup differences were insignificant. The microbiological analysis revealed no significant differences in P. gingivalis and F. nucleatum ratios across time points. While intergroup differences were insignificant, there was a tendency for the P. gingivalis and F. nucleatum ratios to decrease in the test group. Conclusions: Mechanical debridement in patients receiving maintenance therapy resulted in clinically significant improvement; the effectiveness of additional local delivery of antibiotics was not significant. The ratios of P. gingivalis and F. nucleatum showed a tendency to decrease in the test group, although it was not significant.

• Journal of Periodontal and Implant Science
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• v.48 no.4
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• pp.261-271
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• 2018

Purpose: Few studies have examined periodontal pathogens from saliva samples in periodontally healthy young adults. The purposes of this study were to determine the prevalence of periodontopathic bacteria and to quantify periodontal pathogens in saliva samples using real-time polymerase chain reaction (PCR) assays in periodontally healthy Korean young adults under 35 years of age. Methods: Nine major periodontal pathogens were analyzed by real-time PCR in saliva from 94 periodontally healthy young adults. Quantification of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Prevotella intermedia, Fusobacterium nucleatum, Campylobacter rectus, Peptostreptococcus anaerobius, and Eikenella corrodens was performed by DNA copy number measurement. Results: F. nucleatum and E. corrodens were detected in all subjects; the numbers of positive samples were 87 (92.6%), 91 (96.8%), and 90 (95.7%) for P. gingivalis, P. anaerobius, and C. rectus, respectively. Other pathogens were also detected in periodontally healthy subjects. Analysis of DNA copy numbers revealed that the most abundant periodontal pathogen was F. nucleatum, which was significantly more prevalent than all other bacteria (P<0.001), followed by P. anaerobius, P. gingivalis, E. corrodens, C. rectus, and T. denticola. There was no significant difference in the prevalence of each bacterium between men and women. The DNA copy number of total bacteria was significantly higher in men than in women. Conclusions: Major periodontal pathogens were prevalent in the saliva of periodontally healthy Korean young adults. Therefore, we suggest that the development of periodontal disease should not be overlooked in periodontally healthy young people, as it can arise due to periodontal pathogen imbalance and host susceptibility.

• International Journal of Clinical Preventive Dentistry
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• v.14 no.4
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• pp.264-270
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• 2018

Objective: This study performed a quantitative analysis using the real-time polymerase chain reaction technique to examine the oral microbial prevalence in adults and intended to examine the correlations between risk factors of periodontal disease and oral bacteria and correlation between oral test scores and oral microorganisms. Methods: We examined papillary marginal attached (PMA) index, modified patient hygiene performance (M-PHP) index, probing depth (PD), modified gingival index, and oral bacteria counts and surveyed 117, 20 years or older adult males and females who visited dental clinics in the Daejeon region to analyze the prevalence and oral health. Results: The prevalence was 100% for Fusobacterium nucleatum, meaning it was observed in all examined subject, 85.5% for Parvimonas micra, 76.1% for Prevotella intermedia, and 72.6% for Tannerella forsythia. The averages of P. gingivalis and T. forsythia increased as the examined subjects were older, and there was a statistically significant difference between T. forsythia and E. nodatum in relation to medical history, between P. intermedia and P. micra in relation to gender, and between P. intermedia and E. corrodens in relation to smoking (p<0.05). For a correlation between the oral test scores and oral microorganisms, P. gingivalis and F. nucleatum was highly correlated with PD (correlation coefficient of 0.51 and 0.41) (p<0.01) while P. gingivalis, P. micra, C. rectus, and E. nodatum were significantly correlated with M-PHP index, gingival index, PD, and PMA index (p<0.01, p<0.05). Conclusion: For oral health management of adults, the age, systemic disease, and smoking are closely related to oral bacteria, and P. gingivalis, T. forsythia, F. nucleatum, P. intermedia, P. micra, C. rectus, E. corrodens, and E. nodatum are considered to be the oral microorganisms that indicate periodontal health.

• Journal of Oral Medicine and Pain
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• v.47 no.1
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• pp.10-26
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• 2022

Purpose: The purpose of this study was to investigate whether various saliva collection methods affect the observed salivary microbiome and whether microbiomes of stimulated and unstimulated saliva and plaque differ in richness and diversity. Methods: Seven sampling methods for unstimulated saliva, stimulated saliva, and plaque samples were applied to six orally and systemically healthy participants. Bacterial 16S ribosomal RNA genes of 10 major oral bacterial species, namely, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum, Prevotella intermedia, Prevotella nigrescens, Streptococcus mitis, Streptococcus sobrinus, and Lactobacillus casei, were analyzed by real-time polymerase chain reaction. We comprehensively examined the dependence of the amount of bacterial ribosomal DNA (rDNA), bacterial-community composition, and relative abundance of each species on sample collection methods. Results: There were significant differences in the bacterial rDNA copy number depending on the collection method in three species: F. nucleatum, P. nigrescens, and S. mitis. The species with the highest richness was S. mitis, with the range from 89.31% to 100.00%, followed by F. nucleatum, P. nigrescens, T. denticola, T. forsythia, and P. intermedia, and the sum of the proportions of the remaining five species was less than 1%. The species with the lowest observed richness was P. gingivalis (<0.1%). The Shannon diversity index was the highest in unstimulated saliva collected with a funnel (4.449). The Shannon diversity index was higher in plaque samples (3.623) than in unstimulated (3.171) and stimulated (3.129) saliva and in mouthwash saliva samples (2.061). Conclusions: The oral microbial profile of saliva samples can be affected by sample collection methods, and saliva differs from plaque in the microbiome. An easy and rapid technique for saliva collection is desirable; however, observed microbial-community composition may more accurately reflect the actual microbiome when unstimulated saliva is assayed.

