Journal of Microbiology

Journal Articles

The Salmonella enterica EnvE is an Outer Membrane Lipoprotein and Its Gene Expression Leads to Transcriptional Repression of the Virulence Gene msgA: Sinyeon Kim, Yong Heon Lee; J. Microbiol. 2024;62(11):1013-1022. Published online November 15, 2024; DOI: https://doi.org/10.1007/s12275-024-00183-4

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Abstract: The envE gene of Salmonella enterica serovar Typhimurium is encoded within Salmonella Pathogenicity Island-11 (SPI-11) and is located immediately upstream of the virulence gene msgA (macrophage survival gene A) in the same transcriptional orientation. To date, the characteristics and roles of envE remain largely unexplored. In this study, we show that EnvE, a predicted lipoprotein, is localized on the outer membrane using sucrose gradient ultracentrifugation. Under oxidative stress conditions, envE transcription is suppressed, while msgA transcription is induced, indicating an inverse correlation between the mRNA levels of the two neighboring genes. Importantly, inactivation of envE leads to constitutive transcription of msgA regardless of the presence of oxidative stress. Moreover, trans-complementation of the envE mutant with a plasmid-borne envE fails to prevent the induction of msgA transcription, suggesting that envE functions as a cis-regulatory element rather than a trans-acting factor. We further show that both inactivation and complementation of envE confer wild-type levels of resistance to oxidative stress by ensuring the expression of msgA. Our data suggest that the S. enterica envE gene encodes an outer membrane lipoprotein, and its transcription represses msgA expression in a cis-acting manner, probably by transcriptional interference, although the exact molecular details are yet unclear.

Whole-Genome Sequencing Reveals the Population Structure and Genetic Diversity of Salmonella Typhimurium ST34 and ST19 Lineages: Zhen-Xu Zhuo, Yu-Lian Feng, Xi-Wei Zhang, Hao Liu, Fang-Yin Zeng, Xiao-Yan Li; J. Microbiol. 2024;62(10):859-870. Published online November 4, 2024; DOI: https://doi.org/10.1007/s12275-024-00170-9

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Abstract: Salmonella Typhimurium is an invasive gastrointestinal pathogen for both humans and animals. To investigate the genetic framework and diversity of S. Typhimurium, a total of 194 S. Typhimurium isolates were collected from patients in a tertiary hospital between 2020 and 2021. Antimicrobial susceptibility testing was used to confirm the resistance phenotype. Whole-genome sequencing and bioinformatics analysis were performed to determine the sequence type, phylogenetic relationships, resistance gene profiles, Salmonella pathogenicity island (SPI) and the diversity of the core and pan genome. The result showed that 57.22% of S. Typhimurium isolates were multidrug resistant and resistance of total isolates to the first-line drug ciprofloxacin was identified in 60.82%. The population structure of S. Typhimurium was categorized into three lineages: ST19 (20.10%, 39/194), ST34-1 (47.42%, 92/194) and ST34-2 (40.65%, 63/194), with the population size exhibiting increasing trends. All lineages harbored variety of fimbrial operons, prophages, SPIs and effectors that contributed to the virulence and long-term infections of S. Typhimurium. Importantly, ST34-1 lineage might potentially be more invasive due to the possession of SPI1-effector gene sopE which was essential for the proliferation, internalization and intracellular presence of S. Typhimurium in hosts. Multiple antimicrobial resistance genes were characteristically distributed across three lineages, especially carbapenem genes only detected in ST34-1&2 lineages. The distinct functional categories of pan genome among three lineages were observed in metabolism, signaling and gene information processing. This study provides a theoretical foundation for the evolved adaptation and genetic diversity of S. Typhimurium ST19 and ST34, among which ST34 lineages with multidrug resistance and potential hypervirulence need to pay more attention to epidemiological surveillance.

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

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

Exploring the Therapeutic Potential of Scorpion‑Derived Css54 Peptide Against Candida albicans: Jonggwan Park , Hyeongsun Kim , Da Dam Kang , Yoonkyung Park; J. Microbiol. 2024;62(2):101-112. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00113-4

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Abstract

Candida albicans (C. albicans) is one of the most common opportunistic fungi worldwide, which is associated with a high mortality rate. Despite treatment, C. albicans remains the leading cause of life-threatening invasive infections. Consequently, antimicrobial peptides (AMPs) are potential alternatives as antifungal agents with excellent antifungal activity. We previously reported that Css54, found in the venom of Centrurodies suffusus suffusus (C. s. suffusus) showed antibacterial activity against zoonotic bacteria. However, the antifungal activity of Css54 has not yet been elucidated. The obj!ective of this study was to identify the antifungal activity of Css54 against C. albicans and analyze its mechanism. Css54 showed high antifungal activity against C. albicans. Css54 also inhibited biofilm formation in fluconazole-resistant fungi. The antifungal mechanism of action of Css54 was investigated using membrane-related assays, including the membrane depolarization assay and analysis of the membrane integrity of C. albicans after treatment with Css54. Css54 induced reactive oxygen species (ROS) production in C. albicans, which affected its antifungal activity. Our results indicate that Css54 causes membrane damage in C. albicans, highlighting its value as a potential therapeutic agent against C. albicans infection.

