Journal of Microbiology

Journal Article

[Protocol] Use of Cas9 Targeting and Red Recombination for Designer Phage Engineering: Shin-Yae Choi , Danitza Xiomara Romero-Calle , Han-Gyu Cho , Hee-Won Bae , You-Hee Cho; J. Microbiol. 2024;62(1):1-10. Published online February 1, 2024; DOI: https://doi.org/10.1007/s12275-024-00107-2

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Bacteriophages (phages) are natural antibiotics and biological nanoparticles, whose application is significantly boosted by recent advances of synthetic biology tools. Designer phages are synthetic phages created by genome engineering in a way to increase the benefits or decrease the drawbacks of natural phages. Here we report the development of a straightforward genome engineering method to efficiently obtain engineered phages in a model bacterial pathogen, Pseudomonas aeruginosa. This was achieved by eliminating the wild type phages based on the Streptococcus pyogenes Cas9 (SpCas9) and facilitating the recombinant generation based on the Red recombination system of the coliphage λ (λRed). The producer (PD) cells of P. aeruginosa strain PAO1 was created by miniTn7-based chromosomal integration of the genes for SpCas9 and λRed under an inducible promoter. To validate the efficiency of the recombinant generation, we created the fluorescent phages from a temperate phage MP29. A plasmid bearing the single guide RNA (sgRNA) gene for selectively targeting the wild type gp35 gene and the editing template for tagging the Gp35 with superfolder green fluorescent protein (sfGFP) was introduced into the PD cells by electroporation. We found that the targeting efficiency was affected by the position and number of sgRNA. The fluorescent phage particles were efficiently recovered from the culture of the PD cells expressing dual sgRNA molecules. This protocol can be used to create designer phages in P. aeruginosa for both application and research purposes.

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Pilin regions that select for the small RNA phages in Pseudomonas aeruginosa type IV pilus
Hee-Won Bae, Hyeong-Jun Ki, Shin-Yae Choi, You-Hee Cho, Kristin N. Parent
Journal of Virology.2025;[Epub] CrossRef
Characteristics of bioaerosols under high-ozone periods, haze episodes, dust storms, and normal days in Xi’an, China
Yiming Yang, Liu Yang, Xiaoyan Hu, Zhenxing Shen
Particuology.2024; 90: 140. CrossRef
Airborne desert dust and aeromicrobiology over the Turkish Mediterranean coastline
Dale W. Griffin, Nilgün Kubilay, Mustafa Koçak, Mike A. Gray, Timothy C. Borden, Eugene A. Shinn
Atmospheric Environment.2007; 41(19): 4050. CrossRef

Review

The “Cins” of Our Fathers: Rejuvenated Interest in Colicins to Combat Drug Resistance: Sumudu Upatissa , Robert J. Mitchell; J. Microbiol. 2023;61(2):145-158. Published online February 8, 2023; DOI: https://doi.org/10.1007/s12275-023-00023-x

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Abstract

With the growing threat of antibiotic resistance, researchers around the globe are seeking alternatives to stem bacterial pathogenesis. One such alternative is bacteriocins, proteins produced by bacterial species to inhibit the growth and viability of related bacterial species. With their diverse mechanisms, which include pore formation and nuclease activities, and narrow spectrum of activities, which limit their impact to only certain bacterial species, unlike many chemical antibiotics, bacteriocins offer intriguing possibilities to selectively control individual bacterial populations. Within this review, therefore, we highlight current research exploring the application of colicins and microcins, a subset of bacteriocins, with an emphasis on their activities against drug-resistant pathogens, both in in vitro and in vivo settings.

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Isolation, Genomics-Based and Biochemical Characterization of Bacteriocinogenic Bacteria and Their Bacteriocins, Sourced from the Gastrointestinal Tract of Meat-Producing Pigs
Ester Sevillano, Irene Lafuente, Nuria Peña, Luis M. Cintas, Estefanía Muñoz-Atienza, Pablo E. Hernández, Juan Borrero
International Journal of Molecular Sciences.2024; 25(22): 12210. CrossRef
Intelligent Biological Networks: Improving Anti-Microbial Resistance Resilience through Nutritional Interventions to Understand Protozoal Gut Infections
Avinash V. Karpe, David J. Beale, Cuong D. Tran
Microorganisms.2023; 11(7): 1800. CrossRef
Pairing Colicins B and E5 with Bdellovibrio bacteriovorus To Eradicate Carbapenem- and Colistin-Resistant Strains of Escherichia coli
Sumudu Upatissa, Wonsik Mun, Robert J. Mitchell, Minsu Kim
Microbiology Spectrum.2023;[Epub] CrossRef
Bacteriocin-Producing Escherichia coli Q5 and C41 with Potential Probiotic Properties: In Silico, In Vitro, and In Vivo Studies
Veronika S. Mihailovskaya, Dmitry A. Sutormin, Marina O. Karipova, Anna B. Trofimova, Victor A. Mamontov, Konstantin Severinov, Marina V. Kuznetsova
International Journal of Molecular Sciences.2023; 24(16): 12636. CrossRef

