Review
- Membrane Proteins as a Regulator for Antibiotic Persistence in Gram‑Negative Bacteria
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Jia Xin Yee , Juhyun Kim , Jinki Yeom
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J. Microbiol. 2023;61(3):331-341. Published online February 17, 2023
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DOI: https://doi.org/10.1007/s12275-023-00024-w
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Antibiotic treatment failure threatens our ability to control bacterial infections that can cause chronic diseases. Persister bacteria
are a subpopulation of physiological variants that becomes highly tolerant to antibiotics. Membrane proteins play crucial
roles in all living organisms to regulate cellular physiology. Although a diverse membrane component involved in persistence
can result in antibiotic treatment failure, the regulations of antibiotic persistence by membrane proteins has not been fully
understood. In this review, we summarize the recent advances in our understanding with regards to membrane proteins in
Gram-negative bacteria as a regulator for antibiotic persistence, highlighting various physiological mechanisms in bacteria.
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- Cardamom essential oil-loaded zinc oxide nanoparticles: A sustainable antimicrobial strategy against multidrug-resistant foodborne pathogens
Mabrouk Sobhy, Tamer Elsamahy, Esraa A. Abdelkarim, Ebtihal Khojah, Haiying Cui, Lin Lin
Microbial Pathogenesis.2025; 205: 107661. CrossRef - Amino Acid and Au(III) Self-Assembled Supramolecular Nanozymes for Antimicrobial Applications
Yunzhu Xu, Dahai Hou, Min Zhao, Tong Zhao, Yong Ma, Yafeng Zhang, Yang Guo, Weiwei Tao, Hui Wang
ACS Applied Nano Materials.2024; 7(19): 22505. CrossRef -
PhoPQ-mediated lipopolysaccharide modification governs intrinsic resistance to tetracycline and glycylcycline antibiotics in
Escherichia coli
Byoung Jun Choi, Umji Choi, Dae-Beom Ryu, Chang-Ro Lee, Mehrad Hamidian, You-Hee Cho
mSystems.2024;[Epub] CrossRef - Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms’ Complex Regulation
Jin-Won Lee
Journal of Microbiology.2023; 61(3): 273. CrossRef
Journal Articles
- Mutational analysis on stable expression and LasB inhibition of LasB propeptide in Pseudomonas aeruginosa
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Youngsun Shin , Xi-Hui Li , Cheol Seung Lee , Joon-Hee Lee
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J. Microbiol. 2022;60(7):727-734. Published online May 25, 2022
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DOI: https://doi.org/10.1007/s12275-022-1671-5
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Three major proteases, elastase B (LasB), protease IV (PIV),
and elastase A (LasA) expressed in Pseudomonas aeruginosa
play important roles in infections and pathogeneses. These
are activated by a proteolytic cascade initiated by the activation
of LasB. In this study, we investigated whether LasB
could be inhibited using its propeptide (LasBpp). Although
LasA and PIV were inhibited by their propeptides, LasB was
not inhibited by purified LasBpp because LasB degraded LasBpp.
To address this problem, mutant LasBpp variants were constructed
to obtain a mutant LasBpp resistant to LasB degradation.
A C-terminal deletion series of LasBpp was tested in
vivo, and two positive candidates, T2 and T2-1, were selected.
However, both caused growth retardation and were unstably
expressed in vivo. Since deleting the C-terminal end of LasBpp
significantly affected its stable expression, substitution mutations
were introduced at the two amino acids near the
truncation site of T2-1. The resulting mutants, LasBppE172D,
LasBppG173A, and LasBppE172DG173A, significantly diminished LasB
activity when overexpressed in vivo and were stably expressed
in MW1, a quorum sensing mutant that does not produce
LasB. In vitro analysis showed that purified LasBppE172DG173A
inhibited LasB activity to a small extent. Summarizing, Cterminal
modification of LasBpp profoundly affected the stable
expression of LasBpp, and little enhanced the ability of
LasBpp to resist degradation by LasB.
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- LasB activation in Pseudomonas aeruginosa: Quorum sensing-mediated release of an auto-activation inhibitor
Cheol Seung Lee, Xi-Hui Li, Chae-Ran Jeon, Joon-Hee Lee
Journal of Microbiology.2025; 63(2): e2411005. CrossRef
- Lactobacillus plantarum-derived metabolites sensitize the tumorsuppressive effects of butyrate by regulating the functional expression of SMCT1 in 5-FU-resistant colorectal cancer cells
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Hye-Ju Kim , JaeJin An , Eun-Mi Ha
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J. Microbiol. 2022;60(1):100-117. Published online December 29, 2021
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DOI: https://doi.org/10.1007/s12275-022-1533-1
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A critical obstacle to the successful treatment of colorectal
cancer (CRC) is chemoresistance. Chemoresistant CRC cells
contribute to treatment failure by providing a mechanism
of drug lethargy and modifying chemoresistance-associated
molecules. The gut microbiota provide prophylactic and therapeutic
effects by targeting CRC through anticancer mechanisms.
Among them, Lactobacillus plantarum contributes
to the health of the host and is clinically effective in treating
CRC. This study confirmed that 5-fluorouracil (5-FU)-resistant
CRC HCT116 (HCT116/5FUR) cells acquired butyrateinsensitive
properties. To date, the relationship between 5-
FU-resistant CRC and butyrate resistance has not been elucidated.
Here, we demonstrated that the acquisition of butyrate
resistance in HCT116/5FUR cells was strongly correlated
with the inhibition of the expression and function of
SMCT1, a major transporter of butyrate in colonocytes. L.
plantarum-cultured cell-free supernatant (LP) restored the
functional expression of SMCT1 in HCT116/5FUR cells, leading
to butyrate-induced antiproliferative effect and apoptosis.
These results suggest that LP has a synergistic effect on the
SMCT1/butyrate-mediated tumor suppressor function and
is a potential chemosensitizer to overcome dual 5-FU and butyrate
resistance in HCT116 cells.
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Citations
Citations to this article as recorded by

- Advancements in the Pathogenesis, Diagnosis, and Therapeutic Implications of Intestinal Bacteria
Duofei Lu, Xianxiong Ma, Kaixiong Tao, Hongwei Lei
Current Issues in Molecular Biology.2025; 47(2): 106. CrossRef - The benefits of Lactiplantibacillus plantarum: From immunomodulator to vaccine vector
Joshua Tobias, Stefan Heinl, Kristina Dendinovic, Ajša Ramić, Anna Schmid, Catherine Daniel, Ursula Wiedermann
Immunology Letters.2025; 272: 106971. CrossRef - Advances in understanding therapeutic mechanisms of probiotics in cancer management, with special emphasis on breast cancer: A comprehensive review
A S Angel Nama, G Mary Sandeepa, Viswanath Buddolla, Anthati Mastan
European Journal of Pharmacology.2025; 995: 177410. CrossRef - Unlocking the power of probiotics, postbiotics: targeting apoptosis for the treatment and prevention of digestive diseases
Qiuyan Xie, Ji Liu, Ping Yu, Ting Qiu, Shanyu Jiang, Renqiang Yu
Frontiers in Nutrition.2025;[Epub] CrossRef - Unveiling the Interplay Between the Human Microbiome and Gastric Cancer: A Review of the Complex Relationships and Therapeutic Avenues
Jenan Al-Matouq, Hawra Al-Ghafli, Noura N. Alibrahim, Nida Alsaffar, Zaheda Radwan, Mohammad Daud Ali
Cancers.2025; 17(2): 226. CrossRef - The role of gut microbiota and metabolites in cancer chemotherapy
Shiyu Li, Shuangli Zhu, Jun Yu
Journal of Advanced Research.2024; 64: 223. CrossRef - Sodium Butyrate Inhibits the Expression of Thymidylate Synthase and Induces Cell Death in Colorectal Cancer Cells
Nayeon Kim, Changwon Yang
International Journal of Molecular Sciences.2024; 25(3): 1572. CrossRef - Anticancer Properties of Saccharomyces boulardii Metabolite Against Colon Cancer Cells
Babak Pakbin, Samaneh Allahyari, Shaghayegh Pishkhan Dibazar, Amir Peymani, Mozhdeh Khajeh Haghverdi, Khadijeh Taherkhani, Maryam Javadi, Razzagh Mahmoudi
Probiotics and Antimicrobial Proteins.2024; 16(1): 224. CrossRef - The effect of oral butyrate on colonic short-chain fatty acid transporters and receptors depends on microbial status
Karla Vagnerová, Tomáš Hudcovic, Martin Vodička, Peter Ergang, Petra Klusoňová, Petra Petr Hermanová, Dagmar Šrůtková, Jiří Pácha
Frontiers in Pharmacology.2024;[Epub] CrossRef - Exploiting lactic acid bacteria for colorectal cancer: a recent update
Yang Chen, Bo Yang, Jianxin Zhao, R. Paul Ross, Catherine Stanton, Hao Zhang, Wei Chen
Critical Reviews in Food Science and Nutrition.2024; 64(16): 5433. CrossRef - Gut microbial metabolites: Shaping future diagnosis and treatment against gastrointestinal cancer
Hongyan Gou, Ruijie Zeng, Harry Cheuk Hay Lau, Jun Yu
Pharmacological Research.2024; 208: 107373. CrossRef - Probiotics intervention in colorectal cancer: From traditional approaches to novel strategies
Suki Ha, Xiang Zhang, Jun Yu
Chinese Medical Journal.2024; 137(1): 8. CrossRef - A Narrative Review on the Advance of Probiotics to Metabiotics
Hye Ji Jang, Na-Kyoung Lee, Hyun-Dong Paik
Journal of Microbiology and Biotechnology.2024; 34(3): 487. CrossRef - Pharmacomicrobiomics of cell-cycle specific anti-cancer drugs – is it a new perspective for personalized treatment of cancer patients?
