Journal of Microbiology

Editor’s Choice articles are curated by our senior editors, who represent each section, to highlight research published in 2024 that they consider particularly interesting to our readers and/or important within the respective research area.

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Evolutionary Microbiology and Systematics
Microbial Ecology and Environmental Microbiology
Microbial Physiology and Biochemistry
Microbial Genetics, Genomics
and Molecular Biology (Prokaryote)
Microbial Genetics, Genomics
and Molecular Biology (Eukaryote)
Microbial Pathogenesis
and Host-Microbe Interaction
Synthetic Microbiology and Biotechnology
Virology

Microbial Pathogenesis and Host-Microbe Interaction

Journal Articles

[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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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
Synthetic and Functional Engineering of Bacteriophages: Approaches for Tailored Bactericidal, Diagnostic, and Delivery Platforms
Ola Alessa, Yoshifumi Aiba, Mahmoud Arbaah, Yuya Hidaka, Shinya Watanabe, Kazuhiko Miyanaga, Dhammika Leshan Wannigama, Longzhu Cui
Molecules.2025; 30(15): 3132. 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
Particuology.2024; 90: 140. CrossRef
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
Atmospheric Environment.2007; 41(19): 4050. 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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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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Natural product-derived antifungals against Candida albicans: Chemical diversity and mechanisms of action
Runchu Li, Xiaoxu Yang, Wenjia Dan, Jiangkun Dai
Bioorganic & Medicinal Chemistry.2026; 132: 118435. CrossRef
Animal-derived peptides from Traditional Chinese medicines: medicinal potential, mechanisms, and prospects
Jiahui Zhang, Siyi Li, Yueyi Qi, Jieyu Shen, Aijing Leng, Jialin Qu
Journal of Ethnopharmacology.2025; 349: 119872. CrossRef
Scorpion venom as a natural peptide source for innovative therapeutic solutions: A comprehensive review of its potential in emerging medical frontiers
Radwa Abdallnasser Amen, Rawan Atef Essmat, Alyaa Farid, Mohamed A. Abdel-Rahman, Ahmed A. El-Sherif, Yonghong Zhang
Toxicon.2025; 268: 108603. CrossRef
Design and Characterization of Antibacterial Peptide Nanofibrils as Components of Composites for Biomaterial Applications
Justyna Sawicka, Piotr Bollin, Anna Sylla, Miroslawa Panasiuk, Michalina Wilkowska, Lidia Ciolek, Mateusz Leśniewski, Aleksandra Konopka, Karol Struniawski, Gabriela Calka-Kuc, Adam Liwo, Piotr Hanczyc, Maciej Kozak, Beata Gromadzka, Monika Biernat, Sylwi
Current Protein & Peptide Science.2025; 26(10): 875. CrossRef
Properties and Pharmacology of Scorpion Toxins and Their Biotechnological Potential in Agriculture and Medicine
Cháriston André Dal Belo, Stephen Hyslop, Célia Regina Carlini
Toxins.2025; 17(10): 497. CrossRef
Antimicrobial Potential of Scorpion-Venom-Derived Peptides
Zhiqiang Xia, Lixia Xie, Bing Li, Xiangyun Lv, Hongzhou Zhang, Zhijian Cao
Molecules.2024; 29(21): 5080. CrossRef
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

Genetically Engineered CLDN18.2 CAR-T Cells Expressing Synthetic PD1/CD28 Fusion Receptors Produced Using a Lentiviral Vector: Heon Ju Lee, Seo Jin Hwang, Eun Hee Jeong, Mi Hee Chang; J. Microbiol. 2024;62(7):555-568. Published online May 3, 2024; DOI: https://doi.org/10.1007/s12275-024-00133-0

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This study aimed to develop synthetic Claudin18.2 (CLDN18.2) chimeric antigen receptor (CAR)-T (CAR-T) cells as a treatment for advanced gastric cancer using lentiviral vector genetic engineering technology that targets the CLDN18.2 antigen and simultaneously overcomes the immunosuppressive environment caused by programmed cell death protein 1 (PD-1). Synthetic CAR T cells are a promising approach in cancer immunotherapy but face many challenges in solid tumors. One of the major problems is immunosuppression caused by PD-1. CLDN18.2, a gastric-specific membrane protein, is considered a potential therapeutic target for gastric and other cancers. In our study, CLDN18.2 CAR was a second-generation CAR with inducible T-cell costimulatory (CD278), and CLDN18.2-PD1/CD28 CAR was a third-generation CAR, wherein the synthetic PD1/CD28 chimeric-switch receptor (CSR) was added to the second-generation CAR. In vitro, we detected the secretion levels of different cytokines and the killing ability of CAR-T cells. We found that the secretion of cytokines such as interferon-gamma (IFN-γ) and tumor necrosis factor-alpha (TNF-α) secreted by three types of CAR-T cells was increased, and the killing ability against CLDN18.2-positive GC cells was enhanced. In vivo, we established a xenograft GC model and observed the antitumor effects and off-target toxicity of CAR-T cells. These results support that synthetic anti-CLDN18.2 CAR-T cells have antitumor effect and anti-CLDN18.2-PD1/CD28 CAR could provide a promising design strategy to improve the efficacy of CAR-T cells in advanced gastric cancer.