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Antimicrobial Potential of Scorpion-Venom-Derived Peptides
Zhiqiang Xia, Lixia Xie, Bing Li, Xiangyun Lv, Hongzhou Zhang, Zhijian Cao
Molecules.2024; 29(21): 5080. CrossRef
Synthetic Short Cryptic Antimicrobial Peptides as Templates for the Development of Novel Biotherapeutics Against WHO Priority Pathogen
Manjul Lata, Vrushti Telang, Pooja Gupta, Garima Pant, Mitra Kalyan, Jesu Arockiaraj, Mukesh Pasupuleti
International Journal of Peptide Research and Therapeutics.2024;[Epub] CrossRef

Lactobacillus acidophilus KBL409 Ameliorates Atopic Dermatitis in a Mouse Model: Woon-ki Kim , You Jin Jang , SungJun Park , Sung-gyu Min , Heeun Kwon , Min Jung Jo , GwangPyo Ko; J. Microbiol. 2024;62(2):91-99. Published online February 22, 2024; DOI: https://doi.org/10.1007/s12275-024-00104-5

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Abstract

Atopic dermatitis (AD) is a chronic inflammatory skin disease with repeated exacerbations of eczema and pruritus. Probiotics can prevent or treat AD appropriately via modulation of immune responses and gut microbiota. In this study, we evaluated effects of Lactobacillus acidophilus (L. acidophilus) KBL409 using a house dust mite (Dermatophagoides farinae)-induced in vivo AD model. Oral administration of L. acidophilus KBL409 significantly reduced dermatitis scores and decreased infiltration of immune cells in skin tissues. L. acidophilus KBL409 reduced in serum immunoglobulin E and mRNA levels of T helper (Th)1 (Interferon-γ), Th2 (Interleukin [IL]-4, IL-5, IL-13, and IL-31), and Th17 (IL-17A) cytokines in skin tissues. The anti-inflammatory cytokine IL-10 was increased and Foxp3 expression was up-regulated in AD-induced mice with L. acidophilus KBL409. Furthermore, L. acidophilus KBL409 significantly modulated gut microbiota and concentrations of short-chain fatty acids and amino acids, which could explain its effects on AD. Our results suggest that L. acidophilus KBL409 is the potential probiotic for AD treatment by modulating of immune responses and gut microbiota of host.

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The Skin Histopathology of Pro- and Parabiotics in a Mouse Model of Atopic Dermatitis
Hun Hwan Kim, Se Hyo Jeong, Min Yeong Park, Pritam Bhagwan Bhosale, Abuyaseer Abusaliya, Jeong Doo Heo, Hyun Wook Kim, Je Kyung Seong, Tae Yang Kim, Jeong Woo Park, Byeong Soo Kim, Gon Sup Kim
Nutrients.2024; 16(17): 2903. CrossRef
Limosilactobacillus fermentum KBL674 Alleviates Vaginal Candidiasis
Sung Jae Jang, Eun Jung Jo, Cheonghoon Lee, Bo-Ram Cho, Yun Jeong Shin, Jun Soo Song, Woon-Ki Kim, Nanhee Lee, Hyungjin Lee, SungJun Park, GwangPyo Ko
Probiotics and Antimicrobial Proteins.2024;[Epub] CrossRef

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

Editorial

Editorial] Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms’ Complex Regulation: Jin-Won Lee; J. Microbiol. 2023;61(3):273-276. Published online April 3, 2023; DOI: https://doi.org/10.1007/s12275-023-00036-6