Karolina Kaźmierczak-Siedlecka, Nikola Bulman, Paweł Ulasiński, Bartosz Kamil Sobocki, Karol Połom, Luigi Marano, Leszek Kalinowski, Karolina Skonieczna-Żydecka
Gut Microbes.2023;[Epub] CrossRef - Participation of protein metabolism in cancer progression and its potential targeting for the management of cancer
Dalong Liu, Yun Wang, Xiaojiang Li, Yan Wang, Zhiqiang Zhang, Zhifeng Wang, Xudong Zhang
Amino Acids.2023; 55(10): 1223. CrossRef - Microbial metabolites in colorectal tumorigenesis and cancer therapy
Yali Liu, Harry Cheuk-Hay Lau, Jun Yu
Gut Microbes.2023;[Epub] CrossRef - Lactobacillus plantarum Metabolites Elicit Anticancer Effects by Inhibiting Autophagy-Related Responses
Sihyun Jeong, Yuju Kim, Soyeong Park, Doyeon Lee, Juho Lee, Shwe Phyu Hlaing, Jin-Wook Yoo, Sang Hoon Rhee, Eunok Im
Molecules.2023; 28(4): 1890. CrossRef - Lactobacillus plantarum modulate gut microbiota and intestinal immunity in cyclophosphamide-treated mice model
Zhibo Zeng, Zonghao Huang, Wen Yue, Shah Nawaz, Xinzhu Chen, Jing Liu
Biomedicine & Pharmacotherapy.2023; 169: 115812. CrossRef - Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment
Yali Liu, Harry Cheuk-Hay Lau, Wing Yin Cheng, Jun Yu
Genomics, Proteomics & Bioinformatics.2023; 21(1): 84. CrossRef - Research progress of traditional Chinese medicine as sensitizer in reversing chemoresistance of colorectal cancer
Xiang Lin, Xinyu Yang, Yushang Yang, Hangbin Zhang, Xuan Huang
Frontiers in Oncology.2023;[Epub] CrossRef - Characterization of Wnt signaling pathway under treatment of Lactobacillus acidophilus postbiotic in colorectal cancer using an integrated in silico and in vitro analysis
Nafiseh Erfanian, Saeed Nasseri, Adib Miraki Feriz, Hossein Safarpour, Mohammad Hassan Namaei
Scientific Reports.2023;[Epub] CrossRef - A Review of Gut Microbiota‐Derived Metabolites in Tumor Progression and Cancer Therapy
Qiqing Yang, Bin Wang, Qinghui Zheng, Heyu Li, Xuli Meng, Fangfang Zhou, Long Zhang
Advanced Science.2023;[Epub] CrossRef - Anti-tumour effect of Huangqin Decoction on colorectal cancer mice through microbial butyrate mediated PI3K/Akt pathway suppression
Jia-Jie Zhu, Hai-Yan Liu, Liang-Jun Yang, Zheng Fang, Rui Fu, Jia-Bin Chen, Shan Liu, Bao-Ying Fei
Journal of Medical Microbiology
.2023;[Epub] CrossRef - Fecal levels of SCFA and BCFA during capecitabine in patients with metastatic or unresectable colorectal cancer
Janine Ziemons, Romy Aarnoutse, Anne Heuft, Lars Hillege, Janneke Waelen, Judith de Vos-Geelen, Liselot Valkenburg-van Iersel, Irene E. G. van Hellemond, Geert-Jan M. Creemers, Arnold Baars, Johanna H. M. J. Vestjens, John Penders, Koen Venema, Marjolein
Clinical and Experimental Medicine.2023; 23(7): 3919. CrossRef - Probiotic-Derived Bioactive Compounds in Colorectal Cancer Treatment
Christina Thoda, Maria Touraki
Microorganisms.2023; 11(8): 1898. CrossRef - Gut microbiota and microbiota-derived metabolites in colorectal cancer: enemy or friend
Xinyi Wang, Xicai Sun, Jinjin Chu, Wenchang Sun, Shushan Yan, Yaowen Wang
World Journal of Microbiology and Biotechnology.2023;[Epub] CrossRef - Determination of the effect of L. plantarum AB6-25, L. plantarum MK55 and S. boulardii T8-3C microorganisms on colon, cervix, and breast cancer cell lines: Molecular docking, and molecular dynamics study
Seda Yalçınkaya, Serap Yalçın Azarkan, Aynur Gül Karahan Çakmakçı
Journal of Molecular Structure.2022; 1261: 132939. CrossRef - Extracellular vesicles derived from Lactobacillus plantarum restore chemosensitivity through the PDK2-mediated glucose metabolic pathway in 5-FU-resistant colorectal cancer cells
JaeJin An, Eun-Mi Ha
Journal of Microbiology.2022; 60(7): 735. CrossRef
- Short-chain fatty acids inhibit the biofilm formation of Streptococcus gordonii through negative regulation of competence-stimulating peptide signaling pathway
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Taehwan Park , Jintaek Im , A Reum Kim , Dongwook Lee , Sungho Jeong , Cheol-Heui Yun , Seung Hyun Han
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J. Microbiol. 2021;59(12):1142-1149. Published online December 4, 2021
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DOI: https://doi.org/10.1007/s12275-021-1576-8
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Streptococcus gordonii, a Gram-positive commensal bacterium,
is an opportunistic pathogen closely related to initiation
and progression of various oral diseases, such as periodontitis
and dental caries. Its biofilm formation is linked
with the development of such diseases by enhanced resistance
against antimicrobial treatment or host immunity. In the
present study, we investigated the effect of short-chain fatty
acids (SCFAs) on the biofilm formation of S. gordonii. SCFAs,
including sodium acetate (NaA), sodium propionate (NaP),
and sodium butyrate (NaB), showed an effective inhibitory
activity on the biofilm formation of S. gordonii without reduction
in bacterial growth. SCFAs suppressed S. gordonii
biofilm formation at early time points whereas SCFAs did
not affect its preformed biofilm. A quorum-sensing system
mediated by competence-stimulating peptide (CSP) is known
to regulate biofilm formation of streptococci. Interestingly,
SCFAs substantially decreased mRNA expression of comD
and comE, which are CSP-sensor and its response regulator
responsible for CSP pathway, respectively. Although S. gordonii
biofilm formation was enhanced by exogenous synthetic
CSP treatment, such effect was not observed in the
presence of SCFAs. Collectively, these results suggest that
SCFAs have an anti-biofilm activity on S. gordonii through
inhibiting comD and comE expression which results in negative
regulation of CSP quorum-sensing system. SCFAs could
be an effective anti-biofilm agent against S. gordonii for the
prevention of oral diseases.
