Journal of Microbiology

Journal Articles

Deletion of IRC19 Causes Defects in DNA Double-Strand Break Repair Pathways in Saccharomyces cerevisiae: Ju-Hee Choi, Oyungoo Bayarmagnai, Sung-Ho Bae; J. Microbiol. 2024;62(9):749-758. Published online July 12, 2024; DOI: https://doi.org/10.1007/s12275-024-00152-x

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Abstract: DNA double-strand break (DSB) repair is a fundamental cellular process crucial for maintaining genome stability, with homologous recombination and non-homologous end joining as the primary mechanisms, and various alternative pathways such as single-strand annealing (SSA) and microhomology-mediated end joining also playing significant roles under specific conditions. IRC genes were previously identified as part of a group of genes associated with increased levels of Rad52 foci in Saccharomyces cerevisiae. In this study, we investigated the effects of IRC gene mutations on DSB repair, focusing on uncharacterized IRC10, 19, 21, 22, 23, and 24. Gene conversion (GC) assay revealed that irc10Δ, 22Δ, 23Δ, and 24Δ mutants displayed modest increases in GC frequencies, while irc19Δ and irc21Δ mutants exhibited significant reductions. Further investigation revealed that deletion mutations in URA3 were not generated in irc19Δ mutant cells following HO-induced DSBs. Additionally, irc19Δ significantly reduced frequency of SSA, and a synergistic interaction between irc19Δ and rad52Δ was observed in DSB repair via SSA. Assays to determine the choice of DSB repair pathways indicated that Irc19 is necessary for generating both GC and deletion products. Overall, these results suggest a potential role of Irc19 in DSB repair pathways, particularly in end resection process.

Development of a Novel Korean H9‑Specific rRT‑PCR Assay and Its Application for Avian Influenza Virus Surveillance in Korea: Mingeun Sagong , Yong-Myung Kang , Na Yeong Kim , Eun Bi Noh , Gyeong-Beom Heo , Se-Hee An , Youn-Jeong Lee , Young Ki Choi , Kwang-Nyeong Lee; J. Microbiol. 2023;61(10):929-936. Published online November 27, 2023; DOI: https://doi.org/10.1007/s12275-023-00088-8

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Since the 2000s, the Y439 lineage of H9N2 avian influenza virus (AIV) has been the predominant strain circulating in poultry in Korea; however, in 2020, the Y280 lineage emerged and spread rapidly nationwide, causing large economic losses. To prevent further spread and circulation of such viruses, rapid detection and diagnosis through active surveillance programs are crucial. Here, we developed a novel H9 rRT-PCR assay that can detect a broad range of H9Nx viruses in situations in which multiple lineages of H9 AIVs are co-circulating. We then evaluated its efficacy using a large number of clinical samples. The assay, named the Uni Kor-H9 assay, showed high sensitivity for Y280 lineage viruses, as well as for the Y439 lineage originating in Korean poultry and wild birds. In addition, the assay showed no cross-reactivity with other subtypes of AIV or other avian pathogens. Furthermore, the Uni Kor-H9 assay was more sensitive, and had higher detection rates, than reference H9 rRT-PCR methods when tested against a panel of domestically isolated H9 AIVs. In conclusion, the novel Uni Kor-H9 assay enables more rapid and efficient diagnosis than the “traditional” method of virus isolation followed by subtyping RT-PCR. Application of the new H9 rRT-PCR assay to AI active surveillance programs will help to control and manage Korean H9 AIVs more efficiently.

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Development and evaluation of a multiplex real-time RT-PCR assay for simultaneous detection of H5, H7, and H9 subtype avian influenza viruses
Se-Hee An, Na-Yeong Kim, Gyeong-Beom Heo, Yong-Myung Kang, Youn-Jeong Lee, Kwang-Nyeong Lee
Journal of Virological Methods.2024; 327: 114942. CrossRef

Review

Potential of Bacillus velezensis as a probiotic in animal feed: a review: Fatima Khalid , Anam Khalid , Yuechi Fu , Qian Hu , Yunfang Zheng , Salman Khan , Zaigui Wang; J. Microbiol. 2021;59(7):627-633. Published online July 1, 2021; DOI: https://doi.org/10.1007/s12275-021-1161-1

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Abstract

Bacillus velezensis is a plant growth-promoting bacterium that can also inhibit plant pathogens. However, based on its properties, it is emerging as a probiotic in animal feed. This review focuses on the potential characteristics of B. velezensis for use as a probiotic in the animal feed industry. The review was conducted by collecting recently published articles from peer-reviewed journals. Google Scholar and PubMed were used as search engines to access published literature. Based on the information obtained, the data were divided into three groups to discuss the (i) probiotic characteristics of B. velezensis, (ii) probiotic potential for fish, and (iii) the future potential of this species to be developed as a probiotic for the animal feed industry. Different strains of B. velezensis isolated from different sources were found to have the ability to produce antimicrobial compounds and have a beneficial effect on the gut microbiota, with the potential to be a candidate probiotic in the animal feed industry. This review provides valuable information about the characteristics of B. velezensis, which can provide researchers with a better understanding of the use of this species in the animal feed industry.

