Journal of Microbiology

Review

Recent Advances in CRISPR‑Cas Technologies for Synthetic Biology: Song Hee Jeong , Ho Joung Lee , Sang Jun Lee; J. Microbiol. 2023;61(1):13-36. Published online February 1, 2023; DOI: https://doi.org/10.1007/s12275-022-00005-5

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With developments in synthetic biology, “engineering biology” has emerged through standardization and platformization based on hierarchical, orthogonal, and modularized biological systems. Genome engineering is necessary to manufacture and design synthetic cells with desired functions by using bioparts obtained from sequence databases. Among various tools, the CRISPR-Cas system is modularly composed of guide RNA and Cas nuclease; therefore, it is convenient for editing the genome freely. Recently, various strategies have been developed to accurately edit the genome at a single nucleotide level. Furthermore, CRISPR-Cas technology has been extended to molecular diagnostics for nucleic acids and detection of pathogens, including disease-causing viruses. Moreover, CRISPR technology, which can precisely control the expression of specific genes in cells, is evolving to find the target of metabolic biotechnology. In this review, we summarize the status of various CRISPR technologies that can be applied to synthetic biology and discuss the development of synthetic biology combined with CRISPR technology in microbiology.

Citations

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Advanced Sustainable Systems.2025;[Epub] CrossRef
CRISPR applications in microbial World: Assessing the opportunities and challenges
Farhan Kursheed, Esha Naz, Sana Mateen, Ume Kulsoom
Gene.2025; 935: 149075. CrossRef
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Ratnesh Singh Kanwar, Kirtida Gambhir, Tanishka Aggarwal, Akash Godiwal, Kuntal Bhadra
Military Medicine.2025; 190(3-4): e569. CrossRef
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Pankaj Garg, Gargi Singhal, Siddhika Pareek, