Journal of Microbiology

Journal Articles

Different Adaption Strategies of Abundant and Rare Microbial Communities in Sediment and Water of East Dongting Lake: Yabing Gu, Junsheng Li, Zhenghua Liu, Min Zhang, Zhaoyue Yang, Huaqun Yin, Liyuan Chai, Delong Meng, Nengwen Xiao; J. Microbiol. 2024;62(10):829-843. Published online October 22, 2024; DOI: https://doi.org/10.1007/s12275-024-00171-8

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Abstract: The dynamics of aquatic microbes is of great importance for comprehending the acclimatisation and evolution of microorganisms in lake ecology. However, little is known about the adaption strategies of microbial communities in East Dongting Lake, which had special and complexity geographical characteristics. A semi-enclosed lake area (A) and a waterway connected to Yangtze River (B) both existed in the lake zone. Here, we investigated bacterial and fungal community diversity, community network and community assembly processes in sediment and water. The results indicated that the proportion of OTU numbers and their relative abundance for rare and abundant taxa were different obviously between sediment and water, but not between bacteria and fungi. However, abundant subcommunities dominated the shifts of bacterial community diversity and structure in A region, while rare subcommunities for fungal community diversity. Compared to fungal community, bacterial network was more compact and more key stones were identified as rare taxa. In addition, stochastic processes (dispersal limitation) drove the community assembly of abundant and rare subcommunities, but the effects of deterministic processes (including variable and heterogeneous selections) affected more on rare rather than abundant taxa. Partial Mantel test further indicated that the effect of environmental factors was a stronger force in shaping abundant bacterial subcommunities (TOC, NH₄⁺-N, TN, and ORP) and rare fungal subcommunities (ORP). Environmental factors explained more of the variation in bacterial community structure than that in fungal community structure, although they had additional effects on fungal community diversity and community assembly. Moreover, bacterial community affected the fungal community as a biotic factor in water. This research provided new insights into better understanding of microbial communities in the complex environment of the East Dongting Lake.

Environmental Adaptability and Roles in Ammonia Oxidation of Aerobic Ammonia-Oxidizing Microorganisms in the Surface Sediments of East China Sea: Wenhui Li, Yu Zhen, Yuhong Yang, Daling Wang, Hui He; J. Microbiol. 2024;62(10):845-858. Published online August 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00166-5

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This study investigated the community characteristics and environmental influencing factors of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the surface sediments of the East China Sea. The research found no consistent pattern in the richness and diversity of AOA and AOB with respect to the distance from the shore, indicating a complex interplay of factors. The expression levels of AOA amoA gene and AOB amoA gene in the surface sediments of the East China Sea ranged from 4.49 × 10² to 2.17 × 10⁶ copies per gram of sediment and from 6.6 × 10¹ to 7.65 × 10⁴ copies per gram of sediment, respectively. Salinity (31.77 to 34.53 PSU) and nitrate concentration (1.51 to 10.12 μmol/L) were identified as key environmental factors significantly affecting the AOA community, while salinity and temperature (13.71 to 19.50 °C) were crucial for the AOB community. The study also found that AOA, dominated by the Nitrosopumilaceae family, exhibited higher gene expression levels than AOB, suggesting a more significant role in ammonia oxidation. The expression of AOB was sensitive to multiple environmental factors, indicating a responsive role in nitrogen cycles and ecosystem health. The findings contribute to a better understanding of the biogeochemical processes and ecological roles of ammonia-oxidizing microorganisms in marine sediments.

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Metabolism diversification of ammonia-oxidizing archaea and bacteria under different precipitation gradients and land legacies
Soumyadev Sarkar, Anna Kazarina, Paige M. Hansen, Kaitlyn Ward, Christopher Hargreaves, Nicholas Reese, Qinghong Ran, Willow Kessler, Ligia F.T. de Souza, Terry D. Loecke, Marcos V.M. Sarto, Charles W. Rice, Lydia H. Zeglin, Benjamin A. Sikes, Sonny T.M.
Applied Soil Ecology.2025; 206: 105831. CrossRef

Review

The Role of Extracellular Vesicles in Pandemic Viral Infections: Woosung Shim, Anjae Lee, Jung-Hyun Lee; J. Microbiol. 2024;62(6):419-427. Published online June 25, 2024; DOI: https://doi.org/10.1007/s12275-024-00144-x

