Journal of Microbiology

Research Articles

Enoxacin adversely affects Salmonella enterica virulence and host pathogenesis through interference with type III secretion system type II (T3SS-II) and disruption of translocation of Salmonella Pathogenicity Island-2 (SPI2) effectors: El-Sayed Khafagy, Gamal A. Soliman, Maged S. Abdel-Kader, Mahmoud M. Bendary, Wael A. H. Hegazy, Momen Askoura; J. Microbiol. 2025;63(2):e2410015. Published online February 27, 2025; DOI: https://doi.org/10.71150/jm.2410015

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Abstract PDF: Salmonella enterica is a clinically significant oro-fecal pathogen that causes a wide variety of illnesses and can lead to epidemics. S. enterica expresses a lot of virulence factors that enhance its pathogenesis in host. For instance, S. enterica employs a type three secretion system (T3SS) to translocate a wide array of effector proteins that could change the surrounding niche ensuring suitable conditions for the thrive of Salmonella infection. Many antimicrobials have been recently introduced to overcome the annoying bacterial resistance to antibiotics. Enoxacin is member of the second-generation quinolones that possesses a considerable activity against S. enterica. The present study aimed to evaluate the effect of enoxacin at sub-minimum inhibitory concentration (sub-MIC) on S. enterica virulence capability and pathogenesis in host. Enoxacin at sub-MIC significantly diminished both Salmonella invasion and intracellular replication within the host cells. The observed inhibitory effect of enoxacin on S. enterica internalization could be attributed to its ability to interfere with translocation of the T3SS effector proteins. These results were further confirmed by the finding that enoxacin at sub-MIC down-regulated the expression of the genes encoding for T3SS-type II (T3SS-II). Moreover, enoxacin at sub-MIC lessened bacterial adhesion to abiotic surface and biofilm formation which indicates a potential anti-virulence activity. Importantly, in vivo results showed a significant ability of enoxacin to protect mice against S. enterica infection and decreased bacterial colonization within animal tissues. In nutshell, current findings shed light on an additional mechanism of enoxacin at sub-MIC by interfering with Salmonella intracellular replication. The outcomes presented herein could be further invested in conquering bacterial resistance and open the door for additional effective clinical applications.

PneusPage: A WEB-BASED TOOL for the analysis of Whole-Genome Sequencing Data of Streptococcus pneumonia: Eunju Hong, Youngjin Shin, Hyunseong Kim, Woo Young Cho, Woo-Hyun Song, Seung-Hyun Jung, Minho Lee; J. Microbiol. 2025;63(1):e.2409020. Published online January 24, 2025; DOI: https://doi.org/10.71150/jm.2409020

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Abstract PDF Supplementary Material: With the advent of whole-genome sequencing, opportunities to investigate the population structure, transmission patterns, antimicrobial resistance profiles, and virulence determinants of Streptococcus pneumoniae at high resolution have been increasingly expanding. Consequently, a user-friendly bioinformatics tool is needed to automate the analysis of Streptococcus pneumoniae whole-genome sequencing data, summarize clinically relevant genomic features, and further guide treatment options. Here, we developed PneusPage, a web-based tool that integrates functions for species prediction, molecular typing, drug resistance determination, and data visualization of Streptococcus pneumoniae. To evaluate the performance of PneusPage, we analyzed 80 pneumococcal genomes with different serotypes from the Global Pneumococcal Sequencing Project and compared the results with those from another platform, PathogenWatch. We observed a high concordance between the two platforms in terms of serotypes (100% concordance rate), multilocus sequence typing (100% concordance rate), penicillin-binding protein typing (88.8% concordance rate), and the Global Pneumococcal Sequencing Clusters (98.8% concordance rate). In addition, PneusPage offers integrated analysis functions for the detection of virulence and mobile genetic elements that are not provided by previous platforms. By automating the analysis pipeline, PneusPage makes whole-genome sequencing data more accessible to non-specialist users, including microbiologists, epidemiologists, and clinicians, thereby enhancing the utility of whole-genome sequencing in both research and clinical settings. PneusPage is available at https://pneuspage.minholee.net/.