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Abstract

Bacteria employ a diverse array of cellular regulatory mechanisms to successfully adapt and thrive in ever-changing environments, including but not limited to temperature changes, fluctuations in nutrient availability, the presence or absence of electron acceptors such as oxygen, the availability of metal ions crucial for enzyme activity, and the existence of antibiotics. Bacteria can virtually modulate any step of gene expression from transcr!ptional initiation to posttranslational modification of a protein for the control of cellular processes. Furthermore, one gene regulator often controls another in a complex gene regulatory network. Thus, it is not easy to fully understand the intricacies of bacterial regulatory mechanisms in various environments. In this special issue, while acknowledging the challenge of covering all aspects of bacterial regulatory mechanisms across diverse environments, seven review articles are included to provide insight into the recent progress in understanding such mechanisms from different perspectives: positive regulatory mechanisms by secondary messenger (cAMP receptor protein), two-component signal transduction mechanisms (Rcs and Cpx), diverse regulatory mechanisms by a specific environmental factor in specific bacteria (oxygen availability in Mycobacterium and manganese ion availability in Salmonella), diverse regulatory mechanisms by a specific environmental factor (temperature and antibiotics), and regulatory mechanisms by antibiotics in cell wall synthesis. Bacteria, as ubiquitous organisms that can be found in almost every environment, carry out complex cellular processes that allow them to survive and thrive in a variety of different conditions despite their small size and relative simplicity. One of the key factors that allows bacteria to carry out these complex processes is their ability to regulate gene expression through various mechanisms. Gene expression is a fundamental biological process by which the genetic information encoded in a gene is transcribed into an RNA molecule and subsequently translated into a functional gene product, often a protein. Furthermore, the activity levels of proteins may further be altered by posttranslational modification. Regulation of gene expression refers to the control of the amount and timing of gene expression, and thus it can be divided into transcr!ptional, translational, and posttranslational levels.

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The PhoBR two-component system upregulates virulence in Aeromonas dhakensis C4–1
Wei Feng, Xuesong Li, Nuo Yang, Lixia Fan, Guiying Guo, Jun Xie, Xiuqing Cai, Yuqi Meng, Jifeng Zeng, Yu Han, Jiping Zheng
Aquaculture.2025; 595: 741665. CrossRef
Molecular mechanisms of cold stress response in cotton: Transcriptional reprogramming and genetic strategies for tolerance
Washu Dev, Fahmida Sultana, Hongge Li, Daowu Hu, Zhen Peng, Shoupu He, Haobo Zhang, Muhammad Waqas, Xiaoli Geng, Xiongming Du
Plant Science.2025; 352: 112390. CrossRef
PhoPQ-mediated lipopolysaccharide modification governs intrinsic resistance to tetracycline and glycylcycline antibiotics in Escherichia coli
Byoung Jun Choi, Umji Choi, Dae-Beom Ryu, Chang-Ro Lee, Mehrad Hamidian, You-Hee Cho
mSystems.2024;[Epub] CrossRef
Navigating the signaling landscape of Ralstonia solanacearum: a study of bacterial two-component systems
Mohit Yadav, Janhavi Sathe, Valentina Teronpi, Aditya Kumar
World Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef

Journal Articles

Eradication of drug-resistant Acinetobacter baumannii by cell-penetrating peptide fused endolysin: Jeonghyun Lim , Jaeyeon Jang , Heejoon Myung , Miryoung Song; J. Microbiol. 2022;60(8):859-866. Published online May 25, 2022; DOI: https://doi.org/10.1007/s12275-022-2107-y

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Abstract

Antimicrobial agents targeting peptidoglycan have shown successful results in eliminating bacteria with high selective toxicity. Bacteriophage encoded endolysin as an alternative antibiotics is a peptidoglycan degrading enzyme with a low rate of resistance. Here, the engineered endolysin was developed to defeat multiple drug-resistant (MDR) Acinetobacter baumannii. First, putative endolysin PA90 was predicted by genome analysis of isolated Pseudomonas phage PBPA. The His-tagged PA90 was purified from BL21(DE3) pLysS and tested for the enzymatic activity using Gram-negative pathogens known for having a high antibiotic resistance rate including A. baumannii. Since the measured activity of PA90 was low, probably due to the outer membrane, cell-penetrating peptide (CPP) DS4.3 was introduced at the N-terminus of PA90 to aid access to its substrate. This engineered endolysin, DS-PA90, completely killed A. baumannii at 0.25 μM, at which concentration PA90 could only eliminate less than one log in CFU/ml. Additionally, DS-PA90 has tolerance to NaCl, where the ~50% of activity could be maintained in the presence of 150 mM NaCl, and stable activity was also observed with changes in pH or temperature. Even MDR A. baumannii strains were highly susceptible to DS-PA90 treatment: five out of nine strains were entirely killed and four strains were reduced by 3–4 log in CFU/ml. Consequently, DS-PA90 could protect waxworm from A. baumannii-induced death by ~70% for ATCC 17978 or ~44% for MDR strain 1656-2 infection. Collectively, our data suggest that CPP-fused endolysin can be an effective antibacterial agent against Gramnegative pathogens regardless of antibiotics resistance mechanisms.