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Abstract

Extracellular vesicles (EVs), of diverse origin and content, are membranous structures secreted by a broad range of cell types. Recent advances in molecular biology have highlighted the pivotal role of EVs in mediating intercellular communication, facilitated by their ability to transport a diverse range of biomolecules, including proteins, lipids, DNA, RNA and metabolites. A striking feature of EVs is their ability to exert dual effects during viral infections, involving both proviral and antiviral effects. This review explores the dual roles of EVs, particularly in the context of pandemic viruses such as HIV-1 and SARS-CoV-2. On the one hand, EVs can enhance viral replication and exacerbate pathogenesis by transferring viral components to susceptible cells. On the other hand, they have intrinsic antiviral properties, including activation of immune responses and direct inhibition of viral infection. By exploring these contrasting functions, our review emphasizes the complexity of EV-mediated interactions in viral pathogenesis and highlights their potential as targets for therapeutic intervention. The insights obtained from investigating EVs in the context of HIV-1 and SARS-CoV-2 provide a deeper understanding of viral mechanisms and pathologies, and offer a new perspective on managing and mitigating the impact of these global health challenges.

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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 Article

Antiviral Activity Against SARS‑CoV‑2 Variants Using in Silico and in Vitro Approaches: Hee-Jung Lee , Hanul Choi , Aleksandra Nowakowska , Lin-Woo Kang , Minjee Kim , Young Bong Kim; J. Microbiol. 2023;61(7):703-711. Published online June 26, 2023; DOI: https://doi.org/10.1007/s12275-023-00062-4

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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emergence in 2019 led to global health crises and the persistent risk of viral mutations. To combat SARS-CoV-2 variants, researchers have explored new approaches to identifying potential targets for coronaviruses. This study aimed to identify SARS-CoV-2 inhibitors using drug repurposing. In silico studies and network pharmacology were conducted to validate targets and coronavirus-associated diseases to select potential candidates, and in vitro assays were performed to evaluate the antiviral effects of the candidate drugs to elucidate the mechanisms of the viruses at the molecular level and determine the effective antiviral drugs for them. Plaque and cytopathic effect reduction were evaluated, and real-time quantitative reverse transcription was used to evaluate the antiviral activity of the candidate drugs against SARS-CoV-2 variants in vitro. Finally, a comparison was made between the molecular docking binding affinities of fenofibrate and remdesivir (positive control) to conventional and identified targets validated from protein–protein interaction (PPI). Seven candidate drugs were obtained based on the biological targets of the coronavirus, and potential targets were identified by constructing complex disease targets and PPI networks. Among the candidates, fenofibrate exhibited the strongest inhibition effect 1 h after Vero E6 cell infection with SARS-CoV-2 variants. This study identified potential targets for coronavirus disease (COVID-19) and SARS-CoV-2 and suggested fenofibrate as a potential therapy for COVID-19.

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Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant
Tae-Hun Kim, Sojung Bae, Sunggeun Goo, Jinjong Myoung
Journal of Microbiology and Biotechnology.2023; 33(12): 1587. CrossRef

Review

Manganese Transporter Proteins in Salmonella enterica serovar Typhimurium: Nakyeong Ha , Eun-Jin Lee; J. Microbiol. 2023;61(3):289-296. Published online March 2, 2023; DOI: https://doi.org/10.1007/s12275-023-00027-7

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Abstract

The metal cofactors are essential for the function of many enzymes. The host restricts the metal acquisition of pathogens for their immunity and the pathogens have evolved many ways to obtain metal ions for their survival and growth. Salmonella enterica serovar Typhimurium also needs several metal cofactors for its survival, and manganese has been found to contribute to Salmonella pathogenesis. Manganese helps Salmonella withstand oxidative and nitrosative stresses. In addition, manganese affects glycolysis and the reductive TCA, which leads to the inhibition of energetic and biosynthetic metabolism. Therefore, manganese homeostasis is crucial for full virulence of Salmonella. Here, we summarize the current information about three importers and two exporters of manganese that have been identified in Salmonella. MntH, SitABCD, and ZupT have been shown to participate in manganese uptake. mntH and sitABCD are upregulated by low manganese concentration, oxidative stress, and host NRAMP1 level. mntH also contains a Mn2+- dependent riboswitch in its 5′ UTR. Regulation of zupT expression requires further investigation. MntP and YiiP have been identified as manganese efflux proteins. mntP is transcr!ptionally activated by MntR at high manganese levels and repressed its activity by MntS at low manganese levels. Regulation of yiiP requires further analysis, but it has been shown that yiiP expression is not dependent on MntS. Besides these five transporters, there might be additional transporters that need to be identified.

