Journal of Microbiology

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Genomic profiling of soil nitrifying microorganisms enriched on floating membrane filter: Christiana Abiola, Joo-Han Gwak, Ui-Ju Lee, Aderonke Odunayo Adigun, Sung-Keun Rhee; J. Microbiol. 2025;63(4):e2502002. Published online April 29, 2025; DOI: https://doi.org/10.71150/jm.2502002

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Abstract PDF Supplementary Material: Recently, floating membrane filter cultivation was adopted to simulate solid surface and enrich surface-adapted soil ammonia-oxidizing archaea (AOA) communities from agricultural soil, as opposed to the conventional liquid medium. Here, we conducted metagenomic sequencing to recover nitrifier bins from the floating membrane filter cultures and reveal their genomic properties. Phylogenomic analysis showed that AOA bins recovered from this study, designated FF_bin01 and FF_bin02, are affiliated with the Nitrososphaeraceae family, while the third bin, FF_bin03, is a nitrite-oxidizing bacterium affiliated with the Nitrospiraceae family. Based on the ANI/AAI analysis, FF_bin01 and FF_bin02 are identified as novel species within the genera “Candidatus Nitrosocosmicus” and Nitrososphaera, respectively, while FF_bin03 represents a novel species within the genus Nitrospira. The pan and core genome analysis for the 29 AOA genomes considered in this study revealed 5,784 orthologous clusters, out of which 653 were core orthologous clusters. Additionally, 90 unique orthologous clusters were conserved among the Nitrososphaeraceae family, suggesting their potential role in enhancing culturability and adaptation to diverse environmental conditions. Intriguingly, FF_bin01 and FF_bin02 harbor a gene encoding manganese catalase and FF_bin03 also possesses a heme catalase gene, which might enhance their growth on the floating membrane filter. Overall, the floating membrane filter cultivation has proven to be a promising approach for isolating distinct soil AOA, and further modifications to this technique could stimulate the growth of a broader range of uncultivated nitrifiers from diverse soil environments.

Genetic insights into novel lysis suppression by phage CSP1 in Escherichia coli: Moosung Kim, Sangryeol Ryu; J. Microbiol. 2025;63(4):e2501013. Published online April 29, 2025; DOI: https://doi.org/10.71150/jm.2501013

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Abstract PDF Supplementary Material: Lysis inhibition (LIN) in bacteriophage is a strategy to maximize progeny production. A clear plaque-forming mutant, CSP1C, was isolated from the turbid plaque-forming CSP1 phage. CSP1C exhibited an adsorption rate and replication dynamics similar to CSP1. Approximately 90% of the phages were adsorbed to the host cell within 12 min, and both phages had a latent period of 25 min. Burst sizes were 171.42 ± 31.75 plaque-forming units (PFU) per infected cell for CSP1 and 168.94 ± 51.67 PFU per infected cell for CSP1C. Both phages caused comparable reductions in viable E. coli cell counts at a low multiplicity of infection (MOI). However, CSP1 infection did not reduce turbidity, suggesting a form of LIN distinct from the well-characterized LIN of T4 phage. Genomic analysis revealed that a 4,672-base pairs (bp) DNA region, encompassing part of the tail fiber gene, CSP1_020, along with three hypothetical genes, CSP1_021, CSP1_022, and part of CSP1_023, was deleted from CSP1 to make CSP1C. Complementation analysis in CSP1C identified CSP1_020, CSP1_021, and CSP1_022 as a minimal gene set required for the lysis suppression in CSP1. Co-expression of these genes in E. coli with holin (CSP1_092) and endolysin (CSP1_091) resulted in lysis suppression. Lysis suppression was abolished by disrupting the proton motive force (PMF), supporting their potential role as antiholin. Additionally, CSP1_021 directly interacts with holin, suggesting that it may function as an antiholin. These findings identify new genetic factors involved in lysis suppression in CSP1, providing broader insights into phage strategies for modulating host cell lysis.

