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Editor's Choice 2024
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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.
- editor_pick
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- Evolutionary Microbiology and Systematics
- Microbial Ecology and Environmental Microbiology
- Microbial Physiology and Biochemistry
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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 Genetics, Genomics
and Molecular Biology (Prokaryote)
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
- 821 View
- 25 Download
- 3 Web of Science
- 6 Crossref
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Abstract
PDF - 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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Citations
Citations to this article as recorded by
- Climate change and the immune system
Ger T. Rijkers, Zhibek Timraliyeva, Emma Mackie, Matei Lupuşoara
Expert Review of Clinical Immunology.2026; 22(1): 61. CrossRef - CRISPR/Cas9-engineered Salmonella phage displaying antimicrobial peptide LL37 for enhanced antibacterial activity
Su Jin Jo, Se Chang Park, Sang Guen Kim
International Journal of Antimicrobial Agents.2026; 67(4): 107734. CrossRef -
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
- Climate change and the immune system
- A PadR family transcriptional repressor regulates the transcription of chromate efflux transporter in Enterobacter sp. Z1
- Xueqi Huo, Zijie Zhou, Hongliang Liu, Gejiao Wang, Kaixiang Shi
- J. Microbiol. 2024;62(5):355-365. Published online April 8, 2024
- DOI: https://doi.org/10.1007/s12275-024-00117-0
- 700 View
- 11 Download
- 1 Web of Science
- 1 Crossref
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Abstract
PDF
- Chromium is a prevalent toxic heavy metal, and chromate [Cr(VI)] exhibits high mutagenicity and carcinogenicity. The presence of the Cr(VI) efflux protein ChrA has been identified in strains exhibiting resistance to Cr(VI). Nevertheless, certain strains of bacteria that are resistant to Cr(VI) lack the presence of ChrB, a known regulatory factor. Here, a PadR family transcriptional repressor, ChrN, has been identified as a regulator in the response of Enterobacter sp. Z1(CCTCC NO: M 2019147) to Cr(VI). The chrN gene is cotranscribed with the chrA gene, and the transcriptional expression of this operon is induced by Cr(VI). The binding capacity of the ChrN protein to Cr(VI) was demonstrated by both the tryptophan fluorescence assay and Ni-NTA purification assay. The interaction between ChrN and the chrAN operon promoter was validated by reporter gene assay and electrophoretic mobility shift assay. Mutation of the conserved histidine residues His14 and His50 resulted in loss of ChrN binding with the promoter of the chrAN operon. This observation implies that these residues are crucial for establishing a DNA-binding site. These findings demonstrate that ChrN functions as a transcriptional repressor, modulating the cellular response of strain Z1 to Cr(VI) exposure.
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Citations
Citations to this article as recorded by- High antimony resistance strain Enterobacter sp. Z1 mediates biomineralization of antimony trioxide
Zijie Zhou, Hongbo Yu, Gejiao Wang, Mingshun Li, Kaixiang Shi
Environment International.2025; 195: 109237. CrossRef
- High antimony resistance strain Enterobacter sp. Z1 mediates biomineralization of antimony trioxide
- 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
- 715 View
- 10 Download
- 11 Web of Science
- 13 Crossref
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Abstract
PDF
- 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.