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Citations
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- Recent progress in understanding the role of bacterial extracellular DNA: focus on dental biofilm
Fengxue Geng, Junchao Liu, Jinwen Liu, Ze Lu, Yaping Pan
Critical Reviews in Microbiology.2025; 51(5): 898. CrossRef - Potential effects of prebiotic fibers on dental caries: a systematic review
Constanza E. Fernández, Catalina Maturana‐Valenzuela, Nicol Rojas‐Castillo, Bob Rosier
Journal of the Science of Food and Agriculture.2025; 105(11): 5640. CrossRef - Formation, architecture, and persistence of oral biofilms: recent scientific discoveries and new strategies for their regulation
Chengyuan Lv, Ziyi Wang, Zehui Li, Xialing Shi, Mingming Xiao, Yan Xu
Frontiers in Microbiology.2025;[Epub] CrossRef - The human skin microbiome: from metagenomes to therapeutics
Julia Oh, Anita Y. Voigt
Nature Reviews Microbiology.2025;[Epub] CrossRef - Serotype-Dependent Inhibition of Streptococcus pneumoniae Growth by Short-Chain Fatty Acids
Suwon Lim, Dongwook Lee, Sungho Jeong, Jeong Woo Park, Jintaek Im, Bokeum Choi, Donghyun Gwak, Cheol-Heui Yun, Ho Seong Seo, Seung Hyun Han
Journal of Microbiology and Biotechnology.2024; 34(1): 47. CrossRef - Comprehensive Multi-Omic Evaluation of the Microbiota and Metabolites in the Colons of Diverse Swine Breeds
Yanbin Zhu, Guangming Sun, Yangji Cidan, Bin Shi, Zhankun Tan, Jian Zhang, Wangdui Basang
Animals.2024; 14(8): 1221. CrossRef - Effects of Epigallocatechin gallate on Biofilm adherence and Glycolytic pH in Streptococcus gordonii
Prawati Nuraini, Dimas Prasetianto Wicaksono, Ardianti Maartrina Dewi, Adinda Ayu Fitriana, Sili Han
Research Journal of Pharmacy and Technology.2024; : 4711. CrossRef - Oral Pathogens and Their Antibiotics from Marine Organisms: A Systematic Review of New Drugs for Novel Drug Targets
Sehyeok Im, Jun Hyuck Lee, Youn-Soo Shim
Journal of Dental Hygiene Science.2024; 24(2): 84. CrossRef - Effects of the gut microbiota and its metabolite short-chain fatty acids on endometriosis
Menghe Liu, Ru Peng, Chunfang Tian, Jianping Shi, Jiannan Ma, Ruiwen Shi, Xiao Qi, Rongwei Zhao, Haibin Guan
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef - Butyrate potentiates Enterococcus faecalis lipoteichoic acid-induced inflammasome activation via histone deacetylase inhibition
Ok-Jin Park, Ye-Eun Ha, Ju-Ri Sim, Dongwook Lee, Eun-Hye Lee, Sun-Young Kim, Cheol-Heui Yun, Seung Hyun Han
Cell Death Discovery.2023;[Epub] CrossRef - Gut microbiota short-chain fatty acids and their impact on the host thyroid function and diseases
María José Mendoza-León, Ashutosh K. Mangalam, Alejandro Regaldiz, Enrique González-Madrid, Ma. Andreina Rangel-Ramírez, Oscar Álvarez-Mardonez, Omar P. Vallejos, Constanza Méndez, Susan M. Bueno, Felipe Melo-González, Yorley Duarte, Ma. Cecilia Opazo, Al
Frontiers in Endocrinology.2023;[Epub] CrossRef - Crosstalk between microbial biofilms in the gastrointestinal tract and chronic mucosa diseases
Yumeng Wang, Shixi Xu, Qiurong He, Kun Sun, Xiaowan Wang, Xiaorui Zhang, Yuqing Li, Jumei Zeng
Frontiers in Microbiology.2023;[Epub] CrossRef - Listening to enteric bacteria from the perspective of antibiotic alternatives in animal husbandry
Leli Wang, Yiru Zhang, Juan Xu, Qingqing Shi, Yao Peng, Cimin Long, Lan Li, Yulong Yin
The Innovation Life.2023; 1(2): 100022. CrossRef - The Complicated Relationship of Short-Chain Fatty Acids and Oral Microbiome: A Narrative Review
Georgy E. Leonov, Yurgita R. Varaeva, Elena N. Livantsova, Antonina V. Starodubova
Biomedicines.2023; 11(10): 2749. CrossRef - Social networking at the microbiome-host interface
Richard J. Lamont, George Hajishengallis, Hyun Koo, Anthony R. Richardson
Infection and Immunity.2023;[Epub] CrossRef - Making Sense of Quorum Sensing at the Intestinal Mucosal Interface
Friederike Uhlig, Niall P. Hyland
Cells.2022; 11(11): 1734. CrossRef - Food-Grade Bacteria Combat Pathogens by Blocking AHL-Mediated Quorum Sensing and Biofilm Formation
Kirsi Savijoki, Paola San-Martin-Galindo, Katriina Pitkänen, Minnamari Edelmann, Annika Sillanpää, Cim van der Velde, Ilkka Miettinen, Jayendra Z. Patel, Jari Yli-Kauhaluoma, Mataleena Parikka, Adyary Fallarero, Pekka Varmanen
Foods.2022; 12(1): 90. CrossRef - Innate immunity and microbial dysbiosis in hidradenitis suppurativa – vicious cycle of chronic inflammation
Divya Chopra, Rachel A. Arens, Watcharee Amornpairoj, Michelle A. Lowes, Marjana Tomic-Canic, Natasa Strbo, Hadar Lev-Tov, Irena Pastar
Frontiers in Immunology.2022;[Epub] CrossRef - Drugs for the Quorum Sensing Inhibition of Oral Biofilm: New Frontiers and Insights in the Treatment of Periodontitis
Alessandro Polizzi, Martina Donzella, Giada Nicolosi, Simona Santonocito, Paolo Pesce, Gaetano Isola
Pharmaceutics.2022; 14(12): 2740. CrossRef
- [PROTOCOL] Flow cytometric monitoring of the bacterial phenotypic diversity in aquatic ecosystems
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Jin-Kyung Hong , Soo Bin Kim , Seok Hyun Ahn , Yongjoo Choi , Tae Kwon Lee
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J. Microbiol. 2021;59(10):879-885. Published online September 23, 2021
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DOI: https://doi.org/10.1007/s12275-021-1443-7
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Flow cytometry is a promising tool used to identify the phenotypic
features of bacterial communities in aquatic ecosystems
by measuring the physical and chemical properties of
cells based on their light scattering behavior and fluorescence.
Compared to molecular or culture-based approaches, flow
cytometry is suitable for the online monitoring of microbial
water quality because of its relatively simple sample preparation
process, rapid analysis time, and high-resolution phenotypic
data. Advanced statistical techniques (e.g., denoising
and binning) can be utilized to successfully calculate phenotypic
diversity by processing the scatter data obtained from
flow cytometry. These phenotypic diversities were well correlated
with taxonomic-based diversity computed using nextgeneration
16S RNA gene sequencing. The protocol provided
in this paper should be a useful guide for a fast and reliable
flow cytometric monitoring of bacterial phenotypic diversity
in aquatic ecosystems.
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Citations
Citations to this article as recorded by

- Enhancing Bacterial Phenotype Classification Through the Integration of Autogating and Automated Machine Learning in Flow Cytometric Analysis
In Jae Jeong, Jin‐Kyung Hong, Young Jun Bae, Tea Kwon Lee
Cytometry Part A.2025; 107(3): 203. CrossRef - Assessing long-term ecological impacts of PCE contamination in groundwater using a flow cytometric fingerprint approach
Jin-Kyung Hong, Soo Bin Kim, Gui Nam Wee, Bo Ram Kang, Jee Hyun No, Susmita Das Nishu, Joonhong Park, Tae Kwon Lee
Science of The Total Environment.2024; 931: 172698. CrossRef - Phenotypic shifts induced by environmental pre-stressors modify antibiotic resistance in Staphylococcus aureus
Gui Nam Wee, Eun Sun Lyou, Susmita Das Nishu, Tae Kwon Lee
Frontiers in Microbiology.2023;[Epub] CrossRef
- Full-repertoire comparison of the microscopic objects composing the human gut microbiome with sequenced and cultured communities
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Edmond Kuete Yimagou , Jean-Pierre Baudoin , Rita Abou Abdallah , Fabrizio Di Pinto , Jacques Yaacoub Bou Khalil , Didier Raoult
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J. Microbiol. 2020;58(5):377-386. Published online April 11, 2020
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DOI: https://doi.org/10.1007/s12275-020-9365-3
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The study of the human gut microbiome is essential in microbiology
and infectious diseases as specific alterations in the
gut microbiome might be associated with various pathologies,
such as chronic inflammatory disease, intestinal infection
and colorectal cancer. To identify such dysregulations,
several strategies are being used to create a repertoire of the
microorganisms composing the human gut microbiome. In
this study, we used the “microscomics” approach, which consists
of creating an ultrastructural repertoire of all the cell-like
objects composing stool samples from healthy donors using
transmission electron microscopy (TEM). We used TEM to
screen ultrathin sections of 8 resin-embedded stool samples.
After exploring hundreds of micrographs, we managed to
elaborate ultrastructural categories based on morphological
criteria or features. This approach explained many inconsistencies
observed with other techniques, such as metagenomics
and culturomics. We highlighted the value of our cultureindependent
approach by comparing our microscopic images
to those of cultured bacteria and those reported in the
literature. This study helped to detect “minimicrobes” Candidate
Phyla Radiation (CPR) for the first time in human
stool samples. This “microscomics” approach is non-exhaustive
but complements already existing approaches and adds
important data to the puzzle of the microbiota.
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Citations
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- Tips and tricks for gut microbiota investigation using scanning electron microscopy (SEM): going from sample preparation to imaging and landscape analysis
Meriem Boukili, Omar Zmerli, Florence Fenollar, Sara Bellali, Jacques Bou Khalil
Gut Microbes.2025;[Epub] CrossRef - Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease
Sabrina Naud, Ahmad Ibrahim, Camille Valles, Mohamad Maatouk, Fadi Bittar, Maryam Tidjani Alou, Didier Raoult
Clinical Microbiology Reviews.2022;[Epub] CrossRef - Radiotherapy and the gut microbiome: facts and fiction
Jing Liu, Chao Liu, Jinbo Yue
Radiation Oncology.2021;[Epub] CrossRef - Host–microbiota maladaptation in colorectal cancer
Alina Janney, Fiona Powrie, Elizabeth H. Mann
Nature.2020; 585(7826): 509. CrossRef
- Differential expression of the major catalase, KatA in the two wild type Pseudomonas aeruginosa strains, PAO1 and PA14
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Bi-o Kim , In-Young Chung , You-Hee Cho
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J. Microbiol. 2019;57(8):704-710. Published online June 11, 2019
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DOI: https://doi.org/10.1007/s12275-019-9225-1
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KatA is the major catalase required for hydrogen peroxide
(H2O2) resistance and acute virulence in Pseudomonas aeruginosa
PA14, whose transcription is governed by its dual
promoters (katAp1 and katAp2). Here, we observed that KatA
was not required for acute virulence in another wild type P.
aeruginosa strain, PAO1, but that PAO1 exhibited higher
KatA expression than PA14 did. This was in a good agreement
with the observation that PAO1 was more resistant
than PA14 to H2O2 as well as to the antibiotic peptide, polymyxin
B (PMB), supposed to involve reactive oxygen species
(ROS) for its antibacterial activity. The higher KatA expression
in PAO1 than in PA14 was attributed to both katAp1
and katAp2 transcripts, as assessed by S1 nuclease mapping.