Journal Articles

Hydroxychloroquine an Antimalarial Drug, Exhibits Potent Antifungal Efficacy Against Candida albicans Through Multitargeting: Sargun Tushar Basrani, Tanjila Chandsaheb Gavandi, Shivani Balasaheb Patil, Nandkumar Subhash Kadam, Dhairyasheel Vasantrao Yadav, Sayali Ashok Chougule, Sankunny Mohan Karuppayil, Ashwini Khanderao Jadhav; J. Microbiol. 2024;62(5):381-391. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00111-6

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Abstract: Candida albicans is the primary etiological agent associated with candidiasis in humans. Unrestricted growth of C. albicans can progress to systemic infections in the worst situation. This study investigates the antifungal activity of Hydroxychloroquine (HCQ) and mode of action against C. albicans. HCQ inhibited the planktonic growth and yeast to hyphal form morphogenesis of C. albicans significantly at 0.5 mg/ml concentration. The minimum inhibitory concentrations (MIC(50)) of HCQ for C. albicans adhesion and biofilm formation on the polystyrene surface was at 2 mg/ml and 4 mg/ml respectively. Various methods, such as scanning electron microscopy, exploration of the ergosterol biosynthesis pathway, cell cycle analysis, and assessment of S oxygen species (ROS) generation, were employed to investigate HCQ exerting its antifungal effects. HCQ was observed to reduce ergosterol levels in the cell membranes of C. albicans in a dose-dependent manner. Furthermore, HCQ treatment caused a substantial arrest of the C. albicans cell cycle at the G0/G1 phase, which impeded normal cell growth. Gene expression analysis revealed upregulation of SOD2, SOD1, and CAT1 genes after HCQ treatment, while genes like HWP1, RAS1, TEC1, and CDC 35 were downregulated. The study also assessed the in vivo efficacy of HCQ in a mice model, revealing a reduction in the pathogenicity of C. albicans after HCQ treatment. These results indicate that HCQ holds for the development of novel antifungal therapies.

Comparative Transcriptomic Analysis of Flagellar‑Associated Genes in Salmonella Typhimurium and Its rnc Mutant: Seungmok Han , Ji-Won Byun , Minho Lee; J. Microbiol. 2024;62(1):33-48. Published online January 5, 2024; DOI: https://doi.org/10.1007/s12275-023-00099-5

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Abstract

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

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CspA regulates stress resistance, flagellar motility and biofilm formation in Salmonella Enteritidis
Xiang Li, Yan Cui, Xiaohui Sun, Chunlei Shi, Shoukui He, Xianming Shi
Food Bioscience.2025; 66: 106237. CrossRef
Influence of Flagella on Salmonella Enteritidis Sedimentation, Biofilm Formation, Disinfectant Resistance, and Interspecies Interactions
Huixue Hu, Jingguo Xu, Jingyu Chen, Chao Tang, Tianhao Zhou, Jun Wang, Zhuangli Kang
Foodborne Pathogens and Disease.2024;[Epub] CrossRef

Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov., Isolated from Freshwater and Soil: Yong-Seok Kim , Eun-Mi Hwang , Chang-Myeong Jeong , Chang-Jun Cha; J. Microbiol. 2023;61(10):891-901. Published online October 18, 2023; DOI: https://doi.org/10.1007/s12275-023-00081-1

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Abstract

Two novel bacterial strains CJ74T and CJ75T belonging to the genus Flavobacterium were isolated from freshwater of Han River and ginseng soil, South Korea, respectively. Strain CJ74T was Gram-stain-negative, aerobic, rod-shaped, non-motile, and non-flagellated, and did not produce flexirubin-type pigments. Strain CJ75T was Gram-stain-negative, aerobic, rodshaped, motile by gliding, and non-flagellated, and produced flexirubin-type pigments. Both strains were shown to grow optimally at 30 °C in the absence of NaCl on R2A medium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ74T and CJ75T belonged to the genus Flavobacterium and were most closely related to Flavobacterium niveum TAPW14T and Flavobacterium foetidum CJ42T with 96.17% and 97.29% 16S rRNA sequence similarities, respectively. Genomic analyses including the reconstruction of phylogenomic tree, average nucleotide identity, and digital DNA-DNA hybridization suggested that they were novel species of the genus Flavobacterium. Both strains contained menaquinone 6 (MK-6) as the primary respiratory quinone and phosphatidylethanolamine as a major polar lipid. The predominant fatty acids of both strains were iso-C15:0 and summed feature 3 ( C16:1 ω7c and/or C16: 1 ω6c). Based on the polyphasic taxonomic study, strains CJ74T and CJ75T represent novel species of the genus Flavobacterium, for which names Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov. are proposed, respectively. The type strains are CJ74T (=KACC 19819T =JCM 32889T) and CJ75T (=KACC 23149T =JCM 36132T).