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Enhancing the antitumor activity of CD19/BCMA CAR-T cells in vitro with a PD1IL7R chimeric switch receptor
Kai Yan, Zhongdang Xiao
Cellular Immunology.2025; 415-416: 105001. CrossRef
Research progress on mechanisms of tumor immune microenvironment and gastrointestinal resistance to immunotherapy: mini review
Zheng Zhang, Yangping Wu
Frontiers in Immunology.2025;[Epub] CrossRef
On-target off-tumor toxicity of claudin18.2-directed CAR-T cells in preclinical models
Filippo Birocchi, Antonio J. Almazan, Aiyana Parker, Amanda A. Bouffard, Sadie Goncalves, Christopher Kelly, Jessica Frank, Mark B. Leick, Nicholas J. Haradhvala, Shaw Kagawa, Gad Getz, Giulia Escobar, Diego Salas-Benito, Adele Mucci, Trisha R. Berger, Ma
Nature Communications.2025;[Epub] CrossRef
Innovative CAR-T approaches targeting Claudin 18.2 to counteract drug resistance in gastric cancer
Giovanni Calice, Carlo Calabrese, Tiziana Notarangelo
Biomedicine & Pharmacotherapy.2025; 193: 118863. CrossRef

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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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
Phage therapy as a revitalized weapon for treating clinical diseases
Yingjie Wang, Yamei Yu
Microbiome Research Reports.2025;[Epub] CrossRef

Mammaliicoccus sciuri's Pan-Immune System and the Dynamics of Horizontal Gene Transfer among Staphylococcaceae: a One-Health CRISPR Tale: Allan de Carvalho, Marcia Giambiagi-deMarval, Ciro César Rossi; J. Microbiol. 2024;62(9):775-784. Published online July 22, 2024; DOI: https://doi.org/10.1007/s12275-024-00156-7

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Recently emancipated from the Staphylococcus genus due to genomic differences, Mammaliicoccus sciuri, previously classified as an occasional pathogen, emerges as a significant player in the landscape of resistance gene dissemination among Staphylococcaceae. Despite its classification, its role remained enigmatic. In this study, we delved into the genomic repertoire of M. sciuri to unravel its contribution to resistance and virulence gene transfer in the context of One Health. Through comprehensive analysis of publicly available genomes, we unveiled a diverse pan-immune system adept at defending against exogenous genetic elements, yet concurrently fostering horizontal gene transfer (HGT). Specifically, exploration of CRISPR-Cas systems, with spacer sequences as molecular signatures, elucidated a global dissemination pattern spanning environmental, animal, and human hosts. Notably, we identified the integration of CRISPR-Cas systems within SCCmecs (Staphylococcal Cassette Chromosome mec), harboring key genes associated with pathogenicity and resistance, especially the methicillin resistance gene mecA, suggesting a strategic adaptation to outcompete other mobile genetic elements. Our findings underscored M. sciuri's active engagement in HGT dynamics and evolutionary trajectories within Staphylococcaceae, emphasizing its central role in shaping microbial communities and highlighting the significance of understanding its implications in the One Health framework, an interdisciplinary approach that recognizes the interconnectedness of human, animal, and environmental health to address global health challenges.

