Journal of Microbiology

Review

Progress and challenges in CRISPR/Cas applications in microalgae: Quynh-Giao Tran, Trang Thi Le, Dong-Yun Choi, Dae-Hyun Cho, Jin-Ho Yun, Hong Il Choi, Hee-Sik Kim, Yong Jae Lee; J. Microbiol. 2025;63(3):e2501028. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501028

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Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technologies have emerged as powerful tools for precise genome editing, leading to a revolution in genetic research and biotechnology across diverse organisms including microalgae. Since the 1950s, microalgal production has evolved from initial cultivation under controlled conditions to advanced metabolic engineering to meet industrial demands. However, effective genetic modification in microalgae has faced significant challenges, including issues with transformation efficiency, limited target selection, and genetic differences between species, as interspecies genetic variation limits the use of genetic tools from one species to another. This review summarized recent advancements in CRISPR systems applied to microalgae, with a focus on improving gene editing precision and efficiency, while addressing organism-specific challenges. We also discuss notable successes in utilizing the class 2 CRISPR-associated (Cas) proteins, including Cas9 and Cas12a, as well as emerging CRISPR-based approaches tailored to overcome microalgal cellular barriers. Additionally, we propose future perspectives for utilizing CRISPR/Cas strategies in microalgal biotechnology.

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Advancing microbial engineering through synthetic biology
Ki Jun Jeong
Journal of Microbiology.2025; 63(3): e2503100. CrossRef

Research Article

Single nucleotide genome recognition and selective bacterial lysis using synthetic phages loaded with CRISPR-Cas12f1-truncated sgRNA: Ho Joung Lee, Song Hee Jeong, Sang Jun Lee; J. Microbiol. 2025;63(2):e2501012. Published online February 27, 2025; DOI: https://doi.org/10.71150/jm.2501012

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Abstract PDF Supplementary Material: Phage specificity primarily relies on host cell-surface receptors. However, integrating cas genes and guide RNAs into phage genomes could enhance their target specificity and regulatory effects. In this study, we developed a CRISPR-Cas12f1 system-equipped bacteriophage λ model capable of detecting Escherichia coli target genes. We demonstrated that synthetic λ phages carrying Cas12f1-sgRNA can effectively prevent lysogen formation. Furthermore, we showcased that truncating the 3'-end of sgRNA enables precise identification of single-nucleotide variations in the host genome. Moreover, infecting E. coli strains carrying various stx2 gene subtypes encoding Shiga toxin with bacteriophages harboring Cas12f1 and truncated sgRNAs resulted in the targeted elimination of strains with matching subtype genes. These findings underscore the ability of phages equipped with the CRISPR-Cas12f1 system to precisely control microbial hosts by recognizing genomic sequences with high resolution.

Journal Articles

H-NS is a Transcriptional Repressor of the CRISPR-Cas System in Acinetobacter baumannii ATCC 19606: Kyeongmin Kim, Md Maidul Islam, Seunghyeok Bang, Jeongah Kim, Chung-Young Lee, Je Chul Lee, Minsang Shin; J. Microbiol. 2024;62(11):999-1012. Published online November 11, 2024; DOI: https://doi.org/10.1007/s12275-024-00182-5

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Abstract: Acinetobacter baumannii is a multidrug-resistant opportunistic pathogen primarily associated with hospital-acquired infections. The bacterium can gain multidrug resistance through several mechanisms, including horizontal gene transfer. A CRISPR-Cas system including several Cas genes could restrict the horizontal gene transfer. However, the molecular mechanism of CRISPR- Cas transcriptional regulation remains unclear. We identified a type I-F CRISPR-Cas system in A. baumannii ATCC 19606^T standard strain based on sequence analysis. We focused on the transcriptional regulation of Cas3, a key protein of the CRISPR-Cas system. We performed a DNA affinity chromatography-pulldown assay to identify transcriptional regulators of the Cas3 promoter. We identified several putative transcriptional factors, such as H-NS, integration host factor, and HU, that can bind to the promoter region of Cas3. We characterized AbH-NS using size exclusion chromatography and cross-linking experiments and demonstrated that the Cas3 promoter can be regulated by AbH-NS in a concentration-dependent manner via an in vitro transcription assay. CRISPR-Cas expression levels in wild-type and hns mutant strains in the early stationary phase were examined by qPCR and β-galactosidase assay. We found that H-NS can act as a repressor of Cas3. Our transformation efficiency results indicated that the hns mutation decreased the transformation efficiency, while the Cas3 mutation increased it. We report the existence and characterization of the CRISPR-Cas system in A. baumannii 19606^T and demonstrate that AbH-NS is a transcriptional repressor of CRISPR-Cas-related genes in A. baumannii.