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Discovery of two novel Flavobacterium species with potential for complex polysaccharide degradation
Xu-Dong Lian, Yong Guan, Yue Jiang, Dong-Heui Kwak, Mi-Kyung Lee, Zhun Li
Scientific Reports.2025;[Epub] CrossRef
Ammonia-oxidizing activity and microbial structure of ammonia-oxidizing bacteria, ammonia-oxidizing archaea and complete ammonia oxidizers in biofilm systems with different salinities
Haojie Qiu, Weihua Zhao, Yingying Qin, Yanyan Wang, Meng Bai, Shaoqing Su, Chao Wang, Zhisheng Zhao
Bioresource Technology.2025; : 132248. CrossRef
Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef
Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream
Sumin Kim, Miri S. Park, Ilnam Kang, Jang-Cheon Cho
Current Microbiology.2024;[Epub] CrossRef
Validation List no. 218. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef

Genetic Characteristics and Phylogeographic Dynamics of Echovirus: Yan Wang , Pir Tariq Shah , Yue Liu , Amina Nawal Bahoussi , Li Xing; J. Microbiol. 2023;61(9):865-877. Published online September 15, 2023; DOI: https://doi.org/10.1007/s12275-023-00078-w

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Abstract: Echoviruses belong to the genus Enterovirus in the Picornaviridae family, forming a large group of Enterovirus B (EVB) within the Enteroviruses. Previously, Echoviruses were classified based on the coding sequence of VP1. In this study, we performed a reliable phylogenetic classification of 277 sequences isolated from 1992 to 2019 based on the full-length genomes of Echovirus. In this report, phylogenetic, phylogeographic, recombination, and amino acid variability landscape analyses were performed to reveal the evolutional characteristics of Echovirus worldwide. Echoviruses were clustered into nine major clades, e.g., G1–G9. Phylogeographic analysis showed that branches G2–G9 were linked to common strains, while the branch G1 was only linked to G5. In contrast, strains E12, E14, and E16 clustered separately from their G3 and G7 clades respectively, and became a separate branch. In addition, we identified a total of 93 recombination events, where most of the events occurred within the VP1-VP4 coding regions. Analysis of amino acid variation showed high variability in the a positions of VP2, VP1, and VP3. This study updates the phylogenetic and phylogeographic information of Echovirus and indicates that extensive recombination and significant amino acid variation in the capsid proteins drove the emergence of new strains.

Review

The Fatal Role of Enterohaemorrhagic Escherichia coli Shiga Toxin‑associated Extracellular Vesicles in Host Cells: Kyung-Soo Lee , Jun-Young Park , Yu-Jin Jeong , Moo-Seung Lee; J. Microbiol. 2023;61(8):715-727. Published online September 4, 2023; DOI: https://doi.org/10.1007/s12275-023-00066-0

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Abstract

Enterohemorrhagic Escherichia coli (EHEC) is a specific subset of Shiga toxin-producing Escherichia coli (STEC) strains that are characterized by their ability to cause bloody diarrhea (hemorrhagic colitis) and potentially life-threatening, extraintestinal complications such as hemolytic uremic syndrome (HUS), which is associated with acute renal failure., contributing to severe clinical outcomes. The Shiga toxins (Stxs), produced by EHEC, are primary virulence factors. These potent cytotoxins are composed of one enzymatically active A subunit (StxA) and five receptor-binding B subunits (StxB). Although the toxins are primarily associated with cytotoxic effects, they also elicit other pathogenic consequences due to their induction of a number of biological processes, including apoptosis through ER-stress, pro-inflammatory responses, autophagy, and post-translational modification (PTM). Moreover, several studies have reported the association between Stxs and extracellular vesicles (EVs), including microvesicles and exosomes, demonstrating that Stx-containing EVs secreted by intoxicated macrophages are taken up by recipient cells, such as toxin-sensitive renal proximal tubular epithelial cells. This mechanism likely contributes to the spreading of Stxs within the host, and may exacerbate gastrointestinal illnesses and kidney dysfunction. In this review, we summarize recent findings relating to the host responses, in different types of cells in vitro and in animal models, mediated by Stxs-containing exosomes. Due to their unique properties, EVs have been explored as therapeutic agents, drug delivery systems, and diagnostic tools. Thus, potential therapeutic applications of EVs in EHEC Stxs-mediated pathogenesis are also briefly reviewed.

Citations

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Estimation of IL-8 and TNF-α Levels in Pediatric Diarrhea Patients Infected with Enterohemorrhagic E. coli O157:H7
Safaa A. AL-Isawi, Shaimaa Jassim Alsultany
Medical Journal of Babylon.2024; 21(3): 533. CrossRef
Structural basis to identify a target site in Shiga toxin for the inhibitor discovery against growth of Shiga toxin-producing E. coli
Anuja Prabhudesai, Samir Shaikh, Kayasth Zarna Ashwinbhai, Reeshu Gupta
Bulletin of the National Research Centre.2024;[Epub] CrossRef

Journal Articles

Ten Novel Species Belonging to the Genus Flavobacterium, Isolated from Freshwater Environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum sp. nov., F. limnophilum sp. nov., F. lacustre: Hyunyoung Jo , Miri S. Park , Yeonjung Lim , Ilnam Kang , Jang-Cheon Cho; J. Microbiol. 2023;61(5):495-510. Published online May 23, 2023; DOI: https://doi.org/10.1007/s12275-023-00054-4

