Journal of Microbiology

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[PROTOCOL]Analyzing viral epitranscriptomes using nanopore direct RNA sequencing: Ari Hong , Dongwan Kim , V. Narry Kim , Hyeshik Chang; J. Microbiol. 2022;60(9):867-876. Published online August 24, 2022; DOI: https://doi.org/10.1007/s12275-022-2324-4

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RNA modifications are a common occurrence across all domains of life. Several chemical modifications, including N6- methyladenosine, have also been found in viral transcripts and viral RNA genomes. Some of the modifications increase the viral replication efficiency while also helping the virus to evade the host immune system. Nonetheless, there are numerous examples in which the host's RNA modification enzymes function as antiviral factors. Although established methods like MeRIP-seq and miCLIP can provide a transcriptome- wide overview of how viral RNA is modified, it is difficult to distinguish between the complex overlapping viral transcript isoforms using the short read-based techniques. Nanopore direct RNA sequencing (DRS) provides both long reads and direct signal readings, which may carry information about the modifications. Here, we describe a refined protocol for analyzing the RNA modifications in viral transcriptomes using nanopore technology.

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Utilization of nanopore direct RNA sequencing to analyze viral RNA modifications
Lu Tan, Zhihao Guo, Xiaoming Wang, Dal Young Kim, Runsheng Li, Pedro H. Oliveira
mSystems.2024;[Epub] CrossRef
Current progress in strategies to profile transcriptomic m6A modifications
Yuening Yang, Yanming Lu, Yan Wang, Xianghui Wen, Changhai Qi, Weilan Piao, Hua Jin
Frontiers in Cell and Developmental Biology.2024;[Epub] CrossRef
Improved sub-genomic RNA prediction with the ARTIC protocol
Thomas Baudeau, Kristoffer Sahlin
Nucleic Acids Research.2024; 52(17): e82. CrossRef
Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases
Stephen Spatz, Claudio L. Afonso
Veterinary Sciences.2024; 11(6): 239. CrossRef
Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data
Shenglun Chen, Jia Meng, Yuxin Zhang
Methods.2024; 228: 30. CrossRef
Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis
Caroline A. McCormick, Stuart Akeson, Sepideh Tavakoli, Dylan Bloch, Isabel N. Klink, Miten Jain, Sara H. Rouhanifard
Gigabyte.2024; 2024: 1. CrossRef
Dissecting the effects of METTL3 on alternative splicing in prostate cancer
Lin Wang, Ling Shi, Yonghao Liang, Judy Kin-Wing Ng, Chan Hoi Yin, Lingyi Wang, Jinpao Hou, Yiwei Wang, Cathy Sin-Hang Fung, Peter Ka-Fung Chiu, Chi-Fai Ng, Stephen Kwok-Wing Tsui
Frontiers in Oncology.2023;[Epub] CrossRef

Whole-genome sequencing analysis of Shiga toxin-producing Escherichia coli O22:H8 isolated from cattle prediction pathogenesis and colonization factors and position in STEC universe phylogeny: Wanderson Marques Da Silva , Mariano Larzabal , Flavia Figueira Aburjaile , Nahuel Riviere , Luisina Martorelli , James Bono , Ariel Amadio , Angel Cataldi; J. Microbiol. 2022;60(7):689-704. Published online June 22, 2022; DOI: https://doi.org/10.1007/s12275-022-1616-z

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Abstract

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen capable of causing illness in humans. In a previous study, our group showed that a STEC isolate belonging to O22:H8 serotype (strain 154) can interfere with STEC O157:H7 colonization both in vitro and in vivo. Using whole-genome sequencing and genomic comparative, we predicted a subset of genes acquired by O22:H8 strain 154 through horizontal gene transfer that might be responsible for the phenotype previously described by our group. Among them were identified genes related to the pathogenesis of non-LEE (locus of enterocyte effacement) STEC, specific metabolic processes, antibiotic resistance and genes encoding for the T6SS-1 that is related to inter-bacterial competition. In addition, we showed that this strain carries stx1c and stx2dact, a mucus-inducible variant. The results obtained in this study provide insights into STEC genomic plasticity and the importance of genomic islands in the adaptation and pathogenesis of this pathogen.