Citations

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From Farm to Community: Dispersal of Potentially Pathogenic Staphylococcus and Mammaliicoccus Species and Antimicrobial Resistance Across Shared Environments
Faizan Ahmad, Samuel Sathler Martuchelle, Ana Luisa Andrade-Oliveira, Vitor Emanuel Lanes Viana, Maria Antônia Silva Melo Sousa, Felipe Sicchierolli da Silveira, Marisa Alves Nogueira-Diaz, Monalessa Fábia Pereira, Marcia Giambiagi-deMarval, Ciro César Ro
Current Microbiology.2025;[Epub] CrossRef
Genomic insights into multidrug and heavy metal resistance in Chryseobacterium sp. BI5 isolated from sewage sludge
Mrinmoy Patra, Anand Kumar Pandey, Suresh Kumar Dubey
Total Environment Microbiology.2025; 1(1): 100005. CrossRef
The Arms Race Between Actinobacillus pleuropneumoniae and Its Genetic Environment: A Comprehensive Analysis of Its Defensome and Mobile Genetic Elements
Giarlã Cunha da Silva, Ciro César Rossi
Molecular Microbiology.2025; 124(1): 40. CrossRef
Defense systems and mobile elements in Staphylococcus haemolyticus: a genomic view of resistance dissemination
Giarlã Cunha da Silva, Ciro César Rossi
Microbial Pathogenesis.2025; 206: 107808. CrossRef
Frequency, Distribution, and Antimicrobial Resistance of Methicillin-Resistant Staphylococci and Mammaliicoccus sciuri Isolated from Dogs and Their Owners in Rio de Janeiro
Fernanda Cruz Bonnard, Luciana Guimarães, Izabel Mello Teixeira, Sandryelle Mercês Freire, Alessandra Maia, Patrícia Câmara de Castro Abreu Pinto, Thais Veiga Blanchart, Bruno Penna
Antibiotics.2025; 14(4): 409. CrossRef
From farm effluent to biotechnological potential: pGLS, a novel and resilient temperate bacteriophage with synergistic activity and broad antibiofilm properties against Staphylococcus and Mammaliicoccus
Vitor Emanuel Lanes Viana, Faizan Ahmad, Samuel Sathler Martuchelle, Sandy de Almada Estanislau, Nohman Rasheed, Marinella Silva Laport, Monalessa Fábia Pereira, Marcia Giambiagi-deMarval, Ciro César Rossi
Journal of Applied Microbiology.2025;[Epub] CrossRef
Staphylococcus parequorum sp. nov. and Staphylococcus halotolerans sp. nov., isolated from traditional Korean soybean foods
Ju Hye Baek, Dong Min Han, Dae Gyu Choi, Chae Yeong Moon, Jae Kyeong Lee, Chul-Hong Kim, Jung-Woong Kim, Che Ok Jeon
Journal of Microbiology.2025; 63(8): e2503003. CrossRef
Discovery of phage CSF, a novel generalist bacteriophage targeting multidrug-resistant and potentially pathogenic Staphylococcus spp. and Mammaliicoccus spp.
Faizan Ahmad, Vitor Emanuel Lanes Viana, Rafael Reis de Rezende, Samuel Sathler Martuchelle, Anderson Souza Cabral, Ana Luisa Andrade-Oliveira, Isabella Monteiro Carvalho, Sandy de Almada Estanislau, Nohman Rasheed, Poliane Alfenas Zerbini, Monalessa Fábi
Archives of Virology.2025;[Epub] CrossRef
Characterization of Phylogenetically Distinct Temperate Phages from Kenyan Mammaliicoccus sciuri
Jérémy D.R. Cherbuin, Jaime Llodrá, Loïc Borcard, Sabine Kaessmeyer, Alban Ramette, Javier Eduardo Fernandez, Theresa Maria Wagner, Sergi Torres-Puig, Peter Kuhnert, Dann Turner, Fabien Labroussaa, Jörg Jores
PHAGE.2025; 6(4): 259. CrossRef
Human Pathogenic Bacteria Within the Nasal and Rectal Microbiome of Macropus giganteus
David Arroyo, Amy Peart, Brian Vesely, Andrew Trudgian, Jessica Chellappah
Tropical Medicine and Infectious Disease.2025; 10(11): 322. CrossRef

Lipoteichoic Acid from Lacticaseibacillus rhamnosus GG as a Novel Intracanal Medicament Targeting Enterococcus faecalis Biofilm Formation: Ji-Young Yoon, Somin Park, Dongwook Lee, Ok-Jin Park, WooCheol Lee, Seung Hyun Han; J. Microbiol. 2024;62(10):897-905. Published online September 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00165-6