Review

Recent advances in targeted mutagenesis to expedite the evolution of biological systems: Seungjin Kim, Seungwon Lee, Hyun Gyu Lim; J. Microbiol. 2025;63(3):e2501008. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501008

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Abstract PDF

Evolution has been systematically exploited to engineer biological systems to obtain improved or novel functionalities by selecting beneficial mutations. Recent innovations in continuous targeted mutagenesis within living cells have emerged to generate large sequence diversities without requiring multiple steps. This review comprehensively introduces recent advancements in this field, categorizing them into three approaches depending on methods to create mutations: orthogonal error-prone DNA polymerases, site-specific base editors, and homologous recombination of mutagenic DNA fragments. Combined with high-throughput screening methods, these advances expedited evolution processes with significant reduction of labor and time. These approaches promise broader industrial and research applications, including enzyme improvement, metabolic engineering, and drug resistance studies.

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Advancing microbial engineering through synthetic biology
Ki Jun Jeong
Journal of Microbiology.2025; 63(3): e2503100. CrossRef

Research Article

Single nucleotide genome recognition and selective bacterial lysis using synthetic phages loaded with CRISPR-Cas12f1-truncated sgRNA: Ho Joung Lee, Song Hee Jeong, Sang Jun Lee; J. Microbiol. 2025;63(2):e2501012. Published online February 27, 2025; DOI: https://doi.org/10.71150/jm.2501012

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Abstract PDF Supplementary Material: Phage specificity primarily relies on host cell-surface receptors. However, integrating cas genes and guide RNAs into phage genomes could enhance their target specificity and regulatory effects. In this study, we developed a CRISPR-Cas12f1 system-equipped bacteriophage λ model capable of detecting Escherichia coli target genes. We demonstrated that synthetic λ phages carrying Cas12f1-sgRNA can effectively prevent lysogen formation. Furthermore, we showcased that truncating the 3'-end of sgRNA enables precise identification of single-nucleotide variations in the host genome. Moreover, infecting E. coli strains carrying various stx2 gene subtypes encoding Shiga toxin with bacteriophages harboring Cas12f1 and truncated sgRNAs resulted in the targeted elimination of strains with matching subtype genes. These findings underscore the ability of phages equipped with the CRISPR-Cas12f1 system to precisely control microbial hosts by recognizing genomic sequences with high resolution.

Journal Articles

Characterization of Newly Isolated Bacteriophages Targeting Carbapenem-Resistant Klebsiella pneumoniae: Bokyung Kim, Shukho Kim, Yoon-Jung Choi, Minsang Shin, Jungmin Kim; J. Microbiol. 2024;62(12):1133-1153. Published online December 10, 2024; DOI: https://doi.org/10.1007/s12275-024-00180-7

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Abstract: Klebsiella pneumoniae, a Gram-negative opportunistic pathogen, is increasingly resistant to carbapenems in clinical settings. This growing problem necessitates the development of alternative antibiotics, with phage therapy being one promising option. In this study, we investigated novel phages targeting carbapenem-resistant Klebsiella pneumoniae (CRKP) and evaluated their lytic capacity against clinical isolates of CRKP. First, 23 CRKP clinical isolates were characterized using Multi-Locus Sequence Typing (MLST), carbapenemase test, string test, and capsule typing. MLST classified the 23 K. pneumoniae isolates into 10 sequence types (STs), with the capsule types divided into nine known and one unknown type. From sewage samples collected from a tertiary hospital, 38 phages were isolated. Phenotypic and genotypic characterization of these phages was performed using Random Amplification of Polymorphic DNA-PCR (RAPD-PCR), transmission electron microscopy (TEM), and whole genome sequencing (WGS) analysis. Host spectrum analysis revealed that each phage selectively lysed strains sharing the same STs as their hosts, indicating ST-specific activity. These phages were subtyped based on their host spectrum and RAPD-PCR, identifying nine and five groups, respectively. Fourteen phages were selected for further analysis using TEM and WGS, revealing 13 Myoviruses and one Podovirus. Genomic analysis grouped the phages into three clusters: one closely related to Alcyoneusvirus, one to Autographiviridae, and others to Straboviridae. Our results showed that the host spectrum of K. pneumoniae-specific phages corresponds to the STs of the host strain. These 14 novel phages also hold promise as valuable resources for phage therapy against CRKP.

