Journal of Microbiology

Journal Article

Environmental Adaptation of Psychrophilic Bacteria Subtercola spp. Isolated from Various Cryospheric Habitats: Hanbyul Lee , Yong-Joon Cho , Ahnna Cho , Ok-Sun Kim; J. Microbiol. 2023;61(7):663-672. Published online August 24, 2023; DOI: https://doi.org/10.1007/s12275-023-00068-y

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Abstract: Subtercola boreus K300T is a novel psychrophilic strain that was isolated from permanently cold groundwater in Finland and has also been found in several places in Antarctica including lake, soil, and rocks. We performed genomic and transcriptomic analyses of 5 strains from Antarctica and a type strain to understand their adaptation to different environments. Interestingly, the isolates from rocks showed a low growth rate and smaller genome size than strains from the other isolation sources (lake, soil, and groundwater). Based on these habitat-dependent characteristics, the strains could be classified into two ecotypes, which showed differences in energy production, signal transduction, and transcription in the clusters of orthologous groups of proteins (COGs) functional category. In addition, expression pattern changes revealed differences in metabolic processes, including uric acid metabolism, DNA repair, major facilitator superfamily (MFS) transporters, and xylose degradation, depending on the nutritional status of their habitats. These findings provide crucial insights into the environmental adaptation of bacteria, highlighting genetic diversity and regulatory mechanisms that enable them to thrive in the cryosphere.

Review

Envelope‑Stress Sensing Mechanism of Rcs and Cpx Signaling Pathways in Gram‑Negative Bacteria: Seung-Hyun Cho , Kilian Dekoninck , Jean-Francois Collet; J. Microbiol. 2023;61(3):317-329. Published online March 9, 2023; DOI: https://doi.org/10.1007/s12275-023-00030-y

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The global public health burden of bacterial antimicrobial resistance (AMR) is intensified by Gram-negative bacteria, which have an additional membrane, the outer membrane (OM), outside of the peptidoglycan (PG) cell wall. Bacterial twocomponent systems (TCSs) aid in maintaining envelope integrity through a phosphorylation cascade by controlling gene expression through sensor kinases and response regulators. In Escherichia coli, the major TCSs defending cells from envelope stress and adaptation are Rcs and Cpx, which are aided by OM lipoproteins RcsF and NlpE as sensors, respectively. In this review, we focus on these two OM sensors. β-Barrel assembly machinery (BAM) inserts transmembrane OM proteins (OMPs) into the OM. BAM co-assembles RcsF, the Rcs sensor, with OMPs, forming the RcsF-OMP complex. Researchers have presented two models for stress sensing in the Rcs pathway. The first model suggests that LPS perturbation stress disassembles the RcsF-OMP complex, freeing RcsF to activate Rcs. The second model proposes that BAM cannot assemble RcsF into OMPs when the OM or PG is under specific stresses, and thus, the unassembled RcsF activates Rcs. These two models may not be mutually exclusive. Here, we evaluate these two models critically in order to elucidate the stress sensing mechanism. NlpE, the Cpx sensor, has an N-terminal (NTD) and a C-terminal domain (CTD). A defect in lipoprotein trafficking
results
in NlpE retention in the inner membrane, provoking the Cpx response. Signaling requires the NlpE NTD, but not the NlpE CTD; however, OM-anchored NlpE senses adherence to a hydrophobic surface, with the NlpE CTD playing a key role in this function.

Citations

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Metal-based antimicrobial agents in wound Dressings: Infection management and the challenge of antibiotic resistance
Haoyang Peng, Deqiao Dong, Shiquan Feng, Yueping Guo, Jiaqi Yu, Changran Gan, Xue Hu, Zhenmao Qin, Yan Liu, Yanan Gao
Chemical Engineering Journal.2025; 507: 160726. CrossRef
Transcriptome reveals the role of the htpG gene in mediating antibiotic resistance through cell envelope modulation in Vibrio mimicus SCCF01
Zhenyang Qin, Kun Peng, Yang Feng, Yilin Wang, Bowen Huang, Ziqi Tian, Ping Ouyang, Xiaoli Huang, Defang Chen, Weimin Lai, Yi Geng
Frontiers in Microbiology.2024;[Epub] CrossRef
Rcs signal transduction system in Escherichia coli: Composition, related functions, regulatory mechanism, and applications
Zeyu Li, Yingying Zhu, Wenli Zhang, Wanmeng Mu
Microbiological Research.2024; 285: 127783. CrossRef
Identification of genes used by Escherichia coli to mitigate climatic stress conditions
Styliani Roufou, Sholeem Griffin, Lydia Katsini, Monika Polańska, Jan F.M. Van Impe, Panagiotis Alexiou, Vasilis P. Valdramidis
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International Journal of Molecular Sciences.2024; 25(18): 10118. CrossRef
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Tong Jin, Xiangjun Zhan, Liuxin Pang, Bo Peng, Xinpeng Zhang, Wenxiu Zhu, Baowei Yang, Xiaodong Xia
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Breaking Barriers: Exploiting Envelope Biogenesis and Stress Responses to Develop Novel Antimicrobial Strategies in Gram-Negative Bacteria
Renu Bisht, Pierre D. Charlesworth, Paola Sperandeo, Alessandra Polissi
Pathogens.2024; 13(10): 889. CrossRef
The protective role of potassium in the adaptation of Pseudomonas protegens SN15-2 to hyperosmotic stress
Jian Wang, Yaping Wang, Shouquan Lu, Haibo Lou, XiaoBing Wang, Wei Wang
Microbiological Research.2024; 289: 127887. CrossRef
Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms’ Complex Regulation
Jin-Won Lee
Journal of Microbiology.2023; 61(3): 273. CrossRef
Physiological and Transcriptomic Analyses of Escherichia coli Serotype O157:H7 in Response to Rhamnolipid Treatment
Shuo Yang, Lan Ma, Xiaoqing Xu, Qing Peng, Huiying Zhong, Yuxin Gong, Linbo Shi, Mengxin He, Bo Shi, Yu Qiao
Microorganisms.2023; 11(8): 2112. CrossRef