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Abstract

Eleven bacterial strains were isolated from freshwater environments and identified as Flavobacterium based on 16S rRNA gene sequence analyses. Complete genome sequences of the 11 strains ranged from 3.45 to 5.83 Mb with G + C contents of 33.41–37.31%. The average nucleotide identity (ANI) values showed that strains IMCC34515T and IMCC34518 belonged to the same species, while the other nine strains represented each separate species. The ANI values between the strains and their closest Flavobacterium species exhibited ≤ 91.76%, indicating they represent each novel species. All strains had similar characteristics such as being Gram-stain-negative, rod-shaped, and contained iso-C15:0 as the predominant fatty acid, menaquinone-6 as the respiratory quinone, and phosphatidylethanolamine and aminolipids as major polar lipids. Genomic, phylogenetic, and phenotypic characterization confirmed that the 11 strains were distinct from previously recognized Flavobacterium species. Therefore, Flavobacterium praedii sp. nov. (IMCC34515T = KACC 22282T = NBRC 114937T), Flavobacterium marginilacus sp. nov. (IMCC34673T = KACC 22284T = NBRC 114940T), Flavobacterium aestivum sp. nov. (IMCC34774T = KACC 22285T = NBRC 114941T), Flavobacterium flavigenum sp. nov. (IMCC34775T = KACC22286T = NBRC 114942T), Flavobacterium luteolum sp. nov. (IMCC34776T = KACC 22287T = NBRC 114943T), Flavobacterium gelatinilyticum sp. nov. (IMCC34777T = KACC 22288T = NBRC 114944T), Flavobacterium aquiphilum sp.nov. (IMCC34779T = KACC 22289T = NBRC 114945T), Flavobacterium limnophilum sp. nov. (IMCC36791T = KACC22290T = NBRC 114947T), Flavobacterium lacustre sp. nov. (IMCC36792T = KACC 22291T = NBRC 114948T), and Flavobacterium eburneipallidum sp. nov. (IMCC36793T = KACC 22292T = NBRC 114949T) are proposed as novel species.

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Indoor pollution of funeral homes and potential health risk of workers: A case study in central China
Jinjun Ye, Zhengtao Ai, Lup Wai Chew
Building and Environment.2025; 272: 112677. CrossRef
Flavobacterium magnesitis sp. nov. and Flavobacterium zubiriense sp. nov., two novel Flavobacterium species isolated from alkaline magnesite residues
Leonor Matos, Lorrie Maccarrio, Ana Paula Chung, Diogo N. Proença, Søren Sørensen, Paula V. Morais, Romeu Francisco
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Comprehensive genome analysis of five novel flavobacteria: Flavobacterium piscisymbiosum sp. nov., Flavobacterium pisciphilum sp. nov., Flavobacterium flavipigmentatum sp. nov., Flavobacterium lipolyticum sp. nov. and Flavobacterium cupriresistens sp. nov
Izzet Burcin Saticioglu, Hilal Ay, Soner Altun, Nihed Ajmi, Enes Said Gunduz, Huban Gocmen, Muhammed Duman
Systematic and Applied Microbiology.2024; 47(4): 126518. CrossRef
Leuconostoc aquikimchii sp. nov., a Lactic Acid Bacterium Isolated from Cabbage Watery Kimchi
Subin Kim, Se Hee Lee, Ki Hyun Kim, Misun Yun
Journal of Microbiology.2024; 62(12): 1089. CrossRef
Overproduction of Xanthophyll Pigment in Flavobacterium sp. JSWR-1 under Optimized Culture Conditions
Jegadeesh Raman, Young-Joon Ko, Jeong-Seon Kim, Da-Hye Kim, Soo-Jin Kim
Journal of Microbiology and Biotechnology.2024; 34(3): 710. CrossRef
Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream
Sumin Kim, Miri S. Park, Ilnam Kang, Jang-Cheon Cho
Current Microbiology.2024;[Epub] CrossRef
Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef
Validation List no. 213. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef

Rhizosphere Microbial Community and Metabolites of Susceptible and Resistant Tobacco Cultivars to Bacterial Wilt: Wan Zhao , Yanyan Li , Chunlei Yang , Yong Yang , Yun Hu; J. Microbiol. 2023;61(4):389-402. Published online March 7, 2023; DOI: https://doi.org/10.1007/s12275-023-00012-0