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MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing
Nathalie Bonin, Enrique Doster, Hannah Worley, Lee J Pinnell, Jonathan E Bravo, Peter Ferm, Simone Marini, Mattia Prosperi, Noelle Noyes, Paul S Morley, Christina Boucher
Nucleic Acids Research.2023; 51(D1): D744. CrossRef
Genomes-based MLST, cgMLST, wgMLST and SNP analysis of Salmonella Typhimurium from animals and humans
Shigan Yan, Zhaoxu Jiang, Wencheng Zhang, Zhenhai Liu, Xiaorui Dong, Donghui Li, Zijun Liu, Chengyu Li, Xu Liu, Liping Zhu
Comparative Immunology, Microbiology and Infectious Diseases.2023; 96: 101973. CrossRef
Escherichia coli O157:H7 tir 255 T > A allele strains differ in chromosomal and plasmid composition
Margaret D. Weinroth, Michael L. Clawson, Gregory P. Harhay, Mark Eppinger, Dayna M. Harhay, Timothy P. L. Smith, James L. Bono
Frontiers in Microbiology.2023;[Epub] CrossRef
Occurrence and genetic characterization of Shiga toxin-producing Escherichia coli on bovine and pork carcasses and the environment from transport trucks
Rocío Colello, Manuela Baigorri, Felipe Del Canto, Juliana González, Ariel Rogé, Claudia van der Ploeg, Federico Sánchez Chopa, Mónica Sparo, Analía Etcheverría, Nora Lía Padola
World Journal of Microbiology and Biotechnology.2023;[Epub] CrossRef

Lipocalin2 as a potential antibacterial drug against Acinetobacter baumannii infection: Daejin Lim , Su-Jin Park , Ha Young Kim , Minsang Shin , Miryoung Song; J. Microbiol. 2022;60(4):444-449. Published online March 28, 2022; DOI: https://doi.org/10.1007/s12275-022-2007-1

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Abstract

Available antibiotics to treat Acinetobacter baumannii infection is limited due to increasing resistance and the emergence of multiple drug-resistant strains. Hence, discovering effective agents against A. baumannii to reduce the number of infectionrelated deaths is imperative. In search of novel and alternative antibiotics, the antibacterial function of lipocalin2 (Lcn2) was investigated to treat systemic infections of A. baumannii using a mouse neutropenia model. We observed a significant increase in serum Lcn2 levels upon bacterial injection into the mouse, and the administration of recombinant Lcn2 (rmLcn2) extended their survival. Such protective effects were also observed in rmLcn2-pretreated macrophages, where rmLcn2 reduced the survival of the pathogen inside the macrophages. The underlying molecular mechanism of Lcn2 protection was also investigated. We observed that pretreatment of the Raw- 264.7 macrophages with rmLcn2 markedly altered the expression of tonB3, which encodes a component of the transporter for ferrisiderophores in A. baumannii. However, the expression of katG, the gene encoding catalase, remained unaffected. These indicate that Lcn2-mediated defense against the pathogen is related to nutritional immunity rather than reactive oxygen species (ROS) production. Furthermore, the addition of rmLcn2 in infected mice diminished bacterial burden in multiple organs and enhanced the expression of tonB3 in the liver, spleen, and lungs of the infected mice. Increased survival rate due to rmLcn2 treatment declined when the infection model was established using lcn2-defective (lcn2-/-) mice, which indicated the necessity of endogenous Lcn2. Therefore, the antibacterial function of Lcn2 can be exploited to develop an alternative therapeutic agent against A. baumannii.

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Antimicrobial peptide thanatin fused endolysin PA90 (Tha-PA90) for the control of Acinetobacter baumannii infection in mouse model
Jeonghyun Lim, Heejoon Myung, Daejin Lim, Miryoung Song
Journal of Biomedical Science.2024;[Epub] CrossRef
Dynamic changes and clinical value of lipocalin 2 in liver diseases caused by microbial infections
Feng Chen, Shan-Shan Wu, Chao Chen, Cheng Zhou
World Journal of Hepatology.2024; 16(2): 177. CrossRef
Lipocalin-2 is an essential component of the innate immune response to Acinetobacter baumannii infection
Jessica R. Sheldon, Lauren E. Himmel, Dillon E. Kunkle, Andrew J. Monteith, K. Nichole Maloney, Eric P. Skaar, David S. Weiss
PLOS Pathogens.2022; 18(9): e1010809. CrossRef

