Journal of Microbiology

Research Article

Efficiency of reverse genetics methods for rescuing severe acute respiratory syndrome coronavirus 2: Chang-Joo Park, Taehun Kim, Seung-Min Yoo, Myung-Shin Lee, Nam-Hyuk Cho, Changhoon Park; J. Microbiol. 2025;63(2):e2411023. Published online February 27, 2025; DOI: https://doi.org/10.71150/jm.2411023

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Abstract PDF: Bacteria-free reverse genetics techniques are crucial for the efficient generation of recombinant viruses, bypassing the need for labor-intensive bacterial cloning. These methods are particularly relevant for studying the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19. This study compared the efficiency of three bacteria-free approaches—circular polymerase extension reaction (CPER) with and without nick sealing and infectious sub-genomic amplicons (ISA)—to bacterial artificial chromosome (BAC)-based technology for rescuing SARS-CoV-2. Significant differences in viral titers following transfection were observed between methods. CPER with nick sealing generated virus titers comparable to those of the BAC-based method and 10 times higher than those of the standard CPER. In contrast, ISA demonstrated extremely low efficiency, as cytopathic effects were detected only after two passages. All rescued viruses exhibited replication kinetics consistent with those of the original strain, with no significant deviation in replication capacity. Furthermore, the utility of CPER and ISA in genetically modifying SARS-CoV-2 was demonstrated by successfully inserting the gene encoding green fluorescent protein into the genome. Overall, this study underscores the potential of bacteria-free methods, such as CPER and ISA, in advancing SARS-CoV-2 research while highlighting their significant differences in efficiency.

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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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

Licochalcone A Protects Vaginal Epithelial Cells Against Candida albicans Infection Via the TLR4/NF-κB Signaling Pathway: Wei Li, Yujun Yin, Taoqiong Li, Yiqun Wang, Wenyin Shi; J. Microbiol. 2024;62(7):525-533. Published online May 31, 2024; DOI: https://doi.org/10.1007/s12275-024-00134-z

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Abstract: Vulvovaginal candidiasis (VVC) is a prevalent condition affecting a significant portion of women worldwide. Licochalcone A (LA), a natural compound with diverse biological activities, holds promise as a protective agent against Candida albicans (C. albicans) infection. This study aims to investigate the potential of LA to safeguard vaginal epithelial cells (VECs) from C. albicans infection and elucidate the underlying molecular mechanisms. To simulate VVC in vitro, VK2-E6E7 cells were infected with C. albicans. Candida albicans biofilm formation, C. albicans adhesion to VK2-E6E7 cells, and C. albicans-induced cell damage and inflammatory responses were assessed by XTT reduction assay, fluorescence assay, LDH assay, and ELISA. CCK-8 assay was performed to evaluate the cytotoxic effects of LA on VK2-E6E7 cells. Western blotting assay was performed to detect protein expression. LA dose-dependently hindered C. albicans biofilm formation and adhesion to VK2-E6E7 cells. Furthermore, LA mitigated cell damage, inhibited the Bax/Bcl-2 ratio, and attenuated the secretion of pro-inflammatory cytokines in C. albicans-induced VK2-E6E7 cells. The investigation into LA's impact on the Toll-like receptor 4 (TLR4)/nuclear factor-kappa B (NF-κB) pathway revealed that LA downregulated TLR4 expression and inhibited NF-κB activation in C. albicans-infected VK2-E6E7 cells. Furthermore, TLR4 overexpression partially abated LA-mediated protection, further highlighting the role of the TLR4/NF-κB pathway. LA holds the potential to safeguard VECs against C. albicans infection, potentially offering therapeutic avenues for VVC management.

Review

Reverse Zoonotic Transmission of SARS-CoV-2 and Monkeypox Virus: A Comprehensive Review: Chiranjib Chakraborty, Manojit Bhattacharya, Md Aminul Islam, Hatem Zayed, Elijah Ige Ohimain, Sang-Soo Lee, Prosun Bhattacharya, Kuldeep Dhama; J. Microbiol. 2024;62(5):337-354. Published online May 23, 2024; DOI: https://doi.org/10.1007/s12275-024-00138-9

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Abstract

Reverse zoonosis reveals the process of transmission of a pathogen through the human-animal interface and the spillback of the zoonotic pathogen. In this article, we methodically demonstrate various aspects of reverse zoonosis, with a comprehensive discussion of SARS-CoV-2 and MPXV reverse zoonosis. First, different components of reverse zoonosis, such as humans, different pathogens, and numerous animals (poultry, livestock, pets, wild animals, and zoo animals), have been demonstrated. Second, it explains the present status of reverse zoonosis with different pathogens during previous occurrences of various outbreaks, epidemics, and pandemics. Here, we present 25 examples from literature. Third, using several examples, we comprehensively illustrate the present status of the reverse zoonosis of SARS-CoV-2 and MPXV. Here, we have provided 17 examples of SARS-CoV-2 reverse zoonosis and two examples of MPXV reverse zoonosis. Fourth, we have described two significant aspects of reverse zoonosis: understanding the fundamental aspects of spillback and awareness. These two aspects are required to prevent reverse zoonosis from the current infection with two significant viruses. Finally, the One Health approach was discussed vividly, where we urge scientists from different areas to work collaboratively to solve the issue of reverse zoonosis.