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Antimicrobial peptide thanatin fused endolysin PA90 (Tha-PA90) for the control of Acinetobacter baumannii infection in mouse model
Jeonghyun Lim, Heejoon Myung, Daejin Lim, Miryoung Song
Journal of Biomedical Science.2024;[Epub] CrossRef
Tissue damage alleviation and mucin inhibition by P5 in a respiratory infection mouse model with multidrug-resistant Acinetobacter baumannii
Jun Hee Oh, Jonggwan Park, Hee Kyoung Kang, Hee Joo Park, Yoonkyung Park
Biomedicine & Pharmacotherapy.2024; 181: 117724. CrossRef
Potential of antimicrobial peptide-fused endolysin LysC02 as therapeutics for infections and disinfectants for food contact surfaces to control Cronobacter sakazakii
Doyeon Kim, Jinwoo Kim, Minsik Kim
Food Control.2024; 157: 110190. CrossRef
Gram-negative endolysins: overcoming the outer membrane obstacle
Hazel M Sisson, Simon A Jackson, Robert D Fagerlund, Suzanne L Warring, Peter C Fineran
Current Opinion in Microbiology.2024; 78: 102433. CrossRef
LysJEP8: A promising novel endolysin for combating multidrug‐resistant Gram‐negative bacteria
Jose Vicente Carratalá, Neus Ferrer‐Miralles, Elena Garcia‐Fruitós, Anna Arís
Microbial Biotechnology.2024;[Epub] CrossRef
You get what you test for: The killing effect of phage lysins is highly dependent on buffer tonicity and ionic strength
Roberto Vázquez, Diana Gutiérrez, Zoë Dezutter, Bjorn Criel, Philippe de Groote, Yves Briers
Microbial Biotechnology.2024;[Epub] CrossRef
Endolysins: a new antimicrobial agent against antimicrobial resistance. Strategies and opportunities in overcoming the challenges of endolysins against Gram-negative bacteria
Fazal Mehmood Khan, Fazal Rasheed, Yunlan Yang, Bin Liu, Rui Zhang
Frontiers in Pharmacology.2024;[Epub] CrossRef
Characterization of Three Different Endolysins Effective against Gram-Negative Bacteria
Tae-Hwan Jeong, Hye-Won Hong, Min Soo Kim, Miryoung Song, Heejoon Myung
Viruses.2023; 15(3): 679. CrossRef
Design strategies for positively charged endolysins: Insights into Artilysin development
Jose Vicente Carratalá, Anna Arís, Elena Garcia-Fruitós, Neus Ferrer-Miralles
Biotechnology Advances.2023; 69: 108250. CrossRef

Characterization and bioefficacy of green nanosilver particles derived from fungicide-tolerant Tricho-fusant for efficient biocontrol of stem rot (Sclerotium rolfsii Sacc.) in groundnut (Arachis hypogaea L.): Darshna G. Hirpara , Harsukh P. Gajera , Disha D. Savaliya , Rushita V. Bhadani; J. Microbiol. 2021;59(11):1031-1043. Published online October 6, 2021; DOI: https://doi.org/10.1007/s12275-021-1344-9

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Abstract

An efficient and eco-friendly bioefficacy of potent Trichofusant (Fu21) and its green nanosilver formulation against stem rot (Sclerotium rolfsii) in groundnut was established. Fu21 demonstrated higher in-vitro growth inhibition of pathogen with better fungicide tolerance than the parental strains. The green nanosilver particles were synthesized from the extracellular metabolites of Fu21 and characterized for shape (spherical, 59.34 nm in scanning electron microscope), purity (3.00 KeV, energy dispersive X-ray analysis), size (54.3 nm in particle size analyzer), and stability (53.7 mv, zeta). The field efficacy study exhibited that the seedling emergence was high in seeds treated with green nanosilver (minimum inhibitory concentration-[MIC] 20 μg Ag/ml), and a low disease severity index of stem rot during the crop growth was followed by the live antagonist (Fu21) in addition to seed treatment with a fungicide mix under pathogen infestation. The seed quality analysis of harvested pods revealed a high oil content with balanced fatty acid composition (3.10 oleic/linoleic acid ratio) in green nanosilver treatment under pathogen infestation. The residual analysis suggested that green nanosilver applied at the MIC level as seed treatment yielded similar effects as the control for silver residue in the harvested groundnut seeds. The green nanosilver at MIC has a high pod-yield under S. rolfsii infestation, demonstrating green chemistry and sustainability of the nanoproduct.