In addition, it was confirmed that the PMB resistance is attributed
to both katAp1 and katAp2 in a complementary manner
in PA14 and PAO1, by exploiting the promoter mutants
for each -10 box (p1m, p2m, and p1p2m). These results provide
an evidence that the two widely used P. aeruginosa strains
display different virulence mechanisms associated with OxyR
and Anr, which need to be further characterized for better
understanding of the critical virulence pathways that may
differ in various P. aeruginosa strains.
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Citations
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- hmuSTUV operon positively regulates the alginate gene cluster to mediate the pathogenicity of Pseudomonas donghuensis HYS
Yaqian Xiao, Wang Xiang, Donghao Gao, Bowen Zheng, Zhiqian Wang, Dechang Rong, Hasan Bayram, Reza A. Ghiladi, George H. Lorimer, Zhixiong Xie, Jun Wang
International Journal of Biological Macromolecules.2025; 306: 141430. CrossRef - Enhancing the compost maturation of deer manure and corn straw by supplementation via black liquor
Shijun Pan, Gang Wang, Yide Fan, Xiqing Wang, Juan Liu, Mingzhu Guo, Huan Chen, Sitong Zhang, Guang Chen
Heliyon.2023; 9(2): e13246. CrossRef - The small RNA PrrH of Pseudomonas aeruginosa regulates hemolysis and oxidative resistance in bloodstream infection
Shenghe Zeng, Qixuan Shi, YinZhen Liu, Mo Li, Dongling Lin, Shebin Zhang, Qiwei Li, Jieying Pu, Cong Shen, Bin Huang, Cha Chen, Jianming Zeng
Microbial Pathogenesis.2023; 180: 106124. CrossRef - Eco-evolutionary dynamics of experimental Pseudomonas aeruginosa populations under oxidative stress
Taoran Fu, Danna R. Gifford, Christopher G. Knight, Michael A. Brockhurst
Microbiology
.2023;[Epub] CrossRef - The Pseudomonas aeruginosa DksA1 protein is involved in H2O2 tolerance and within-macrophages survival and can be replaced by DksA2
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Yilin Zhang, Huimin Tan, Shiping Yang, Yucong Huang, Shuanghu Cai, Jichang Jian, Jia Cai, Qiwei Qin
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Antioxidants & Redox Signaling.2021; 34(6): 442. CrossRef - The Bactericidal Tandem Drug, AB569: How to Eradicate Antibiotic-Resistant Biofilm Pseudomonas aeruginosa in Multiple Disease Settings Including Cystic Fibrosis, Burns/Wounds and Urinary Tract Infections
Daniel J. Hassett, Rhett A. Kovall, Michael J. Schurr, Nalinikanth Kotagiri, Harshita Kumari, Latha Satish
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Hyo-Young Oh, Shivakumar S. Jalde, In-Young Chung, Yeon-Ji Yoo, Hye-Jeong Jang, Hyun-Kyung Choi, You-Hee Cho
Journal of Medical Microbiology
.2021;[Epub] CrossRef
- Low-density lipoprotein as an opsonin promoting the phagocytosis of Pseudomonas aeruginosa by U937 cells
-
Yuxin Li , Zhi Liu , Jinli Yang , Ling Liu , Runlin Han
-
J. Microbiol. 2019;57(8):711-716. Published online May 11, 2019
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DOI: https://doi.org/10.1007/s12275-019-8413-3
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383
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2
Web of Science
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2
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Abstract
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Low-density lipoprotein (LDL) was recently reported to be an
opsonin, enhancing the phagocytosis of group A Streptococcus
(GAS) by human monocytic leukemia U937 cells due to the
binding of LDL to some GAS strains. We postulated that LDL
might also promote the opsonophagocytosis of Pseudomonas
aeruginosa by U937 cells since this bacterium interacts with
LDL. In this study, P. aeruginosa (CMCC10104), U937 cells,
and human LDL were used in phagocytosis assays to test our
hypothesis. Escherichia coli strain BL21, which does not interact
with LDL, was used as a negative control. Colony counting
and fluorescence microscopy were used to determine the
bacterial quantity in the opsonophagocytosis assays. After
incubation of U937 cells and P. aeruginosa with LDL (100
μg/ml) for 15 and 30 min, phagocytosis was observed to be
increased by 22.71% and 32.90%, respectively, compared to
that seen in the LDL-free group. However, LDL did not increase
the phagocytosis of E. coli by U937 cells. In addition,
we identified CD36 as a major opsonin receptor on U937 cells,
since an anti-CD36 monoclonal antibody, but not an anti-
CD4 monoclonal antibody, almost completely abolished the
opsonophagocytosis of P. aeruginosa by U937 cells.
-
Citations
Citations to this article as recorded by

- Adhesion of Enteropathogenic, Enterotoxigenic, and Commensal Escherichia coli to the Major Zymogen Granule Membrane Glycoprotein 2
Christin Bartlitz, Rafał Kolenda, Jarosław Chilimoniuk, Krzysztof Grzymajło, Stefan Rödiger, Rolf Bauerfeind, Aamir Ali, Veronika Tchesnokova, Dirk Roggenbuck, Peter Schierack, Isaac Cann
Applied and Environmental Microbiology.2022;[Epub] CrossRef - Lipoprotein(a), an Opsonin, Enhances the Phagocytosis of Nontypeable Haemophilus influenzae by Macrophages
Zhi Liu, Yuxin Li, Yu Wang, Zhe Liu, Yan Su, Qiang Ma, Runlin Han, Enrique Ortega
Journal of Immunology Research.2021; 2021: 1. CrossRef
- Antibiofilm effect of biofilm-dispersing agents on clinical isolates of Pseudomonas aeruginosa with various biofilm structures
-
Soo-Kyoung Kim , Xi-Hui Li , Hyeon-Ji Hwang , Joon-Hee Lee
-
J. Microbiol. 2018;56(12):902-909. Published online October 25, 2018
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DOI: https://doi.org/10.1007/s12275-018-8336-4
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365
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0
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8
Crossref
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Abstract
PDF
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Pseudomonas aeruginosa, an opportunistic human pathogen,
causes many biofilm-mediated chronic infections. In this study,
biofilm structures of various clinical strains of P. aeruginosa
isolated from hospitalized patients were examined and their
influence on the biofilm-dispersing effects of chemicals was
investigated. The clinical isolates formed structurally distinct
biofilms that could be classified into three different groups:
1) mushroom-like, 2) thin flat, and 3) thick flat structures.
A dispersion of these differently structured biofilms was induced
using two biofilm-dispersing agents, anthranilate and
sodium nitroprusside (SNP). Although both SNP and anthranilate
could disperse all types of biofilms, the thick flat biofilms
were dispersed less efficiently than the biofilms of other
structures. This suggests that biofilm-dispersing agents have
higher potency on the biofilms of porous structures than on
densely packed biofilms.
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Citations
Citations to this article as recorded by

- Effects of Anti-Pseudomonal Agents, Individually and in Combination, With or Without Clarithromycin, on Growth and Biofilm Formation by Antibiotic-Susceptible and -Resistant Strains of Pseudomonas aeruginosa, and the Impact of Exposure to Cigarette Smoke
Moloko C. Cholo, Charles Feldman, Ronald Anderson, Lebogang Sekalo, Naledi Moloko, Guy A. Richards
Antibiotics.2025; 14(3): 325. CrossRef - Interspecies electron transfer of mixed-species biofilms in microbial corrosion of metals: mechanisms and mitigation strategies
Mohammed Arroussi, Khaled Al-Athel, Ihsan ulhaq Toor, Ruiyong Zhang
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Ashaimaa Y. Moussa, Shaimaa Fayez, Hang Xiao, Baojun Xu
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Alicia Grace, Robert Murphy, Aoife Dillon, Diarmuid Smith, Sally-Ann Cryan, Andreas Heise, Deirdre Fitzgerald-Hughes
HRB Open Research.2022; 5: 4. CrossRef - Anthranilate Acts as a Signal to Modulate Biofilm Formation, Virulence, and Antibiotic Tolerance of Pseudomonas aeruginosa and Surrounding Bacteria
Hyeon-Ji Hwang, Xi-Hui Li, Soo-Kyoung Kim, Joon-Hee Lee, Cezar M. Khursigara
Microbiology Spectrum.2022;[Epub] CrossRef - Early plaque formation on PTFE membranes with expanded or dense surface structures applied in the oral cavity of human volunteers
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Microbiology Spectrum.2021;[Epub] CrossRef -
Thermoregulation of
Pseudomonas aeruginosa
Biofilm Formation
Suran Kim, Xi-Hui Li, Hyeon-Ji Hwang, Joon-Hee Lee, Danilo Ercolini
Applied and Environmental Microbiology.2020;[Epub] CrossRef
- [PROTOCOL] Drosophila melanogaster as a polymicrobial infection model for Pseudomonas aeruginosa and Staphylococcus aureus
-
Young-Joon Lee , Hye-Jeong Jang , In-Young Chung , You-Hee Cho
-
J. Microbiol. 2018;56(8):534-541. Published online July 25, 2018
-
DOI: https://doi.org/10.1007/s12275-018-8331-9
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470
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1
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17
Crossref
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Abstract
PDF
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Non-mammalian infection models have been developed over
the last two decades, which is a historic milestone to understand
the molecular basis of bacterial pathogenesis. They also
provide small-scale research platforms for identification of
virulence factors, screening for antibacterial hits, and evaluation
of antibacterial efficacy. The fruit fly, Drosophila melanogaster
is one of the model hosts for a variety of bacterial
pathogens, in that the innate immunity pathways and tissue
physiology are highly similar to those in mammals. We here
present a relatively simple protocol to assess the key aspects
of the polymicrobial interaction in vivo between the human
opportunistic pathogens, Pseudomonas aeruginosa and Staphylococcus
aureus, which is based on the systemic infection
by needle pricking at the dorsal thorax of the flies. After infection,
fly survival and bacteremia over time for both P.
aeruginosa and S. aureus within the infected flies can be monitored
as a measure of polymicrobial virulence potential.