Gold nanoparticle-DNA aptamer-assisted delivery of antimicrobial peptide effectively inhibits Acinetobacter baumannii infection in mice: Jaeyeong Park , Eunkyoung Shin , Ji-Hyun Yeom , Younkyung Choi , Minju Joo , Minho Lee , Je Hyeong Kim , Jeehyeon Bae , Kangseok Lee; J. Microbiol. 2022;60(1):128-136. Published online December 29, 2021; DOI: https://doi.org/10.1007/s12275-022-1620-3

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Abstract

Acinetobacter baumannii causes multidrug resistance, leading to fatal infections in humans. In this study, we showed that Lys AB2 P3-His–a hexahistidine-tagged form of an antimicrobial peptide (AMP) loaded onto DNA aptamer-functionalized gold nanoparticles (AuNP-Apt)–can effectively inhibit A. baumannii infection in mice. When A. baumannii-infected mice were intraperitoneally injected with AuNP-Apt loaded with Lys AB2 P3-His, a marked reduction in A. baumannii colonization was observed in the mouse organs, leading to prominently increased survival time and rate of the mice compared to those of the control mice treated with AuNP-Apt or Lys AB2 P3-His only. This study shows that AMPs loaded onto AuNP-Apt could be an effective therapeutic tool against infections caused by multidrug-resistant pathogenic bacteria in humans.

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Challenges and Emerging Molecular Approaches in Combating Antimicrobial Resistance
Gene Philip Levee Ynion, Christian Jay Rosal, Arvin Zulueta, Angelo Ordanel, Christopher Marlowe Caipang
Journal of Bacteriology and Virology.2024; 54(1): 12. CrossRef
Gold Nanoparticles and Antimicrobial Peptides: A Novel Combination
Şule Balcı, Bengü Ergüden
ChemistrySelect.2024;[Epub] CrossRef
Aptamers: A Cutting-Edge Approach for Gram-Negative Bacterial Pathogen Identification
María Guadalupe Córdova-Espinoza, Rosa González-Vázquez, Rolando Rafik Barron-Fattel, Raquel Gónzalez-Vázquez, Marco Antonio Vargas-Hernández, Exsal Manuel Albores-Méndez, Ana Laura Esquivel-Campos, Felipe Mendoza-Pérez, Lino Mayorga-Reyes, María Angélica
International Journal of Molecular Sciences.2024; 25(2): 1257. CrossRef
Antimicrobial Peptide Delivery Systems as Promising Tools Against Resistant Bacterial Infections
Kamila Botelho Sampaio de Oliveira, Michel Lopes Leite, Nadielle Tamires Moreira Melo, Letícia Ferreira Lima, Talita Cristina Queiroz Barbosa, Nathalia Lira Carmo, Douglas Afonso Bittencourt Melo, Hugo Costa Paes, Octávio Luiz Franco
Antibiotics.2024; 13(11): 1042. CrossRef
Optimizing Treatment for Carbapenem-Resistant Acinetobacter baumannii Complex Infections: A Review of Current Evidence
Seong Jin Choi, Eu Suk Kim
Infection & Chemotherapy.2024; 56(2): 171. CrossRef
Advances in skin gene therapy: utilizing innovative dressing scaffolds for wound healing, a comprehensive review
Fatemeh Karimzadeh, Elahe Soltani Fard, Akram Nadi, Rahim Malekzadeh, Fatemeh Elahian, Seyed Abbas Mirzaei
Journal of Materials Chemistry B.2024; 12(25): 6033. CrossRef
Colistin Resistance Mechanism and Management Strategies of Colistin-Resistant Acinetobacter baumannii Infections
Md Minarul Islam, Da Eun Jung, Woo Shik Shin, Man Hwan Oh
Pathogens.2024; 13(12): 1049. CrossRef
Progress in Programmable DNA-Aided Self-Assembly of the Master Frame of a Drug Delivery System
Gary Q. Yang, Weibin Cai, Zhiwen Zhang, Yujun Wang
ACS Applied Bio Materials.2023; 6(12): 5125. CrossRef
Neglected Zoonotic Diseases: Advances in the Development of Cell-Penetrating and Antimicrobial Peptides against Leishmaniosis and Chagas Disease
Sara M. Robledo, Silvia Pérez-Silanes, Celia Fernández-Rubio, Ana Poveda, Lianet Monzote, Víctor M. González, Paloma Alonso-Collado, Javier Carrión
Pathogens.2023; 12(7): 939. CrossRef
Applications and Challenges of Bacteriostatic Aptamers in the Treatment of Common Pathogenic Bacteria Infections
Diandian Li, Yuan Su, Jie Li, Rong Liu, Bing Fang, Jingjing He, Wentao Xu, Longjiao Zhu
Biomacromolecules.2023; 24(11): 4568. CrossRef
Promising Acinetobacter baumannii Vaccine Candidates and Drug Targets in Recent Years
Yong Chiang Tan, Chandrajit Lahiri
Frontiers in Immunology.2022;[Epub] CrossRef
Advances and Perspective on Antimicrobial Nanomaterials for Biomedical Applications
Preeti Garg, Prerna Attri, Rohit Sharma, Moondeep Chauhan, Ganga Ram Chaudhary
Frontiers in Nanotechnology.2022;[Epub] CrossRef
Aptamer Decorated Emodin Nanoparticles-Assisted Delivery of Dermcidin-Derived Peptide DCD-1L: Photoactive Bio-Theragnostic Agent for Enterococcus Faecalis Biofilm Destruction
Maryam Pourhajibagher, Abbas Bahador
SSRN Electronic Journal .2022;[Epub] CrossRef
Development of DNA aptamers specific for small therapeutic peptides using a modified SELEX method
Jaemin Lee, Minkyung Ryu, Dayeong Bae, Hong-Man Kim, Seong-il Eyun, Jeehyeon Bae, Kangseok Lee
Journal of Microbiology.2022; 60(7): 659. CrossRef
Aptamer decorated emodin nanoparticles-assisted delivery of dermcidin-derived peptide DCD-1L: Photoactive bio-theragnostic agent for Enterococcus faecalis biofilm destruction
Maryam Pourhajibagher, Abbas Bahador
Photodiagnosis and Photodynamic Therapy.2022; 39: 103020. CrossRef