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Functional characterization of a TerC family protein of Riemerella anatipestifer in manganese detoxification and virulence
Qinyuan Chen, Fang Guo, Li Huang, Mengying Wang, Chunfeng Shi, Shutong Zhang, Yizhou Yao, Mingshu Wang, Dekang Zhu, Renyong Jia, Shun Chen, Xinxin Zhao, Qiao Yang, Ying Wu, Shaqiu Zhang, Bin Tian, Juan Huang, Xumin Ou, Qun Gao, Di Sun, Ling Zhang, Yanling
Applied and Environmental Microbiology.2024;[Epub] CrossRef
NO enhances the adaptability to high-salt environments by regulating osmotic balance, antioxidant defense, and ion homeostasis in eelgrass based on transcriptome and metabolome analysis
Xianyan Wang, Tongtong Wang, Pei Yu, Yuchun Li, Xinfang Lv
Frontiers in Plant Science.2024;[Epub] CrossRef
High-throughput fitness experiments reveal specific vulnerabilities of human-adapted Salmonella during stress and infection
Benjamin X. Wang, Dmitry Leshchiner, Lijuan Luo, Miles Tuncel, Karsten Hokamp, Jay C. D. Hinton, Denise M. Monack
Nature Genetics.2024; 56(6): 1288. CrossRef
Biological characteristics of manganese transporter MntP in Klebsiella pneumoniae
Wei Peng, Yafei Xu, Yilin Yin, Jichen Xie, Renhui Ma, Guoyuan Song, Zhiqiang Zhang, Qiuhang Quan, Qinggen Jiang, Moran Li, Bei Li, Michael David Leslie Johnson
mSphere.2024;[Epub] CrossRef
Exploring resource competition by protective lactic acid bacteria cultures to control Salmonella in food: an Achilles’ heel to target?
Ludovico Screpanti, Nathalie Desmasures, Margot Schlusselhuber
Critical Reviews in Food Science and Nutrition.2024; : 1. CrossRef
Substrate-Induced Structural Dynamics and Evolutionary Linkage of Siderophore-Iron ABC Transporters of Mycobacterium tuberculosis
Aisha Farhana, Abdullah Alsrhani, Hasan Ejaz, Muharib Alruwaili, Ayman A. M. Alameen, Emad Manni, Zafar Rasheed, Yusuf Saleem Khan
Medicina.2024; 60(11): 1891. CrossRef
Structures and coordination chemistry of transporters involved in manganese and iron homeostasis
Shamayeeta Ray, Rachelle Gaudet
Biochemical Society Transactions.2023; 51(3): 897. 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

Journal Articles

Transcript-specific selective translation by specialized ribosomes bearing genome-encoded heterogeneous rRNAs in V. vulnificus CMCP6: Younkyung Choi , Minju Joo , Wooseok Song , Minho Lee , Hana Hyeon , Hyun-Lee Kim , Ji-Hyun Yeom , Kangseok Lee , Eunkyoung Shin; J. Microbiol. 2022;60(12):1162-1167. Published online November 24, 2022; DOI: https://doi.org/10.1007/s12275-022-2437-9

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Abstract

Ribosomes composed of genome-encoded heterogeneous rRNAs are implicated in the rapid adaptation of bacterial cells to environmental changes. A previous study showed that ribosomes bearing the most heterogeneous rRNAs expressed from the rrnI operon (I-ribosomes) are implicated in the preferential translation of a subset of mRNAs, including hspA and tpiA, in Vibrio vulnificus CMCP6. In this study, we show that HspA nascent peptides were predominantly bound to I-ribosomes. Specifically, I-ribosomes were enriched more than two-fold in ribosomes that were pulled down by immunoprecipitation of HspA peptides compared with the proportion of I-ribosomes in crude ribosomes and ribosomes pulled down by immunoprecipitation of RNA polymerase subunit ß peptides in the wild-type (WT) and rrnI-completed strains. Other methods that utilized the incorporation of an affinity tag in 23S rRNA or chimeric rRNA tethering 16S and 23S rRNAs, which generated specialized functional ribosomes in Escherichia coli, did not result in functional I-ribosomes in V. vulnificus CMCP6. This study provides direct evidence of the preferential translation of hspA mRNA by I-ribosomes.

