Journal of Microbiology

Journal Articles

Predicting quorum sensing peptides using stacked generalization ensemble with gradient boosting based feature selection: Muthusaravanan Sivaramakrishnan , Rahul Suresh , Kannapiran Ponraj; J. Microbiol. 2022;60(7):756-765. Published online June 22, 2022; DOI: https://doi.org/10.1007/s12275-022-2044-9

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Bacteria exist in natural environments for most of their life as complex, heterogeneous, and multicellular aggregates. Under these circumstances, critical cell functions are controlled by several signaling molecules known as quorum sensing (QS) molecules. In Gram-positive bacteria, peptides are deployed as QS molecules. The development of antibodies against such QS molecules has been identified as a promising therapeutic intervention for bacterial control. Hence, the identification of QS peptides has received considerable attention. Availability of a fast and reliable predictive model to effectively identify QS peptides can help the existing high throughput experiments. In this study, a stacked generalization ensemble model with Gradient Boosting Machine (GBM)-based feature selection, namely EnsembleQS was developed to predict QS peptides with high accuracy. On selected GBM features (791D), the EnsembleQS outperformed finely tuned baseline classifiers and demonstrated robust performance, indicating the superiority of the model. The accuracy of EnsembleQS is 4% higher than those resulting from ensemble model on hybrid dataset. When evaluating an independent data set of 40 QS peptides, the EnsembleQS model showed an accuracy of 93.4% with Matthew’s Correlation Coefficient (MCC) and area under the ROC curve (AUC) values 􀁇􀁇of 0.91 and 0.951, respectively. These
results
suggest that EnsembleQS will be a useful computational framework for predicting QS peptides and will efficiently support proteomics research. The source code and all datasets used in this study are publicly available at https:// github.com/proteinexplorers/EnsembleQS.

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Revolutionizing physics: a comprehensive survey of machine learning applications
Rahul Suresh, Hardik Bishnoi, Artem V. Kuklin, Atharva Parikh, Maxim Molokeev, R. Harinarayanan, Sarvesh Gharat, P. Hiba
Frontiers in Physics.2024;[Epub] CrossRef
DeepQSP: Identification of Quorum Sensing Peptides Through Neural Network Model
Md. Ashikur Rahman, Md. Mamun Ali, Kawsar Ahmed, Imran Mahmud, Francis M. Bui, Li Chen, Santosh Kumar, Mohammad Ali Moni
Results in Engineering.2024; 24: 102878. CrossRef
Computational tools for exploring peptide-membrane interactions in gram-positive bacteria
Shreya Kumar, Rex Devasahayam Arokia Balaya, Saptami Kanekar, Rajesh Raju, Thottethodi Subrahmanya Keshava Prasad, Richard K. Kandasamy
Computational and Structural Biotechnology Journal.2023; 21: 1995. CrossRef
DeepTPpred: A Deep Learning Approach With Matrix Factorization for Predicting Therapeutic Peptides by Integrating Length Information
Zhen Cui, Si-Guo Wang, Ying He, Zhan-Heng Chen, Qin-Hu Zhang
IEEE Journal of Biomedical and Health Informatics.2023; 27(9): 4611. CrossRef
PSRQSP: An effective approach for the interpretable prediction of quorum sensing peptide using propensity score representation learning
Phasit Charoenkwan, Pramote Chumnanpuen, Nalini Schaduangrat, Changmin Oh, Balachandran Manavalan, Watshara Shoombuatong
Computers in Biology and Medicine.2023; 158: 106784. CrossRef

Fluorescence change of Fusobacterium nucleatum due to Porphyromonas gingivalis: Min-Ah Lee , Si-Mook Kang , Se-Yeon Kim , Ji-Soo Kim , Jin-Bom Kim , Seung-Hwa Jeong; J. Microbiol. 2018;56(9):628-633. Published online August 23, 2018; DOI: https://doi.org/10.1007/s12275-018-7515-7