Journal Articles

Simultaneous detection of Salmonella spp., Pseudomonas aeruginosa, Bacillus cereus, and Escherichia coli O157:H7 in environmental water using PMA combined with mPCR: Guoyang Xie , Shuang Yu , Wen Li , Dan Mu , Zoraida P. Aguilar , Hengyi Xu; J. Microbiol. 2020;58(8):668-674. Published online June 25, 2020; DOI: https://doi.org/10.1007/s12275-020-0084-6

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Abstract

A multiplex polymerase chain reaction (mPCR) with propidium monoazide (PMA) and internal amplification control (IAC) for the simultaneous detection of waterborne pathogens Salmonella spp., Pseudomonas aeruginosa, Bacillus cereus, and Escherichia coli O157:H7, was developed. This PMA-IAC-mPCR assay used four new specific primers based on the genes for invA, ecfX, cesB, and fliC, respectively. A 16S rRNA primer was chosen for IAC to eliminate false negative
results
. The photosensitive dye, propidium monoazide (PMA) was used to exclude signals from dead bacteria that could lead to false positive results. In pure culture, the limits of detection (LOD) were 101 CFU/ml for P. aeruginosa, 102 CFU/ml for both Salmonella spp. and E. coli O157:H7, and 103 CFU/ml for B. cereus, respectively. In addition, with a 6–8 h enrichment of all four bacteria that were combined in a mixture that was spiked in water sample matrix, the LOD was 3 CFU/ml for Salmonella spp., 7 CFU/ml for E. coli O157:H7, 10 CFU/ml for B. cereus and 2 CFU/ml for P. aeruginosa. This PMA-IAC-mPCR assay holds potential for application in the multiplex assay of waterborne pathogens.

Citations

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Rapid, sensitive, and user-friendly detection of Pseudomonas aeruginosa using the RPA/CRISPR/Cas12a system
Wenjing Zhang, Hai Qu, Xin Wu, Jingjing Shi, Xinling Wang
BMC Infectious Diseases.2024;[Epub] CrossRef
Review of Detection Limits for Various Techniques for Bacterial Detection in Food Samples
Xinyi Zhao, Abhijnan Bhat, Christine O’Connor, James Curtin, Baljit Singh, Furong Tian
Nanomaterials.2024; 14(10): 855. CrossRef
The dual nucleic acid amplification with dynamic light scattering strategy for ultrasensitive detection of Salmonella in milk
Qian Xu, Guoyang Xie, Qiang Shi, Ju Liu, Baoqing Zhou, Ping Tong, Zoraida P. Aguilar, Hengyi Xu
Microchemical Journal.2023; 184: 108143. CrossRef
An Assay Combining Droplet Digital PCR With Propidium Monoazide Treatment for the Accurate Detection of Live Cells of Vibrio vulnificus in Plasma Samples
Ling Hu, Yidong Fu, Shun Zhang, Zhilei Pan, Jiang Xia, Peng Zhu, Jing Guo
Frontiers in Microbiology.2022;[Epub] CrossRef
Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality
Lisa Paruch
International Journal of Environmental Research and Public Health.2022; 19(9): 5128. CrossRef
Rapid-Response Magnetic Enrichment Strategy for Significantly Improving Sensitivity of Multiplex PCR Analysis of Pathogenic Listeria Species
Fangbin Xiao, Xuekun Bai, Keyu Wang, Yifan Sun, Hengyi Xu
Applied Sciences.2022; 12(13): 6415. CrossRef
Real-time and visual detection of viableSalmonellain milk by a competitive annealing mediated isothermal amplification (CAMP) combined with propidium monoazide (PMA)
Xu Chen, Wei Li, Yue Ma
Analytical Methods.2022; 14(38): 3773. CrossRef
Hybrid RCA-DLS assay combined with aPCR for sensitive Salmonella enteritidis detection
Guoyang Xie, Zhongxu Zhan, Yu Ye, Baoqing Zhou, Ping Tong, Zoraida P. Aguilar, Hengyi Xu
Analytical Biochemistry.2022; 646: 114647. CrossRef
How to Evaluate Non-Growing Cells—Current Strategies for Determining Antimicrobial Resistance of VBNC Bacteria
Susanne Fleischmann, Christian Robben, Thomas Alter, Peter Rossmanith, Patrick Mester
Antibiotics.2021; 10(2): 115. CrossRef
Development of a simple, rapid multiplex PCR tool kit by using the 16S rRNA gene for the identification of faecal and non-faecal coliforms in drinking water
A. Shiva Shanker, N. Rajesh, Pavan Kumar Pindi
Water Supply.2021; 21(7): 3319. CrossRef