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Citations
Citations to this article as recorded by- Metagenomic Comparison of Bat Colony Resistomes Across Anthropogenic and Pristine Habitats
Julio David Soto-López, Omar Velásquez-González, Manuel A. Barrios-Izás, Moncef Belhassen-García, Juan Luis Muñoz-Bellido, Pedro Fernández-Soto, Antonio Muro
Antibiotics.2026; 15(1): 51. CrossRef - Staphylococcal phages as agents of evolution and innovation: From gene flow to next-generation therapeutics
Ciro César Rossi, Felipe Castro Oliveira de Brito Teixeira, Giarlã Cunha da Silva, Monalessa Fábia Pereira, Marcia Giambiagi-deMarval
Genetics and Molecular Biology.2026;[Epub] CrossRef - pTJK, a rare Mammaliicoccus lentus phage with broad-host-range, antibiofilm, and synergistic interactions with antimicrobials against resistant Staphylococcaceae
Faizan Ahmad, Pedro Rocha Garcia, Vitor Emanuel Lanes Viana, Sandy de Almada Estanislau, Nohman Rasheed, Rafael Reis de Rezende, Eduardo Luís Menezes de Almeida, Poliane Alfenas Zerbini, Marisa Alves Nogueira Diaz, Monalessa Fábia Pereira, Marcia Giambiag
Archives of Microbiology.2026;[Epub] CrossRef - 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
- Metagenomic Comparison of Bat Colony Resistomes Across Anthropogenic and Pristine Habitats
- Whole-Genome Sequencing Reveals the Population Structure and Genetic Diversity of Salmonella Typhimurium ST34 and ST19 Lineages
- Zhen-Xu Zhuo, Yu-Lian Feng, Xi-Wei Zhang, Hao Liu, Fang-Yin Zeng, Xiao-Yan Li
- J. Microbiol. 2024;62(10):859-870. Published online November 4, 2024
- DOI: https://doi.org/10.1007/s12275-024-00170-9
- 560 View
- 17 Download
- 1 Web of Science
- 1 Crossref
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Abstract
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- Salmonella Typhimurium is an invasive gastrointestinal pathogen for both humans and animals. To investigate the genetic framework and diversity of S. Typhimurium, a total of 194 S. Typhimurium isolates were collected from patients in a tertiary hospital between 2020 and 2021. Antimicrobial susceptibility testing was used to confirm the resistance phenotype. Whole-genome sequencing and bioinformatics analysis were performed to determine the sequence type, phylogenetic relationships, resistance gene profiles, Salmonella pathogenicity island (SPI) and the diversity of the core and pan genome. The result showed that 57.22% of S. Typhimurium isolates were multidrug resistant and resistance of total isolates to the first-line drug ciprofloxacin was identified in 60.82%. The population structure of S. Typhimurium was categorized into three lineages: ST19 (20.10%, 39/194), ST34-1 (47.42%, 92/194) and ST34-2 (40.65%, 63/194), with the population size exhibiting increasing trends. All lineages harbored variety of fimbrial operons, prophages, SPIs and effectors that contributed to the virulence and long-term infections of S. Typhimurium. Importantly, ST34-1 lineage might potentially be more invasive due to the possession of SPI1-effector gene sopE which was essential for the proliferation, internalization and intracellular presence of S. Typhimurium in hosts. Multiple antimicrobial resistance genes were characteristically distributed across three lineages, especially carbapenem genes only detected in ST34-1&2 lineages. The distinct functional categories of pan genome among three lineages were observed in metabolism, signaling and gene information processing. This study provides a theoretical foundation for the evolved adaptation and genetic diversity of S. Typhimurium ST19 and ST34, among which ST34 lineages with multidrug resistance and potential hypervirulence need to pay more attention to epidemiological surveillance.
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Citations
Citations to this article as recorded by- Genomic Evidence for the Rise of Salmonella Typhimurium ST34 with Increased Plasmid-Mediated Resistance in the Thailand Pork Chain
Hongmei Liu, Ning Wang, Sunpetch Angkititrakul, Wengui Li, Zhongyang Luo, Mingpeng Hou, Yi Wu, Yubo Shi, Yuelin Wang, Fengyun Li, Yaowen Liu, Xin Wu, Fanan Suksawat
Pathogens.2025; 14(12): 1190. CrossRef
- Genomic Evidence for the Rise of Salmonella Typhimurium ST34 with Increased Plasmid-Mediated Resistance in the Thailand Pork Chain
Review
- Extensive Genomic Rearrangement of Catalase-Less Cyanobloom-Forming Microcystis aeruginosa in Freshwater Ecosystems
- Minkyung Kim, Jaejoon Jung, Wonjae Kim, Yerim Park, Che Ok Jeon, Woojun Park
- J. Microbiol. 2024;62(11):933-950. Published online October 8, 2024
- DOI: https://doi.org/10.1007/s12275-024-00172-7
- 670 View
- 14 Download
- 5 Web of Science
- 4 Crossref
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Abstract
PDF
- Many of the world's freshwater ecosystems suffer from cyanobacteria-mediated blooms and their toxins. However, a mechanistic understanding of why and how Microcystis aeruginosa dominates over other freshwater cyanobacteria during warmer summers is lacking. This paper utilizes comparative genomics with other cyanobacteria and literature reviews to predict the gene functions and genomic architectures of M. aeruginosa based on complete genomes. The primary aim is to understand this species' survival and competitive strategies in warmer freshwater environments. M. aeruginosa strains exhibiting a high proportion of insertion sequences (~ 11%) possess genomic structures with low synteny across different strains. This indicates the occurrence of extensive genomic rearrangements and the presence of many possible diverse genotypes that result in greater population heterogeneities than those in other cyanobacteria in order to increase survivability during rapidly changing and threatening environmental challenges. Catalase-less M. aeruginosa strains are even vulnerable to low light intensity in freshwater environments with strong ultraviolet radiation. However, they can continuously grow with the help of various defense genes (e.g., egtBD, cruA, and mysABCD) and associated bacteria. The strong defense strategies against biological threats (e.g., antagonistic bacteria, protozoa, and cyanophages) are attributed to dense exopolysaccharide (EPS)-mediated aggregate formation with efficient buoyancy and the secondary metabolites of M. aeruginosa cells. Our review with extensive genome analysis suggests that the ecological vulnerability of M. aeruginosa cells can be overcome by diverse genotypes, secondary defense metabolites, reinforced EPS, and associated bacteria.