Repositioning of a mucolytic drug to a selective antibacterial against Vibrio cholerae: In-Young Chung† , Bi-o Kim† , Hye-Jeong Jang† , You-Hee Cho; J. Microbiol. 2020;58(1):61-66. Published online January 2, 2020; DOI: https://doi.org/10.1007/s12275-020-9590-9

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Abstract

Drug repositioning, the approach to explore existing drugs for use in new therapeutic indications, has emerged as an alternative drug development strategy. In this study, we found that a mucolytic drug, N-acetylcysteine (NAC) showed antibacterial activity against Vibrio cholerae. NAC can provide acid stress that selectively inhibited the growth of V. cholerae among other bacterial pathogens. To address the antibacterial mechanism of NAC against V. cholerae, six acr (acetylcysteine- resistant) mutants were isolated from 3,118 random transposon insertion clones. The transposon insertion sites of the six mutants were mapped at the five genes. All these mutants did not display NAC resistance under acidic conditions, despite their resistance to NAC under alkaline conditions, indicating that the NAC resistance directed by the acr mutations was independent of the unusual pH-sensitivity of V. cholerae. Furthermore, all these mutants displayed attenuated virulence and reduced biofilm formation, suggesting that the acr genes are required for pathogenesis of V. cholerae. This study validates the relevance of drug repositioning for antibacterials with new modes of action and will provide an insight into a novel antibacterial therapy for V. cholerae infections to minimize side effects and resistance emergence.

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Identification of brevinin-1EMa-derived stapled peptides as broad-spectrum virus entry blockers
Mi Il Kim, Thanh K. Pham, Dahee Kim, Minkyung Park, Bi-o Kim, You-Hee Cho, Young-Woo Kim, Choongho Lee
Virology.2021; 561: 6. CrossRef

Brevibacillus antibioticus sp. nov., with a broad range of antibacterial activity, isolated from soil in the Nakdong River: Ahyoung Choi , Young Ho Nam , Kiwoon Baek , Eu Jin Chung; J. Microbiol. 2019;57(11):991-996. Published online October 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9325-y