The infection takes ~24 h including bacterial cultivation. Fly
survival and bacteremia are assessed using the infected flies
that are monitored up to ~60 h post-infection. These methods
can be used to identify presumable as well as unexpected phenotypes
during polymicrobial interaction between P. aeruginosa
and S. aureus mutants, regarding bacterial pathogenesis
and host immunity.
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Drosophila melanogaster
as an organism model for studying cystic fibrosis and its major associated microbial infections
Hamadoun Touré, Jean-Louis Herrmann, Sébastien Szuplewski, Fabienne Girard-Misguich, Anthony R. Richardson
Infection and Immunity.2023;[Epub] CrossRef - Drosophila melanogaster Systemic Infection Model to Study Altered Virulence during Polymicrobial Infection by Aeromonas
Alexandre Robert, Emilie Talagrand-Reboul, Maria-Jose Figueras, Raymond Ruimy, Laurent Boyer, Brigitte Lamy
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Hyo-Young Oh, Shivakumar S. Jalde, In-Young Chung, Yeon-Ji Yoo, Hye-Jeong Jang, Hyun-Kyung Choi, You-Hee Cho
Journal of Medical Microbiology
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Chenchen Xu, Qiao Cao, Lefu Lan
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Atmika Paudel, Yoshikazu Furuta, Hideaki Higashi
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Deborah Bow Yue Yung, Kathleen Jean Sircombe, Daniel Pletzer
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Frontiers in Microbiology.2019;[Epub] CrossRef - Brain and bone cancer targeting by a ferrofluid composed of superparamagnetic iron-oxide/silica/carbon nanoparticles (earthicles)
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Review
- [MINIREVIEW] Interdependence between iron acquisition and biofilm formation in Pseudomonas aeruginosa
-
Donghoon Kang , Natalia V. Kirienko
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J. Microbiol. 2018;56(7):449-457. Published online June 14, 2018
-
DOI: https://doi.org/10.1007/s12275-018-8114-3
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434
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95
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Abstract
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Bacterial biofilms remain a persistent threat to human healthcare
due to their role in the development of antimicrobial
resistance. To combat multi-drug resistant pathogens, it is
crucial to enhance our understanding of not only the regulation
of biofilm formation, but also its contribution to bacterial
virulence. Iron acquisition lies at the crux of these two
subjects. In this review, we discuss the role of iron acquisition
in biofilm formation and how hosts impede this mechanism
to defend against pathogens. We also discuss recent findings
that suggest that biofilm formation can also have the reciprocal
effect, influencing siderophore production and iron
sequestration.
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Journal Articles
- A common evolutionary pathway for maintaining quorum sensing in Pseudomonas aeruginosa
-
Bai-min Lai , Hui-cong Yan , Mei-zhen Wang , Na Li , Dong-sheng Shen
-
J. Microbiol. 2018;56(2):83-89. Published online February 2, 2018
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DOI: https://doi.org/10.1007/s12275-018-7286-1
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360
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0
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12
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Abstract
PDF
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In the bacterium Pseudomonas aeruginosa, the synthesis and
secretion of extracellular protease is a typical cooperative
behavior regulated by quorum sensing. However, this type
of cooperative behavior is easily exploited by other individuals
who do not synthesize public goods, which is known
as the “tragedy of the commons”. Here P. aeruginosa was inoculated
into casein media with different nitrogen salts added.
In casein broth, protease (a type of public good) is necessary
for bacterial growth. After 30 days of sequential transfer,
some groups propagated stably and avoided “tragedy of the
commons”. The evolved cooperators who continued to synthesize
protease were isolated from these stable groups. By
comparing the characteristics of quorum sensing in these
cooperators, an identical evolutionary pattern was found. A
variety of cooperative behaviors regulated by quorum sensing,
such as the synthesis and secretion of protease and signals,
were significantly reduced during the process of evolution.
Such reductions improved the efficiency of cooperation, helping
to prevent cheating. In addition, the production of pyocyanin,
which is regulated by the RhlIR system, increased
during the process of evolution, possibly due to its role in
stabilizing the cooperation. This study contributes towards
our understanding of the evolution of quorum sensing of P.
aeruginosa.
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Brazilian Journal of Microbiology.2025; 56(1): 225. CrossRef - Challenging the paradigm: non-canonical exoprotease cheating in clinical Pseudomonas aeruginosa isolates
Katya Dafne Guadarrama-Orozco, Diego Armando Esquivel-Hernández, Miguel Ángel Islas-Tolentino, Fohad Mabood Husain, Héctor Quezada, Selene García-Reyes, Bernardo Franco, Diana Laura Marroquin-Mendiola, María Guadalupe Lucero-Gil, Lorena Paola Olvera-Falfa
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Katya Dafne Guadarrama-Orozco, Caleb Perez-Gonzalez, Kokila Kota, Miguel Cocotl-Yañez, Jesús Guillermo Jiménez-Cortés, Miguel Díaz-Guerrero, Mariel Hernández-Garnica, Julia Munson, Frederic Cadet, Luis Esaú López-Jácome, Ángel Yahir Estrada-Velasco, Ana M
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Akhter Ahmed Ahmed, Fraidoon Abdulqadir Salih
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Daniel Loarca, Dánae Díaz, Héctor Quezada, Ana Laura Guzmán-Ortiz, Abril Rebollar-Ruiz, Ana María Fernández Presas, Jimena Ramírez-Peris, Rafael Franco-Cendejas, Toshinari Maeda, Thomas K. Wood, Rodolfo García-Contreras
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Paulina Castañeda-Tamez, Jimena Ramírez-Peris, Judith Pérez-Velázquez, Christina Kuttler, Ammar Jalalimanesh, Miguel Á. Saucedo-Mora, J. Guillermo Jiménez-Cortés, Toshinari Maeda, Yael González, María Tomás, Thomas K. Wood, Rodolfo García-Contreras
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- Imipenem-resistant Gram-negative bacterial isolates carried by persons upon medical examination in Korea
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So Yeon Kim , Sang Yop Shin , Ji-Young Rhee , Kwan Soo Ko
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J. Microbiol. 2017;55(8):612-618. Published online July 18, 2017
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DOI: https://doi.org/10.1007/s12275-017-6555-8
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393
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0
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3
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Abstract
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Carbapenem-resistant Gram-negative bacteria (CR-GNB)
have emerged and disseminated worldwide, become a great
concern worldwide including Korea. The prevalence of fecal
carriage of imipenem-resistant Gram-negative bacteria (IRGNB)
in persons in Korea was investigated. Stool samples
were collected from 300 persons upon medical examination.
Samples were screened for IR-GNB by using MacConkey
agar with 2 μl/ml imipenem. Species were identified by 16S
rRNA gene sequence analysis, and antimicrobial susceptibility
was determined by the broth microdilution method.
In total, 82 IR-GNB bacterial isolates were obtained from
79 (26.3%) out of 300 healthy persons. Multilocus sequence
typing analysis showed very high diversity among IR P. aeruginosa,
S. maltophilia, and E. cloacae isolates, and pulsedfield
gel electrophoresis revealed five main pulsotypes of IR
P. mirabilis. As for the presence of metallo-β-lactamases
(MBLs), only one IMP-25-producing S. marcescens isolate
was identified. Although only one carbapenemase-producing
isolate was identified, the high colonization rates with IRGNB
isolates in this study is notable because carriers may
be a reservoir for the dissemination of resistant pathogens
within the community as well as in health care institutions.
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Diagnostic Microbiology and Infectious Disease.2020; 97(2): 115027. CrossRef
- Antibacterial compound produced by Pseudomonas aeruginosa strain UICC B-40, an endophytic bacterium isolated from Neesia altissima
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Rina Hidayati Pratiwi , Iman Hidayat , Muhammad Hanafi , Wibowo Mangunwardoyo
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J. Microbiol. 2017;55(4):289-295. Published online January 26, 2017
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DOI: https://doi.org/10.1007/s12275-017-6311-0
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403
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15
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Abstract
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This study’s aim was to determine the identity of antibacte-rial compounds produced by Pseudomonas aeruginosa strain UICC B-40 and describe the antibacterial compounds’ me-chanisms of action for damaging pathogenic bacteria cells. Isolation and identification of the compounds were carried out using thin layer chromatography (TLC), nuclear mag-netic resonance (NMR) spectroscopy and liquid chromato-graphy mass spectrometry (LC-MS) analyses. Antibacterial activity was assayed via minimum inhibitory concentration (MIC) and the antibacterial compound mechanism was ob-served morphologically through scanning electron micros-copy (SEM). This study successfully identified the (2E,5E)- phenyltetradeca-2,5-dienoate antibacterial compound (mole-cular weight 300 g/mol), composed of a phenolic ester, fatty acid and long chain of aliphatic group structures. MIC values for this compound were determined at 62.5 μg/ml against Staphylococcus aureus strain ATCC 25923. The mechanism of the compound involved breaking down the bacterial cell walls through the lysis process. The (2E,5E)-phenyltetradeca- 2,5-dienoate compound exhibited inhibitory activity on the growth of Gram-positive bacteria.