Citations

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Development of a multiplex real-time PCR for the simultaneous detection of monkeypox virus clades I, II, and goatpox virus
Yongqiang Lin, Zijing Guo, Jinsong Chen, Xianwen Zhang, Long Zhou, Yanmin Li, Zhidong Zhang
Frontiers in Veterinary Science.2024;[Epub] CrossRef

Journal Articles

The Regulation of Phosphorus Release by Penicillium chrysogenum in Different Phosphate via the TCA Cycle and Mycelial Morphology: Liyan Wang , Da Tian , Xiaoru Zhang , Mingxue Han , Xiaohui Cheng , Xinxin Ye , Chaochun Zhang , Hongjian Gao , Zhen Li; J. Microbiol. 2023;61(8):765-775. Published online September 4, 2023; DOI: https://doi.org/10.1007/s12275-023-00072-2

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Abstract: Phosphate-solubilizing fungi (PSF) efficiently dissolve insoluble phosphates through the production of organic acids. This study investigates the mechanisms of organic acid secretion by PSF, specifically Penicillium chrysogenum, under tricalcium phosphate ( Ca3(PO4)2, Ca–P) and ferric phosphate ( FePO4, Fe–P) conditions. Penicillium chrysogenum exhibited higher phosphorus (P) release efficiency from Ca-P (693.6 mg/L) than from Fe–P (162.6 mg/L). However, Fe–P significantly enhanced oxalic acid (1193.7 mg/L) and citric acid (227.7 mg/L) production by Penicillium chrysogenum compared with Ca–P (905.7 and 3.5 mg/L, respectively). The presence of Fe–P upregulated the expression of genes and activity of enzymes related to the tricarboxylic acid cycle, including pyruvate dehydrogenase and citrate synthase. Additionally, Fe–P upregulated the expression of chitinase and endoglucanase genes, inducing a transformation of Penicillium chrysogenum mycelial morphology from pellet to filamentous. The filamentous morphology exhibited higher efficiency in oxalic acid secretion and P release from Fe–P and Ca–P. Compared with pellet morphology, filamentous morphology enhanced P release capacity by > 40% and > 18% in Ca–P and Fe–P, respectively. This study explored the strategies employed by PSF to improve the dissolution of different insoluble phosphates.

Promoter exchange of the cryptic nonribosomal peptide synthetase gene for oligopeptide production in Aspergillus oryzae: Chanikul Chutrakul , Sarocha Panchanawaporn , Sukanya Jeennor , Jutamas Anantayanon , Kobkul Laoteng; J. Microbiol. 2022;60(1):47-56. Published online November 9, 2021; DOI: https://doi.org/10.1007/s12275-022-1442-3

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Abstract

Oligopeptides with functional activities are of current interest in the nutraceutical and medical sectors. The development of the biosynthetic process of oligopeptides through a nonribosomal peptide synthetase (NRPS) system has become more challenging. To develop a production platform for nonribosomal peptides (NRPs), reprogramming of transcriptional regulation of the acv gene encoded ACV synthetase (ACVS) was implemented in Aspergillus oryzae using the CRISPRCas9 system. Awakening silent acv expression was successfully achieved by promoter substitution. Among the three exchanged promoters, AoPgpdA, AoPtef1, and PtPtoxA, the replacement of the native promoter with AoPgpdA led to the highest ACV production in A. oryzae. However, the ACV production of the AoPGpdA strain was also dependent on the medium composition, in which urea was the best nitrogen source, and a C:N ratio of 20:1 was optimal for tripeptide production. In addition to cell growth, magnesium ions are an essential element for ACV production and might participate in ACVS activity. It was also found that ACV was the growthassociated product of the engineered strain that might be a
result
of constitutive transcriptional control by the AoPgpdA promoter. This study offers a potential strategy for nonribosomal ACV production using the fungal system, which is applicable for redesigning bioactive oligopeptides with industrial relevance.