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The demand for safe and effective endodontic medicaments to control Enterococcus faecalis biofilms, a contributor to apical periodontitis, is increasing. Recently, lipoteichoic acid (LTA) of family Lactobacillaceae has been shown to have anti-biofilm effects against various oral pathogens. Preliminary experiments showed that LTA purified from Lacticaseibacillus rhamnosus GG (Lgg.LTA) was the most effective against E. faecalis biofilms among LTAs from three Lactobacillaceae including L. rhamnosus GG, Lacticaseibacillus casei, and Lactobacillus acidophilus. Therefore, in this study, we investigated the potential of Lgg.LTA as an intracanal medicament in human root canals infected with E. faecalis. Twenty eight dentinal cylinders were prepared from extracted human teeth, where two-week-old E. faecalis biofilms were formed followed by intracanal treatment with sterile distilled water (SDW), N-2 methyl pyrrolidone (NMP), calcium hydroxide (CH), or Lgg.LTA. Bacteria and biofilms that formed in the root canals were analyzed by scanning electron microscopy and confocal laser scanning microscopy. The remaining E. faecalis cells in the root canals after intracanal medicament treatment were enumerated by culturing and counting. When applied to intracanal biofilms, Lgg.LTA effectively inhibited E. faecalis biofilm formation as much as CH, while SDW and NMP had little effect. Furthermore, Lgg.LTA reduced both live and dead bacteria within the dentinal tubules, indicating the possibility of minimal re-infection in the root canals. Collectively, intracanal application of Lgg.LTA effectively inhibited E. faecalis biofilm formation, implying that Lgg.LTA can be used as a novel endodontic medicament.

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A critical review on innovative targets for signal disruption in Enterococcus faecalis infection management
Kayeen Vadakkan, Gajanan Sampatrao Ghodake, Chin Wei Lai, Selvaraj Vijayanand, Janarthanam Hemapriya
Microbial Pathogenesis.2025; 207: 107876. CrossRef
Assessing the Diagnostic Accuracy of Soluble Urokinase Plasminogen Activator Receptor and Lipoteichoic Acid Biomarkers in Gram-Positive Bacterial Pathogen for Timely Detection and Differentiation of Colonization versus Active Infection
Mohammed Sadeq Khalife, Sawsan M. Jabbar AL-Hasnawi, May Mohammed Ali
Journal of Bacteriology and Virology.2025; 55(3): 222. CrossRef

H-NS is a Transcriptional Repressor of the CRISPR-Cas System in Acinetobacter baumannii ATCC 19606: Kyeongmin Kim, Md Maidul Islam, Seunghyeok Bang, Jeongah Kim, Chung-Young Lee, Je Chul Lee, Minsang Shin; J. Microbiol. 2024;62(11):999-1012. Published online November 11, 2024; DOI: https://doi.org/10.1007/s12275-024-00182-5

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Acinetobacter baumannii is a multidrug-resistant opportunistic pathogen primarily associated with hospital-acquired infections. The bacterium can gain multidrug resistance through several mechanisms, including horizontal gene transfer. A CRISPR-Cas system including several Cas genes could restrict the horizontal gene transfer. However, the molecular mechanism of CRISPR- Cas transcriptional regulation remains unclear. We identified a type I-F CRISPR-Cas system in A. baumannii ATCC 19606^T standard strain based on sequence analysis. We focused on the transcriptional regulation of Cas3, a key protein of the CRISPR-Cas system. We performed a DNA affinity chromatography-pulldown assay to identify transcriptional regulators of the Cas3 promoter. We identified several putative transcriptional factors, such as H-NS, integration host factor, and HU, that can bind to the promoter region of Cas3. We characterized AbH-NS using size exclusion chromatography and cross-linking experiments and demonstrated that the Cas3 promoter can be regulated by AbH-NS in a concentration-dependent manner via an in vitro transcription assay. CRISPR-Cas expression levels in wild-type and hns mutant strains in the early stationary phase were examined by qPCR and β-galactosidase assay. We found that H-NS can act as a repressor of Cas3. Our transformation efficiency results indicated that the hns mutation decreased the transformation efficiency, while the Cas3 mutation increased it. We report the existence and characterization of the CRISPR-Cas system in A. baumannii 19606^T and demonstrate that AbH-NS is a transcriptional repressor of CRISPR-Cas-related genes in A. baumannii.

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The H-NS homologues MvaT and MvaU repress CRISPR-Cas in Pseudomonas aeruginosa
Kira Céline Koonce, Jesper Juel Mauritzen, Ida Friberg Hitz, Emil Funk Vangsgaard, Elizabeth H. M. Putz, Anne Sofie Wajn, Frederik Hagelund Leth, Nina Molin Høyland-Kroghsbo
Philosophical Transactions of the Royal Society B: Biological Sciences.2025;[Epub] CrossRef
BaeR and H-NS control CRISPR-Cas-mediated immunity and virulence in Acinetobacter baumannii
Ting Yu, Jun Xie, Xinyue Huang, Jiayuan Huang, Guangyu Bao, Wenjie Yuan, Chengfeng Gao, Cuicui Liu, Jian Hu, Weixuan Yang, Guocai Li, Ryan McClure
mSystems.2025;[Epub] CrossRef

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Editor's Choice 2024