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Abstract

The aim of this study was to measure changes in the fluorescence of Fusobacterium nucleatum interacting with Porphyromonas gingivalis for excitation with blue light at 405-nm. P. gingivalis was mono- and co-cultivated in close proximity with F. nucleatum. The fluorescence of the bacterial colonies was photographed using a QLF-D (Quantitative Light-induced Fluorescence-Digital) Biluminator camera system with a 405 nm light source and a specific filter. The red, green and blue intensities of fluorescence images were analyzed using the image analysis software. A fluorescence spectrometer was used to detect porphyrin synthesized by each bacterium. F. nucleatum, which emitted green fluorescence in single cultures, showed intense red fluorescence when it was grown in close proximity with P. gingivalis. F. nucleatum co-cultivated with P. gingivalis showed the same pattern of fluorescence peaks as for protoporphyrin IX in the red part of the spectrum. We conclude that the green fluorescence of F. nucleatum can change to red fluorescence in the presence of adjacent co-cultured with P. gingivalis, indicating that the fluorescence character of each bacterium might depend on the presence of other bacteria.

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Red/Orange Autofluorescence in Selected Candida Strains Exposed to 405 nm Laser Light
Rafał Wiench, Dariusz Paliga, Anna Mertas, Elżbieta Bobela, Anna Kuśka-Kiełbratowska, Sonia Bordin-Aykroyd, Aleksandra Kawczyk-Krupka, Kinga Grzech-Leśniak, Monika Lukomska-Szymanska, Edward Lynch, Dariusz Skaba
Dentistry Journal.2024; 12(3): 48. CrossRef
Autofluorescence Detection Method for Dental Plaque Bacteria Detection and Classification: Example of Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, and Streptococcus mutans
Yung-Jhe Yan, Bo-Wen Wang, Chih-Man Yang, Ching-Yi Wu, Mang Ou-Yang
Dentistry Journal.2021; 9(7): 74. CrossRef
Fluorescence image and microbiological analysis of biofilm retained around healthy and inflamed orthodontic miniscrews
A.S. Garcez, L.C. Barros, M.R.U. Fernandes, D.N. Fujii, S.S. Suzuki, R. Nepomuceno
Photodiagnosis and Photodynamic Therapy.2020; 30: 101707. CrossRef

Reducing the Bioactivity of Tannerella forsythia Lipopolysaccharide by Porphyromonas gingivalis: Young-Jae Kim , Sung-Hoon Lee; J. Microbiol. 2014;52(8):702-708. Published online August 1, 2014; DOI: https://doi.org/10.1007/s12275-014-4324-5

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Abstract

Tannerella forsythia is considered a pathogen of periodontitis and forms a biofilm with multi-species bacteria in oral cavity. Lipopolysaccharide is a powerful immunostimulator and induces inflammation and shock. The purpose of this study was to investigate the characteristics of T. forsythia LPS in its co-cultivation with Fusobacterium nucleatum or Porphyromonas gingivalis. T. forsythia was co-cultured in the presence and absence of F. nucleatum and P. gingivalis and then T. forsythia LPS was extracted. The extracts were analyzed by SDS-PAGE and NF-κB reporter CHO cell lines. THP-1 cells were treated with the LPS and evaluated induction of cytokine expression by real-time RT-PCR and ELISA. For analysis of the bioactivity of T. forsythia LPS, the binding assay on LPS-binding protein (LBP) and CD14 was processed. The extracts did not contaminate other molecules except LPS and showed TLR4 agonists. Co-cultured T. forsythia LPS with P. gingivalis exhibited a lower level of induction of TNF-α, IL-1β, and IL-6 expression than singleor co-cultured T. forsythia LPS with F. nucleatum in the conditions of human serum. However, the three T. forsythia LPS did not show difference of cytokine induction in the serum free conditions. Co-cultured T. forsythia LPS with P. gingivalis exhibited a lower affinity to LBP and CD14 as binding site of O-antigen and attached at a lower level to THP-1 cells compared to single- or co-cultured T. forsythia LPS with F. nucleatum. The virulence of T. forsythia LPS was decreased by co-culturing with P. gingivalis and their affinity to LBP and CD14 was reduced, which may due to modification of O-antigen chain by P. gingivalis.