Citations

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Strategies for the Enhancement of Secondary Metabolite Production via Biosynthesis Gene Cluster Regulation in Aspergillus oryzae
Xiao Jia, Jiayi Song, Yijian Wu, Sai Feng, Zeao Sun, Yan Hu, Mengxue Yu, Rui Han, Bin Zeng
Journal of Fungi.2024; 10(5): 312. 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
Journal of Microbiology.2023; 61(2): 199. 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
Synthetic microbes and biocatalyst designs in Thailand
Duangthip Trisrivirat, Ruchanok Tinikul, Pimchai Chaiyen
Biotechnology Notes.2023; 4: 28. CrossRef
Potential of Aspergillus oryzae as a biosynthetic platform for indigoidine, a non-ribosomal peptide pigment with antioxidant activity
Sarocha Panchanawaporn, Chanikul Chutrakul, Sukanya Jeennor, Jutamas Anantayanon, Nakul Rattanaphan, Kobkul Laoteng, Daniel Cullen
PLOS ONE.2022; 17(6): e0270359. CrossRef
CRISPR/Cas9-Based Genome Editing and Its Application in Aspergillus Species
Feng-Jie Jin, Bao-Teng Wang, Zhen-Dong Wang, Long Jin, Pei Han
Journal of Fungi.2022; 8(5): 467. CrossRef

Review

Application of computational approaches to analyze metagenomic data: Ho-Jin Gwak , Seung Jae Lee , Mina Rho; J. Microbiol. 2021;59(3):233-241. Published online February 10, 2021; DOI: https://doi.org/10.1007/s12275-021-0632-8

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Abstract

Microorganisms play a vital role in living systems in numerous ways. In the soil or ocean environment, microbes are involved in diverse processes, such as carbon and nitrogen cycle, nutrient recycling, and energy acquisition. The relation between microbial dysbiosis and disease developments has been extensively studied. In particular, microbial communities in the human gut are associated with the pathophysiology of several chronic diseases such as inflammatory bowel disease and diabetes. Therefore, analyzing the distribution of microorganisms and their associations with the environment is a key step in understanding nature. With the advent of nextgeneration sequencing technology, a vast amount of metagenomic data on unculturable microbes in addition to culturable microbes has been produced. To reconstruct microbial genomes, several assembly algorithms have been developed by incorporating metagenomic features, such as uneven depth. Since it is difficult to reconstruct complete microbial genomes from metagenomic reads, contig binning approaches were suggested to collect contigs that originate from the same genome. To estimate the microbial composition in the environment, various methods have been developed to classify individual reads or contigs and profile bacterial proportions. Since microbial communities affect their hosts and environments through metabolites, metabolic profiles from metagenomic or metatranscriptomic data have been estimated. Here, we provide a comprehensive review of computational
methods
that can be applied to investigate microbiomes using metagenomic and metatranscriptomic sequencing data. The limitations of metagenomic studies and the key approaches to overcome such problems are discussed.

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A Review of Web-Based Metagenomics Platforms for Analysing Next-Generation Sequence Data
Arunmozhi Bharathi Achudhan, Priya Kannan, Annapurna Gupta, Lilly M. Saleena
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Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities
Alexander Van Uffelen, Andrés Posadas, Nancy H. C. Roosens, Kathleen Marchal, Sigrid C. J. De Keersmaecker, Kevin Vanneste
Scientific Data.2024;[Epub] CrossRef
Metagenomic approaches and opportunities in arid soil research
Muhammad Riaz Ejaz, Kareem Badr, Zahoor Ul Hassan, Roda Al-Thani, Samir Jaoua
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DeepCheck: multitask learning aids in assessing microbial genome quality
Guo Wei, Nannan Wu, Kunyang Zhao, Sihai Yang, Long Wang, Yan Liu
Briefings in Bioinformatics.2024;[Epub] CrossRef
Integrated multi-omics analyses of microbial communities: a review of the current state and future directions
Muzaffer Arıkan, Thilo Muth
Molecular Omics.2023; 19(8): 607. CrossRef
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Yan Zhang, Jiao Jin, Biyan Huang, Huimin Ying, Jie He, Liang Jiang
Biomolecules.2022; 12(7): 917. CrossRef
Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels
Juan José González-Plaza, Cristina Furlan, Tomaž Rijavec, Aleš Lapanje, Rocío Barros, Juan Antonio Tamayo-Ramos, Maria Suarez-Diez
Frontiers in Microbiology.2022;[Epub] CrossRef
Efficient and Quality-Optimized Metagenomic Pipeline Designed for Taxonomic Classification in Routine Microbiological Clinical Tests
Sylvie Buffet-Bataillon, Guillaume Rizk, Vincent Cattoir, Mohamed Sassi, Vincent Thibault, Jennifer Del Giudice, Jean-Pierre Gangneux
Microorganisms.2022; 10(4): 711. CrossRef
Establishment and Validation of a New Analysis Strategy for the Study of Plant Endophytic Microorganisms
Feng Chen, Xianjin Wang, Guiping Qiu, Haida Liu, Yingquan Tan, Beijiu Cheng, Guomin Han
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Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease
Alba Boix-Amorós, Hilary Monaco, Elisa Sambataro, Jose C. Clemente
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Current Understanding on the Genetic Basis of Key Metabolic Disorders: A Review
Kenneth Francis Rodrigues, Wilson Thau Lym Yong, Md. Safiul Alam Bhuiyan, Shafiquzzaman Siddiquee, Muhammad Dawood Shah, Balu Alagar Venmathi Maran
Biology.2022; 11(9): 1308. CrossRef
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Journal Articles