• Journal of dental hygiene science
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• v.24 no.2
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• pp.97-106
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• 2024

Background: Periodontitis and peri-implantitis are diseases caused by pathogenic microorganisms that cause tissue damage and alveolar bone destruction resulting in the loss of teeth and implants. Due to the biological differences in the tissues surrounding the implants, peri-implantitis progresses more rapidly and intensely than periodontitis, underscoring the importance of understanding the characteristics and interactions of pathogenic bacteria. This study aimed to quantitatively analyze the pathogenic microorganisms associated with periodontitis and peri-implantitis in Korean patients and evaluate the correlation between these bacteria. Methods: A total of 98 (52 males and 46 females) were randomly selected and classified into three groups (healthy group [HG]=25; periodontitis group [PG]=31; and peri-implantitis group [PIG]=42). The relative expression levels of 11 pathogenic microorganisms collected from the gingival sulcus fluid were determined using multiplex real-time polymerase chain reaction. Results: Eikenella corrodens, Fusobacterium nucleatum, and Prevotella nigrescens were highly prevalent in the HG, PG, and PIG patients. The results of the relative quantitative analysis of microorganisms showed that all bacteria belonging to the green, orange, and red complexes were significantly more abundant in the PG and PIG than in the HG (p<0.05). Porphyromonas gingivalis in the red complex showed a positive correlation with all microorganisms in the orange complex (p<0.05). Campylobacter rectus in the orange complex showed a significant positive correlation with all microorganisms in the red complex, and with F. nucleatum, P. nigrescens, Prevotella intermedia, and Eubacterium nodatum (p<0.05). Conclusion: P. gingivalis, C. rectus, and F. nucleatum exhibit strong interactions. Removing these bacteria can block complex formation and enhance the prevention and treatment of periodontitis and peri-implantitis.

• Korean Journal of Microbiology
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• v.40 no.2
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• pp.111-114
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• 2004

This study was carried out to evaluate the inhibition of growth and collagenase activity of Salvia miltiorrhiza Bunge against microorganisms causing periodontal diseases. The ethanol extract of Salvia miltiorrhiza showed sig-nificant growth inhibition against microorganisms causing periodontal diseases. Ethanol extract was further fractionated with organic solvents in the order of hexane, chloroform and ethyl acetate. Among the fractions tested, the hexane fraction showed the highest cell growth inhibition. The minimal inhibitory concentration (MIC) of the extract against C. curvus, C. rectus, E. corrodens, F nucleatum, P. gingivalis, P. intermedia and W. succinogenes were 200, 50, 50, 250, 150, 250 and 200 ${\mu}g$/ml, respectively. The inhibition of collagenase activity by organic solvent fractions were higher than that of minocycline, and the inhibition ratio of collagenase activity was $88.2{\pm}2.1$ % in the chloroform fraction.

• Journal of Microbiology and Biotechnology
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• v.17 no.5
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• pp.858-864
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• 2007

This study investigated the antibacterial activities of sophoraflavanone G from Sophora flavescens in combination with two antimicrobial agents against oral bacteria. The combined effect of sophoraflavanone G and the antimicrobial agents was evaluated using the checkerboard method to obtain a fractional inhibitory concentration(FIC) index. The sophoraflavanone G+ampicillin(AM) combination was found to have a synergistic effect against S. mutans, S. sanguinis, S. sobrinus, S. gordonii, A. actinomycetemcomitans, F nucleatum, P. intermedia, and P. gingivalis, whereas the sophoraflavanone G+gentamicin(GM) combination had a synergistic effect against S. sanguinis, S. criceti, S. anginosus, A. actinomycetemcomitans, F nucleatum, P. intermedia, and P. gingivalis. Neither combination exhibited any antagonistic interactions(FIC index>4). In particular, the MICs/MBCs for all the bacteria were reduced to one-half$\sim$one-sixteenth as a result of the drug combinations. A synergistic interaction was also confirmed by time-kill studies for nine bacteria where the checkerboard suggested synergy. Thus, a strong bactericidal effect was exerted through the drug combinations, plus in vitro data suggested that sophoraflavanone G combined with other antibiotics may be microbiologically beneficial rather than antagonistic.