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Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species
Younkyung Choi, Eunkyoung Shin, Minho Lee, Ji-Hyun Yeom, Kangseok Lee, Bashir Sajo Mienda
PLOS ONE.2023; 18(12): e0289072. CrossRef
Relaxed Cleavage Specificity of Hyperactive Variants of Escherichia coli RNase E on RNA I
Dayeong Bae, Hana Hyeon, Eunkyoung Shin, Ji-Hyun Yeom, Kangseok Lee
Journal of Microbiology.2023; 61(2): 211. CrossRef

The efficacy of a 2,4-diaminoquinazoline compound as an intranasal vaccine adjuvant to protect against influenza A virus infection in vivo: Kyungseob Noh , Eun Ju Jeong , Timothy An , Jin Soo Shin , Hyejin Kim , Soo Bong Han , Meehyein Kim; J. Microbiol. 2022;60(5):550-559. Published online April 18, 2022; DOI: https://doi.org/10.1007/s12275-022-1661-7

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Abstract

Adjuvants are substances added to vaccines to enhance antigen- specific immune responses or to protect antigens from rapid elimination. As pattern recognition receptors, Toll-like receptors 7 (TLR7) and 8 (TLR8) activate the innate immune system by sensing endosomal single-stranded RNA of RNA viruses. Here, we investigated if a 2,4-diaminoquinazolinebased TLR7/8 agonist, (S)-3-((2-amino-8-fluoroquinazolin- 4-yl)amino)hexan-1-ol (named compound 31), could be used as an adjuvant to enhance the serological and mucosal immunity of an inactivated influenza A virus vaccine. The compound induced the production of proinflammatory cytokines in macrophages. In a dose-response analysis, intranasal administration of 1 μg compound 31 together with an inactivated vaccine (0.5 μg) to mice not only enhanced virus-specific IgG and IgA production but also neutralized influenza A virus with statistical significance. Notably, in a virus-challenge model, the combination of the vaccine and compound 31 alleviated viral infection-mediated loss of body weight and increased survival rates by 40% compared with vaccine only-treated mice. We suggest that compound 31 is a promising lead compound for developing mucosal vaccine adjuvants to protect against respiratory RNA viruses such as influenza viruses and potentially coronaviruses.

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Efflux-Enhanced Imidazoquinolines To Exploit Chemoresistance
Muhammad Haroon, Sharmin Sultana, Seyedeh A. Najibi, Emily T. Wang, Abbey Michaelson, Pranto S. M. Al Muied, Amy E. Nielsen, Rock J. Mancini
ACS Omega.2025;[Epub] CrossRef
Design, Synthesis, and Biological Evaluation of New 2,6,7-Substituted Purine Derivatives as Toll-like Receptor 7 Agonists for Intranasal Vaccine Adjuvants
Morgan Kim, Kyungseob Noh, Pyeongkeun Kim, Jae Ho Kim, Byeong Wook Choi, Ravi Singh, Jun-Ho Choi, Soo Bong Han, Seong Soon Kim, Eun-Young Lee, Myung Ae Bae, Daeho Shin, Meehyein Kim, Jin Hee Ahn
Journal of Medicinal Chemistry.2024; 67(11): 9389. CrossRef
Evaluation of Antiviral Activity of Gemcitabine Derivatives against Influenza Virus and Severe Acute Respiratory Syndrome Coronavirus 2
Hyeon-Min Cha, Uk-Il Kim, Soo Bin Ahn, Myoung Kyu Lee, Haemi Lee, Hyungtae Bang, Yejin Jang, Seong Soon Kim, Myung Ae Bae, Kyungjin Kim, Meehyein Kim
ACS Infectious Diseases.2023; 9(4): 1033. CrossRef
Identification of broad-spectrum neutralizing antibodies against influenza A virus and evaluation of their prophylactic efficacy in mice
Sumin Son, Soo Bin Ahn, Geonyeong Kim, Yejin Jang, Chunkyu Ko, Meehyein Kim, Sang Jick Kim
Antiviral Research.2023; 213: 105591. CrossRef
Inhibition of KIF20A suppresses the replication of influenza A virus by inhibiting viral entry
Hoyeon Jeon, Younghyun Lim, In-Gu Lee, Dong-In Kim, Keun Pil Kim, So-Hee Hong, Jeongkyu Kim, Youn-Sang Jung, Young-Jin Seo
Journal of Microbiology.2022; 60(11): 1113. CrossRef

Reviews

Protective and pathogenic role of humoral responses in COVID-19: Uni Park , Nam-Hyuk Cho; J. Microbiol. 2022;60(3):268-275. Published online March 2, 2022; DOI: https://doi.org/10.1007/s12275-022-2037-8

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Abstract

Since the advent of SARS-CoV-2 in Dec. 2019, the global endeavor to identify the pathogenic mechanism of COVID-19 has been ongoing. Although humoral immunity including neutralizing activity play an important role in protection from the viral pathogen, dysregulated antibody responses may be associated with the pathogenic progression of COVID-19, especially in high-risk individuals. In addition, SARS-CoV-2 spike-specific antibodies acquired by prior infection or vaccination act as immune pressure, driving continuous population turnover by selecting for antibody-escaping mutations. Here, we review accumulating knowledge on the potential role of humoral immune responses in COVID-19, primarily focusing on their beneficial and pathogenic properties. Understanding the multifaceted regulatory mechanisms of humoral responses during SARS-CoV-2 infection can help us to develop more effective therapeutics, as well as protective measures against the ongoing pandemic.