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Comparative impact of seed priming with zinc oxide nanoparticles and zinc sulphate on biocompatibility, zinc uptake, germination, seedling vitality, and antioxidant modulation in groundnut
M. N. Ashwini, H. P. Gajera, Darshna G. Hirpara, Disha D. Savaliya, U. K. Kandoliya
Journal of Nanoparticle Research.2024;[Epub] CrossRef
Biotechnological trends and optimization of Arachis hypogaea residues valorization: A bibliometric analysis and comprehensive review
Oyetola Ogunkunle, Micheal Olusoji Olusanya
Bioresource Technology.2024; 414: 131585. CrossRef
Intracellular metabolomics and microRNAomics unveil new insight into the regulatory network for potential biocontrol mechanism of stress‐tolerant Tricho‐fusants interacting with phytopathogen Sclerotium rolfsii Sacc
Darshna G. Hirpara, Harsukh P. Gajera
Journal of Cellular Physiology.2023; 238(6): 1288. CrossRef
Antifungal Properties of Nanosilver Clay Composites Against Fungal Pathogens of Agaricus bisporus
Tebogo Levy Ramakutoane, Magaretha Petronella Roux‐van der Merwe, Jacqueline Badenhorst, Sreejarani Kesavan Pillai, Suprakas Sinha Ray
ChemistrySelect.2023;[Epub] CrossRef
Exploring conserved and novel MicroRNA-like small RNAs from stress tolerant Trichoderma fusants and parental strains during interaction with fungal phytopathogen Sclerotium rolfsii Sacc.
Darshna G. Hirpara, H.P. Gajera, Disha D. Savaliya, M.V. Parakhia
Pesticide Biochemistry and Physiology.2023; 191: 105368. CrossRef
Biochemical and molecular depictions to develop ech42 gene-specific SCAR markers for recognition of chitinolytic Trichoderma inhibiting Macrophomina phaseolina (Maubl.) Ashby
H. P. Gajera, Darshna G. Hirpara, Disha D. Savaliya, M. V. Parakhia
Archives of Microbiology.2023;[Epub] CrossRef
Salicylic acid-functionalised chitosan nanoparticles restore impaired sucrose metabolism in the developing anther of cotton (Gossypium hirsutum) under heat stress
Khyati R. Savani, H. P. Gajera, Darshna G. Hirpara, Disha D. Savaliya, U. K. Kandoliya, Honghong Wu
Functional Plant Biology.2023; 50(9): 736. CrossRef

Fungal diversity in deep-sea sediments from Magellan seamounts environment of the western Pacific revealed by high-throughput Illumina sequencing: Shuai Yang , Wei Xu , Yuanhao Gao , Xiaoyao Chen , Zhu-Hua Luo; J. Microbiol. 2020;58(10):841-852. Published online September 2, 2020; DOI: https://doi.org/10.1007/s12275-020-0198-x

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Abstract

There are lots of seamounts globally whose primary production is disproportionally greater than the surrounding areas. Compared to other deep-sea environments, however, the seamounts environment is relatively less explored for fungal diversity. In the present study, we explored the fungal community structure in deep-sea sediments from four different stations of the Magellan seamounts environment by using high-throughput sequencing of the ITS1 region. A total of 1,897,618 ITS1 sequences were obtained. Among these sequences, fungal ITS1 sequences could be clustered into 1,662 OTUs. The majority of these sequences belonged to Ascomycota. In the genera level, the most abundant genus was Mortierella (4.79%), which was reported as a common fungal genus in soil and marine sediments, followed by Umbelopsis (3.80%), Cladosporium (2.98%), Saccharomycopsis (2.53%), Aspergillus (2.42%), Hortaea (2.36%), Saitozyma (2.20%), Trichoderma (2.12%), Penicillium (2.11%), Russula (1.86%), and Verticillium (1.40%). Most of these recovered genera belong to Ascomycota. The Bray-Curtis analysis showed that there was 37 to 85% dissimilarity of fungal communities between each two sediment samples. The Principal coordinates analysis clearly showed variations in the fungal community among different sediment samples. These results suggested that there was a difference in fungal community structures not only among four different sampling stations but also for different layers at the same station. The depth and geographical distance significantly affect the fungal community, and the effect of depth and geographical distance on the structure of the fungal community in the Magellan seamounts is basically same. Most of the fungi were more or less related to plants, these plant parasitic/symbiotic/endophytic fungi constitute a unique type of seamounts environmental fungal ecology, different from other marine ecosystems.