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Abstract

A Gram-stain-positive, aerobic, motile, and rod-shaped bacterial strain designated TGS2-1T was isolated from sediment soil in the Nakdong River, Republic of Korea. The optimal growth of strain TGS2-1T was observed at 28°C and pH 7.0 without NaCl supplementation. Strain TGS2-1T revealed antibiosis against various bacteria, including Staphylococcus aureus KCCM 4051, CCARM 3089 (methicillin resistant strains), Enterococcus faecalis KCCM 11814, Escherichia coli KCTC 2443, Candida albicans KACC 7270, and Filobasidium neoformans KCTC 7902. Phylogenetic analyses based on the 16S rRNA gene sequences indicated that strain TGS2-1T belonged to the genus Brevibacillus and shared 93.8–99.7% sequence similarity with Brevibacillus species. Whole-genome sequencing of strain TGS2-1T revealed a genome size of 6.2 Mbp and DNA G + C content of 47.0 mol%. The TGS2-1T genome shared an average nucleotide identity and digital DNA-DNA hybridization of 74.6–93.3% and 18.6–67.1%, respectively, with six related Brevibacillus genomes. The major fatty acid constituents of strain TGS2-1T were anteiso-C15:0 (62.3%) and anteiso-C17:0 (10.8%). Cells of strain TGS2-1T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, seven unidentified aminophospholipids, and five unidentified lipids. The isoprenoid quinone detected in the strain was menaquinone-7 (MK-7). Based on data obtained from this polyphasic taxonomic study, strain TGS2-1T represents a novel species belonging to genus Brevibacillus, for which the name B. antibioticus sp. nov. is proposed. The type strain is TGS2-1T (= KCCM 90326T = NBRC 113840T = FBCC-B2501).

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Traditional processing increases biological activities of Dendrobium offificinale Kimura et. Migo in Southeast Yunnan, China
Di Zhou, Ying Zhao, Zhilin Chen, Xiuxiang Yan, Yanqiang Zhao, Lu Gao, Lixin Yang
Scientific Reports.2022;[Epub] CrossRef
Marine Bacterial Secondary Metabolites: A Treasure House for Structurally Unique and Effective Antimicrobial Compounds
Ramanathan Srinivasan, Arunachalam Kannappan, Chunlei Shi, Xiangmin Lin
Marine Drugs.2021; 19(10): 530. CrossRef

Antimicrobial effect and proposed action mechanism of cordycepin against Escherichia coli and Bacillus subtilis: Qi Jiang , Zaixiang Lou , Hongxin Wang , Chen Chen; J. Microbiol. 2019;57(4):288-297. Published online March 30, 2019; DOI: https://doi.org/10.1007/s12275-019-8113-z

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Abstract

The detailed antibacterial mechanism of cordycepin efficacy against food-borne germs remains ambiguous. In this study, the antibacterial activity and action mechanism of cordycepin were assessed. The results showed that cordycepin effectively inhibited the growth of seven bacterial pathogens including both Gram-positive and Gram-negative bacterial pathogens; the minimum inhibitory concentrations (MIC) were 2.5 and 1.25 mg/ml against Escherichia coli and Bacillus subtilis, respectively. Scanning electron microscope and transmission electron microscope examination confirmed that cordycepin caused obvious damages in the cytoplasmatic membranes of both E. coli and B. subtilis. Outer membrane permeability assessment indicated the loss of barrier function and the leakage of cytoplasmic contents. Propidium iodide and carboxyfluorescein diacetate double staining approach coupled with flow cytometry analysis indicated that the integrity of cell membrane was severely damaged during a short time, while the intracellular enzyme system still remained active. This clearly suggested that membrane damage was one of the reasons for cordycepin efficacy against bacteria. Additionally, results from circular dichroism and fluorescence analysis indicated cordycepin could insert to genome DNA base and double strand, which disordered the structure of genomic DNA. Basis on these results, the mode of bactericidal action of cordycepin against E. coli and B. subtilis was found to be a dual mechanism, disrupting bacterial cell membranes and binding to bacterial genomic DNA to interfere in cellular functions, ultimately leading to cell death.

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Prospects for cordycepin biosynthesis in microbial cell factories
Xiang Li, Rongshuai Jiang, Shenghou Wang, Chenyang Li, Yongping Xu, Shuying Li, Qian Li, Liang Wang
Frontiers in Chemical Engineering.2024;[Epub] CrossRef
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Hong Kyu Lee, Yun-Jung Na, Su-Min Seong, Dohee Ahn, Kyung-Chul Choi
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Gold nanoparticle-DNA aptamer-assisted delivery of antimicrobial peptide effectively inhibits Acinetobacter baumannii infection in mice
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Journal of Microbiology.2022; 60(1): 128. CrossRef
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Liying Shi, He Cao, Siyu Fu, Zixian Jia, Xuan Lu, Zhengguo Cui, Dayong Yu
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Review