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Rise in broadly cross-reactive adaptive immunity against human β-coronaviruses in MERS-recovered patients during the COVID-19 pandemic
So-Hee Kim, Yuri Kim, Sangeun Jeon, Uni Park, Ju-Il Kang, Kyeongseok Jeon, Hye-Ran Kim, Songhyeok Oh, Ji-Young Rhee, Jae-Phil Choi, Wan Beom Park, Sang Won Park, Jeong-Sun Yang, Joo-Yeon Lee, Jihye Kang, Hyoung-Shik Shin, Yeonjae Kim, Seungtaek Kim, Yeon-
Science Advances.2024;[Epub] CrossRef
Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant
Tae-Hun Kim, Sojung Bae, Sunggeun Goo, Jinjong Myoung
Journal of Microbiology and Biotechnology.2023; 33(12): 1587. CrossRef
Two years of COVID-19 pandemic: where are we now?
Jinjong Myoung
Journal of Microbiology.2022; 60(3): 235. CrossRef

Transmissibility and pathogenicity of SARS-CoV-2 variants in animal models: Young-Il Kim , Mark Anthony B. Casel , Young Ki Choi; J. Microbiol. 2022;60(3):255-267. Published online March 2, 2022; DOI: https://doi.org/10.1007/s12275-022-2033-z

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Abstract

As of February 2022, SARS-CoV-2 is still one of the most serious public health threats due to its high mortality rate and rapid spread of novel variants. Since the first outbreak in 2019, general understanding of SARS-CoV-2 has been improved through basic and clinical studies; however, knowledge gaps still exist in our understanding of the emerging novel SARSCoV- 2 variants, which impacts the corresponding development of vaccines and therapeutics. Especially, accumulation of mutations in SARS-CoV-2 and rapid spread in populations with previous immunity has resulted in selection of variants that evade the host immune response. This phenomenon threatens to render current SARS-CoV-2 vaccines ineffective for controlling the pandemic. Proper animal models are essential for detailed investigations into the viral etiology, transmission and pathogenesis mechanisms, as well as evaluation of the efficacy of vaccine candidates against recent SARS-CoV-2 variants. Further, the choice of animal model for each research topic is important for researchers to gain better knowledge of recent SARS-CoV-2 variants. Here, we review the advantages and limitations of each animal model, including mice, hamsters, ferrets, and non-human primates, to elucidate variant SARS-CoV-2 etiology and transmission and to evaluate therapeutic and vaccine efficacy.

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In vivo characterization of ACE2 expression in Sprague-Dawley rats and cultured primary brain pericytes highlights the utility of Rattus norvegicus in the study of COVID-19 brain pathophysiology
Eugene Park, Elaine Liu, Andrew J. Baker
Brain Research.2025; 1848: 149333. CrossRef
Utilizing non‐human primate models to combat recent COVID‐19/SARS‐CoV‐2 and viral infectious disease outbreaks
Taeho Kwon
Journal of Medical Primatology.2024;[Epub] CrossRef
Early detection of highly transmissible viral variants using phylogenomics
Michael R. May, Bruce Rannala
Science Advances.2024;[Epub] CrossRef
Animal Models, Zoonotic Reservoirs, and Cross-Species Transmission of Emerging Human-Infecting Coronaviruses
Yakhouba Kane, Gary Wong, George F. Gao
Annual Review of Animal Biosciences.2023; 11(1): 1. CrossRef
SARS-CoV-2 Aerosol and Intranasal Exposure Models in Ferrets
Elizabeth E. Zumbrun, Samantha E. Zak, Eric D. Lee, Philip A. Bowling, Sara I. Ruiz, Xiankun Zeng, Jeffrey W. Koehler, Korey L. Delp, Russel R. Bakken, Shannon S. Hentschel, Holly A. Bloomfield, Keersten M. Ricks, Tamara L. Clements, April M. Babka, John
Viruses.2023; 15(12): 2341. CrossRef
The Isolation and In Vitro Differentiation of Primary Fetal Baboon Tracheal Epithelial Cells for the Study of SARS-CoV-2 Host-Virus Interactions
Bharathiraja Subramaniyan, Sunam Gurung, Manish Bodas, Andrew R. Moore, Jason L. Larabee, Darlene Reuter, Constantin Georgescu, Jonathan D. Wren, Dean A. Myers, James F. Papin, Matthew S. Walters
Viruses.2023; 15(4): 862. CrossRef
Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant
Tae-Hun Kim, Sojung Bae, Sunggeun Goo, Jinjong Myoung
Journal of Microbiology and Biotechnology.2023; 33(12): 1587. CrossRef
Two years of COVID-19 pandemic: where are we now?
Jinjong Myoung
Journal of Microbiology.2022; 60(3): 235. CrossRef
SARS CoV-2 (Delta Variant) Infection Kinetics and Immunopathogenesis in Domestic Cats
Miruthula Tamil Selvan, Sachithra Gunasekara, Ping Xiao, Kristen Griffin, Shannon R. Cowan, Sai Narayanan, Akhilesh Ramachandran, Darren E. Hagen, Jerry W. Ritchey, Jennifer M. Rudd, Craig A. Miller
Viruses.2022; 14(6): 1207. CrossRef