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Biodiversity and community structures across the Magellan seamounts and abyssal plains in the western Pacific Ocean revealed by environmental DNA metabarcoding analysis
Eun-Bi Kim, Se-Jong Ju, Yeon Jee Suh
Frontiers in Marine Science.2024;[Epub] CrossRef
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Miaoyin Dong, Hongyan Su, Jinjuan Li, Dan Zhang, Wenzhi Yao, Delong Yang, Jianhe Wei, Mengfei Li, Paul W. Paré
Industrial Crops and Products.2024; 222: 119953. CrossRef
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Microbiology Spectrum.2023;[Epub] CrossRef
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Xiaojiao An, Shuaibo Han, Xin Ren, John Sichone, Zhiwei Fan, Xinxing Wu, Yan Zhang, Hui Wang, Wei Cai, Fangli Sun
Journal of Fungi.2023; 9(6): 691. CrossRef
Depth-Dependent Distribution of Prokaryotes in Sediments of the Manganese Crust on Nazimov Guyots of the Magellan Seamounts
Jianxing Sun, Hongbo Zhou, Haina Cheng, Zhu Chen, Jichao Yang, Yuguang Wang, Chunlei Jing
Microbial Ecology.2023; 86(4): 3027. CrossRef
Ecological and Oceanographic Perspectives in Future Marine Fungal Taxonomy
Nalin N. Wijayawardene, Don-Qin Dai, Prabath K. Jayasinghe, Sudheera S. Gunasekara, Yuriko Nagano, Saowaluck Tibpromma, Nakarin Suwannarach, Nattawut Boonyuen
Journal of Fungi.2022; 8(11): 1141. CrossRef
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Hong-Wei Shen, Dan-Feng Bao, Darbhe J. Bhat, Hong-Yan Su, Zong-Long Luo
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Environmental Science and Pollution Research.2022; 29(30): 45793. CrossRef
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Natasha Maria Barnes, Samir R. Damare, Belle Damodara Shenoy
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Stefano Varrella, Giulio Barone, Michael Tangherlini, Eugenio Rastelli, Antonio Dell’Anno, Cinzia Corinaldesi
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Zhimin Zhang, Qinghui Deng, Xiuyun Cao, Yiyong Zhou, Chunlei Song
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Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina
Anna Muszewska, Alicja Okrasińska, Kamil Steczkiewicz, Olga Drgas, Małgorzata Orłowska, Urszula Perlińska-Lenart, Tamara Aleksandrzak-Piekarczyk, Katarzyna Szatraj, Urszula Zielenkiewicz, Sebastian Piłsyk, Ewa Malc, Piotr Mieczkowski, Joanna S. Kruszewska
Frontiers in Microbiology.2021;[Epub] CrossRef

Azohydromonas aeria sp. nov., isolated from air: Han Xue , Chun-gen Piao , Dan-ran Bian , Min-wei Guo , Yong Li; J. Microbiol. 2020;58(7):543-549. Published online June 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9423-x

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Abstract

A grey pink colored bacterium, strain t3-1-3T, was isolated from the air at the foot of the Xiangshan Mountain in Beijing, China. The cells are aerobic, Gram-stain-negative, non-sporeforming, motile and coccoid-rod shaped (0.9–1.2 × 1.9–2.1 μm). Strain t3-1-3T was catalase-positive and oxidase-negative and this strain grew at 4–42°C (optimum 28°C), a pH of 4.0–9.0 (optimum pH 7.0) and under 0–2% (w/v) NaCl (optimum 0–1% NaCl). A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain t3-1-3T was closely related to Azohydromonas riparia UCM-11T (97.4% similarity), followed by Azohydromonas australica G1-2T (96.8%) and Azohydromonas ureilytica UCM-80T (96.7%). The genome of strain t3-1-3T contains 6,895 predicted protein-encoding genes, 8 rRNA genes, 62 tRNA genes and one sRNA gene, as well as five potential biosynthetic gene clusters, including clusters of genes coding for non-ribosomal peptide synthetase (NRPS), bacteriocin and arylpolyene and two clusters of genes for terpene. The predominant cellular fatty acids (> 10.0% of the total) in strain t3-1-3T were summed feature 3 (C16:1ω7c and/or C16:1ω6c, 37.8%), summed feature 8 (C18:1ω7c and/or C18:1ω6c, 29.7%) and C16:0 (17.3%). Strain t3-1-3T contained ubiquinone-8 (Q-8) as the predominant respiratory quinone. The polar lipids of strain t3-1-3T comprised phosphatidyl ethanolamine (PE), phosphatidyl glycerol (PG), diphosphatidyl glycerol (DPG), an unidentified glycolipid (GL), an unidentified aminophospholipid (APL), two unidentified phospholipid (PL1-2) and five unidentified lipid (L1-5). The DNA G + C content of the type strain is 70.3%. The broader range of growth temperature, assimilation of malic acid and trisodium citrate, presence of C18:3ω6c and an unidentified glycolipid and absence of C12:0 2-OH and C16:0iso differentiate strain t3-1-3T from related species. Based on the taxonomic data presented in this study, we suggest that strain t3-1-3T represents a novel species within the genus Azohydromonas, for which the name Azohydromonas aeria sp. nov. is proposed. The type strain of Azohydromonas aeria is t3-1-3T (= CFCC 13393T = LMG 30135T).