REVIEW] Antibacterial strategies inspired by the oxidative stress and response networks: So Youn Kim , Chanseop Park , Hye-Jeong Jang , Bi-o Kim , Hee-Won Bae , In-Young Chung , Eun Sook Kim , You-Hee Cho; J. Microbiol. 2019;57(3):203-212. Published online February 26, 2019; DOI: https://doi.org/10.1007/s12275-019-8711-9

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Abstract

Oxidative stress arises from an imbalance between the excessive accumulation of reactive oxygen species (ROS) and a cell’s capability to readily detoxify them. Although ROS are spontaneously generated during the normal oxygen respiration and metabolism, the ROS generation is usually augmented by redox-cycling agents, membrane disrupters, and bactericidal antibiotics, which contributes their antimicrobial bioactivity. It is noted that all the bacteria deploy an arsenal of inducible antioxidant defense systems to cope with the devastating effect exerted by the oxidative stress: these systems include the antioxidant effectors such as catalases and the master regulators such as OxyR. The oxidative stress response is not essential for normal growth, but critical to survive the oxidative stress conditions that the bacterial pathogens may encounter due to the host immune response and/or the antibiotic treatment. Based on these, we here define the ROS-inspired antibacterial strategies to enhance the oxidative stress of ROS generation and/or to compromise the bacterial response of ROS detoxification, by delineating the ROSgenerating antimicrobials and the core concept of the bacterial response against the oxidative stress.

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Journal Articles

The antibacterial activity of E. coli bacteriophage lysin lysep3 is enhanced by fusing the Bacillus amyloliquefaciens bacteriophage endolysin binding domain D8 to the C-terminal region: Shuang Wang , Jingmin Gu , Meng Lv , Zhimin Guo , Guangmou Yan , Ling Yu , Chongtao Du , Xin Feng , Wenyu Han , Changjiang Sun , Liancheng Lei; J. Microbiol. 2017;55(5):403-408. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6431-6

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Abstract

Bacteriophage endolysin is one of the most promising anti-biotic substitutes, but in Gram-negative bacteria, the outer membrane prevents the lysin from hydrolyzing peptidogly-cans and blocks the development of lysin applications. The prime strategy for new antibiotic substitutes is allowing lysin to access the peptidoglycan from outside of the bacteria by reformation of the lysin. In this study, the novel Escherichia coli (E. coli) phage lyase lysep3, which lacks outside-in cata-lytic ability, was fused with the N-terminal region of the Bacillus amyloliquefaciens lysin including its cell wall bind-ing domain D8 through the best manner of protein fusion based on the predicted tertiary structure of lysep3-D8 to ob-tain an engineered lysin that can lyse bacteria from the out-side. Our results showed that lysep3-D8 could lyse both Gram- negative and Gram-positive bacteria, whereas lysep3 and D8 have no impact on bacterial growth. The MIC of lysep3-D8 on E. coli CVCC1418 is 60 μg/ml; lysep3-D8 can inhibit the growth of bacteria up to 12 h at this concentration. The bac-tericidal spectrum of lysep3-D8 is broad, as it can lyse of all of 14 E. coli strains, 3 P. aeruginosa strains, 1 Acinetobacter baumannii strain, and 1 Streptococcus strain. Lysep3-D8 has sufficient bactericidal effects on the 14 E. coli strains tested at the concentration of 100 μg/ml. The cell wall binding do-main of the engineered lysin can destroy the integrity of the outer membrane of bacteria, thus allowing the catalytic do-main to reach its target, peptidoglycan, to lyse the bacteria. Lysep3-D8 can be used as a preservative in fodder to benefit the health of animals. The method we used here proved to be a successful exploration of the reformation of phage lysin.

Citations

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New-Generation Antibacterial Agent—Cellulose-Binding Thermostable TP84_Endolysin
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Antibacterial compound produced by Pseudomonas aeruginosa strain UICC B-40, an endophytic bacterium isolated from Neesia altissima: Rina Hidayati Pratiwi , Iman Hidayat , Muhammad Hanafi , Wibowo Mangunwardoyo; J. Microbiol. 2017;55(4):289-295. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6311-0

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Abstract

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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Research Support, Non-U.S. Gov'ts

Antibacterial effects of N-acetylcysteine against endodontic pathogens: Ji-Hoi Moon , Young-Suk Choi , Hyeon-Woo Lee , Jung Sun Heo , Seok Woo Chang , Jin-Yong Lee; J. Microbiol. 2016;54(4):322-329. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-5534-9