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Abstract

Soil-borne diseases are closely related to rhizosphere microecosystem. While, plant species and genotypes are important factors affected rhizosphere microecosystem. In this study, the rhizosphere soil microbial community and metabolites of susceptible and resistant tobacco cultivars were investigated. The results showed that there were significant differences in the rhizosphere microbial community and metabolites between susceptible cultivar Yunyan87 and resistant cultivar Fandi3. Furthermore, the rhizosphere soil of Fandi3 showed a higher microbial diversity than that of Yunyan87. The abundance of R. solanacearum was much higher in the rhizosphere soil of Yunyan87 than in the rhizosphere soil of Fandi3, resulting in a higher disease incidence and index. While the abundance of beneficial bacteria in the rhizosphere soil of Fandi3 were higher than that of Yunyan87. Additionally, there were significant differences in metabolites between Yunyan87 and Fandi3 cultivars, and 4-hydroxybenzaldehyde, 3-hydroxy-4-methoxybenzoic acid, vamillic aldehyde, benzoic acid, 4-hydroxybenzyl alcohol, p-hydroxybenzoic acid and phthalic acid were notably high in Yunyan87. Redundancy analysis (RDA) indicated that the rhizosphere microbial community of Fandi3 and Yunyan87 were highly correlated with various environmental factors and metabolites. Overall, susceptible and resistant tobacco cultivars had different impact on rhizosphere microbial community and metabolites. The results expand our understanding of the roles of tobacco cultivars in plant-micro-ecosystem interactions, and provide a basis for the control of tobacco bacterial wilt.

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MAPK Cascades in Plant Microbiota Structure and Functioning
Thijs Van Gerrewey, Hoo Sun Chung
Journal of Microbiology.2024; 62(3): 231. CrossRef
Response of Soil Microorganisms and Phenolic to Pseudostelariae heterophylla Cultivation in Different Soil Types
Yingying Liu, Dan Wu, Yongjun Kan, Li Zhao, Chang Jiang, Wensheng Pang, Juan Hu, Meilan Zhou
Eurasian Soil Science.2024; 57(3): 446. CrossRef
Response of bacterial community metabolites to bacterial wilt caused by Ralstonia solanacearum: a multi-omics analysis
Chengjian Wei, Jinchang Liang, Rui Wang, Luping Chi, Wenjing Wang, Jun Tan, Heli Shi, Xueru Song, Zhenzhen Cui, Qiang Xie, Dejie Cheng, Xiaoqiang Wang
Frontiers in Plant Science.2024;[Epub] CrossRef
The Composition and Function of the Rhizosphere Bacterial Community of Paeonia lactiflora Varies with the Cultivar
Liping Yang, Xin Wan, Runyang Zhou, Yingdan Yuan
Biology.2023; 12(11): 1363. CrossRef
Analysis of the response mechanisms of Pinellia ternata to terahertz wave stresses using transcriptome and metabolic data
Dongdong Wang, Surendra Sarsaiya, Xu Qian, Leilei Jin, Fuxing Shu, Chuanyou Zhang, Jishuang Chen
Frontiers in Plant Science.2023;[Epub] CrossRef

Transcriptome‑based Mining of the Constitutive Promoters for Tuning Gene Expression in Aspergillus oryzae: Kobkul Laoteng , Jutamas Anantayanon , Chanikul Chutrakul , Sarocha Panchanawaporn , Sukanya Jeennor; J. Microbiol. 2023;61(2):199-210. Published online February 6, 2023; DOI: https://doi.org/10.1007/s12275-023-00020-0

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Abstract

Transcriptional regulation has been adopted for developing metabolic engineering tools. The regulatory promoter is a crucial genetic element for strain optimization. In this study, a gene set of Aspergillus oryzae with highly constitutive expression across different growth stages was identified through transcriptome data analysis. The candidate promoters were functionally characterized in A. oryzae by transcriptional control of β-glucuronidase (GUS) as a reporter. The results showed that the glyceraldehyde triphosphate dehydrogenase promoter (PgpdA1) of A. oryzae with a unique structure displayed the most robust strength in constitutively controlling the expression compared to the PgpdA2 and other putative promoters tested. In addition, the ubiquitin promoter (Pubi) of A. oryzae exhibited a moderate expression strength. The deletion analysis revealed that the 5' untranslated regions of gpdA1 and ubi with the length of 1028 and 811 nucleotides, counted from the putative translation start site (ATG), respectively, could efficiently drive the GUS expression. Interestingly, both promoters could function on various carbon sources for cell growth. Glucose was the best fermentable carbon source for allocating high constitutive expressions during cell growth, and the high concentrations (6–8% glucose, w/v) did not repress their functions. It was also demonstrated that the secondary metabolite gene coding for indigoidine could express under the control of PgpdA1 or Pubi promoter. These strong and moderate promoters of A. oryzae provided beneficial options in tuning the transcriptional expression for leveraging the metabolic control towards the targeted products.