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Anti-Inflammatory Efficacy of Human-Derived Streptococcus salivarius on Periodontopathogen-Induced Inflammation
Dong-Heon Baek, Sung-Hoon Lee
Journal of Microbiology and Biotechnology.2023; 33(8): 998. CrossRef
Virulence of Filifactor alocis lipoteichoic acid on human gingival fibroblast
Hyun-Jun Yoo, Sung-Hoon Lee
Archives of Oral Biology.2022; 135: 105370. CrossRef
Effects of Shiitake mushroom extract on antimicrobial activity against periodontopathogens and inflammatory condition of human gingival fibroblast
Yeol-Mae Jeon
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Characteristics of Treponema denticola lipooligosaccharide in presence of hemin and quorum-sensing molecule
Dong-Heon Baek, Sung-Hoon Lee
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The Associations of Periodontopathic Bacteria and Oral Candida with Periodontal Inflamed Surface Area in Older Adults Receiving Supportive Periodontal Therapy
Hideo Shigeishi, Mariko Nakamura, Iori Oka, Cheng-Yih Su, Kanako Yano, Momoko Ishikawa, Yoshino Kaneyasu, Masaru Sugiyama, Kouji Ohta
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Hyun-Jun Yoo, Su-Kyung Jwa
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Inhibitory effect of Lactococcus lactis on the bioactivity of periodontopathogens
Hyun-Seung Shin, Dong-Heon Baek, Sung-Hoon Lee
The Journal of General and Applied Microbiology.2018; 64(2): 55. CrossRef
Consistent and reproducible long-term in vitro growth of health and disease-associated oral subgingival biofilms
Irina M. Velsko, Luciana M. Shaddox
BMC Microbiology.2018;[Epub] CrossRef
Quantification by qPCR of Pathobionts in Chronic Periodontitis: Development of Predictive Models of Disease Severity at Site-Specific Level
Inmaculada Tomás, Alba Regueira-Iglesias, Maria López, Nora Arias-Bujanda, Lourdes Novoa, Carlos Balsa-Castro, Maria Tomás
Frontiers in Microbiology.2017;[Epub] CrossRef
Gingipain‐dependent augmentation by Porphyromonas gingivalis of phagocytosis of Tannerella forsythia
Y.‐J. Jung, H.‐K. Jun, B.‐K. Choi
Molecular Oral Microbiology.2016; 31(6): 457. CrossRef
Development of Filifactor alocis media for single- and co-cultivation with periodontopathogens
조인우, 이성훈
Oral Biology Research.2016; 40(4): 193. CrossRef
Antagonistic effect of peptidoglycan of Streptococcus sanguinis on lipopolysaccharide of major periodontal pathogens
Sung-Hoon Lee
Journal of Microbiology.2015; 53(8): 553. CrossRef
Polymicrobial Oral Infection with Four Periodontal Bacteria Orchestrates a Distinct Inflammatory Response and Atherosclerosis in ApoEnull Mice
Sasanka S. Chukkapalli, Irina M. Velsko, Mercedes F. Rivera-Kweh, Donghang Zheng, Alexandra R. Lucas, Lakshmyya Kesavalu, Salomon Amar
PLOS ONE.2015; 10(11): e0143291. CrossRef

Research Support, Non-U.S. Gov't

Plasminogen Activator Inhibitor Type 1 Expression Induced by Lipopolysaccharide of Porphyromonas gingivalis in Human Gingival Fibroblast: Hee Sam Na , Eun J. Lim , So Y. Jeong , Mi H. Ryu , Mi Hee Park , Jin Chung; J. Microbiol. 2014;52(2):154-160. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3022-7

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Abstract

In the gingival tissues of patients with periodontitis, inflammatory responses are mediated by a wide variety of genes. In our previous screening study, plasminogen activator inhibitor type 1 (PAI-1) mRNA binding protein expression was increased in gingiva from periodontitis patients. In this study, we further investigated the signaling pathway involved in PAI-1 expression induced by Porphyromonas gingivalis LPS (Pg LPS) in human gingival fibroblasts (HGF). When HGFs were treated with Pg LPS, both PAI-1 mRNA expression and PAI-1 protein were induced in a dose-dependent manner. Pg LPS induced NF-κB activation and the expressions of PAI-1 mRNA and protein were suppressed by pretreating with a NF-κB inhibitor. Pg LPS also induced ERK, p38, and JNK activation, and Pg LPS-induced PAI-1 expression was inhibited by ERK/p38/JNK inhibitor pretreatment. In conclusion, Pg LPS induced PAI-1 expression through NF-κB and MAP kinases activation in HGF.