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A Novel Bacillus amyloliquefaciens Specifically Improving the Solubility and Antioxidant Activities of Edible Bird’s Nest
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Comparative genomic and transcriptome analysis of Bacillus velezensis CL-4 fermented corn germ meal
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Antibacterial Activity of Two Metabolites Isolated From Endophytic Bacteria Bacillus velezensis Ea73 in Ageratina adenophora
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Frontiers in Microbiology.2022;[Epub] CrossRef
Dynamic analysis of physicochemical characteristics and microbial communities of Aspergillus-type douchi during fermentation
Panwen Zhang, Hao Li, Wenpeng Zhao, Kai Xiong, He Wen, Huilin Yang, Xiaolan Wang
Food Research International.2022; 153: 110932. CrossRef
Metagenomic insights to understand the role of polluted river Yamuna in shaping the gut microbial communities of two invasive fish species
Meghali Bharti, Shekhar Nagar, Himani Khurana, Ram Krishan Negi
Archives of Microbiology.2022;[Epub] CrossRef
Bacillus velezensis MT9 and Pseudomonas chlororaphis MT5 as biocontrol agents against citrus sooty mold and associated insect pests
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Comparative Genome Analysis Reveals Phylogenetic Identity of Bacillus velezensis HNA3 and Genomic Insights into Its Plant Growth Promotion and Biocontrol Effects
Doaa S. Zaid, Shuyun Cai, Chang Hu, Ziqi Li, Youguo Li, Jeffrey A. Gralnick
Microbiology Spectrum.2022;[Epub] CrossRef
The safety and technological properties of Bacillus velezensis DMB06 used as a starter candidate were evaluated by genome analysis
Hong-Eun Na, Sojeong Heo, Yoon-Su Kim, Tao Kim, Gawon Lee, Jong-Hoon Lee, Do-Won Jeong
LWT.2022; 161: 113398. CrossRef
Structural and genetic insights into a poly-γ-glutamic acid with in vitro antioxidant activity of Bacillus velezensis VCN56
Ngoc Tung Quach, Thi Hanh Nguyen Vu, Thi Thu An Nguyen, Hoang Ha, Phu-Ha Ho, Son Chu-Ky, Lan-Huong Nguyen, Hai Van Nguyen, Thi Thu Thuy Thanh, Ngoc Anh Nguyen, Hoang Ha Chu, Quyet-Tien Phi
World Journal of Microbiology and Biotechnology.2022;[Epub] CrossRef
Autoclaved Diet with Inactivated Spores of Bacillus spp. Decreased Reproductive Performance of Muc2−/− and Muc2+/− Mice
Maryana V. Morozova, Galina V. Kalmykova, Nadezhda I. Akulova, Yuriy V. Ites, Valentina I. Korkina, Ekaterina A. Litvinova
Animals.2022; 12(18): 2399. CrossRef
Comparative genomics analysis of Bacillus velezensis LOH112 isolated from a nonagenarian provides insights into its biocontrol and probiotic traits
Zhenhuang Ge, Zhiqi Kuang, Jiahao Chen, Junyi Chen, Tianhao Liu, Zhigang She, Yongjun Lu
Gene.2022; 835: 146644. CrossRef
Fermentation of NaHCO3-treated corn germ meal by Bacillus velezensis CL-4 promotes lignocellulose degradation and nutrient utilization
Long Chen, Wanying Chen, Boyu Zheng, Wei Yu, Lin Zheng, Zihui Qu, Xiaogang Yan, Bingdong Wei, Zijian Zhao
Applied Microbiology and Biotechnology.2022; 106(18): 6077. CrossRef
Suppression of Grape White Rot Caused by Coniella vitis Using the Potential Biocontrol Agent Bacillus velezensis GSBZ09
Xiangtian Yin, Tinggang Li, Xilong Jiang, Xiaoning Tang, Jiakui Zhang, Lifang Yuan, Yanfeng Wei
Pathogens.2022; 11(2): 248. CrossRef
Effects of Dietary Bacillus velezensis LSG2-5 on Growth, Immunity, Antioxidant Capacity, and Disease Resistance of Amur minnow (Rhynchocypris lagowskii Dybowski)
Yurou Zhang, Mengnan Yu, Lili Lin, Jiajing Wang, Dongming Zhang, Qiuju Wang, Mahmoud M. Elsadek, Guiqin Wang, Qi Yao, Yuke Chen, Zhixin Guo, Xiangjun Leng
Aquaculture Nutrition.2022; 2022: 1. CrossRef
In Vivo Efficacy of Bacillus velezensis Isolated from Korean Gochang Bokbunja Vinegar against Carbapenem-Resistant Klebsiella pneumoniae Infections
Fatemeh Ghorbanian, Hoonhee Seo, Hanieh Tajdozian, Youngkyoung Lee, MD Abdur Rahim, Sukyung Kim, Il-Yun Jung, Saebim Lee, Ho-Yeon Song
Polish Journal of Microbiology.2022; 71(4): 553. CrossRef
Analysis of the probiotic activity of Bacillus velezensis RT-26 strain isolated from reindeer rumen by whole-genome sequencing
L.A. Ilina, V.A. Filippova, E.S. Ponomareva, E.A. Brazhnik, T.P. Dunyashev, K.A. Laishev, S. Eliseeva, E.A. Vatskel
BIO Web of Conferences.2022; 48: 03002. CrossRef
Antimicrobial Effects of Potential Probiotics of Bacillus spp. Isolated from Human Microbiota: In Vitro and In Silico Methods
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Microorganisms.2021; 9(8): 1615. CrossRef