Journal Article

Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov., isolated from the rhizosphere of tomato (Solanum lycopersicum): Shin Ae Lee , Tae-Wan Kim , Mee-Kyung Sang , Jaekyeong Song , Soon-Wo Kwon , Hang-Yeon Weon; J. Microbiol. 2020;58(10):832-840. Published online September 29, 2020; DOI: https://doi.org/10.1007/s12275-020-0258-2

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Abstract

Two Gram-stain-positive, rod-shaped, endospore-forming bacteria, designated 12200R-189T and 14171R-81T were isolated from the rhizosphere of tomato plants. The 16S rRNA gene sequence similarity between strains 12200R-189T and 14171R-81T were 97.2%. Both strains showed the highest 16S rRNA gene sequence similarities to Paenibacillus sacheonensis SY01T (96.3% and 98.0%, respectively). The genome of strain 12200R-189T was approximately 6.7 Mb in size with 5,750 protein-coding genes (CDSs) and the G + C content was 58.1 mol%, whereas that of strain 14171R-81T comprised one chromosome of 7.0 Mb and two plasmids (0.2 Mb each) with 6,595 CDSs and the G + C content was 54.5 mol%. Comparative genome analysis revealed that average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among 12200R-189T, 14171R-81T, and other closely related species were below the cut-off levels 95% and 70%, respectively. Strain 12200R-189T grew at a temperature range of 15–40°C, pH 6.0–9.0, and 0–3% NaCl (w/v), whereas strain 14171R-81T grew at a temperature range of 10–37°C, pH 6.0– 8.0, and 0–1% NaCl (w/v). Menaquinone-7 (MK-7) was the only isoprenoid quinone detected in both strains. The predominant cellular fatty acids (> 10%) were iso-C15:0, anteiso- C15:0, and iso-C16:0. The polar lipids of strain 12200R- 189T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), aminophospholipid (APL), phospholipid (PL), phosphatidylglycolipid (PGL), and four aminophosphoglycolipids (APGLs) and those of strain 14171R-81T were DPG, PG, PE, APL, three PLs, two PGLs, and three APGLs. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic analyses, strains 12200R- 189T and 14171R-81T represent two novel species of the genus Paenibacillus, for which the names Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov. are proposed. The type strains are 12200R-189T (= KACC 19916T = CCTCC AB 2020027T) and 14171R-81T (= KACC 19915T = CCTCC AB 2020026T).

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Description and genomic characterization of Jiella flava sp. nov., isolated from Acrostichum aureum
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Minh Hong Nguyen, Mai Thi Ngoc Dinh, Keun Chul Lee, Ji-Sun Kim, Thao Kim Nu Nguyen, Jung-Sook Lee
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
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Journal of Microbiology.2021; 59(8): 729. CrossRef

Review

MINIREVIEW] Fungi in salterns: Dawoon Chung† , Haryun Kim† , Hyun Seok Choi; J. Microbiol. 2019;57(9):717-724. Published online August 27, 2019; DOI: https://doi.org/10.1007/s12275-019-9195-3

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Abstract

Salterns are hypersaline extreme environments with unique physicochemical properties such as a salinity gradient. Although the investigation of microbiota in salterns has focused on archaea and bacteria, diverse fungi also thrive in the brine and soil of salterns. Fungi isolated from salterns are represented by black yeasts (Hortaea werneckii, Phaeotheca triangularis, Aureobasidium pullulans, and Trimmatostroma salinum), Cladosporium, Aspergillus, and Penicillium species. Most studies on saltern-derived fungi gave attention to black yeasts and their physiological characteristics, including growth under various culture conditions. Since then, biochemical and molecular tools have been employed to explore adaptation of these fungi to salt stress. Genome databases of several fungi in salterns are now publicly available and being used to elucidate salt tolerance mechanisms and discover the target genes for agricultural and industrial applications. Notably, the number of enzymes and novel metabolites known to be produced by diverse saltern-derived fungi has increased significantly. Therefore, fungi in salterns are not only interesting and important subjects to study fungal biodiversity and adaptive mechanisms in extreme environments, but also valuable bioresources with potential for biotechnological applications.