CalR Inhibits the Swimming Motility and Polar Flagellar Gene Expression in Vibrio parahaemolyticus: Jingyang Chang, Yining Zhou, Miaomiao Zhang, Xue Li, Nan Zhang, Xi Luo, Bin Ni, Haisheng Wu, Renfei Lu, Yiquan Zhang; J. Microbiol. 2024;62(12):1125-1132. Published online December 6, 2024; DOI: https://doi.org/10.1007/s12275-024-00179-0

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Abstract: Vibrio parahaemolyticus has two flagellar systems, the polar flagellum and lateral flagella, which are both intricately regulated by a multitude of factors. CalR, a LysR-type transcriptional regulator, is sensitive to calcium (Ca) and plays a crucial role in regulating the virulence and swarming motility of V. parahaemolyticus. In this study, we have demonstrated that the deletion of calR significantly enhances the swimming motility of V. parahaemolyticus under low Ca conditions but not under high Ca conditions or in the absence of Ca. CalR binds to the regulatory DNA regions of flgM, flgA, and flgB, which are located within the polar flagellar gene loci, with the purpose of repressing their transcription. Additionally, it exerts an indirect negative control over the transcription of flgK. The overexpression of CalR in Escherichia coli resulted in a reduction in the expression levels of flgM, flgA, and flgB, while having no impact on the expression of flgK. In summary, this research demonstrates that the negative regulation of V. parahaemolyticus swimming motility by CalR under low Ca conditions is achieved through its regulation on the transcription of polar flagellar genes.

Characterization and Comparative Genomic Analysis of vB_BceM_CEP1: A Novel Temperate Bacteriophage Infecting Burkholderia cepacia Complex: Momen Askoura, Eslam K Fahmy, Safya E Esmaeel, Wael A H Hegazy, Aliaa Abdelghafar; J. Microbiol. 2024;62(11):1035-1055. Published online November 18, 2024; DOI: https://doi.org/10.1007/s12275-024-00185-2

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Abstract: The increasing prevalence of multidrug-resistant bacteria imminently threatens public health and jeopardizes nearly all aspects of modern medicine. The Burkholderia cepacia complex (Bcc) comprises Burkholderia cepacia and the related species of Gram-negative bacteria. Members of the Bcc group are opportunistic pathogens responsible for various chronic illnesses, including cystic fibrosis and chronic granulomatous disease. Phage therapy is emerging as a potential solution to combat the antimicrobial resistance crisis. In this study, a temperate phage vB_BceM_CEP1 was isolated from sewage and fully characterized. Transmission electron microscopy indicated that vB_BceM_CEP1 belongs to the family Peduoviridae. The isolated phage demonstrated enhanced environmental stability and antibiofilm potential. One-step growth analysis revealed a latent period of 30 min and an average burst size of 139 plaque-forming units per cell. The genome of vB_BceM_CEP1 consists of 32,486 bp with a GC content of 62.05%. A total of 40 open reading frames were annotated in the phage genome, and none of the predicted genes was annotated as tRNA. Notably, genes associated with antibiotic resistance, host virulence factors, and toxins were absent from the vB_BceM_CEP1 genome. Based on its unique phenotype and phylogeny, the isolated phage vB_BceM_CEP1 is classified as a new temperate phage with lytic activity. The findings of this study enhance our understanding of the diversity of Bcc phages.

Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture: Meora Rajeev, Jang-Cheon Cho; J. Microbiol. 2024;62(11):985-997. Published online November 15, 2024; DOI: https://doi.org/10.1007/s12275-024-00187-0

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Abstract

Bioflocs are microbial aggregates primarily composed of heterotrophic bacteria that play essential ecological roles in maintaining animal health, gut microbiota, and water quality in biofloc aquaculture systems. Despite the global adoption of biofloc aquaculture for shrimp and fish cultivation, our understanding of biofloc microbiota-particularly the dominant bacterial members and their ecological functions-remains limited. In this study, we employed integrated metataxonomic and metagenomic approaches to demonstrate that the family Rhodobacteraceae of Alphaproteobacteria consistently dominates the biofloc microbiota and plays essential ecological roles. We first analyzed a comprehensive metataxonomic dataset consisting of 200 16S rRNA gene amplicons collected across three Asian countries: South Korea, China, and Vietnam. Taxonomic investigation identified Rhodobacteraceae as the dominant and consistent bacterial members across the datasets. The predominance of this taxon was further validated through metagenomics approaches, including read taxonomy and read recruitment analyses. To explore the ecological roles of Rhodobacteraceae, we applied genome-centric metagenomics, reconstructing 45 metagenome-assembled genomes. Functional annotation of these genomes revealed that dominant Rhodobacteraceae genera, such as Marivita, Ruegeria, Dinoroseobacter, and Aliiroseovarius, are involved in vital ecological processes, including complex carbohydrate degradation, aerobic denitrification, assimilatory nitrate reduction, ammonium assimilation, and sulfur oxidation. Overall, our study reveals that the common practice of carbohydrate addition in biofloc aquaculture systems fosters the growth of specific heterotrophic bacterial communities, particularly Rhodobacteraceae. These bacteria contribute to maintaining water quality by removing toxic nitrogen and sulfur compounds and enhance animal health by colonizing gut microbiota and exerting probiotic effects.

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Ecological disposal of bauxite tailings and red mud: A sustainable strategy for bauxite industrial waste reuse
Xusheng Jiang, Xuehong Zhang, Xijun Liu, Hui Qiu, Mengting Lin, Guo Yu, Shouhui Zhang, Jie Liu
Resources, Conservation and Recycling.2025; 218: 108259. CrossRef
Variation of Microorganisms and Water Quality, and Their Impacts on the Production of Penaeus vannamei in Small-Scale Greenhouse Ponds
Siyu Wu, Haochang Su, Lei Su, Yucheng Cao, Guoliang Wen, Yu Xu, Bin Shen, Shanshan Wu, Yuting Su, Xiaojuan Hu
Microorganisms.2025; 13(3): 546. CrossRef
Effect of hydraulic retention time of sponge-based trickling filter for shrimp culture recirculating tank
Penpicha Satanwat, Mami Nagai, Tharin Boonprasertsakul, Akihiro Nagano, Tsutomu Okubo, Nur Adlin, Takahiro Watari, Masashi Hatamoto, Takashi Yamaguchi, Sitthakarn Sitthi, Wiboonluk Pungrasmi, Rapeepun Vanichviriyakit, Sorawit Powtongsook
Process Safety and Environmental Protection.2025; : 107154. CrossRef

Meta-Analysis

Exploring COVID-19 Pandemic Disparities with Transcriptomic Meta-analysis from the Perspective of Personalized Medicine: Medi Kori, Ceyda Kasavi, Kazim Yalcin Arga; J. Microbiol. 2024;62(9):785-798. Published online July 9, 2024; DOI: https://doi.org/10.1007/s12275-024-00154-9

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Abstract

Infection with SARS-CoV2, which is responsible for COVID-19, can lead to differences in disease development, severity and mortality rates depending on gender, age or the presence of certain diseases. Considering that existing studies ignore these differences, this study aims to uncover potential differences attributable to gender, age and source of sampling as well as viral load using bioinformatics and multi-omics approaches. Differential gene expression analyses were used to analyse the phenotypic differences between SARS-CoV-2 patients and controls at the mRNA level. Pathway enrichment analyses were performed at the gene set level to identify the activated pathways corresponding to the differences in the samples. Drug repurposing analysis was performed at the protein level, focusing on host-mediated drug candidates to uncover potential therapeutic differences. Significant differences (i.e. the number of differentially expressed genes and their characteristics) were observed for COVID-19 at the mRNA level depending on the sample source, gender and age of the samples. The results of the pathway enrichment show that SARS-CoV-2 can be combated more effectively in the respiratory tract than in the blood samples. Taking into account the different sample sources and their characteristics, different drug candidates were identified. Evaluating disease prediction, prevention and/or treatment strategies from a personalised perspective is crucial. In this study, we not only evaluated the differences in COVID-19 from a personalised perspective, but also provided valuable data for further experimental and clinical efforts. Our findings could shed light on potential pandemics.

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Differential Impact of Spike Protein Mutations on SARS-CoV-2 Infectivity and Immune Evasion: Insights from Delta and Kappa Variants
Tae-Hun Kim, Sojung Bae, Jinjong Myoung
Journal of Microbiology and Biotechnology.2024; 34(12): 2506. CrossRef

Journal Articles

Enterococcus Phage vB_EfaS_HEf13 as an Anti-Biofilm Agent Against Enterococcus faecalis: Dongwook Lee, Jintaek Im, A Reum Kim, Woohyung Jun, Cheol-Heui Yun, Seung Hyun Han; J. Microbiol. 2024;62(8):683-693. Published online June 27, 2024; DOI: https://doi.org/10.1007/s12275-024-00150-z

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Abstract

Enterococcus faecalis is a Gram-positive bacterium that is frequently found in the periapical lesion of patients with apical periodontitis. Its biofilm formation in root canal is closely related to the development of refractory apical periodontitis by providing increased resistance to endodontic treatments. Phage therapy has recently been considered as an efficient therapeutic strategy in controlling various periodontal pathogens. We previously demonstrated the bactericidal capacities of Enterococcus phage vB_EfaS_HEf13 (phage HEf13) against clinically-isolated E. faecalis strains. Here, we investigated whether phage HEf13 affects biofilm formation and pre-formed biofilm of clinically-isolated E. faecalis, and its combinatory effect with endodontic treatments, including chlorhexidine (CHX) and penicillin. The phage HEf13 inhibited biofilm formation and disrupted pre-formed biofilms of E. faecalis in a dose- and time-dependent manner. Interestingly, phage HEf13 destroyed E. faecalis biofilm exopolysaccharide (EPS), which is known to be a major component of bacterial biofilm. Furthermore, combined treatment of phage HEf13 with CHX or penicillin more potently inhibited biofilm formation and disrupted pre-formed biofilm than either treatment alone. Confocal laser scanning microscopic examination demonstrated that these additive effects of the combination treatments on disruption of pre-formed biofilm are mediated by relatively enhanced reduction in thickness distribution and biomass of biofilm. Collectively, our results suggest that the effect of phage HEf13 on E. faecalis biofilm is mediated by its EPS-degrading property, and its combination with endodontic treatments more potently suppresses E. faecalis biofilm, implying that phage HEf13 has potential to be used as a combination therapy against E. faecalis infections.

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Size-dependent ecotoxicological impacts of tire wear particles on zebrafish physiology and gut microbiota: Implications for aquatic ecosystem health
Yun Zhang, Qianqian Song, Qingxuan Meng, Tianyu Zhao, Xiaolong Wang, Xinrui Meng, Jing Cong
Journal of Hazardous Materials.2025; 487: 137215. CrossRef

Quorum Quenching Potential of Reyranella sp. Isolated from Riverside Soil and Description of Reyranella humidisoli sp. nov.: Dong Hyeon Lee, Seung Bum Kim; J. Microbiol. 2024;62(6):449-461. Published online May 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00131-2