Research Support, Non-U.S. Gov'ts

Recombinant Expression and Purification of Functional XorII, a Restriction Endonuclease from Xanthomonas oryzae pv. oryzae: Dong Kyu Hwang , Jae-Yong Cho , Young Kee Chae; J. Microbiol. 2007;45(2):175-178.; DOI: https://doi.org/2515 [pii]

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Abstract: An endonuclease from Xanthomonas oryzae pathovar oryzae KACC 10331, XorII, was recombinantly produced in Escherichia coli using a T7 system. XorII was purified using a combination of ion exchange and immobilized metal affinity chromatography (IMAC). An optimized washing protocol was carried out on an IMAC in order to obtain a high purity product. The final amount of purified XorII was approximately 2.5 mg/L of LB medium. The purified recombinant XorII was functional and showed the same cleavage pattern as PvuI. The enzyme activity tested the highest at 25°C in 50 mM NaCl, 10 mM Tris-HCl, 10 mM MgCl2, and 1 mM dithiothreitol at a pH of 7.9.

Biochemical Quantitation of PM2 Phage DNA as a Substrate for Endonuclease Assay: Yoo Jin Joo , Hee-Ju Kim , Jae Yung Lee , Joon Kim; J. Microbiol. 2004;42(2):99-102.; DOI: https://doi.org/2038 [pii]

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Abstract: Bacteriophage PM2 has a closed circular form of double stranded DNA as a genome. This DNA from the phage is a useful source for nick-circle endonuclease assay in the fmol range. Due to difficulties in the maintenance of viral infectivity, storage conditions of the phage should be considered for the purification of PM2 DNA. The proper condition for a short-term storage of less than 2 months is to keep the PM2 phage at 4^oC; whereas the proper condition for a long-term storage of the PM2 phage for over 2 months is to keep it under liquid nitrogen in 7.5% glycerol. The optimal conditions for a high yield of phage progeny were also considered with the goal to achieve a successful PM2 DNA preparation. A MOI(Multiplicity Of Infection) of 0.03, in which the OD_600 of the host bacteria was between 0.3 and 0.5, turned out to be optimal for the mass production of PM2 phage with a burst size of about 214. Considerations of PM2 genome size, and the concentrations and radiospecific activities of purified PM2 DNA, are required to measure the endonuclease activity in the fmol range. This study reports the proper quantitation of radioactivity and the yield of purified DNA based on these conditions.

Restriction pattern of the nucleic acid of Synechococcus sp. cyanophage: Park, Jong Geun , Kim, Min , Choi, Yong Keel , Yoon, Sung Nyu; J. Microbiol. 1996;34(1):1-6.

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Abstract: The nucleic acid of Synechococcus sp. cyanophage was identified as double-stranded DNA by the result of digestion with enzymes such as exonucleases, DNase, and S1 nuclease, and by acridine orange staining. The cyanophage DNA was cleaved with several restriciton ehdonucleases such as ApaI, BamHI, Bg/II, HaeIII, Eco RI, HindIII, PstI, AND aPAI gave the clearest sets of bands on agarose gels and the fragment numbers for each were 12, 20, 29, 20, and 7, respectively. The sums of the size from Bam HI and PstI digestions were estimated approximately 227±4 kb, which are in agreement with the result of the pulsed field gel electrphoresis. This virus is thought to have the largest genosome among those of known cyanophages, which corresponds to the largest head of 90 nm when compared with the head sizes of cyanophages discovered since 1963.

Expression and Characterization of the Human rpS3 in a Methylotrophic Yeast Pichia pastoris: Jae Yung Lee , Sang Oun Jung , BuHyun Youn , Oh Sik Kwon , Joon Kim; J. Microbiol. 2000;38(2):88-92.

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Abstract: A human ribosomal protein S3 (rpS3), which also functions as a DNA repair enzyme (UV endonuclease III), was expressed in a methylotrophic yeast, Pichia pastoris, and biochemically characterized. UV endonuclease activity was previously characterized, and this activity of mammalian rpS3 was found to be non-specific upon purification and storage. Under the Pichia expression system, the subcloned cDNA of the human rpS3 gene revealed a peptide of 42 kDa by SDS-PAGE and Western blot. The secreted form of human rpS3 rendered no endonuclease activity while the intracellular form showed UV specific endonuclease activity by the nick circle assay.

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