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Journal Article

Comprehensive analysis of fungal diversity and enzyme activity in nuruk, a Korean fermenting starter, for acquiring useful fungi: Emily Carroll , Tran Ngoc Trinh , Hokyoung Son , Yin-Won Lee , Jeong-Ah Seo; J. Microbiol. 2017;55(5):357-365. Published online April 29, 2017; DOI: https://doi.org/10.1007/s12275-017-7114-z

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Abstract

Nuruk is a fermenting starter that is involved in the pro-duction of alcoholic beverages, and has been used in South Korea for a very long time. To analyze the fungal diversity, we collected a total of 59 nuruk samples from several com-panies and persons in 2013 to 2014, and obtained 364 iso-lates. All of the single isolated fungi were identified, both morphologically and molecularly, based on the sequences of ribosomal RNA gene [18S, ITS1-5.8S-ITS2, and 26S (D1/D2 region)]. In 46 nuruk samples out of 59 (78%), Saccharo-mycopsis fibuligera, a dimorphic yeast, was most frequently isolated. Among the filamentous fungi, Aspergillus and Lich-theimia were found in more than 50% of the samples with lower colony forming unit (CFU/g of sample) than those of yeasts. The yeasts S. fibuligera and Wickerhamomyces ano-malus were counted with maximum 1.3 – 1.8 × 108 CFU/g. Among Mucorales fungi, Lichtheimia and Mucor were iso-lated in much higher numbers than Rhizopus and Rhizo-mucor. Overall, the home-made nuruks tend to contain more diverse filamentous fungi than the commercial nuruks. To acquire industrially useful filamentous fungi and yeasts, we analyzed the enzyme activities of α-amylase, glucoamylase and acid protease associated with brewing properties for 131 strains. Aspergillus oryzae and S. fibuligera had high α- and glucoamylase activities and most isolates of Lichtheimia ramosa had high acid protease activity. For further applica-tions, 27 fungal strains were chosen based on isolation fre-quencies from nuruk, and the ability to produce useful en-zyme.

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Applied Biological Chemistry.2021;[Epub] CrossRef
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Environmental Microbiology.2021; 23(7): 3499. CrossRef
pH Changes Have a Profound Effect on Gene Expression, Hydrolytic Enzyme Production, and Dimorphism in Saccharomycopsis fibuligera
Mohamed El-Agamy Farh, Najib Abdellaoui, Jeong-Ah Seo
Frontiers in Microbiology.2021;[Epub] CrossRef
Saccharomycopsis fibuligera in liquor production: A review
Zai-Bin Xie, Kai-Zheng Zhang, Zhen-Hui Kang, Jian-Gang Yang
European Food Research and Technology.2021; 247(7): 1569. CrossRef
Diversity of Filamentous Fungi Isolated From Some Amylase and Alcohol-Producing Starters of India
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Frontiers in Microbiology.2020;[Epub] CrossRef
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Journal of Pure and Applied Microbiology.2020; 14(1): 233. CrossRef
Natural Occurrence of Aflatoxigenic Aspergillus Species and Aflatoxins in Traditional Korean Fermentation Starters, Meju and Nuruk
So Young Woo, Sang Yoo Lee, Fei Tian, A-Yeong Jeong, Cha Nee Yoo, Seung Yoon Kang, Hyang Sook Chun
Journal of Food Hygiene and Safety.2020; 35(5): 438. CrossRef
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Journal of the Institute of Brewing.2020; 126(1): 105. CrossRef
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Xiaoning Huang, Yi Fan, Ting Lu, Jiamu Kang, Xiaona Pang, Beizhong Han, Jingyu Chen
Microorganisms.2020; 8(9): 1281. CrossRef
Comprehensive analysis of different grades of roasted-sesame-like flavored Daqu
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International Journal of Food Properties.2019; 22(1): 1205. CrossRef
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Overexpression of RAD51 Enables PCR-Based Gene Targeting in Lager Yeast
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Expansion of a Telomeric FLO/ALS-Like Sequence Gene Family in Saccharomycopsis fermentans
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Food Research International.2018; 109: 596. CrossRef
Bioformation of Volatile and Nonvolatile Metabolites by Saccharomycopsis fibuligera KJJ81 Cultivated under Different Conditions—Carbon Sources and Cultivation Times
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Molecules.2018; 23(11): 2762. CrossRef

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