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Construction of an Aspergillus oryzae △nptB△pyrG Host for Homologous Expression of Lipase and Catalytic Property Characterization of Recombinant Lipase
Yueting Zhang, Hongmei Nie, Fei Zhang, Mengmeng Jin, Zhao Wang, Jianyong Zheng
Applied Biochemistry and Biotechnology.2024;[Epub] CrossRef
Mining and Understanding of New Transcriptional Regulatory Elements from Licorice-Derived Endophyte Serratia Rubidaea W12-1
Ying Zhang, Yunyang Ma, Bing Hu, H.M. Zabed, A.K. Singh, M.A. Ibrahim, N. Chen
BIO Web of Conferences.2024; 142: 03018. CrossRef
Exploring and Engineering Novel Strong Promoters for High-Level Protein Expression in Bacillus subtilis DB104 through Transcriptome Analysis
Ji-Su Jun, Hyang-Eun Jeong, Kwang-Won Hong
Microorganisms.2023; 11(12): 2929. CrossRef
Efficient de novo production of bioactive cordycepin by Aspergillus oryzae using a food-grade expression platform
Sukanya Jeennor, Jutamas Anantayanon, Sarocha Panchanawaporn, Chanikul Chutrakul, Wanwipa Vongsangnak, Kobkul Laoteng
Microbial Cell Factories.2023;[Epub] CrossRef

Flavihumibacter fluminis sp. nov. and Flavihumibacter rivuli sp. nov., isolated from a freshwater stream: Miri S. Park , Hyeonuk Sa , Ilnam Kang , Jang-Cheon Cho; J. Microbiol. 2022;60(8):806-813. Published online July 29, 2022; DOI: https://doi.org/10.1007/s12275-022-2298-2

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Abstract

Two Gram-stain-positive, aerobic, chemoheterotrophic, nonmotile, rod-shaped, and yellow-pigmented bacterial strains, designated IMCC34837T and IMCC34838T, were isolated from a freshwater stream. Results of 16S rRNA gene-based phylogenetic analyses showed that strains IMCC34837T and IMCC- 34838T shared 96.3% sequence similarity and were most closely related to Flavihumibacter profundi Chu64-6-1T (99.6%) and Flavihumibacter cheonanensis WS16T (96.4%), respectively. Complete whole-genome sequences of strains IMCC- 34837T and IMCC34838T were 5.0 Mbp and 4.3 Mbp of genome size with 44.5% and 47.9% of DNA G + C contents, respectively. Average nucleotide identity (ANI) and digital DNA- DNA hybridization (dDDH) values between the two strains were 70.0% and 17.9%, repectively, revealing that they are independent species. The two strains showed ≤ 75.2% ANI and ≤ 19.3% dDDH values to each closely related species of the genus Flavihumibacter, indicating that the two strains represent each novel species. Major fatty acid constituents of strain IMCC34837T were iso-C15:0, iso-C15:1 G and anteiso-C15:0 and those of strain IMCC34838T were iso-C15:0 and iso-C15:1 G. The predominant isoprenoid quinone detected in both strains was menaquinone-7 (MK-7). Major polar lipids of both strains were phosphatidylethanolamine, aminolipids, and glycolipids. Based on the phylogenetic and phenotypic characterization, strains IMCC34837T and IMCC34838T were considered to represent two novel species within the genus Flavihumibacter, for which the names Flavihumibacter fluminis sp. nov. and Flavihumibacter rivuli sp. nov. are proposed with IMCC34837T (= KACC 21752T = NBRC 115292T) and IMCC34838T (= KACC 21753T = NBRC 115293T) as the type strains, respectively.

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Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
Raúl Riesco, Martha E. Trujillo
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Leuconostoc aquikimchii sp. nov., a Lactic Acid Bacterium Isolated from Cabbage Watery Kimchi
Subin Kim, Se Hee Lee, Ki Hyun Kim, Misun Yun
Journal of Microbiology.2024; 62(12): 1089. CrossRef
Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef
Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream
Sumin Kim, Miri S. Park, Ilnam Kang, Jang-Cheon Cho
Current Microbiology.2024;[Epub] CrossRef
Validation List no. 211. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Proposal of Flavihumibacter fluvii sp. nov. as a replacement name for the effectively published but invalidated epithet Flavihumibacter fluminis Park et al. 2022
Miri S. Park, Hyeonuk Sa, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2023; 61(6): 649. CrossRef

Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork: So-Yeon Lee , Pil Soo Kim , Hojun Sung , Dong-Wook Hyun , Jin-Woo Bae; J. Microbiol. 2022;60(5):469-477. Published online March 31, 2022; DOI: https://doi.org/10.1007/s12275-022-1647-5