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Abstract

Quorum quenching refers to any mechanism that inhibits quorum sensing processes. In this study, quorum quenching activity among bacteria inhabiting riverside soil was screened, and a novel Gram-stain-negative, rod shaped bacterial strain designated MMS21-HV4-11(T), which showed the highest level of quorum quenching activity, was isolated and subjected to further analysis. Strain MMS21-HV4-11(T) could be assigned to the genus Reyranella of Alphaproteobacteria based on the 16S rRNA gene sequence, as the strain shared 98.74% sequence similarity with Reyranella aquatilis seoho-37(T), and then 97.87% and 97.80% sequence similarity with Reyranella soli KIS14-15(T) and Reyranella massiliensis 521(T), respectively. The decomposed N-acyl homoserine lactone was restored at high concentrations under acidic conditions, implying that lactonase and other enzyme(s) are responsible for quorum quenching. The genome analysis indicated that strain MMS21-HV4-11(T) had two candidate genes for lactonase and one for acylase, and expected protein structures were confirmed. In the quorum sensing inhibition assay using a plant pathogen Pectobacterium carotovorum KACC 14888, development of soft rot was significantly inhibited by strain MMS21-HV4-11(T). Besides, the swarming motility by Pseudomonas aeruginosa PA14 was significantly inhibited in the presence of strain MMS21-HV4-11(T). Since the isolate did not display direct antibacterial activity against either of these species, the inhibition was certainly due to quorum quenching activity. In an extended study with the type strains of all known species of Reyranella, all strains were capable of degrading N-acyl homoserine lactones (AHLs), thus showing quorum quenching potential at the genus level. This is the first study on the quorum quenching potential and enzymes responsible in Reyranella. In addition, MMS21-HV4-11(T) could be recognized as a new species through taxonomic characterization, for which the name Reyranella humidisoli sp. nov. is proposed (type strain = MMS21-HV4-11( T) = KCTC 82780( T) = LMG 32365(T)).

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Study of N-acyl homoserine lactone (AHL) degradation potential of bacteria isolated from environmental samples and their impact on quorum sensing regulated biofilm formation of Pseudomonas aeruginosa
Anju Tomy, Rakesh Yasarla
Journal of Environmental Chemical Engineering.2025; 13(2): 115974. CrossRef
Research progress of bacterial quorum sensing systems in synthetic biology applications
Boyu Luo, Tuoyu Liu, Zhi Sun, Yue Teng
Chinese Science Bulletin.2024; 69(36): 5213. CrossRef
Validation List no. 220. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef

Exploring the Therapeutic Potential of Scorpion‑Derived Css54 Peptide Against Candida albicans: Jonggwan Park , Hyeongsun Kim , Da Dam Kang , Yoonkyung Park; J. Microbiol. 2024;62(2):101-112. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00113-4

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Abstract

Candida albicans (C. albicans) is one of the most common opportunistic fungi worldwide, which is associated with a high mortality rate. Despite treatment, C. albicans remains the leading cause of life-threatening invasive infections. Consequently, antimicrobial peptides (AMPs) are potential alternatives as antifungal agents with excellent antifungal activity. We previously reported that Css54, found in the venom of Centrurodies suffusus suffusus (C. s. suffusus) showed antibacterial activity against zoonotic bacteria. However, the antifungal activity of Css54 has not yet been elucidated. The obj!ective of this study was to identify the antifungal activity of Css54 against C. albicans and analyze its mechanism. Css54 showed high antifungal activity against C. albicans. Css54 also inhibited biofilm formation in fluconazole-resistant fungi. The antifungal mechanism of action of Css54 was investigated using membrane-related assays, including the membrane depolarization assay and analysis of the membrane integrity of C. albicans after treatment with Css54. Css54 induced reactive oxygen species (ROS) production in C. albicans, which affected its antifungal activity. Our results indicate that Css54 causes membrane damage in C. albicans, highlighting its value as a potential therapeutic agent against C. albicans infection.