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The phylogeny of the genus Azohydromonas supports its transfer to the family Comamonadaceae
Ezequiel Gerardo Mogro, Juan Hilario Cafiero, Mauricio Javier Lozano, Walter Omar Draghi
International Journal of Systematic and Evolutionary Microbiology.2022;[Epub] CrossRef
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[Protocol] Detecting Salmonella Type II flagella production by transmission electron microscopy and immunocytochemistry: Yoontak Han , Eun-Jin Lee; J. Microbiol. 2020;58(4):245-251. Published online November 23, 2019; DOI: https://doi.org/10.1007/s12275-020-9297-y

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Abstract

The bacterial flagellum is an appendage structure that provides a means for motility to promote survival in fluctuating environments. For the intracellular pathogen Salmonella enterica serovar Typhimurium to survive within macrophages, flagellar gene expression must be tightly regulated, and thus, is controlled at multiple levels, including DNA recombination, transcription, post-transcription, protein synthesis, and assembly within host cells. To understand the contribution of flagella to Salmonella pathogenesis within the host, it is critical to detect flagella production within macrophages via microscopy. In this paper, we describe two methods for detecting bacterial flagella by microscopy both in vitro and in vivo infection models.

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Qian Zhou, Yu-jing Zhong, Zhu-zhou Shan, Xue-xue Pan, Jing-yu Huang, Jing-shu Xiang, De-zhu Zhang, Wei-wei Li, Jun Li, Ying Liu, Shi-jun Li, Li Zhou
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Xiaohui Liu, Jing Chen, Ying Liu, Zhengfen Wan, Xiaochun Guo, Shaoyong Lu, Dongru Qiu
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Genomic surveillance links livestock production with the emergence and spread of multi-drug resistant non-typhoidal Salmonella in Mexico: Enrique Jesús Delgado-Suárez , Rocío Ortíz-López , Wondwossen A. Gebreyes , Marc W. Allard , Francisco Barona-Gómez , María Salud Rubio-Lozano; J. Microbiol. 2019;57(4):271-280. Published online February 5, 2019; DOI: https://doi.org/10.1007/s12275-019-8421-3

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Abstract

Multi-drug resistant (MDR) non-typhoidal Salmonella (NTS) is increasingly common worldwide. While food animals are thought to contribute to the growing antimicrobial resistance (AMR) problem, limited data is documenting this relationship, especially in low and middle-income countries (LMIC). Herein, we aimed to assess the role of non-clinical NTS of bovine origin as reservoirs of AMR genes of human clinical significance. We evaluated the phenotypic and genotypic AMR profiles in a set of 44 bovine-associated NTS. For comparative purposes, we also included genotypic AMR data of additional isolates from Mexico (n = 1,067) that are publicly available. The most frequent AMR phenotypes in our isolates involved tetracycline (40/44), trimethoprim-sulfamethoxazole (26/44), chloramphenicol (19/44), ampicillin (18/44), streptomycin (16/44), and carbenicillin (13/44), while nearly 70% of the strains were MDR. These phenotypes were correlated with a widespread distribution of AMR genes (i.e. tetA, aadA, dfrA12, dfrA17, sul1, sul2, bla-TEM-1, blaCARB-2) against multiple antibiotic classes, with some of them contributed by plasmids and/or class-1 integrons. We observed different AMR genotypes for betalactams and tetracycline resistance, providing evidence of convergent evolution and adaptive AMR. The probability of MDR genotype occurrence was higher in meat-associated isolates than in those from other sources (odds ratio 11.2, 95% confidence interval 4.5–27.9, P < 0.0001). The study shows that beef cattle are a significant source of MDR NTS in Mexico, highlighting the role of animal production on the emergence and spread of MDR Salmonella in LMIC.