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- Identification of essential genes of Pseudomonas aeruginosa for its growth in airway mucus
-
Mohammed Abd Alrahman , Sang Sun Yoon
-
J. Microbiol. 2017;55(1):68-74. Published online December 30, 2016
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DOI: https://doi.org/10.1007/s12275-017-6515-3
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359
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8
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Abstract
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Pseudomonas aeruginosa has been identified as an important
causative agent of airway infection, mainly in cystic fibrosis.
This disease is characterized by defective mucociliary clearance
induced in part by mucus hyper-production. Mucin is
a major component of airway mucus and is heavily O-glycosylated,
with a protein backbone. Airway infection is known
to be established with bacterial adhesion to mucin. However,
the genes involved in mucin degradation or utilization remain
elusive. In this study, we sought to provide a genetic basis of
P. aeruginosa airway growth by identifying those genes. First,
using RNASeq analyses, we compared genome-wide expression
profiles of PAO1, a prototype P. aeruginosa laboratory
strain, grown in M9-mucin (M9M) and M9-glucose (M9G)
media. Additionally, a PAO1 transposon (Tn) insertion mutants
library was screened for mutants defective in growth
in M9M medium. One mutant with a Tn insertion in the
xcpU gene (PA3100) was determined to exhibit faulty growth
in M9M medium. This gene contributes to the type II secretion
system, suggesting that P. aeruginosa uses this secretion
system to produce a number of proteins to break down and
assimilate the mucin molecule. Furthermore, we screened
the PAO1 genome for genes with protease activity. Of 13 mutants,
one with mutation in PA3247 gene exhibited defective
growth in M9M, suggesting that the PA3247-encoded protease
plays a role in mucin utilization. Further mechanistic
dissection of this particular process will reveal new drug targets,
the inhibition of which could control recalcitrant P. aeruginosa
infections.
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Citrobacter rodentium
possesses a functional type II secretion system necessary for successful host infection
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Review
- MINIREVIEW] Biofilm dispersion in Pseudomonas aeruginosa
-
Soo-Kyoung Kim , Joon-Hee Lee
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J. Microbiol. 2016;54(2):71-85. Published online February 2, 2016
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DOI: https://doi.org/10.1007/s12275-016-5528-7
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411
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97
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Abstract
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In recent decades, many researchers have written numerous
articles about microbial biofilms. Biofilm is a complex community
of microorganisms and an example of bacterial group
behavior. Biofilm is usually considered a sessile mode of life
derived from the attached growth of microbes to surfaces, and
most biofilms are embedded in self-produced extracellular
matrix composed of extracellular polymeric substances (EPSs),
such as polysaccharides, extracellular DNAs (eDNA), and
proteins. Dispersal, a mode of biofilm detachment indicates
active mechanisms that cause individual cells to separate from
the biofilm and return to planktonic life. Since biofilm cells
are cemented and surrounded by EPSs, dispersal is not simple
to do and many researchers are now paying more attention
to this active detachment process. Unlike other modes
of biofilm detachment such as erosion or sloughing, which
are generally considered passive processes, dispersal occurs
as a result of complex spatial differentiation and molecular
events in biofilm cells in response to various environmental
cues, and there are many biological reasons that force bacterial
cells to disperse from the biofilms. In this review, we
mainly focus on the spatial differentiation of biofilm that is
a prerequisite for dispersal, as well as environmental cues
and molecular events related to the biofilm dispersal. More
specifically, we discuss the dispersal-related phenomena and
mechanisms observed in Pseudomonas aeruginosa, an important
opportunistic human pathogen and representative
model organism for biofilm study.
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Research Support, Non-U.S. Gov'ts
- Note] Inhibition of quorum sensing in Pseudomonas aeruginosa by two herbal essential oils from Apiaceae family
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Ehsan Sepahi , Saeed Tarighi , Farajollah Shahriari Ahmadi , Abdolreza Bagheri
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J. Microbiol. 2015;53(2):176-180. Published online January 5, 2015
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DOI: https://doi.org/10.1007/s12275-015-4203-8
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Abstract
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Ferula (Ferula asafoetida L.) and Dorema (Dorema aucheri
Bioss.) both from Apiaceae family were tested for their antiquorum
sensing (QS) activity against Pseudomonas aeruginosa.
Both essential oils exhibited anti-QS activity at 25 μg/ml
of concenteration. At this concenteration Ferula fully abolished
and Dorema reduced the violacein production by C.
violaceum. Pyocyanin, pyoverdine, elastase and biofilm production
were decreased in Ferula oil treatments. Dorema
oil reduced pyoverdine and elastase production, while pyocyanin
and biofilm production were not affacted. Expresion
analysis of QS-dependent genes confirmed our phenotypic
data. Our data introduced native Dorema and Ferula plants
as novel QS and virulence inhibitors.
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Jung-Hoon Lee , Heesung Shin , Yong-Jae Kim , Se-Hwan Paek , Shouguang Jin , Un-Hwan Ha
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J. Microbiol. 2014;52(12):1044-1049. Published online November 29, 2014
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DOI: https://doi.org/10.1007/s12275-014-4512-3
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482
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Abstract
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The proinflammatory cytokine interleukin-1β plays an important role in protecting the host against airway infection; however, it can also trigger a massive influx of neutrophils into the airways, causing tissue damage. Anti-inflammatory treatments are particularly in demand for patients suffering from chronic inflammatory diseases. Sophora flavescens is a traditional herbal medicine used to reduce inflammation, but no study has examined its ability to block IL-1β production. Here, we show that S. flavescens reduced the Pseudomonas aeruginosa-induced expression of IL-1β by lung epithelial cells and macrophages. S. flavescens was also effective at reducing IL-1β production induced by either Staphylococcus aureus or phorbol 12-myristate 13-acetate, indicating that the effect is generalizable to diverse inflammatory stimuli. In addition, S. flavescens blocked the phosphorylation of IKKα/β, key upstream kinases involved in the degradation of IκBα, and the cleavage of caspase-1, a key component of the inflammasome. Thus, this study demonstrates that S. flavescens exerts its anti-inflammatory effects by blocking P. aeruginosa-mediated NF-κB/inflammasome activation and the subsequent production of IL-1β.
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Sung-Chan Choi , Can Zhang , Sooyoung Moon , Young-Sook Oh
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J. Microbiol. 2014;52(9):734-742. Published online August 2, 2014
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DOI: https://doi.org/10.1007/s12275-014-4060-x
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363
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4-Hydroxy-2,5-dimethyl-3(2H)-furanone (HDMF), a nonhalogenated furanone found in a variety of fruits, has been shown to have antimicrobial activity. However, few studies have focused on its inhibitory effect on bacterial quorum sensing (QS) at levels below the non-inhibitory concentration. In this study, 0.1 μM HDMF decreased the production of QS signal molecules and inhibited QS-controlled biofilm formation by Pseudomonas aeruginosa PAO1 without causing growth inhibition. In the presence of 0.1 and 1.0 μM HDMF, biofilm production by PAO1 was reduced by 27.8 and 42.6%, respectively, compared to that by untreated control cells. HDMF (1.0 μM) also significantly affected virulence factor expression (regulated by the las, rhl, and pqs system), resulting in a significant reduction in the production of LasA protease (53.8%), rhamnolipid (40.9%), and pyocyanin (51.4%). This HDMF-dependent inhibition of virulence factor expression was overcome by increasing the levels of two QS signal molecules of P. aeruginosa, N-(3-oxo-dodecanoyl)-L-homoserine lactone and N-butyryl-L-homoserine lactone, suggesting reversible competitive inhibition between HDMF and these molecules. The results of this study indicate that HDMF has great potential as an inhibitor of QS, and that it may be of value as a therapeutic agent and in biofilm control, without increasing selective pressure for resistance development.
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- Superinfection Exclusion Reveals Heteroimmunity between Pseudomonas aeruginosa Temperate Phages
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In-Young Chung , Hee-Won Bae , Hye-Jung Jang , Bi-o Kim , You-Hee Cho
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J. Microbiol. 2014;52(6):515-520. Published online May 29, 2014
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DOI: https://doi.org/10.1007/s12275-014-4012-5
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Abstract
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Temperate siphophages (MP29, MP42, and MP48) were isolated from the culture supernatant of clinical Pseudomonas aeruginosa isolates. The complete nucleotide sequences and annotation of the phage genomes revealed the overall synteny
to the known temperate P. aeruginosa phages such as MP22, D3112, and DMS3. Genome-level sequence analysis showed the conservation of both ends of the linear genome and the divergence at the previously identified dissimilarity
regions (R1 to R9). Protein sequence alignment of the c repressor (ORF1) of each phage enabled us to divide the six phages into two groups: D3112 group (D3112, MP29, MP42, and MP48) and MP22 group (MP22 and DMS3). Superinfection
exclusion was observed between the phages belonging to the same group, which was mediated by the specific interaction between the c repressor and the cognate operator. Based on these, we suggest that the temperate siphophages prevalent in the clinical strains of P. aeruginosa represent at least two distinct heteroimmunity groups.