Mammaliicoccus sciuri's Pan-Immune System and the Dynamics of Horizontal Gene Transfer Among Staphylococcaceae: a One-Health CRISPR Tale: Allan de Carvalho, Marcia Giambiagi-deMarval, Ciro César Rossi; J. Microbiol. 2024;62(9):775-784. Published online July 22, 2024; DOI: https://doi.org/10.1007/s12275-024-00156-7

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Abstract

Recently emancipated from the Staphylococcus genus due to genomic differences, Mammaliicoccus sciuri, previously classified as an occasional pathogen, emerges as a significant player in the landscape of resistance gene dissemination among Staphylococcaceae. Despite its classification, its role remained enigmatic. In this study, we delved into the genomic repertoire of M. sciuri to unravel its contribution to resistance and virulence gene transfer in the context of One Health. Through comprehensive analysis of publicly available genomes, we unveiled a diverse pan-immune system adept at defending against exogenous genetic elements, yet concurrently fostering horizontal gene transfer (HGT). Specifically, exploration of CRISPR-Cas systems, with spacer sequences as molecular signatures, elucidated a global dissemination pattern spanning environmental, animal, and human hosts. Notably, we identified the integration of CRISPR-Cas systems within SCCmecs (Staphylococcal Cassette Chromosome mec), harboring key genes associated with pathogenicity and resistance, especially the methicillin resistance gene mecA, suggesting a strategic adaptation to outcompete other mobile genetic elements. Our findings underscored M. sciuri's active engagement in HGT dynamics and evolutionary trajectories within Staphylococcaceae, emphasizing its central role in shaping microbial communities and highlighting the significance of understanding its implications in the One Health framework, an interdisciplinary approach that recognizes the interconnectedness of human, animal, and environmental health to address global health challenges.

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From Farm to Community: Dispersal of Potentially Pathogenic Staphylococcus and Mammaliicoccus Species and Antimicrobial Resistance Across Shared Environments
Faizan Ahmad, Samuel Sathler Martuchelle, Ana Luisa Andrade-Oliveira, Vitor Emanuel Lanes Viana, Maria Antônia Silva Melo Sousa, Felipe Sicchierolli da Silveira, Marisa Alves Nogueira-Diaz, Monalessa Fábia Pereira, Marcia Giambiagi-deMarval, Ciro César Ro
Current Microbiology.2025;[Epub] CrossRef
Genomic insights into multidrug and heavy metal resistance in Chryseobacterium sp. BI5 isolated from sewage sludge
Mrinmoy Patra, Anand Kumar Pandey, Suresh Kumar Dubey
Total Environment Microbiology.2025; 1(1): 100005. CrossRef

Review

Apoptotic Factors, CaNma111 and CaYbh3, Function in Candida albicans Filamentation by Regulating the Hyphal Suppressors, Nrg1 and Tup1: Suyoung Kim , Se Hyeon Kim , Eunjoong Kweon , Jinmi Kim; J. Microbiol. 2023;61(4):403-409. Published online March 27, 2023; DOI: https://doi.org/10.1007/s12275-023-00034-8

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Abstract: The morphological switch from the yeast to hyphal form is a key virulence attribute of the opportunistic fungal pathogen, Candida albicans. Our recent report showed that deletion of the newly identified apoptotic factor, CaNma111 or CaYbh3, leads to hyperfilamentation and increased virulence in a mouse infection model. CaNma111 and CaYbh3 are homologs of the pro-apoptotic protease, HtrA2/Omi, and BH3-only protein, respectively. In this study, we examined the effects of CaNMA111 and CaYBH3 deletion mutations on the expression levels of the hypha-specific transcr!ption factors, Cph1 (a hyphal activator), Nrg1 (a hyphal repressor), and Tup1 (a hyphal repressor). The protein levels of Nrg1 were decreased in Caybh3/Caybh3 cells while those of Tup1 were decreased in both Canma111/Canma111 and Caybh3/Caybh3 cells. These effects on Nrg1 and Tup1 proteins were retained during serum-induced filamentation and appear to explain the hyperfilamentation phenotypes of the CaNMA111 and CaYBH3 deletion mutants. Treatment with the apoptosis-inducing dose of farnesol decreased the Nrg1 protein levels in the wild-type strain and more evidently in Canma111/Canma111 and Caybh3/Caybh3 mutant strains. Together, our results suggest that CaNma111 and CaYbh3 are key regulators of Nrg1 and Tup1 protein levels in C. albicans.