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Citations
Citations to this article as recorded by- Rapid and selective disruption of photosystem I in toxic cyanobacteria protects aquatic ecosystem health
Wonjae Kim, Yerim Park, Yongjun Son, Nayeon Yoo, Eui-Hwan Chung, Woojun Park
Journal of Hazardous Materials.2026; 501: 140736. CrossRef - Cyanophage Infections in a Sponge Intracellular Cyanobacterial Symbiont
Tzipora Peretz, Esther Cattan‐Tsaushu, Chiara Conti, Benyamin Rosental, Laura Steindler, Sarit Avrani
Environmental Microbiology.2025;[Epub] CrossRef - Public goods-mediated bacterial interplay in aquatic ecosystems
Yerim Park, Wonjae Kim, Jihye Bae, Woojun Park
Water Research.2025; 287: 124310. CrossRef - Horizontal Gene Transfer and Recombination in Cyanobacteriota
Devaki Bhaya, Gabriel Birzu, Eduardo P.C. Rocha
Annual Review of Microbiology .2025; 79(1): 685. CrossRef
- Rapid and selective disruption of photosystem I in toxic cyanobacteria protects aquatic ecosystem health
Journal Articles
- 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
- 657 View
- 10 Download
- 2 Web of Science
- 2 Crossref
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Abstract
PDF
- 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 19606T 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 19606T and demonstrate that AbH-NS is a transcriptional repressor of CRISPR-Cas-related genes in A. baumannii.
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Citations
Citations to this article as recorded by-
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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The H-NS homologues MvaT and MvaU repress CRISPR-Cas in
Pseudomonas aeruginosa
- The Salmonella enterica EnvE is an Outer Membrane Lipoprotein and Its Gene Expression Leads to Transcriptional Repression of the Virulence Gene msgA
- Sinyeon Kim, Yong Heon Lee
- J. Microbiol. 2024;62(11):1013-1022. Published online November 15, 2024
- DOI: https://doi.org/10.1007/s12275-024-00183-4
- 472 View
- 14 Download
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Abstract
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- The envE gene of Salmonella enterica serovar Typhimurium is encoded within Salmonella Pathogenicity Island-11 (SPI-11) and is located immediately upstream of the virulence gene msgA (macrophage survival gene A) in the same transcriptional orientation. To date, the characteristics and roles of envE remain largely unexplored. In this study, we show that EnvE, a predicted lipoprotein, is localized on the outer membrane using sucrose gradient ultracentrifugation. Under oxidative stress conditions, envE transcription is suppressed, while msgA transcription is induced, indicating an inverse correlation between the mRNA levels of the two neighboring genes. Importantly, inactivation of envE leads to constitutive transcription of msgA regardless of the presence of oxidative stress. Moreover, trans-complementation of the envE mutant with a plasmid-borne envE fails to prevent the induction of msgA transcription, suggesting that envE functions as a cis-regulatory element rather than a trans-acting factor. We further show that both inactivation and complementation of envE confer wild-type levels of resistance to oxidative stress by ensuring the expression of msgA. Our data suggest that the S. enterica envE gene encodes an outer membrane lipoprotein, and its transcription represses msgA expression in a cis-acting manner, probably by transcriptional interference, although the exact molecular details are yet unclear.
- 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
- 617 View
- 13 Download
- 1 Web of Science
- 1 Crossref
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Abstract
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- 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.