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Abstract

The success of endodontic treatment depends on the eradication of microorganisms from the root canal system and the prevention of reinfection. The purpose of this investigation was to evaluate the antibacterial and antibiofilm efficacy of N-acetylcysteine (NAC), an antioxidant mucolytic agent, as an intracanal medicament against selected endodontic pathogens. Minimum inhibitory concentrations (MICs) of NAC for Actinomyces naeslundii, Lactobacillus salivarius, Streptococcus mutans, and Enterococcus faecalis were determined using the broth microdilution method. NAC showed antibacterial activity, with MIC values of 0.78–1.56 mg/ml. The effect of NAC on biofilm formation of each bacterium and a multispecies culture consisting of the four bacterial species was assessed by crystal violet staining. NAC significantly inhibited biofilm formation by all the monospecies and multispecies bacteria at minimum concentrations of 0.78–3.13 mg/ml. The efficacy of NAC for biofilm disruption was evaluated by scanning electron microscopy and ATP-bioluminescence quantification using mature multispecies biofilms. Preformed mature multispecies biofilms on saliva-coated hydroxyapatite disks were disrupted within 10 min by treatment with NAC at concentrations of 25 mg/ml or higher. After 24 h of treatment, the viability of mature biofilms was reduced by > 99% compared with the control. Moreover, the biofilm disrupting activity of NAC was significantly higher than that of saturated calcium hydroxide or 2% chlorhexidine solution. Within the limitations of this in vitro study, we conclude that NAC has excellent antibacterial and antibiofilm efficacy against endodontic pathogens and may be used as an alternative intracanal medicament in root canal therapies.

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Antibacterial metabolites from the Actinomycete Streptomyces sp. P294: Huining Su , Hongwei Shao , Keqin Zhang , Guohong Li; J. Microbiol. 2016;54(2):131-135. Published online February 2, 2016; DOI: https://doi.org/10.1007/s12275-016-5311-9

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Abstract

The Actinomycete strain P294 was isolated from soil and identified as Streptomyces sp. based upon the results of 16S rRNA sequence analysis. Three compounds obtained from the solid fermentation products of this strain have been determined by 1D, 2D NMR and HRMS experiments. These compounds include two new compounds angumycinones C (1) and D (2), and the known compound X-14881 E (3). All compounds were assayed for antibacterial and nematicidal activity. The results showed the three compounds had different degrees of inhibitory activity against several target bacteria but no significant toxicity against the nematode Caenorhabditis elegans.

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Diverse ansamycin derivatives from the marine-derived Streptomyces sp. ZYX-F-97 and their antibacterial activities
Ke-Xin Yi, Qing-Yi Xie, Qing-Yun Ma, Li Yang, Hao-Fu Dai, You-Xing Zhao, Yu-E Hao
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Heterologous Expression of Type II PKS Gene Cluster Leads to Diversified Angucyclines in Streptomyces albus J1074
Xiaoting Zhang, Falei Zhang, Chen Li, Jiayi Li, Xiao Xu, Tianjiao Zhu, Qian Che, Deihai Li, Guojian Zhang
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Antibacterial potential of a small peptide from Bacillus sp. RPT-0001 and its capping for green synthesis of silver nanoparticles: Supriya Deepak Patil , Rajnikant Sharma , Tapas Bhattacharyya , Piyush Kumar , Manasi Gupta , Bhupinder Singh Chaddha , Naveen Kumar Navani , Ranjana Pathania; J. Microbiol. 2015;53(9):643-652. Published online August 1, 2015; DOI: https://doi.org/10.1007/s12275-015-4686-3

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Abstract

Infirmity and death from diseases caused by unsafe food are a continual hazard to communal health safety and socio-economic growth throughout the world. Chemical preservatives are associated with health hazards and toxicity issues. In the study reported here, 200 soil isolates from Western Himalayan region in India were screened for potential antibacterial activity against food-borne pathogens. This study led to the isolation of a bacterial strain belonging to the Genus Bacillus and was designated as RPT-0001. The associated antibacterial activity was sensitive to pronase E treatment. Bioassay-guided fractionation using reverse phase high performance liquid chromatography (RP-HPLC) led to isolation of the antibacterial peptide designated as RPT-0001. The molecular weight of RPT-0001 was determined by electro- spray ionization mass spectroscopy (ESI-MS) as 276.9 Da. RPT-0001 was inhibitory to both Gram-negative and Grampositive food-borne bacteria tested. The characteristics of RPT-0001 do not match with that of any other known antibacterial peptides produced by Bacillus sp. or related genera. Purified RPT-0001 was successfully used in synthesis of silver nanoparticles effective against food-borne pathogenic bacteria. The antibacterial peptide and silver nanoparticles synthesized utilizing it as a capping and reducing agent hold promising potential in food preservation, in packaging material and as a therapeutic agent in the treatment of foodborne infections.