Journal Articles

Gut microbiota metabolic characteristics in coronary artery disease patients with hyperhomocysteine: Ran Tian , Hong-Hong Liu , Si-Qin Feng , Yi-Fei Wang , Yi-Yang Wang , Yu-Xiong Chen , Hui Wang , Shu-Yang Zhang; J. Microbiol. 2022;60(4):419-428. Published online March 4, 2022; DOI: https://doi.org/10.1007/s12275-022-1451-2

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Abstract

Hyperhomocysteine (HHcy) is known as a risk factor for coronary artery disease (CAD). Despite the knowledge that gut microbiota related metabolism pathway shares metabolites with that of Hcy, little has been shown concerning the association between HHcy and gut microbiota. To explore their relationship in the context of CAD, 105 patients and 14 healthy controls were recruited from one single medical center located in Beijing, China. Their serum and fecal samples were collected, with multi-omics analyses performed via LC/MS/ MS and 16S rRNA gene V3-V4 region sequencing, respectively. Participants from the prospective cohort were divided into CAD, CAD & HHcy and healthy controls (HC) groups based on the diagnosis and serum Hcy concentration. The
results
revealed significant different metabolic signatures between CAD and CAD & HHcy groups. CAD patients with HHcy suffered a heavier atherosclerotic burden compared to CAD patients, and the difference was closely associated to betaine-homocysteine S-methyltransferase (BHMT)-related metabolites and trimethylamine N-oxide (TMAO)-related metabolites. Dimethylglycine (DMG) exhibited a strong positive correlation with serum total Hcy (tHcy), and TMAO and trimethylysine (TML) were associated with heavier atherosclerotic burden. Multiple other metabolites were also identified to be related to distinct cardiovascular risk factors. Additionally, Clostridium cluster IV and Butyricimonas were enriched in CAD patients with elevated tHcy. Our study suggested that CAD patients with elevated tHcy were correlated with higher atherosclerotic burden, and the impaired Hcy metabolism and cardiovascular risk were closely associated with BHMT-related metabolites, TMAO-related metabolites and impaired gut microbiota homeostasis.

Citations

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Unravelling the Gut Microbiome Role in Cardiovascular Disease: A Systematic Review and a Meta-Analysis
Diana Martins, Cláudia Silva, António Carlos Ferreira, Sara Dourado, Ana Albuquerque, Francisca Saraiva, Ana Beatriz Batista, Pedro Castro, Adelino Leite-Moreira, António S. Barros, Isabel M. Miranda
Biomolecules.2024; 14(6): 731. CrossRef
Gut Commensal Bacteroides thetaiotaomicron Promote Atherothrombosis via Regulating L-Tryptophan Metabolism
Honghong Liu, Siqin Feng, Muyun Tang, Ran Tian, Shuyang Zhang
Reviews in Cardiovascular Medicine.2024;[Epub] CrossRef
Relation between homocysteine-to-adropin ratio and severity of coronary artery disease
Ola Hassan Abd Elaziz, Bassem Mohamed Abdel Hady, Ghada Mohamed S Ahmad, Safaa Abo Alfadl Mohamed, Abeer Ahmed Elmalah, Inass Hassan Ahmad, Entesar O Elsaghier, Marwa FM Elsayed, Hala Naguib Mohamed, Marwa Khairy Abd Elwahab, Ahmed Salah
Electronic Journal of General Medicine.2024; 21(1): em556. CrossRef
Association of serum homocysteine levels with intestinal flora and cognitive function in schizophrenia
Hehua Li, Hanqiu Li, Zhimin Zhu, Xiang Xiong, Yuanyuan Huang, Yangdong Feng, Zezhi Li, Kai Wu, Fengchun Wu
Journal of Psychiatric Research.2023; 159: 258. CrossRef
Association analysis of gut microbiota-metabolites-neuroendocrine changes in male rats acute exposure to simulated altitude of 5500 m
Jianan Wang, Shiying Liu, Yalei Xie, Chengli Xu
Scientific Reports.2023;[Epub] CrossRef