Caspase-3 inhibitor inhibits enterovirus D68 production: Wenbo Huo , Jinghua Yu , Chunyu Liu , Ting Wu , Yue Wang , Xiangling Meng , Fengmei Song , Shuxia Zhang , Ying Su , Yumeng Liu , Jinming Liu , Xiaoyan Yu , Shucheng Hua; J. Microbiol. 2020;58(9):812-820. Published online September 1, 2020; DOI: https://doi.org/10.1007/s12275-020-0241-y

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Abstract

Enterovirus D68 (EVD68) is an emerging pathogen that recently caused a large worldwide outbreak of severe respiratory disease in children. However, the relationship between EVD68 and host cells remains unclear. Caspases are involved in cell death, immune response, and even viral production. We found that caspase-3 was activated during EVD68 replication to induce apoptosis. Caspase-3 inhibitor (Z-DEVDFMK) inhibited viral production, protected host cells from the cytopathic effects of EVD68 infection, and prevented EVD68 from regulating the host cell cycle at G0/G1. Meanwhile, caspase-3 activator (PAC-1) increased EVD68 production. EVD68 infection therefore activates caspase-3 for virus production. This knowledge provides a potential direction for the prevention and treatment of disease related to EVD68.

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Mst1/2-ALK promotes NLRP3 inflammasome activation and cell apoptosis during Listeria monocytogenes infection
Aijiao Gao, Huixin Tang, Qian Zhang, Ruiqing Liu, Lin Wang, Yashan Liu, Zhi Qi, Yanna Shen
Journal of Microbiology.2021; 59(7): 681. CrossRef

Short-term effects of returning granulated straw on soil microbial community and organic carbon fractions in dryland farming: Wei Fan , Jinggui Wu; J. Microbiol. 2020;58(8):657-667. Published online June 25, 2020; DOI: https://doi.org/10.1007/s12275-020-9266-5

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Abstract

We conducted a 2-year field experiment which was comprised of five treatments, namely no straw returning (CK), straw mulching (SM), straw plowed into the soil (SP), and straw returned in granulated form (SG). The aim of this study was to investigate the effects of different straw returning modes on soil bacterial and fungal community structure and their relationships to soil organic carbon (SOC) fractions at three different soil depths (0–20, 20–40, and 40–60 cm) in a dryland under maize cultivation in Northeast (NE) China. SM, SP, and SG treatments significantly increased SOC content. Compared with SM and SP treatments, SG treatment significantly increased the content of SOC and easily oxidizable carbon (EOC) in the topsoil (0–20 cm depth), and increased dissolved organic carbon (DOC) and SOC content of the light fraction (LFOC) in the 20–40 cm layer. Meanwhile, SG treatment exhibited the highest microbial biomass C (MBC) content in all of the three soil depths. SG treatment also enhanced bacterial richness as well as fungal richness and diversity in the upper 40 cm of soil. In addition, SG treatment increased the relative abundance of Proteobacteria in all depths, and had the highest relative abundance of Basidiomycota in the first 20 cm of soil. SP treatment showed the lowest soil organic carbon content in all fractions and soil microbial community composition. SM treatment exhibited similar results to SG treatment in SOC, DOC, and LFOC contents, and bacterial diversity in the topsoil and subsoil. As a whole, treatment SG improved soil quality and maize yield, hence we recommend returning granulated straw as the most effective practice for enhancing labile SOC fractions as well as maintaining soil diversity and microbial richness of arid farmlands in NE China.