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Porphyromonas gingivalis adopts intricate and unique molecular mechanisms to survive and persist within the host: a critical update
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Periodontal Pathogens and Neuropsychiatric Health
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Periodontitis induced byPorphyromonas gingivalisdrives periodontal microbiota dysbiosis and insulin resistance via an impaired adaptive immune response
Vincent Blasco-Baque, Lucile Garidou, Céline Pomié, Quentin Escoula, Pascale Loubieres, Sandrine Le Gall-David, Mathieu Lemaitre, Simon Nicolas, Pascale Klopp, Aurélie Waget, Vincent Azalbert, André Colom, Martine Bonnaure-Mallet, Philippe Kemoun, Matteo
Gut.2017; 66(5): 872. CrossRef
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Kah Yan How, Keang Peng Song, Kok Gan Chan
Frontiers in Microbiology.2016;[Epub] CrossRef
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Jaroslav Mysak, Stepan Podzimek, Pavla Sommerova, Yelena Lyuya-Mi, Jirina Bartova, Tatjana Janatova, Jarmila Prochazkova, Jana Duskova
Journal of Immunology Research.2014; 2014: 1. CrossRef

Journal Article

Porphyromonas gingivalis-Derived Lipopolysaccharide-Mediated Activation of MAPK Signaling Regulates Inflammatory Response and Differentiation in Human Periodontal Ligament Fibroblasts: Taegun Seo , Seho Cha , Tae-Il Kim , Hee-Jung Park , Jeong-Soon Lee , Kyung Mi Woo; J. Microbiol. 2012;50(2):311-319. Published online April 27, 2012; DOI: https://doi.org/10.1007/s12275-012-2146-x

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Abstract

Porphyromonas gingivalis (P.g.), which is a potential pathogen for periodontal diseases, contains lipopolysaccharide (LPS), and this endotoxin stimulates a variety of cellular responses. At present, P.g.-derived LPS-induced cellular responses in human periodontal ligament fibroblasts (PDLFs) are not well characterized. Here, we demonstrate that P.gderived LPS regulates inflammatory responses, apoptosis and differentiation in PDLFs. Interleukin-6 (IL-6) and -8 (IL-8) were effectively upregulated by treatment of P.g.-derived LPS, and we confirmed apoptosis markers including elevated cytochrome c levels, active caspase-3 and morphological change in the presence of P.g.-derived LPS. Moreover, when PDLFs were cultured with differentiation media, P.g.- derived LPS reduced the expression of differentiation marker genes, as well as reducing alkaline phosphatase (ALP) activity and mineralization. P.g.-derived LPS-mediated these cellular responses were effectively abolished by treatment of mitogen-activated protein kinase (MAPK) inhibitors. Taken together, our results suggest that P.g.-derived LPS regulates several cellular responses via activation of MAPK signaling pathways in PDLFs.

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Research Support, Non-U.S. Gov't

NOTE] Development of Porphyromonas gingivalis-Specific Quantitative Real-Time PCR Primers Based on the Nucleotide Sequence of rpoB: Soon-Nang Park , Jae-Yoon Park , Joong-Ki Kook; J. Microbiol. 2011;49(2):315-319. Published online May 3, 2011; DOI: https://doi.org/10.1007/s12275-011-1028-y

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Abstract: Species-specific quantitative real-time PCR (qPCR) primers were developed for the detection of Porphyromonas gingivalis. These primers, Pg-F/Pg-R, were designed based on the nucleotide sequences of RNA polymerase β-subunit gene (rpoB). Species-specific amplicons were obtained from the tested P. gingivalis strains but not in any of the other strains (46 strains of 46 species). The qPCR primers could detect as little as 4 fg of P. gingivalis chromosomal DNA. These findings suggest that these qPCR primers are suitable for applications in epidemiological studies.

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