Screening of small molecules attenuating biofilm formation of Acinetobacter baumannii by inhibition of ompA promoter activity: Seok Hyeon Na , Hyejin Jeon , Man Hwan Oh , Yoo Jeong Kim , Je Chul Lee; J. Microbiol. 2021;59(9):871-878. Published online August 27, 2021; DOI: https://doi.org/10.1007/s12275-021-1394-z

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Abstract

Anti-virulence therapeutic strategies are promising alternatives against drug-resistant pathogens. Outer membrane protein A (OmpA) plays a versatile role in the pathogenesis and antimicrobial resistance of Acinetobacter baumannii. Therefore, OmpA is an innovative target for anti-virulence therapy against A. baumannii. This study aimed to develop a high-throughput screening (HTS) system to discover small molecules inhibiting the ompA promoter activity of A. baumannii and screen chemical compounds using the bacterial growth-based HTS system. The ompA promoter and open reading frame of nptI fusion plasmids that controlled the expression of nptI encoding resistance to kanamycin by the ompA promoter were constructed and then transformed into A. baumannii ATCC 17978. This reporter strain was applied to screen small molecules inhibiting the ompA promoter activity in a chemical library. Of the 7,520 chemical compounds, 15 exhibited ≥ 70% growth inhibition of the report strain cultured in media containing kanamycin. Three compounds inhibited the expression of ompA and OmpA in the outer membrane of A. baumannii ATCC 17978, which subsequently reduced biofilm formation. In conclusion, our reporter strain is useful for large-scale screening of small molecules inhibiting the ompA expression in A. baumannii. Hit compounds identified by the HTS system are promising scaffolds to develop novel therapeutics against A. baumannii.