Development of a neutralization assay based on the pseudotyped chikungunya virus of a Korean isolate: Woo-Chang Chung , Kwang Yeon Hwang , Suk-Jo Kang , Jae-Ouk Kim , Moon Jung Song; J. Microbiol. 2020;58(1):46-53. Published online November 25, 2019; DOI: https://doi.org/10.1007/s12275-020-9384-0

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Abstract

The Chikungunya virus (CHIKV) belongs to the Alphavirus genus of Togaviridae family and contains a positive-sense single stranded RNA genome. Infection by this virus mainly causes sudden high fever, rashes, headache, and severe joint pain that can last for several months or years. CHIKV, a mosquito- borne arbovirus, is considered a re-emerging pathogen that has become one of the most pressing global health concerns due to a rapid increase in epidemics. Because handling of CHIKV is restricted to Biosafety Level 3 (BSL-3) facilities, the evaluation of prophylactic vaccines or antivirals has been substantially hampered. In this study, we first identified the whole structural polyprotein sequence of a CHIKV strain isolated in South Korea (KNIH/2009/77). Phylogenetic analysis showed that this sequence clustered within the East/ Central/South African CHIKV genotype. Using this sequence information, we constructed a CHIKV-pseudotyped lentivirus expressing the structural polyprotein of the Korean CHIKV isolate (CHIKVpseudo) and dual reporter genes of green fluorescence protein and luciferase. We then developed a pseudovirus-based neutralization assay (PBNA) using CHIKVpseudo. Results from this assay compared to those from the conventional plaque reduction neutralization test showed that our PBNA was a reliable and rapid method to evaluate the efficacy of neutralizing antibodies. More importantly, the neutralizing activities of human sera from CHIKVinfected individuals were quantitated by PBNA using CHIKVpseudo. Taken together, these results suggest that our PBNA for CHIKV may serve as a useful and safe method for testing the neutralizing activity of antibodies against CHIKV in BSL-2 facilities.

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Sofiia N. Rizatdinova, Alina E. Ershova, Irina V. Astrakhantseva
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Facile quantitative diagnostic testing for neutralizing antibodies against Chikungunya virus
Hui-Chung Lin, Shu-Fen Chang, Chien-Ling Su, Huai-Chin Hu, Der-Jiang Chiao, Yu-Lin Hsu, Hsuan-ying Lu, Chang-Chi Lin, Pei-Yun Shu, Szu-Cheng Kuo
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Development of a Novel Chikungunya Virus-Like Replicon Particle for Rapid Quantification and Screening of Neutralizing Antibodies and Antivirals
Hui-Chung Lin, Der-Jiang Chiao, Pei-Yun Shu, Hui-Tsu Lin, Chia-Chu Hsiung, Chang-Chi Lin, Szu-Cheng Kuo, Juan E. Ludert
Microbiology Spectrum.2023;[Epub] CrossRef
Preparation and application of chikungunya pseudovirus containing double reporter genes
Chunyan Su, Kaiyun Ding, Jingwen Xu, Jianchao Wu, Jiansheng Liu, Jiayuan Shen, Hongning Zhou, Hongqi Liu
Scientific Reports.2022;[Epub] CrossRef
Prevalence of Malaria and Chikungunya Co-Infection in Febrile Patients: A Systematic Review and Meta-Analysis
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Isolation and identification of infectious pancreatic necrosis virus form rainbow trout cultured in Korea: Lee, Jin Hee , Heo, Gang Joon , Lee, Chan Hee; J. Microbiol. 1996;34(2):124-130.

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Abstract: A survey was conducted to determine the prevalence of infectious pancreatic necrosis virus (IPNV) on fish farms in Korea and the epidemiology of IPNV infection in the farmed rainbow trout. In total, 43 pools of rainbow trout with apparent signs of viral infection from five provinces were obtained and analyzed. Evident cytopathic effects, including karyopycnosis and cell destruction, were observed in CHSE (chinook samlmon embyro)-214 cells infected with the virus isolates. Of these, ten viral isolates were assumed to be IPNV based on biophysical properties. RNA analysis revealed that the isolates contained two-segmented RNA genomes, further indicating that the viral isolates are IPNV. Antigenic comparison of the IPNV isolates identified three distinct serological groups separable by the cross-neutralization test. Of the ten IPNV isolates, six could be classified as strain DRT, two as strain Ab, and two as strain VR299. We were not able to isolate new strain of IPNV or any isolate serologically similar to the standard strain Sp.

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