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Abstract

Two Gram-stain-negative, mesophilic, strictly aerobic, nonspore forming, and yellow-pigmented strains with rod-shaped cells, designated H21R20T and H23M41T, were isolated from the faeces of an Oriental stork (Ciconia boyciana). Based on 16S rRNA gene sequences, both strains showed the highest similarity (98.3−98.4%) to the type strain of Lysobacter concretionis. Phylogenetic analysis based on the 16S rRNA genes and 92 bacterial core genes showed that strains H21R20T and H23M41T were robustly clustered with L. concretionis Ko07T. Whole genome sequencing revealed that the genomes of both strains were approximately 2.9 Mb in size. The DNA G + C contents of the H21R20T and H23M41T strains were 67.3 and 66.6%, respectively. The two strains showed 80.1−81.7% average nucleotide identity with L. concretionis Ko07T. Strain H21R20T grew optimally at 30°C and pH 8.0 and in the presence of 0.5–3% (wt/vol) NaCl, while strain H23M41T grew optimally at 30°C and pH 7.0–8.0 and in the presence of 0–3% (wt/vol) NaCl. Both strains possessed iso-C15:0, iso-C16:0 and summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-methyl) as the major cellular fatty acids, ubiquinone Q-8 as a predominant quinone, and diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine as the major polar lipids. A multifaceted investigation demonstrated that strains H21R20T and H23M41T represent novel species of the genus Lysobacter, for which we propose the names Lysobacter ciconiae sp. nov. and Lysobacter avium sp. nov. for strains H21R20T (= KCTC 82316T = JCM 34832T) and H23M41T (= KCTC 62676T = JCM 33223T), respectively.

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Isolation and Characterization of an Antioxidant Aryl Polyene Pigment from Antarctic Bacterium Lysobacter sp. A03
Maria Elisa Pailliè-Jiménez, Paolo Stincone, Jamile Queiroz Pereira, Patricio Román Santagapita, Eliseu Rodrigues, Adriano Brandelli
Molecular Biotechnology.2024;[Epub] CrossRef
Luteimonas flava sp. nov. and Aquilutibacter rugosus gen. nov., sp. nov., isolated from freshwater environments in China and re-examining the taxonomic status of genera Luteimonas and Lysobacter
Huibin Lu, Li Chen, Yujing Wang, Peng Xing, Qinglong Wu
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
An update on novel taxa and revised taxonomic status of bacteria isolated from non-domestic animals described in 2022
Claire R. Burbick, Sara D. Lawhon, Erik Munson, Elizabeth Thelen, Amanda Zapp, Anastasia Wilson, Romney M. Humphries
Journal of Clinical Microbiology.2023;[Epub] CrossRef
Lysobacter changpingensis sp. nov., a novel species of the genus Lysobacter isolated from a rhizosphere soil of strawberry in China
Bang-Yan Niu, Dong-Jun Ren, Fang-Bo Zhang, Hong-Tu Zhu, Hai-Lei Wei, Ming-Chao Ma, Miao Gao
Folia Microbiologica.2023; 68(6): 991. CrossRef
Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov., isolated from the gastrointestinal tract of lake prawn
Do-Yeon Kim, In-Chul Jeong, So-Yeon Lee, Yun-Seok Jeong, Jeong Eun Han, Euon Jung Tak, June-Young Lee, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Validation List no. 207. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef

The novel antifungal agent AB-22 displays in vitro activity against hyphal growth and biofilm formation in Candida albicans and potency for treating systemic candidiasis: Kyung-Tae Lee , Dong-Gi Lee , Ji Won Choi , Jong-Hyun Park , Ki Duk Park , Jong-Seung Lee , Yong-Sun Bahn; J. Microbiol. 2022;60(4):438-443. Published online March 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2016-0

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Abstract: Systemic candidiasis, which is mainly caused by Candida albicans, is a serious acute fungal infection in the clinical setting. In a previous study, we reported that compound 22h (designated as AB-22 in this study), a vinyl sulfate compound, is a fast-acting fungicidal agent against a broad spectrum of fungal pathogens. In this study, we aimed to further analyze the in vitro and in vivo efficacy of AB-22 against filamentation, biofilm formation, and virulence of C. albicans. Under in vitro hyphal growth-inducing condition, AB-22 effectively inhibited germ tube formation and hyphal growth, which are required for the initiation of biofilm formation. Indeed, AB-22 significantly suppressed C. albicans biofilm formation in a dose-dependent manner. Moreover, AB-22 treatment inhibited the normal induction of ALS3, HWP1, and ECE1, which are all required for hyphal transition in C. albicans. Furthermore, AB-22 treatment increased the survival of mice systemically infected with C. albicans. In conclusion, in addition to its fungicidal activity, AB-22 inhibits filamentation and biofilm formation in C. albicans, which could collectively contribute to its potent in vivo efficacy against systemic candidiasis.