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Yue Yang, Yan'an Tong, Lian-you Liang, Hong-chang Li, Wen-she Han
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Performance comparison of fecal preservative and stock solutions for gut microbiome storage at room temperature: Chanhyeok Park , Kyeong Eui Yun , Jeong Min Chu , Ji Yeon Lee , Chang Pyo Hong , Young Do Nam , Jinuk Jeong , Kyudong Han , Yong Ju Ahn; J. Microbiol. 2020;58(8):703-710. Published online June 25, 2020; DOI: https://doi.org/10.1007/s12275-020-0092-6

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Abstract

The gut microbiome, which is symbiotic within the human body, assists in human digestion. It plays significant roles in identifying intestinal disease as well as in maintaining a healthy body with functional immune and metabolic activities. To confirm the consistency of fecal intestinal microbial research, it is necessary to study the changes in intestinal microbial flora according to the fecal collection solution and storage period. We collected fecal samples from three healthy Korean adults. To examine the efficacy of fecal collection solution, we used NBgene-Gut, OMNIgene-Gut, 70% ethanol (Ethanol-70%), and RNAlater. The samples were stored for up to two months at room temperature using three different
methods
, and we observed changes in microbial communities over time. We analyzed clusters of changes in the microbial flora by observing fecal stock solutions and metagenome sequencing performed over time. In particular, we confirmed the profiling of alpha and beta diversity and microbial classification according to the differences in intestinal environment among individuals. We also confirmed that the microbial profile remained stable for two months and that the microbial profile did not change significantly over time. In addition, our results suggest the possibility of verifying microbial profiling even for long-term storage of a single sample. In conclusion, collecting fecal samples using a stock solution rather than freezing feces seems to be relatively reproducible and stable for GUT metagenome analysis. Therefore, stock solution tubes in intestinal microbial research can be used without problems.

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Critical evaluation of faecal microbiome preservation using metagenomic analysis
Alena L Pribyl, Donovan H Parks, Nicola Z Angel, Joel A Boyd, Alexander G Hasson, Liang Fang, Samantha L MacDonald, Blake A Wills, David L A Wood, Lutz Krause, Gene W Tyson, Philip Hugenholtz
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Simultaneous detection of Salmonella spp., Pseudomonas aeruginosa, Bacillus cereus, and Escherichia coli O157:H7 in environmental water using PMA combined with mPCR: Guoyang Xie , Shuang Yu , Wen Li , Dan Mu , Zoraida P. Aguilar , Hengyi Xu; J. Microbiol. 2020;58(8):668-674. Published online June 25, 2020; DOI: https://doi.org/10.1007/s12275-020-0084-6

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Abstract

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

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Xinyi Zhao, Abhijnan Bhat, Christine O’Connor, James Curtin, Baljit Singh, Furong Tian
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Qian Xu, Guoyang Xie, Qiang Shi, Ju Liu, Baoqing Zhou, Ping Tong, Zoraida P. Aguilar, Hengyi Xu
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Review

Regulation of the AcrAB efflux system by the quorum-sensing regulator AnoR in Acinetobacter nosocomialis: Bindu Subhadra , Surya Surendran , Bo Ra Lim , Jong Sung Yim , Dong Ho Kim , Kyungho Woo , Hwa-Jung Kim , Man Hwan Oh , Chul Hee Choi; J. Microbiol. 2020;58(6):507-518. Published online May 27, 2020; DOI: https://doi.org/10.1007/s12275-020-0185-2

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Abstract

Multidrug efflux pumps play an important role in antimicrobial resistance and pathogenicity in bacteria. Here, we report the functional characterization of the RND (resistance-nodulation- division) efflux pump, AcrAB, in Acinetobacter nosocomialis. An in silico analysis revealed that homologues of the AcrAB efflux pump, comprising AcrA and AcrB, are widely distributed among different bacterial species. Deletion of acrA and/or acrB genes led to decreased biofilm/pellicle formation and reduced antimicrobial resistance in A. nosocomialis. RNA sequencing and mRNA expression analyses showed that expression of acrA/B was downregulated in a quorum sensing (QS) regulator (anoR)-deletion mutant, indicating transcriptional activation of the acrAB operon by AnoR in A. nosocomialis. Bioassays showed that secretion of N-acyl homoserine lactones (AHLs) was unaffected in acrA and acrB deletion mutants; however, AHL secretion was limited in a deletion mutant of acrR, encoding the acrAB regulator, AcrR. An in silico analysis indicated the presence of AcrR-binding motifs in promoter regions of anoI (encoding AHL synthase) and anoR. Specific binding of AcrR was confirmed by electrophoretic mobility shift assays, which revealed that AcrR binds to positions -214 and -217 bp upstream of the translational start sites of anoI and anoR, respectively, demonstrating transcriptional regulation of these QS genes by AcrR. The current study further addresses the possibility that AcrAB is controlled by the osmotic stress regulator, OmpR, in A. nosocomialis. Our data demonstrate that the AcrAB efflux pump plays a crucial role in biofilm/pellicle formation and antimicrobial resistance in A. nosocomialis, and is under the transcriptional control of a number of regulators. In addition, the study emphasizes the interrelationship of QS and AcrAB efflux systems in A. nosocomialis.