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Antimicrobial Potential of Scorpion-Venom-Derived Peptides
Zhiqiang Xia, Lixia Xie, Bing Li, Xiangyun Lv, Hongzhou Zhang, Zhijian Cao
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Synthetic Short Cryptic Antimicrobial Peptides as Templates for the Development of Novel Biotherapeutics Against WHO Priority Pathogen
Manjul Lata, Vrushti Telang, Pooja Gupta, Garima Pant, Mitra Kalyan, Jesu Arockiaraj, Mukesh Pasupuleti
International Journal of Peptide Research and Therapeutics.2024;[Epub] CrossRef

miR-135b Aggravates Fusobacterium nucleatum-Induced Cisplatin Resistance in Colorectal Cancer by Targeting KLF13: Wei Zeng , Jia Pan , Guannan Ye; J. Microbiol. 2024;62(2):63-73. Published online February 24, 2024; DOI: https://doi.org/10.1007/s12275-023-00100-1

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Abstract

Cisplatin resistance is the main cause of colorectal cancer (CRC) treatment failure, and the cause has been reported to be related to Fusobacterium nucleatum (Fn) infection. In this study, we explored the role of Fn in regulating cisplatin resistance of CRC cells and its underlying mechanism involved. The mRNA and protein expressions were examined by qRT-PCR and western blot. Cell proliferation and cell apoptosis were assessed using CCK8 and flow cytometry assays, respectively. Dual-luciferase reporter gene assay was adopted to analyze the molecular interactions. Herein, our results revealed that Fn abundance and miR-135b expression were markedly elevated in CRC tissues, with a favorable association between the two. Moreover, Fn infection could increase miR-135b expression via a concentration-dependent manner, and it also enhanced cell proliferation but reduced apoptosis and cisplatin sensitivity by upregulating miR-135b. Moreover, KLF13 was proved as a downstream target of miR-135b, of which overexpression greatly diminished the promoting effect of miR-135b or Fn-mediated cisplatin resistance in CRC cells. In addition, it was observed that upstream 2.5 kb fragment of miR-135b promoter could be interacted by β-catenin/TCF4 complex, which was proved as an effector signaling of Fn. LF3, a blocker of β-catenin/TCF4 complex, was confirmed to diminish the promoting role of Fn on miR-135b expression. Thus, it could be concluded that Fn activated miR-135b expression through TCF4/β-catenin complex, thereby inhibiting KLF13 expression and promoting cisplatin resistance in CRC.

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miR-135b: A key role in cancer biology and therapeutic targets
Yingchun Shao, Shuangshuang Zhang, Yuxin Pan, Zhan Peng, Yinying Dong
Non-coding RNA Research.2025; 12: 67. CrossRef
miR‐135b: A Potential Biomarker for Pathological Diagnosis and Biological Therapy
Dezhi Yan, Qingliu He, Chunjian Wang, Tian Li, Xueping Yi, Haisheng Yu, Wenfei Wu, Hanyun Yang, Wenzhao Wang, Liang Ma
WIREs RNA.2025;[Epub] CrossRef
Emerging roles of intratumor microbiota in cancer: tumorigenesis and management strategies
Zhuangzhuang Shi, Zhaoming Li, Mingzhi Zhang
Journal of Translational Medicine.2024;[Epub] CrossRef
Fusobacterium nucleatum: a novel regulator of antitumor immune checkpoint blockade therapy in colorectal cancer
Mengjie Luo
American Journal of Cancer Research.2024; 14(8): 3962. CrossRef
Antioxidant Role of Probiotics in Inflammation-Induced Colorectal Cancer
Sevag Hamamah, Andrei Lobiuc, Mihai Covasa
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Identification of Penexanthone A as a Novel Chemosensitizer to Induce Ferroptosis by Targeting Nrf2 in Human Colorectal Cancer Cells
Genshi Zhao, Yanying Liu, Xia Wei, Chunxia Yang, Junfei Lu, Shihuan Yan, Xiaolin Ma, Xue Cheng, Zhengliang You, Yue Ding, Hongwei Guo, Zhiheng Su, Shangping Xing, Dan Zhu
Marine Drugs.2024; 22(8): 357. CrossRef