Journal Articles

Characterization and validation of an alternative reference bacterium Korean Pharmacopoeia Staphylococcus aureus strain: Ye Won An , Young Sill Choi , Mi-ran Yun , Chihwan Choi , Su Yeon Kim; J. Microbiol. 2022;60(2):187-191. Published online January 7, 2022; DOI: https://doi.org/10.1007/s12275-022-1335-5

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Abstract

The National Culture Collection of Pathogens (NCCP) is a microbial resource bank in Korea that collects pathogen resources causing infectious disease in human and distributes them for research and education. The NCCP bank attempts to discover strains with various characteristics and specific purposes to provide diverse resources to researchers. Staphylococcus aureus American Type Culture Collection (ATCC) 6538P is used as a reference strain in the microbial assay for antibiotics in the Korean and in the United States Pharmacopoeias. We aimed to analyze domestically isolated microbial resources from the NCCP to replace the S. aureus reference strain. Staphylococcus aureus strains were identified using matrix- assisted laser desorption/ionization time-of-flight mass spectrometry and the VITEK-2 system and characterized by multilocus sequence typing, 16S rRNA sequencing, and antibiotic susceptibility testing. Several candidate strains had similar characteristics as the reference strain. Among them, the nucleotide sequence of the 16S rRNA region of NCCP 16830 was 100% identical to that of the reference strain; it was sensitive to six types of antibiotics and showed results most similar to the reference strain. A validity evaluation was conducted using the cylinder-plate method. NCCP 16830 presented valid results and had the same performance as ATCC 6538P; therefore, it was selected as an alternative candidate strain.

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Bacterial composition of refrigerators in households and inactivation of airborne Staphylococcus aureus using a TiO2-UVLED module in a 512 L aerobiology chamber
So-Seum Yong, Jae-Ik Lee, Dong-Hyun Kang
Food Microbiology.2023; 114: 104274. CrossRef

Non-mitochondrial aconitase regulates the expression of iron-uptake genes by controlling the RNA turnover process in fission yeast: Soo-Yeon Cho , Soo-Jin Jung , Kyoung-Dong Kim , Jung-Hye Roe; J. Microbiol. 2021;59(12):1075-1082. Published online October 26, 2021; DOI: https://doi.org/10.1007/s12275-021-1438-4

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Abstract

Aconitase, a highly conserved protein across all domains of life, functions in converting citrate to isocitrate in the tricarboxylic acid cycle. Cytosolic aconitase is also known to act as an iron regulatory protein in mammals, binding to the RNA hairpin structures known as iron-responsive elements within the untranslated regions of specific RNAs. Aconitase-2 (Aco2) in fission yeast is a fusion protein consisting of an aconitase and a mitochondrial ribosomal protein, bL21, residing not only in mitochondria but also in cytosol and the nucleus. To investigate the role of Aco2 in the nucleus and cytoplasm of fission yeast, we analyzed the transcriptome of aco2ΔN mutant that is deleted of nuclear localization signal (NLS). RNA sequencing revealed that the aco2ΔN mutation caused increase in mRNAs encoding iron uptake transporters, such as Str1, Str3, and Shu1. The half-lives of mRNAs for these genes were found to be significantly longer in the aco2ΔN mutant than the wild-type strain, suggesting the role of Aco2 in mRNA turnover. The three conserved cysteines required for the catalytic activity of aconitase were not necessary for this role. The UV cross-linking RNA immunoprecipitation analysis revealed that Aco2 directly bound to the mRNAs of iron uptake transporters. Aco2-mediated degradation of iron-uptake mRNAs appears to utilize exoribonuclease pathway that involves Rrp6 as evidenced by genetic interactions. These results reveal a novel role of non-mitochondrial aconitase protein in the mRNA turnover in fission yeast to fine-tune iron homeostasis, independent of regulation by transcriptional repressor Fep1.