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Geography, Antimicrobial Resistance, and Genomics of Salmonella enterica (Serotypes Newport and Anatum) from Meat in Mexico (2021–2023)
Eduardo Canek Reynoso, Enrique Jesús Delgado-Suárez, Cindy Fabiola Hernández-Pérez, Yaselda Chavarin-Pineda, Elizabeth Ernestina Godoy-Lozano, Geny Fierros-Zárate, Omar Alejandro Aguilar-Vera, Santiago Castillo-Ramírez, Luz del Carmen Sierra Gómez-Pedroso
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Genomic surveillance of antimicrobial resistance shows cattle and poultry are a moderate source of multi-drug resistant non-typhoidal Salmonella in Mexico
Enrique Jesús Delgado-Suárez, Tania Palós-Guitérrez, Francisco Alejandro Ruíz-López, Cindy Fabiola Hernández Pérez, Nayarit Emérita Ballesteros-Nova, Orbelín Soberanis-Ramos, Rubén Danilo Méndez-Medina, Marc W. Allard, María Salud Rubio-Lozano, Iddya Karu
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Daniel F. M. Monte, Fábio P. Sellera, Ralf Lopes, Shivaramu Keelara, Mariza Landgraf, Shermalyn Greene, Paula J. Fedorka-Cray, Siddhartha Thakur, Iddya Karunasagar
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Lytic KFS-SE2 phage as a novel bio-receptor for Salmonella Enteritidis detection: In Young Choi , Cheonghoon Lee , Won Keun Song , Sung Jae Jang , Mi-Kyung Park; J. Microbiol. 2019;57(2):170-179. Published online January 31, 2019; DOI: https://doi.org/10.1007/s12275-019-8610-0

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Abstract

Since Salmonella Enteritidis is one of the major foodborne pathogens, on-site applicable rapid detection methods have been required for its control. The purpose of this study was to isolate and purify S. Enteritidis-specific phage (KFS-SE2 phage) from an eel farm and to investigate its feasibility as a novel, efficient, and reliable bio-receptor for its employment. KFS-SE2 phage was successfully isolated at a high concentration of (2.31 ± 0.43) × 1011 PFU/ml, and consisted of an icosahedral head of 65.44 ± 10.08 nm with a non-contractile tail of 135.21 ± 12.41 nm. The morphological and phylogenetic analysis confirmed that it belongs to the Pis4avirus genus in the family of Siphoviridae. KFS-SE2 genome consisted of 48,608 bp with 45.7% of GC content. Genome analysis represented KFS-SE2 to have distinctive characteristics as a novel phage. Comparative analysis of KFS-SE2 phage with closely related strains confirmed its novelty by the presence of unique proteins. KFS-SE2 phage exhibited excellent specificity to S. Enteritidis and was stable under the temperature range of 4 to 50°C and pH of 3 to 11 (P < 0.05). The latent time was determined to be 20 min. Overall, a new lytic KFS-SE2 phage was successfully isolated from the environment at a high concentration and the excellent feasibility of KFS-SE2 phage was demonstrated as a new bio-receptor for S. Enteritidis detection.

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Characterization of a Salmonella Enteritidis bacteriophage showing broad lytic activity against Gram-negative enteric bacteria: Shukho Kim , Sung-Hun Kim , Marzia Rahman , Jungmin Kim; J. Microbiol. 2018;56(12):917-925. Published online October 25, 2018; DOI: https://doi.org/10.1007/s12275-018-8310-1

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Abstract

In this study, we sought to isolate Salmonella Enteritidis-specific lytic bacteriophages (phages), and we found a lytic phage that could lyse not only S. Enteritidis but also other Gramnegative foodborne pathogens. This lytic phage, SS3e, could lyse almost all tested Salmonella enterica serovars as well as other enteric pathogenic bacteria including Escherichia coli, Shigella sonnei, Enterobacter cloacae, and Serratia marcescens. This SS3e phage has an icosahedral head and a long tail, indicating belong to the Siphoviridae. The genome was 40,793 base pairs, containing 58 theoretically determined open reading frames (ORFs). Among the 58 ORFs, ORF49, and ORF25 showed high sequence similarity with tail spike protein and lysozyme-like protein of Salmonella phage SE2, respectively, which are critical proteins recognizing and lysing host bacteria. Unlike SE2 phage whose host restricted to Salmonella enterica serovars Enteritidis and Gallinarum, SS3e showed broader host specificity against Gram-negative enteric bacteria; thus, it could be a promising candidate for the phage utilization against various Gram-negative bacterial infection including foodborne pathogens.

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