[Protocol] Use of Cas9 Targeting and Red Recombination for Designer Phage Engineering: Shin-Yae Choi , Danitza Xiomara Romero-Calle , Han-Gyu Cho , Hee-Won Bae , You-Hee Cho; J. Microbiol. 2024;62(1):1-10. Published online February 1, 2024; DOI: https://doi.org/10.1007/s12275-024-00107-2

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Abstract

Bacteriophages (phages) are natural antibiotics and biological nanoparticles, whose application is significantly boosted by recent advances of synthetic biology tools. Designer phages are synthetic phages created by genome engineering in a way to increase the benefits or decrease the drawbacks of natural phages. Here we report the development of a straightforward genome engineering method to efficiently obtain engineered phages in a model bacterial pathogen, Pseudomonas aeruginosa. This was achieved by eliminating the wild type phages based on the Streptococcus pyogenes Cas9 (SpCas9) and facilitating the recombinant generation based on the Red recombination system of the coliphage λ (λRed). The producer (PD) cells of P. aeruginosa strain PAO1 was created by miniTn7-based chromosomal integration of the genes for SpCas9 and λRed under an inducible promoter. To validate the efficiency of the recombinant generation, we created the fluorescent phages from a temperate phage MP29. A plasmid bearing the single guide RNA (sgRNA) gene for selectively targeting the wild type gp35 gene and the editing template for tagging the Gp35 with superfolder green fluorescent protein (sfGFP) was introduced into the PD cells by electroporation. We found that the targeting efficiency was affected by the position and number of sgRNA. The fluorescent phage particles were efficiently recovered from the culture of the PD cells expressing dual sgRNA molecules. This protocol can be used to create designer phages in P. aeruginosa for both application and research purposes.

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Pilin regions that select for the small RNA phages in Pseudomonas aeruginosa type IV pilus
Hee-Won Bae, Hyeong-Jun Ki, Shin-Yae Choi, You-Hee Cho, Kristin N. Parent
Journal of Virology.2025;[Epub] CrossRef
Characteristics of bioaerosols under high-ozone periods, haze episodes, dust storms, and normal days in Xi’an, China
Yiming Yang, Liu Yang, Xiaoyan Hu, Zhenxing Shen
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Airborne desert dust and aeromicrobiology over the Turkish Mediterranean coastline
Dale W. Griffin, Nilgün Kubilay, Mustafa Koçak, Mike A. Gray, Timothy C. Borden, Eugene A. Shinn
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Comparative Transcriptomic Analysis of Flagellar‑Associated Genes in Salmonella Typhimurium and Its rnc Mutant: Seungmok Han , Ji-Won Byun , Minho Lee; J. Microbiol. 2024;62(1):33-48. Published online January 5, 2024; DOI: https://doi.org/10.1007/s12275-023-00099-5

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Abstract

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a globally recognized foodborne pathogen that affects both animals and humans. Endoribonucleases mediate RNA processing and degradation in the adaptation of bacteria to environmental changes and have been linked to the pathogenicity of S. Typhimurium. Not much is known about the specific regulatory mechanisms of these enzymes in S. Typhimurium, particularly in the context of environmental adaptation. Thus, this study carried out a comparative transcriptomic analysis of wild-type S. Typhimurium SL1344 and its mutant (Δrnc), which lacks the rnc gene encoding RNase III, thereby elucidating the detailed regulatory characteristics that can be attributed to the rnc gene. Global gene expression analysis revealed that the Δrnc strain exhibited 410 upregulated and 301 downregulated genes (fold-change > 1.5 and p < 0.05), as compared to the wild-type strain. Subsequent bioinformatics analysis indicated that these differentially expressed genes are involved in various physiological functions, in both the wild-type and Δrnc strains. This study provides evidence for the critical role of RNase III as a general positive regulator of flagellar-associated genes and its involvement in the pathogenicity of S. Typhimurium.

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CspA regulates stress resistance, flagellar motility and biofilm formation in Salmonella Enteritidis
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