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Iron-mediated post-transcriptional regulation in Toxoplasma gondii
Megan A. Sloan, Adam Scott, Dana Aghabi, Lucia Mrvova, Clare R. Harding, Dominique Soldati-Favre
PLOS Pathogens.2025; 21(2): e1012857. CrossRef
The Key Enzymes of Carbon Metabolism and the Glutathione Antioxidant System Protect Yarrowia lipolytica Yeast Against pH-Induced Stress
Tatyana I. Rakhmanova, Natalia N. Gessler, Elena P. Isakova, Olga I. Klein, Yulia I. Deryabina, Tatyana N. Popova
Journal of Fungi.2024; 10(11): 747. CrossRef
The intricate link between iron, mitochondria and azoles in Candida species
Wouter Van Genechten, Rudy Vergauwen, Patrick Van Dijck
The FEBS Journal.2024; 291(16): 3568. CrossRef
Non-Mitochondrial Aconitase-2 Mediates the Transcription of Nuclear-Encoded Electron Transport Chain Genes in Fission Yeast
Ho-Jung Kim, Soo-Yeon Cho, Soo-Jin Jung, Yong-Jun Cho, Jung-Hye Roe, Kyoung-Dong Kim
Journal of Microbiology.2024; 62(8): 639. CrossRef
Kinetic and Regulatory Properties of Yarrowia lipolytica Aconitate Hydratase as a Model-Indicator of Cell Redox State under pH Stress
Tatyana I. Rakhmanova, Varvara Yu. Sekova, Natalya N. Gessler, Elena P. Isakova, Yulia I. Deryabina, Tatyana N. Popova, Yevgeniya I. Shurubor, Boris F. Krasnikov
International Journal of Molecular Sciences.2023; 24(8): 7670. CrossRef

Zinc-binding domain mediates pleiotropic functions of Yvh1 in Cryptococcus neoformans: Jae-Hyung Jin , Myung Kyung Choi , Hyun-Soo Cho , Yong-Sun Bahn; J. Microbiol. 2021;59(7):658-665. Published online July 1, 2021; DOI: https://doi.org/10.1007/s12275-021-1287-1

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Abstract: Yvh1 is a dual-specificity phosphatase (DUSP) that is evolutionarily conserved in eukaryotes, including yeasts and humans. Yvh1 is involved in the vegetative growth, differentiation, and virulence of animal and plant fungal pathogens. All Yvh1 orthologs have a conserved DUSP catalytic domain at the N-terminus and a zinc-binding (ZB) domain with two zinc fingers (ZFs) at the C-terminus. Although the DUSP domain is implicated in the regulation of MAPK signaling in humans, only the ZB domain is essential for most cellular functions of Yvh1 in fungi. This study aimed to analyze the functions of the DUSP and ZB domains of Yvh1 in the human fungal pathogen Cryptococcus neoformans, whose Yvh1 (CnYvh1) contains a DUSP domain at the C-terminus and a ZB domain at the N-terminus. Notably, CnYvh1 has an extended internal domain between the two ZF motifs in the ZB domain. To elucidate the function of each domain, we constructed individual domain deletions and swapping strains by complementing the yvh1Δ mutant with wild-type (WT) or mutated YVH1 alleles and examined their Yvh1-dependent phenotypes, including growth under varying stress conditions, mating, and virulence factor production. Here, we found that the complementation of the yvh1Δ mutant with the mutated YVH1 alleles having two ZFs of the ZB domain, but not the DUSP and extended internal domains, restored the WT phenotypic traits in the yvh1Δ mutant. In conclusion, the ZB domain, but not the N-terminal DUSP domain, plays a pivotal role in the pathobiological functions of cryptococcal Yvh1.