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Citations
Citations to this article as recorded by- Bacteriophage therapy to combat MDR non-fermenting Gram-negative bacteria causing nosocomial infections: recent progress and challenges
Sunil Kumar, Razique Anwer, Anil Sharma, Mukesh Yadav, Nirmala Sehrawat
Naunyn-Schmiedeberg's Archives of Pharmacology.2025; 398(11): 15037. CrossRef
- Bacteriophage therapy to combat MDR non-fermenting Gram-negative bacteria causing nosocomial infections: recent progress and challenges
- An Optimized Method for Reconstruction of Transcriptional Regulatory Networks in Bacteria Using ChIP-exo and RNA-seq Datasets
- Minchang Jang, Joon Young Park, Gayeon Lee, Donghyuk Kim
- J. Microbiol. 2024;62(12):1075-1088. Published online November 11, 2024
- DOI: https://doi.org/10.1007/s12275-024-00181-6
- 710 View
- 9 Download
- 1 Web of Science
- 1 Crossref
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Abstract
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- Transcriptional regulatory networks (TRNs) in bacteria are crucial for elucidating the mechanisms that regulate gene expression and cellular responses to environmental stimuli. These networks delineate the interactions between transcription factors (TFs) and their target genes, thereby uncovering the regulatory processes that modulate gene expression under varying environmental conditions. Analyzing TRNs offers valuable insights into bacterial adaptation, stress responses, and metabolic optimization from an evolutionary standpoint. Additionally, understanding TRNs can drive the development of novel antimicrobial therapies and the engineering of microbial strains for biofuel and bioproduct production. This protocol integrates advanced data analysis pipelines, including ChEAP, DEOCSU, and DESeq2, to analyze omics datasets that encompass genome-wide TF binding sites and transcriptome profiles derived from ChIP-exo and RNA-seq experiments. This approach minimizes both the time required and the risk of bias, making it accessible to non-expert users. Key steps in the protocol include preprocessing and peak calling from ChIP-exo data, differential expression analysis of RNA-seq data, and motif and regulon analysis. This method offers a comprehensive and efficient framework for TRN reconstruction across various bacterial strains, enhancing both the accuracy and reliability of the analysis while providing valuable insights for basic and applied research.
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Citations
Citations to this article as recorded by- ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens
Joon Young Park, Minchang Jang, Eunna Choi, Sang-Mok Lee, Ina Bang, Jihoon Woo, Seonggyu Kim, Eun-Jin Lee, Donghyuk Kim
Nucleic Acids Research.2025;[Epub] CrossRef
- ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens
- 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
- 597 View
- 15 Download
- 4 Web of Science
- 4 Crossref
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Abstract
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- 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.
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Citations
Citations to this article as recorded by- A DHH/DHHA1 family 3′-phosphoadenosine 5′-monophosphate (pAp) phosphoesterase Vp2835 is essential for regulating motility, biofilm formation and type III secretion system 1 in Vibrio parahaemolyticus
Chenzhi Zhuhuang, Chenxi Wang, Yu Sun, Min Chu, Menghua Yang, Guangzhi Xu
Food Bioscience.2025; 69: 106836. CrossRef - Chlorogenic Acid Targets Cell Integrity and Virulence to Combat Vibrio parahaemolyticus
Huan Liu, Jie Zhao, Yile Shi, Juanjuan Cao, Yanni Zhao
Foods.2025; 14(19): 3416. CrossRef -
CalR is an activator of biofilm formation in
Vibrio parahaemolyticus
Jingyang Chang, Yining Zhou, Miaomiao Zhang, Xue Li, Nan Zhang, Xi Luo, Bin Ni, Renfei Lu, Yiquan Zhang, Sophie Roussel
Applied and Environmental Microbiology.2025;[Epub] CrossRef - LtrA is critical for biofilm formation and colonization of Vibrio parahaemolyticus on food-related surfaces
Shuhui Xiong, Nan Zhang, Hui Sun, Miaomiao Zhang, Xue Li, Xi Luo, Yiquan Zhang, Renfei Lu
International Journal of Food Microbiology.2025; 441: 111327. CrossRef
- A DHH/DHHA1 family 3′-phosphoadenosine 5′-monophosphate (pAp) phosphoesterase Vp2835 is essential for regulating motility, biofilm formation and type III secretion system 1 in Vibrio parahaemolyticus
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