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A peptide targeting outer membrane protein A of Acinetobacter baumannii exhibits antibacterial activity by reducing bacterial pathogenicity
Hui Zhao, Yue Hu, Dan Nie, Na Li, Zhou Chen, Shan Zhou, Mingkai Li, Xiaoyan Xue, James E. Leggett
Antimicrobial Agents and Chemotherapy.2024;[Epub] CrossRef
Acinetobacter baumannii OmpA-like porins: functional characterization of bacterial physiology, antibiotic-resistance, and virulence
Daniela Scribano, Elena Cheri, Arianna Pompilio, Giovanni Di Bonaventura, Manuel Belli, Mario Cristina, Luigi Sansone, Carlo Zagaglia, Meysam Sarshar, Anna Teresa Palamara, Cecilia Ambrosi
Communications Biology.2024;[Epub] CrossRef
Anti-OmpA antibodies as potential inhibitors of Acinetobacter baumannii biofilm formation, adherence to, and proliferation in A549 human alveolar epithelial cells
Hamideh Barati, Zahra Fekrirad, Mohammadreza Jalali Nadoushan, Iraj Rasooli
Microbial Pathogenesis.2024; 186: 106473. CrossRef
Current and novel therapies for management of Acinetobacter baumannii -associated pneumonia
Aye Mya Sithu Shein, Parichart Hongsing, O’Rorke Kevin Smith, Phatthranit Phattharapornjaroen, Kazuhiko Miyanaga, Longzhu Cui, Hitoshi Ishikawa, Mohan Amarasiri, Peter N. Monk, Anthony Kicic, Tanittha Chatsuwan, Daniel Pletzer, Paul G. Higgins, Shuichi Ab
Critical Reviews in Microbiology.2024; : 1. CrossRef
Understanding the mechanisms of antimicrobial resistance and potential therapeutic approaches against the Gram-negative pathogen Acinetobacter baumannii
Vishwani Jamwal, Tashi Palmo, Kuljit Singh
RSC Medicinal Chemistry.2024; 15(12): 3925. CrossRef
Acinetobacter baumannii outer membrane protein A induces autophagy in bone marrow‐derived dendritic cells involving the PI3K/mTOR pathway
Hongyi Tan, Liyan Cao
Immunity, Inflammation and Disease.2023;[Epub] CrossRef
Advances in research on virulence factors ofAcinetobacter baumanniiand their potential as novel therapeutic targets
Jian-Xia Zhou, Ding-Yun Feng, Xia Li, Jia-Xin Zhu, Wen-Bin Wu, Tian-tuo Zhang
Journal of Applied Microbiology.2023;[Epub] CrossRef
Famotidine Enhances Rifampicin Activity against Acinetobacter baumannii by Affecting OmpA
Meng-na Zhang, Xiao-ou Zhao, Qi Cui, Dao-mi Zhu, Muhammad Asif Wisal, Han-dong Yu, Ling-cong Kong, Hong-xia Ma, Laurie E. Comstock
Journal of Bacteriology.2023;[Epub] CrossRef
Factors mediating Acinetobacter baumannii biofilm formation: Opportunities for developing therapeutics
Kirti Upmanyu, Qazi Mohd. Rizwanul Haq, Ruchi Singh
Current Research in Microbial Sciences.2022; 3: 100131. CrossRef
Evaluation the reactivity of a peptide-based monoclonal antibody derived from OmpA with drug resistant pulsotypes of Acinetobacter baumannii as a potential therapeutic approach
Omid Yeganeh, Mahdi Shabani, Parviz Pakzad, Nariman Mosaffa, Ali Hashemi
Annals of Clinical Microbiology and Antimicrobials.2022;[Epub] CrossRef
Therapeutic Effects of Inhibitor of ompA Expression against Carbapenem-Resistant Acinetobacter baumannii Strains
Seok-Hyeon Na, Hyejin Jeon, Man-Hwan Oh, Yoo-Jeong Kim, Mingi Chu, Ill-Young Lee, Je-Chul Lee
International Journal of Molecular Sciences.2021; 22(22): 12257. CrossRef
DksA Modulates Antimicrobial Susceptibility of Acinetobacter baumannii
Nayeong Kim, Joo-Hee Son, Kyeongmin Kim, Hyo-Jeong Kim, Minsang Shin, Je-Chul Lee
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Changes in the microbial community of Litopenaeus vannamei larvae and rearing water during different growth stages after disinfection treatment of hatchery water: Yafei Duan , Yapeng Tang , Jianhua Huang , Jiasong Zhang , Heizhao Lin , Shigui Jiang , Ruixuan Wang , Guofu Wang; J. Microbiol. 2020;58(9):741-749. Published online July 24, 2020; DOI: https://doi.org/10.1007/s12275-020-0053-0

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Abstract

Microbial communities greatly affect rearing water quality and the larvae health during shrimp hatchery periods. In this study, we investigated the microbial communities of rearing water and larvae of Litopenaeus vannamei after treating hatchery water with different kinds of chemical disinfectants: no disinfectants (Con), chlorine dioxide (ClO2), formaldehyde solution (HCHO), bleach powder (CaClO), and iodine (I2). The water and larval samples were collected from nauplius 6 (N6), zoea 1 (Z1), mysis 1 (M1), and postlarvae 1 (P1) shrimp growth periods. 16S rDNA high-throughput sequencing revealed that the bacterial composition of the rearing water was more complex than that of the larvae, and the bacterial community of the rearing water and the larvae fluctuated significantly at the P1 and Z1 periods, respectively. Disinfectants altered the bacterial diversity and composition of the rearing water and larvae. Specifically, in the rearing water of the P1 period, Proteobacteria abundance was increased in the HCHO group; while Bacteroidetes abundance was decreased in the ClO2, HCHO, and I2 groups but increased in the CaClO group. In the larvae of the Z1 period, Firmicutes (especially Bacillus class) abundance was increased in the CaClO group, but decreased in the ClO2, HCHO, and I2 groups. Network analyses revealed that the genera Donghicola, Roseibacterium, Candidatus-Cquiluna, and Nautella were enriched in the rearing water, while Halomonas, Vibrio, and Flavirhabdus had high abundance in the larvae. The survival of shrimp was influenced by disinfectants that were inconsistent with the bacterial community changes. These results will be helpful for using microbial characteristics to facilitate healthy shrimp nursery.