Comparative genomics analysis of Pediococcus acidilactici species: Zhenzhen Li , Qi Song , Mingming Wang , Junli Ren , Songling Liu , Shancen Zhao; J. Microbiol. 2021;59(6):573-583. Published online May 15, 2021; DOI: https://doi.org/10.1007/s12275-021-0618-6

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Abstract

Pediococcus acidilactici is a reliable bacteriocin producer and a promising probiotic species with wide application in the food and health industry. However, the underlying genetic features of this species have not been analyzed. In this study, we performed a comprehensive comparative genomic analysis of 41 P. acidilactici strains from various ecological niches. The bacteriocin production of 41 strains were predicted and three kinds of bacteriocin encoding genes were identified in 11 P. acidilactici strains, namely pediocin PA-1, enterolysin A, and colicin-B. Moreover, whole-genome analysis showed a high genetic diversity within the population, mainly related to a large proportion of variable genomes, mobile elements, and hypothetical genes obtained through horizontal gene transfer. In addition, comparative genomics also facilitated the genetic explanation of the adaptation for host environment, which specify the protection mechanism against the invasion of foreign DNA (i.e. CRISPR/Cas locus), as well as carbohydrate fermentation. The 41 strains of P. acidilactici can metabolize a variety of carbon sources, which enhances the adaptability of this species and survival in different environments. This study evaluated the antibacterial ability, genome evolution, and ecological flexibility of P. acidilactici from the perspective of genetics and provides strong supporting evidence for its industrial development and application.

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Differences in seroprevalence between epicenter and non-epicenter areas of the COVID-19 outbreak in South Korea: Hye Won Jeong , Hyun-Ha Chang , Eun Ji Kim , Yu Kyung Kim , Se-Mi Kim , Eun-Ha Kim , Young-Il Kim , Mark Anthony B. Casel , Seong-Gyu Kim , Rare Rollon , Seung-Gyu Jang , Kwang-Min Yu , Hee-Sung Kim , Hee Sue Park , Su-Jin Park , Yong-Dae Kim , Eung-Gook Kim , Young Ki Choi; J. Microbiol. 2021;59(5):530-533. Published online April 28, 2021; DOI: https://doi.org/10.1007/s12275-021-1095-7

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Abstract

To compare the standardized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence of high epicenter region with non-epicenter region, serological studies were performed with a total of 3,268 sera from Daegu City and 3,981 sera from Chungbuk Province. Indirect immunofluorescence assay (IFA) for SARS-CoV-2 IgG results showed a high seroprevalence rate in the Daegu City (epicenter) compared with a non-epicenter area (Chungbuk Province) (1.27% vs. 0.91%, P = 0.0358). It is noteworthy that the highest seroprevalence in Daegu City was found in elderly patients (70’s) whereas young adult patients (20’s) in Chungbuk Province showed the highest seroprevalence. Neutralizing antibody (NAb) titers were found in three samples from Daegu City (3/3, 268, 0.09%) while none of the samples from Chungbuk Province were NAb positive. These results demonstrated that even following the large outbreak, the seropositive rate of SARS-CoV-2 in the general population remained low in South Korea.

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Review

Aequoribacter fuscus gen. nov., sp. nov., a new member of the family Halieaceae, isolated from coastal seawater: Shan-Hui Li , Jaeho Song , Ilnam Kang , Juchan Hwang , Jang-Cheon Cho; J. Microbiol. 2020;58(6):463-471. Published online May 27, 2020; DOI: https://doi.org/10.1007/s12275-020-0206-1

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A Gram-stain-negative, rod-shaped, obligately aerobic, nonflagellated, and chemoheterotrophic bacterium, designated IMCC3088T, was isolated from coastal seawater of the Yellow Sea. The 16S rRNA gene sequence analysis indicated that this strain belonged to the family Halieaceae which shared the highest sequence similarities with Luminiphilus syltensis NOR5-1BT (94.5%) and Halioglobus pacificus S1-72T (94.5%), followed by 92.3–94.3% sequence similarities with other species within the aforementioned family. Phylogenetic analyses demonstrated that strain IMCC3088T was robustly clustered with Luminiphilus syltensis NOR5-1BT within the family Halieaceae. However, average amino acid identity (AAI), percentages of conserved proteins (POCP), average nucleotide identity (ANI), and alignment fraction (AF) between strain IMCC3088T and Luminiphilus syltensis NOR5-1BT were 54.5%, 47.7%, 68.0%, and 16.5%, respectively, suggesting that they belonged to different genera. Whole-genome sequencing of strain IMCC3088T revealed a 3.1 Mbp genome size with a DNA G + C content of 51.7 mol%. The genome encoded diverse metabolic pathways including sulfur oxidation, phenol degradation, and proteorhodopsin phototrophy. Mono-unsaturated fatty acids were found to be the predominant cellular fatty acid components in the strain. Phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were the primarily identified polar lipids, and ubiquinone-8 was identified as a major respiratory quinone. The taxonomic data collected herein suggested that strain IMCC3088T represented a novel genus and species of the family Halieaceae, for which the name Aequoribacter fuscus gen. nov., sp. nov. is proposed with the type strain (= KACC 15529T = NBRC 108213T).

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