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- Phage against the Machine: The SIE-ence of Superinfection Exclusion
Michael J. Bucher, Daniel M. Czyż
Viruses.2024; 16(9): 1348. CrossRef - Transposition Behavior Revealed by High-Resolution Description of Pseudomonas Aeruginosa Saltovirus Integration Sites
Gilles Vergnaud, Cédric Midoux, Yann Blouin, Maria Bourkaltseva, Victor Krylov, Christine Pourcel
Viruses.2018; 10(5): 245. CrossRef - Evolutionary Ecology of Prokaryotic Immune Mechanisms
Stineke van Houte, Angus Buckling, Edze R. Westra
Microbiology and Molecular Biology Reviews.2016; 80(3): 745. CrossRef - A phage protein that inhibits the bacterial ATPase required for type IV pilus assembly
In-Young Chung, Hye-Jeong Jang, Hee-Won Bae, You-Hee Cho
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Reviews
- REVIEW] Chronic Obstructive Pulmonary Disease (COPD): Evaluation From Clinical, Immunological and Bacterial Pathogenesis Perspectives
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Daniel J. Hassett , Michael T. Borchers , Ralph J. Panos
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J. Microbiol. 2014;52(3):211-226. Published online March 1, 2014
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DOI: https://doi.org/10.1007/s12275-014-4068-2
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360
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50
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Abstract
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Chronic obstructive pulmonary disease (COPD), a disease manifested by significantly impaired airflow, afflicts ~14.2 million cases in the United States alone with an estimated 63 million people world-wide. Although there are a number of causes, the predominant cause is excessive tobacco smoke. In fact, in China, there have been estimates of 315,000,000 people that smoke. Other less frequent causes are associated with indirect cigarette smoke, air pollutants, biomass fuels, and genetic mutations. COPD is often associated with heart disease, lung cancer, osteoporosis and conditions can worsen in patients with sudden falls. COPD also affects both innate and adaptive immune processes. Cigarette smoke increases the expression of matrix metalloproteases and proinflammatory chemokines and increases lung titers of natural killer cells and neutrophils. Yet, neutrophil reactive oxygen species (ROS) mediated by the phagocytic respiratory burst and phagocytosis is impaired by nicotine. In contrast to innate immunity in COPD, dendritic cells represent leukocytes recruited to the lung that link the innate immune responses to adaptive immune responses by activating naïve T cells through antigen presentation. The autoimmune process that is also a significant part of inflammation associated with COPD. Moreover, coupled with restricted FEV1 values, are the prevalence of patients with single or multiple infections by bacteria, viruses and fungi. Finally, we focus on one of the more problematic infectious agents, the Gram-negative opportunistic pathogenic bacterium, Pseudomonas aeruginosa. Specifically, we delve into the development of highly problematic biofilm infections that are highly refractory to conventional antibiotic therapies in COPD. We offer a nonconventional, biocidal treatment that may be effective for COPD airway infections as well as with combinations of current antibiotic regimens for more effective treatment outcomes and relief for patients with COPD.
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- REVIEW] Perturbation of Pulmonary Immune Functions by Carbon Nanotubes and Susceptibility to Microbial Infection
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Brent E. Walling , Gee W. Lau
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J. Microbiol. 2014;52(3):227-234. Published online March 1, 2014
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DOI: https://doi.org/10.1007/s12275-014-3695-y
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386
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Occupational and environmental pulmonary exposure to carbon nanotubes (CNT) is considered to be a health risk with a very low threshold of tolerance as determined by the United States Center for Disease Control. Immortalized airway epithelial cells exposed to CNTs show a diverse range of effects including reduced viability, impaired proliferation, and elevated reactive oxygen species generation. Additionally, CNTs inhibit internalization of targets in multiple macrophage cell lines. Mice and rats exposed to CNTs often develop pulmonary granulomas and fibrosis. Furthermore, CNTs have immunomodulatory properties in these animal models. CNTs themselves are proinflammatory and can exacerbate the allergic response. However, CNTs may also be immunosuppressive, both locally and systemically. Studies that examined the relationship of CNT exposure prior to pulmonary infection have reached different conclusions. In some cases, pre-exposure either had no effect or enhanced clearance of infections while other studies showed CNTs inhibited clearance. Interestingly, most studies exploring this relationship use pathogens which are not considered primary pulmonary pathogens. Moreover, harmony across studies is difficult as different types of CNTs have dissimilar biological effects. We used Pseudomonas aeruginosa as model pathogen to study how helical multi-walled carbon nanotubes (HCNTs) affected internalization and clearance of the pulmonary pathogen. The results showed that, although HCNTs can inhibit internalization through multiple processes, bacterial clearance was not altered, which was attributed to an enhanced inflammatory response caused by pre-exposure to HCNTs. We compare and contrast our findings in relation to other studies to gauge the modulation of pulmonary immune response by CNTs.
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Research Support, Non-U.S. Gov'ts
- A New Quorum-Sensing Inhibitor Attenuates Virulence and Decreases Antibiotic Resistance in Pseudomonas aeruginosa
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Yu-Xiang Yang , Zhen-Hua Xu , Yu-Qian Zhang , Jing Tian , Li-Xing Weng , Lian-Hui Wang
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J. Microbiol. 2012;50(6):987-993. Published online December 30, 2012
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DOI: https://doi.org/10.1007/s12275-012-2149-7
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436
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64
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Abstract
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Quorum sensing (QS) has been a novel target for the treatment of infectious diseases. Here structural analogs of Pseudomonas aeruginosa autoinducer N-acyl homoserine lactone (AHL) were investigated for QS inhibitor (QSI) activity
and a novel QSI was discovered, N-decanoyl-L-homoserine benzyl ester (C2). Virulence assays showed that C2 downregulated total protease and elastase activities, as well as the production of rhamnolipid, that are controlled by QS in P.
aeruginosa wild-type strain PAO1 without affecting growth. C2 was also shown to inhibit swarming motility of PAO1. Using a microdilution checkerboard method, we identified synergistic interactions between C2 and several antibiotics, tobramycin, gentamycin, cefepime, and meropenem. Data from real-time RT-PCR suggested that C2 inhibited the expression of lasR (29.67%), lasI (21.57%), rhlR (28.20%), and
rhlI (29.03%).
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- Antibacterial Efficacy of Lytic Pseudomonas Bacteriophage in Normal and Neutropenic Mice Models
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Birendra R. Tiwari , Shukho Kim , Marzia Rahman , Jungmin Kim
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J. Microbiol. 2011;49(6):994-999. Published online December 28, 2011
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DOI: https://doi.org/10.1007/s12275-011-1512-4
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Recently, lytic bacteriophages (phages) have been focused on treating bacterial infectious diseases. We investigated the protective efficacy of a novel Pseudomonas aeruginosa phage, PA1Ø, in normal and neutropenic mice. A lethal dose of P. aeruginosa PAO1 was administered via the intraperitoneal route and a single
dose of PA1Ø with different multiplicities of infection (MOI) was treated into infected mice. Immunocompetent mice infected with P. aeruginosa PAO1 were successfully protected by PA1Ø of 1 MOI, 10 MOI or 100 MOI with 80% to 100% survival rate. No viable bacteria were found in organ samples after 48 h of the phage treatment. Phage clearing patterns were different in the presence or absence of host bacteria but PA1Ø disappeared from all organs after 72 h except spleen in the presence of host bacteria. On the contrary, PA1Ø treatment could not protect neutropenic mice infected with P. aeruginosa PAO1 even though could extend their lives for a short time. In in vitro phage-neutrophil bactericidal test, a stronger bactericidal effect was observed in phage-neutrophil co-treatment than in phage single treatment without neutrophils, suggesting phage-neutrophil co-work is essential for the efficient killing of bacteria in the mouse model. In conclusion, PA1Ø can be possibly utilized in future phage therapy endeavors since it exhibited strong protective effects against virulent P. aeruginosa infection.
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Yuan Wu† , Hui Li† , Jun Li , Zu Hu Huang
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J. Microbiol. 2008;46(6):687-691. Published online December 24, 2008
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DOI: https://doi.org/10.1007/s12275-008-0021-6
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308
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We report here novel array of gene cassettes found in single variable region of class 1 integron disseminated in Pseudomonas aeruginosa isolated from a teaching hospital in Nanjing, Jiangsu Province, China. 29 of 47 (61%) P. aeruginosa strains were confirmed haboured class 1 integron, and all the positive strains have the same variable region confirmed by PCR and RFLP methods. The variable region contained an unreported order of four gene cassettes aac(6’)-II-aadA13-cmlA8-oxa 10. Of those, cmlA8 gene was a variant of cmlA5 encoding non-enzymatic protein which putatively confer resistance to chloramphenicol. Susceptibility testing revealed multidrug-resistant mechanisms were involved in the class 1 integron positive clinical isolates. And the class 1 integron located on an about 15 kb transferable plasmid was certified by conjugation experiment and plasmid DNA analysis. The macro restriction profile indicated those clinical strains were clonally related.