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Types and Mechanisms of Efflux Pump Systems and the Potential of Efflux Pump Inhibitors in the Restoration of Antimicrobial Susceptibility, with a Special Reference to Acinetobacter baumannii
Kira M. Zack, Trent Sorenson, Suresh G. Joshi
Pathogens.2024; 13(3): 197. CrossRef
Lysine Trimethylation in Planktonic and Pellicle Modes of Growth in Acinetobacter baumannii
Nicolas Nalpas, Takfarinas Kentache, Emmanuelle Dé, Julie Hardouin
Journal of Proteome Research.2023; 22(7): 2339. CrossRef
The Mechanism of Tigecycline Resistance in Acinetobacter baumannii Revealed by Proteomic and Genomic Analysis
Cunwei Liu, Lei Wang, Ping Wang, Di Xiao, Qinghua Zou
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Yijun Li, Guanwen Sun, Jingchan Xie, Suli Xiao, Chen Lin
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The multifaceted genusAcinetobacter: from infection to bioremediation
Ujwal Dahal, Karan Paul, Shelly Gupta
Journal of Applied Microbiology.2023;[Epub] CrossRef
Efflux pumps and microbial biofilm formation
Mahdyeh Neghabi Hajiagha, Hossein Samadi Kafil
Infection, Genetics and Evolution.2023; 112: 105459. CrossRef
Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria
Ronit Vogt Sionov, Doron Steinberg
Microorganisms.2022; 10(6): 1239. CrossRef
Evidence for Complex Interplay between Quorum Sensing and Antibiotic Resistance in Pseudomonas aeruginosa
Rakesh Sikdar, Mikael H. Elias, Giordano Rampioni
Microbiology Spectrum.2022;[Epub] CrossRef
Update on Multidrug Resistance Efflux Pumps in Acinetobacter spp.
Vanessa Kornelsen, Ayush Kumar
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Meletis Rozis, Dimitrios S Evangelopoulos, Spyros G Pneumaticos
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Journal Articles

Endophytic bacterial and fungal microbiota in different cultivars of cassava (Manihot esculenta Crantz): Hong Li , Chengliang Yan , Yanqiong Tang , Xiang Ma , Yinhua Chen , Songbi Chen , Min Lin , Zhu Liu; J. Microbiol. 2020;58(7):614-623. Published online May 18, 2020; DOI: https://doi.org/10.1007/s12275-020-9565-x

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Abstract

Endophytes colonize tissues of healthy host plants and play a crucial role in plant growth and development. However, little attention has been paid to the endophytes of tuber crops such as cassava, which is used as a staple food by approximately 800 million people worldwide. This study aimed to elucidate the diversity and composition of endophytic bacterial and fungal communities in different cassava cultivars using high-throughput sequencing. Although no significant differences in richness or diversity were observed among the different cassava cultivars, the community compositions were diverse. Two cultivars (SC124 and SC205) tolerant to root rot exhibited similar community compositions, while two other cultivars (SC10 and SC5), which are moderately and highly susceptible to root rot, respectively, harboured similar community compositions. Proteobacteria, Firmicutes, and Ascomycota dominated the endophyte assemblages, with Weissella, Serratia, Lasiodiplodia, Fusarium, and Diaporthe being the predominant genera. The differentially abundant taxonomic clades between the tolerant and susceptible cultivars were mainly rare taxa, such as Lachnoclostridium_5, Rhizobium, Lampropedia, and Stenotrophomonas. These seemed to be key genera that affected the susceptibility of cassava to root rot. Moreover, the comparison of KEGG functional profiles revealed that ‘Environmental adaptation’ category was significantly enriched in the tolerant cultivars, while ‘Infectious diseases: Parasitic’ category was significantly enriched in the susceptible cultivars. The present findings open opportunities for further studies on the roles of endophytes in the susceptibility of plants to diseases.