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Arif Jamal Siddiqui, Mitesh Patel, Mohd Adnan, Sadaf Jahan, Juhi Saxena, Mohammed Merae Alshahrani, Abdelmushin Abdelgadir, Fevzi Bardakci, Manojkumar Sachidanandan, Riadh Badraoui, Mejdi Snoussi, Allal Ouhtit
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Keyur Bhatt, Anita Kongor, Mohd Atharb, Vinod Jain
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Nelson G. J. Oliveira, Marlon H. Cardoso, Nadya Velikova, Marcel Giesbers, Jerry M. Wells, Taia M. B. Rezende, Renko de Vries, Octávio L. Franco
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Antimicrobial Effects of Herbal Extracts on Streptococcus mutans and Normal Oral Streptococci: Sung-Hoon Lee; J. Microbiol. 2013;51(4):484-489. Published online August 30, 2013; DOI: https://doi.org/10.1007/s12275-013-3312-5

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Abstract: Streptococcus mutans is associated with dental caries. A cariogenic biofilm, in particular, has been studied extensively for its role in the formation of dental caries. Herbal extracts such as Cudrania tricuspidata, Sophora flavescens, Ginkgo biloba, and Betula Schmidtii have been used as a folk remedy for treating diseases. The purpose of this study was to evaluate and compare the antibacterial activity of herbal extracts against normal oral streptococci, planktonic and biofilm of S. mutans. Streptococcus gordonii, Streptococcus oralis, Streptococcus salivarius, Streptococcus sanguinis, and S. mutans were cultivated with brain heart infusion broth and susceptibility assay for the herbal extracts was performed according to the protocol of Clinical and Laboratory Standard Institute. Also, S. mutans biofilm was formed on a polystyrene 12-well plate and 8-well chamber glass slip using BHI broth containing 2% sucrose and 1% mannose after conditioning the plate and the glass slip with unstimulated saliva. The biofilm was treated with the herbal extracts in various concentrations and inoculated on Mitis-Salivarius bacitracin agar plate for enumeration of viable S. mutans by counting colony forming units. Planktonic S. mutans showed susceptibility to all of the extracts and S. mutans biofilm exhibited the highest level of sensitivity for the extracts of S. flavescens. The normal oral streptococci exhibited a weak susceptibility in comparison to S. mutans. S. oralis, however, was resistant to all of the extracts. In conclusion, the extract of S. flavescens may be a potential candidate for prevention and management of dental caries.

Influence of Culture Conditions and Medium Composition on the Production of Antibacterial Compounds by Marine Serratia sp. WPRA3: Mahtab Jafarzade , Nur Ain Yahya , Fatemeh Shayesteh , Gires Usup , Asmat Ahmad; J. Microbiol. 2013;51(3):373-379. Published online June 28, 2013; DOI: https://doi.org/10.1007/s12275-013-2440-2

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Abstract: This study was undertaken to investigate the influence of culture conditions and medium components on production of antibacterial compounds by Serratia sp. WPRA3 (JX020764) which was isolated from marine water of Port Dickson, Malaysia. Biochemical, morphological, and molecular characteristics suggested that the isolate is a new candidate of the Serratia sp. The isolate showed strong antimicrobial activity against fungi, Gram-negative and Gram-positive bacteria. This bacterium exhibited optimum antibacterial compounds production at 28°C, pH 7 and 200 rev/min aeration during 72 h of incubation period. Highest antibacterial activity was obtained when sodium chloride (2%), yeast extract (0.5%), and glucose concentration (0.75%) were used as salt, nitrogen, and carbon sources respectively. Different active fractions were obtained by Thin-Layer Chromatography (TLC) and Flash Column Chromatography (FCC) from ethyl acetate crude extracts namely OCE and RCE in different culture conditions, OCE (pH 5, 200 rev/min) and RCE (pH 7/without aeration). In conclusion, the results suggested different culture conditions have a significant impact on the types of secondary metabolites produced by the bacterium.

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