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- Modulation of Secreted Virulence Factor Genes by Subinhibitory Concentrations of Antibiotics in Pseudomonas aeruginosa
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Lixin Shen , Ying Shi , Dan Zhang , Jinhua Wei , Michael G. Surette , Kangmin Duan
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J. Microbiol. 2008;46(4):441-447. Published online August 31, 2008
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DOI: https://doi.org/10.1007/s12275-008-0054-x
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232
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Recent studies have shown that subinhibitory antibiotics play important roles in regulating bacterial genes including virulence factor genes. In this study, the expression of 13 secreted virulence related gene clusters of Pseudomonas aeruginosa, an important opportunistic pathogen, was examined in the presence of subinhibitory concentrations of 4 antibiotics: vancomycin, tetracycline, ampicilin and azithromycin. Activation of gene expression was observed with phzA1, rhlAB, phzA2, lasB, exoY, and exoS. Subinhibitory concentrations of vancomycin resulted in more than 10-fold increase of rhlAB and phzA2 transcription. Both rhamnolipid production and pyocyanin production were significantly elevated, correlating phenotypes with the increased transcription. P. aeruginosa swarming and swimming motility also increased. Similar results were observed with subinhibitory tetracycline, azithromycin and ampicillin. These results indicate that the antibiotics at low concentrations can up-regulate virulence factors and therefore influence bacterial
pathogenesis.
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Charlotte Nolan, Volker Behrends
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Fatemeh Hemmati, Reza Ghotaslou, Roya Salehi, Hossein Samadi Kafil, Alka Hasani, Pourya Gholizadeh, Roghayeh Nouri, Mohammad Ahangarzadeh Rezaee
Molecular Biotechnology.2021; 63(8): 746. CrossRef -
Inhibition of Protein Secretion in
Escherichia coli
and Sub-MIC Effects of Arylomycin Antibiotics
Shawn I. Walsh, David S. Peters, Peter A. Smith, Arryn Craney, Melissa M. Dix, Benjamin F. Cravatt, Floyd E. Romesberg
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Kui Zhu, Shang Chen, Tatyana A. Sysoeva, Lingchong You, Nathalie Balaban
PLOS Biology.2019; 17(12): e3000573. CrossRef - Efficacy of Ciprofloxacin and Its Copper Complex against Pseudomonas aeruginosa Biofilms
Frederic Tewes, Tania F. Bahamondez-Canas, Hugh D. C. Smyth
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Ana Margarida Sousa, Rosana Monteiro, Maria Olívia Pereira
International Journal of Medical Microbiology.2018; 308(8): 1053. CrossRef - Inhibitory effect of aminoglycosides and tetracyclines on quorum sensing in Chromobacterium violaceum
D. G. Deryabin, K. S. Inchagova
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Laura Selan, Gianluca Vrenna, Evaristo Ettorre, Rosanna Papa, Marco Artini
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Defne Gümüş, Fatma Kalaycı-Yüksek, Emre Yörük, Gülşen Uz, Eşref Çelik, Cansu Arslan, Elif Merve Aydın, Cem Canlı, Mine Anğ-Küçüker
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Shahin Bahari, Habib Zeighami, Hesam Mirshahabi, Shekoufeh Roudashti, Fakhri Haghi
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Generation of a Stable Plasmid for
In Vitro
and
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Christina N. Krute, Kelsey L. Krausz, Mary A. Markiewicz, Jason A. Joyner, Srijana Pokhrel, Pamela R. Hall, Jeffrey L. Bose, C. Vieille
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- Effect of Titanium Ion and Resistance Encoding Plasmid of Pseudomonas aeruginosa ATCC 10145
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Sung Min Park , Hyun Soo Kim , Tae Shick Yu
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J. Microbiol. 2006;44(3):255-262.
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DOI: https://doi.org/2388 [pii]
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Abstract
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Titanium and its alloys are technically superior and cost-effective materials, with a wide variety of aerospace, industrial, marine, and commercial applications. In this study, the effects of titanium ions on bacterial growth were evaluated. Six strains of bacteria known to be resistant to both metal ions and antibiotics were used in this study. Two strains, Escherichia coli ATCC 15489, and Pseudomonas aeruginosa ATCC 10145, proved to be resistant to titanium ions. Plasmid-cured P. aeruginosa resulted in the loss of one or more resistance markers, indicating plasmid-encoded resistance. The plasmid profile of P. aeruginosa revealed the presence of a 23-kb plasmid. The plasmid was isolated and transformed into DH5α. Interestingly, the untransformed DH5α did not grow in 300 mg/l titanium ions, but the transformed DH5α grew quite well under such conditions. The survival rate of the transformed DH5α also increased more than 3-fold compared to that of untransformed DH5α.
- Microarray-Mediated Transcriptome Analysis of the Tributyltin (TBT)-Resistant Bacterium Pseudomonas aeruginosa 25W in the Presence of TBT
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Santosh K. Dubey , Tsutomu Tokashiki , Satoru Suzuki
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J. Microbiol. 2006;44(2):200-205.
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DOI: https://doi.org/2364 [pii]
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Abstract
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The tributyltin (TBT)-resistant bacterium, Pseudomonas aeruginosa 25W, which was isolated in seawater from the Arabian Sea, was subjected to transcriptome analysis in the presence of high concentrations of TBT. Only slight effects were observed at TBT concentration of 50 μM, but exposure to 500 μM resulted in the upregulation of 6 genes and the downregulation of 75. Among the 75 downregulated genes, 53% (40 out of 75) were of hypothetical function, followed by 14 transcriptional regulation- and translationassociated genes. The results of this study indicated that although the 25W strain was highly resistant to TBT, high concentrations of TBT result in toxic effect on the transcriptional and translational levels. The target genes likely belong to a specific category of transcription- and translation-associated genes rather than to other gene categories.
- Conserved Virulence Factors of Pseudomonas aeruginosa are Required for Killing Bacillus subtilis
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Shin-Young Park , Yun-Jeong Heo , Young-Seok Choi , Eric Deziel , You-Hee Cho
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J. Microbiol. 2005;43(5):443-450.
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DOI: https://doi.org/2277 [pii]
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Abstract
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The multi-host pathogen, Pseudomonas aeruginosa, possesses an extraordinary versatility which makes it capable of surviving the adverse conditions provided by environmental, host, and, presumably, competing microbial factors in its natural habitats. Here, we investigated the P. aeruginosa-Bacillus subtilis interaction in laboratory conditions and found that some P. aeruginosa strains can outcompete B. subtilis in mixed planktonic cultures. This is accompanied by the loss of B. subtilis viability. The bactericidal activity of P. aeruginosa is measured on B. subtilis plate cultures. The bactericidal activity is attenuated in pqsA, mvfR, lasR, pilB, gacA, dsbA, rpoS, and phnAB mutants. These results suggest that P. aeruginosa utilizes a subset of conserved virulence pathways in order to survive the conditions provided by its bacterial neighbors.
- Fungal-sporulation suppressing substances produced by pseudomonas aeruginosa KMCS-1
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Min, Bu Yong , Shim, Jae Young , Kim, Kun Woo , Lee, Jong Kyu , Yoon, Kwon Sang
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J. Microbiol. 1996;34(3):284-288.
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Abstract
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Among the bacteria isolated form compost piles of cattle excretion in a pasture located at the suburbs of Chunchon city, Pseudomonas aeruginosa KMCS-1 was selected for the test of antifungal substances produced. Six fractions were separated by silica gel column chromatography, and then the antifungal activity of each fraction was assayed against Escherichia coli, Bacillus subtilis, Candida albicans, Rhizopus sp., Aspergillus nidulans, Coprinus cinereus, and Pyricularia oryzae by paper disc method. Two fractions showed significant suppressive activities against A. nidulans, C. cinereus, and P. oryzae; however, their mycelial growth was not affected by neither of these fractions. Inhibitory activities of these fractions to sporulation was assayed at the concentration of 50. 25, 12. 5, and 6.25 ㎍/ml and the average inhibition rates against sporulation of A. nidulans, C. cinereus, and P. oryzae were 94.0, 98.3, and 77.9%, respectively. Further purification and analysis of active substances are now being conducted.
- Microscopic Examination of the Suppressive Action of Antifungal Substances from Pseudomonas aeruginosa on Asexual Sporulation of Fungi
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Yoon, Kwon S. , Min, Bu Y. , Choi, Hyoung T. , Lee, Jong K. , Kim, Kun W.
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J. Microbiol. 1999;37(1):27-34.
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Abstract
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Two fractions with unusual antifungal activity that suppress asexual sporulation of several fungi were obtained from culture filtrate of Pseudomonas aeruginosa and were partially purified through the repeated silicagel flash column chromatographies. The sporulation-suppressive actions of these fractions in Aspergillus nidulans, Rhizopus stolonifer, and Coprinus cinereus, were analyzed by light and electron microscopes. The germination ability of the spores produced in the presence of these fractions were also checked to determine the persistent effects of these antifungal substances on the next generation. Light microscopic observation of developing sporangia of R. stolonifer grown in the presence of both fractions revealed that the significant number of sporangia failed to reach maturity, and frequently, uncontrolled growths of hyphae and rhizoids from the sporangiophores were found. In A. nidulans addition of these fractions appeared to cause different classes of morphological abnormality in conidia development, which included aborted formation of conidiogenous cells from the apex of conidiophores and enhanced hyphal growths either at the tip or middle of the conidiophores. Germination abilities of spores obtained from the cultures grown in the presence of antifungal fractions were 40∼60% in Aspergillus, 50∼80% in Coprinus (thallic spores), and 30∼40% in Rhizopus compared to those of normal spores.