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Are rot-causing Botryosphaeriaceae species surviving in healthy Manihot esculenta propagative material in Brazil?
Amanda Cupertino de Queiroz Brito, Juliana Ferreira de Mello, José Vitorino da Silva Neto, Daniele Magna Azevedo de Assis, Ana Elisa de Almeida Souza, Antonio Félix da Costa, Ueder Pedro Lopes, Cristina Maria de Souza-Motta, Alexandre Reis Machado
Tropical Plant Pathology.2025;[Epub] CrossRef
Nutrient Management Under Good Agricultural Practices for Sustainable Cassava Production in Northeastern Thailand
Derrick Keith Thompson, Ornprapa Thepsilvisut, Phanawan Imorachorn, Saowakol Boonkaen, Preuk Chutimanukul, Suthasinee Somyong, Wuttichai Mhuantong, Hiroshi Ehara
Resources.2025; 14(3): 39. CrossRef
Impact of Vanadium–Titanium–Magnetite Mining Activities on Endophytic Bacterial Communities and Functions in the Root Systems of Local Plants
Zhuang Xiong, Yunfeng Zhang, Xiaodie Chen, Ajia Sha, Wenqi Xiao, Yingyong Luo, Lianxin Peng, Liang Zou, Qiang Li
Genes.2024; 15(5): 526. CrossRef
Colorimetric LAMP Assay for Detection of Xanthomonas phaseoli pv. manihotis in Cassava Through Genomics: A New Approach to an Old Problem
Ian C. Bispo Carvalho, Alice Maria Silva Carvalho, Adriane Wendland, Maurício Rossato
Plant Disease.2024; 108(10): 2993. CrossRef
Genetic diversity, plant growth promotion potential, and antimicrobial activity of culturable endophytic actinobacteria isolated from Aconitum carmichaelii Debeaux
Lan Zou, Yaopeng Zhang, Qian Wang, Siyu Wang, Muyi Li, Jing Huang
Journal of Applied Microbiology.2023;[Epub] CrossRef
High-throughput sequencing-based analysis of the composition and diversity of endophytic bacteria community in tubers of Gastrodia elata f.glauca
Heng Zheng, Peng Zhang, Jing Qin, Jiani Guo, Jun Deng
Frontiers in Microbiology.2023;[Epub] CrossRef
Richness of Nigrospora spp. (Apiosporaceae) in Manihot esculenta in Brazil and the description of three new species
Amanda Cupertino de Queiroz Brito, Juliana Ferreira de Mello, Ana Elisa de Almeida Souza, Sandy dos Santos Nascimento, Cristina Maria de Souza-Motta, Alexandre Reis Machado
Mycological Progress.2023;[Epub] CrossRef
Biocontrol de Fusarium spp. en el cultivo de vainilla: Un nuevo modelo de estudio
Laura Steffania Franco-Galindo , Ana Teresa Mosquera-Espinosa
Temas Agrarios.2023; 28(1): 95. CrossRef
Endophytic bacterial community structure and diversity of the medicinal plant Mirabilis himalaica from different locations
Erhao Zhang, Yazhou Lu, Rundong Zhao, Xiu Yin, Jie Zhang, Benxia Yu, Min Yao, Zhihua Liao, Xiaozhong Lan
Brazilian Journal of Microbiology.2023; 54(4): 2991. CrossRef
Diversity of the Bacterial Microbiome Associated With the Endosphere and Rhizosphere of Different Cassava (Manihot esculenta Crantz) Genotypes
Jingwen Ha, Yu Gao, Rui Zhang, Ke Li, Yijie Zhang, Xiaolei Niu, Xin Chen, Kai Luo, Yinhua Chen
Frontiers in Microbiology.2021;[Epub] CrossRef
The Diversity of Culture-Dependent Gram-Negative Rhizobacteria Associated with Manihot esculenta Crantz Plants Subjected to Water-Deficit Stress
Tatiana Zapata, Diana Marcela Galindo, Alba Rocío Corrales-Ducuara, Iván Darío Ocampo-Ibáñez
Diversity.2021; 13(8): 366. CrossRef
Isolation and characterization of cassava root endophytic bacteria with the ability to promote plant growth and control the in vitro and in vivo growth of Phytopythium sp.
Solange da Cunha Ferreira, Alessandra Keiko Nakasone, Silvia Mara Coelho do Nascimento, Danyllo Amaral de Oliveira, Andrei Santos Siqueira, Elisa Ferreira Moura Cunha, Gledson Luiz Salgado de Castro, Cláudia Regina Batista de Souza
Physiological and Molecular Plant Pathology.2021; 116: 101709. CrossRef

Development of a real-time loop-mediated isothermal amplification method for the detection of severe fever with thrombocytopenia syndrome virus: Jae Woong Lee , Yu-Jung Won , Lae Hyung Kang , Sung-Geun Lee , Seung-Won Park , Soon-Young Paik; J. Microbiol. 2020;58(8):711-715. Published online May 18, 2020; DOI: https://doi.org/10.1007/s12275-020-0109-1

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Abstract

Severe fever with thrombocytopenia syndrome (SFTS) is being reported annually in South Korea since its first detection there in 2010. The causal agent is a negative-strand RNA virus 80–100 nm in diameter. It causes fever, thrombocytopenia, leukocytopenia, gastrointestinal symptoms, and neural symptoms. The mortality rate of SFTS was 32.6% among 172
case
s reported from 2012 to 2015 in South Korea. Thus, is necessary to develop an effective diagnostic method that selectively identifies the isolates circulating in South Korea. The real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay is a simple, rapid, and sensitive approach for molecular diagnosis. Here, we designed novel primers for this assay and found that the technique had very high specificity, sensitivity, and efficiency. This real-time RTLAMP approach using the novel primers developed herein can be applied for early diagnosis of SFTSV strains in South Korea to reduce the mortality rate of SFTS.