Antibacterial pathway of cefquinome against Staphylococcus aureus based on label-free quantitative proteomics analysis: Linglin Gao , Hao Zhu , Yun Chen , Yuhui Yang; J. Microbiol. 2021;59(12):1112-1124. Published online November 9, 2021; DOI: https://doi.org/10.1007/s12275-021-1201-x

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Abstract

Cefquinome (CEQ) is a novel β-lactam antibiotic that exhibits excellent antibacterial activity against Staphylococcus aureus. However, the bacterial protein targets of CEQ are unclear. To evaluate the relationship between the pharmacokinetic/ pharmacodynamic (PK/PD) parameters of CEQ and strains with varying degrees of resistance and to elucidate bacterial protein responses to CEQ treatment, label-free quantitative proteomics analysis was conducted. The sensitive S. aureus ATCC6538 and the resistant 2MIC and 8MIC were tested for differentially expressed proteins. An in vitro model was treated with different concentrations of CEQ (3, 5, or 10 μg/ml) with different terminal half-lives (2.5 or 5 h) at different intervals (12 or 24 h). Differentially expressed proteins were evaluated using Gene Ontology analysis followed by KEGG pathway enrichment analysis and STRING network analysis. RT-qPCR was performed to validate the differentially expressed proteins at the molecular level. The results showed that the degree of resistance increased in a cumulative manner and increased gradually with the extension of administration time. The resistant strain would not have appeared in the model only if %T > mutant prevention concentration ≥ 50%. The expression of 45 proteins significantly changed following CEQ treatment, among which 42 proteins were obviously upregulated and 3 were downregulated. GO analysis revealed that the differentially expressed proteins were mainly present on cells and the cell membrane, participated in metabolic and intracellular processes, and had catalytic and binding activities. The RPSO, SDHB, CITZ, ADK, and SAOUHSC 00113 genes in S. aureus may play important roles in the development of resistance to CEQ. These results provided important reference candidate proteins as targets for overcoming S. aureus resistance to CEQ.

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Detection of Antibiotic Resistance in Feline-Origin ESBL Escherichia coli from Different Areas of China and the Resistance Elimination of Garlic Oil to Cefquinome on ESBL E. coli
Yin-Chao Tong, Peng-Cheng Li, Yang Yang, Qing-Yi Lin, Jin-Tong Liu, Yi-Nuo Gao, Yi-Ning Zhang, Shuo Jin, Su-Zhu Qing, Fu-Shan Xing, Yun-Peng Fan, Ying-Qiu Liu, Wei-Ling Wang, Wei-Min Zhang, Wu-Ren Ma
International Journal of Molecular Sciences.2023; 24(11): 9627. CrossRef

[PROTOCOL] Flow cytometric monitoring of the bacterial phenotypic diversity in aquatic ecosystems: Jin-Kyung Hong , Soo Bin Kim , Seok Hyun Ahn , Yongjoo Choi , Tae Kwon Lee; J. Microbiol. 2021;59(10):879-885. Published online September 23, 2021; DOI: https://doi.org/10.1007/s12275-021-1443-7

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Abstract

Flow cytometry is a promising tool used to identify the phenotypic features of bacterial communities in aquatic ecosystems by measuring the physical and chemical properties of cells based on their light scattering behavior and fluorescence. Compared to molecular or culture-based approaches, flow cytometry is suitable for the online monitoring of microbial water quality because of its relatively simple sample preparation process, rapid analysis time, and high-resolution phenotypic data. Advanced statistical techniques (e.g., denoising and binning) can be utilized to successfully calculate phenotypic diversity by processing the scatter data obtained from flow cytometry. These phenotypic diversities were well correlated with taxonomic-based diversity computed using nextgeneration 16S RNA gene sequencing. The protocol provided in this paper should be a useful guide for a fast and reliable flow cytometric monitoring of bacterial phenotypic diversity in aquatic ecosystems.

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Assessing long-term ecological impacts of PCE contamination in groundwater using a flow cytometric fingerprint approach
Jin-Kyung Hong, Soo Bin Kim, Gui Nam Wee, Bo Ram Kang, Jee Hyun No, Susmita Das Nishu, Joonhong Park, Tae Kwon Lee
Science of The Total Environment.2024; 931: 172698. CrossRef
Phenotypic shifts induced by environmental pre-stressors modify antibiotic resistance in Staphylococcus aureus
Gui Nam Wee, Eun Sun Lyou, Susmita Das Nishu, Tae Kwon Lee
Frontiers in Microbiology.2023;[Epub] CrossRef

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