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Metagenomic insights into the rapid recovery mechanisms of prokaryotic community and spread of antibiotic resistance genes after seawater disinfection
Jiaojiao Yan, Xinxu Zhang, Xinyong Shi, Jialin Wu, Ziang Zhou, Yawen Tang, Zhen Bao, Nan Luo, Demin Zhang, Jiong Chen, Huajun Zhang
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Effects of potassium monopersulfate on nitrification activity and bacterial community structure of sponge biocarrier biofilm in Litopenaeus vannamei aquaculture system
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Water Research.2023; 241: 120136. CrossRef
Stocking Density Effects on Pacific White Shrimp Litopenaeus vannamei Hatchery Performance in Algal‐Bacterial Biofloc Systems
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Melatonin attenuates microbiota dysbiosis of jejunum in short-term sleep deprived mice: Ting Gao , Zixu Wang , Jing Cao , Yulan Dong , Yaoxing Chen; J. Microbiol. 2020;58(7):588-597. Published online May 18, 2020; DOI: https://doi.org/10.1007/s12275-020-0094-4

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Abstract

Our study demonstrated that sleep deprivation resulted in homeostasis disorder of colon. Our study goes deeper into the positive effects of melatonin on small intestinal microbiota disorder caused by sleep deprivation. We successfully established a multiplatform 72 h sleep deprivation mouse model with or without melatonin supplementation, and analyzed the change of small intestinal microbiota using high-throughput sequencing of the 16S rRNA. We found melatonin supplementation suppressed the decrease of plasma melatonin level in sleep deprivation mice. Meanwhile, melatonin supplementation improved significantly the reduction in OTU numbers and the diversity and richness of jejunal microbiota and the abundance of Bacteroidaeae and Prevotellaceae, as well as an increase in the Firmicutes-to-Bacteroidetes ratio and the content of Moraxellaceae and Aeromonadaceae in the jejunum of sleep deprived-mice. Moreover, melatonin supplementation reversed the change of metabolic pathway in sleep deprived-mice, including metabolism, signal transduction mechanisms and transcription etc, which were related to intestinal health. Furthermore, melatonin supplementation inverted the sleep deprivation-induced a decline of anti-inflammatory cytokines (IL-22) and an increase of the ROS and proinflammatory cytokines (IL-17) in jejunum. These findings suggested that melatonin, similar to a probiotics agent, can reverse sleep deprivation-induced small intestinal microbiota disorder by suppressing oxidative stress and inflammation response.

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Reviews

[Minireview]Recent advances in genetic engineering tools based on synthetic biology: Jun Ren , Jingyu Lee , Dokyun Na; J. Microbiol. 2020;58(1):1-10. Published online January 2, 2020; DOI: https://doi.org/10.1007/s12275-020-9334-x

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Abstract

Genome-scale engineering is a crucial methodology to rationally regulate microbiological system operations, leading to expected biological behaviors or enhanced bioproduct yields. Over the past decade, innovative genome modification technologies have been developed for effectively regulating and manipulating genes at the genome level. Here, we discuss the current genome-scale engineering technologies used for microbial engineering. Recently developed strategies, such as clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9, multiplex automated genome engineering (MAGE), promoter engineering, CRISPR-based regulations, and synthetic small regulatory RNA (sRNA)-based knockdown, are considered as powerful tools for genome-scale engineering in microbiological systems. MAGE, which modifies specific nucleotides of the genome sequence, is utilized as a genome-editing tool. Contrastingly, synthetic sRNA, CRISPRi, and CRISPRa are mainly used to regulate gene expression without modifying the genome sequence. This review introduces the recent genome-scale editing and regulating technologies and their applications in metabolic engineering.

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REVIEW] When a Virus is not a Parasite: The Beneficial Effects of Prophages: Joseph Bondy-Denomy , Alan R. Davidson; J. Microbiol. 2014;52(3):235-242. Published online March 1, 2014; DOI: https://doi.org/10.1007/s12275-014-4083-3

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Abstract

Most organisms on the planet have viruses that infect them. Viral infection may lead to cell death, or to a symbiotic relationship where the genomes of both virus and host replicate together. In the symbiotic state, both virus and cell potentially experience increased fitness as a result of the other. The viruses that infect bacteria, called bacteriophages (or phages), well exemplify the symbiotic relationships that can develop between viruses and their host. In this review, we will discuss the many ways that prophages, which are phage genomes integrated into the genomes of their hosts, influence bacterial behavior and virulence.

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