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Yumiko Saga, Toshikazu Yoshida, Rieko Yoshida, Shunsuke Yazawa, Takahisa Shimada, Noriko Inasaki, Masae Itamochi, Emiko Yamazaki, Kazunori Oishi, Hideki Tani
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Jing Xue, Qing Ren, Rui Jian, Guang-Cheng Xie, Yongliang Chen, Jiangli Wang, Luanying Du, Wen-Ping Guo
Journal of Microbiological Methods.2022; 202: 106601. CrossRef
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Mengqian Huang, Sihua Liu, Yanan Xu, Aqian Li, Wei Wu, Mifang Liang, Guoyu Niu, Zhiyun Wang, Tao Wang
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Mei Zhang, Yanhua Du, Li Yang, Lin Zhan, Bin Yang, Xueyong Huang, Bianli Xu, Koichi Morita, Fuxun Yu
The Brazilian Journal of Infectious Diseases.2022; 26(4): 102386. CrossRef
Development of an RT-LAMP Assay for the Rapid Detection of SFTS Virus
Shiori Sano, Shuetsu Fukushi, Souichi Yamada, Shizuko Harada, Hitomi Kinoshita, Satoko Sugimoto, Tomoki Yoshikawa, Takeshi Kurosu, Yuki Takamatsu, Masayuki Shimojima, Shoichi Toda, Yuka Hamada, Naoki Fujisawa, Takayuki Sugimoto, Masayuki Saijo
Viruses.2021; 13(4): 693. CrossRef
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Xingan Hao, Licheng Wang, Xudong Zhang, Qinrong Zhong, Jamal-U-Ddin Hajano, Liangsheng Xu, Yunfeng Wu
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Baseline mapping of severe fever with thrombocytopenia syndrome virology, epidemiology and vaccine research and development
Nathen E. Bopp, Jaclyn A. Kaiser, Ashley E. Strother, Alan D. T. Barrett, David W. C. Beasley, Virginia Benassi, Gregg N. Milligan, Marie-Pierre Preziosi, Lisa M. Reece
npj Vaccines.2020;[Epub] CrossRef

Long-term continuously monocropped peanut significantly disturbed the balance of soil fungal communities: Mingna Chen , Jiancheng Zhang , Hu Liu , Mian Wang , LiJuan Pan , Na Chen , Tong Wang , Yu Jing , Xiaoyuan Chi , Binghai Du; J. Microbiol. 2020;58(7):563-573. Published online April 22, 2020; DOI: https://doi.org/10.1007/s12275-020-9573-x

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Abstract

Balancing soil microbial diversity and abundance is critical to sustaining soil health, and understanding the dynamics of soil microbes in a monocropping system can help determine how continuous monocropping practices induce soil sickness mediated by microorganisms. This study used previously constructed gradient continuous monocropping plots and four varieties with different monocropping responses were investigated. The feedback responses of their soil fungal communities to short-term and long-term continuous monocropping were tracked using high-throughput sequencing techniques. The analyses indicated that soil samples from 1 and 2 year monocropped plots were grouped into one class, and samples from the 11 and 12 year plots were grouped into another, regardless of variety. At the species level, the F. solani, Fusarium oxysporum, Neocosmospora striata, Acrophialophora levis, Aspergillus niger, Aspergillus corrugatus, Thielavia hyrcaniae, Emericellopsis minima, and Scedosporium aurantiacum taxa showed significantly increased abundances in the long-term monocropping libraries compared to the short-term cropping libraries. In contrast, Talaromyces flavus, Talaromyces purpureogenus, Mortierella alpina, Paranamyces uniporus, and Volutella citrinella decreased in the long-term monocropping libraries compared to the shortterm libraries. This study, combined with our previous study, showed that fungal community structure was significantly affected by the length of the monocropping period, but peanut variety and growth stages were less important. The increase in pathogen abundances and the decrease in beneficial fungi abundances seem to be the main cause for the yield decline and poor growth of long-term monocultured peanut. Simplification of fungal community diversity could also contribute to peanut soil sickness under long-term monocropping. Additionally, the different responses of peanut varieties to monocropping may be related to variations in their microbial community structure.

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Short-term continuous monocropping reduces peanut yield mainly via altering soil enzyme activity and fungal community
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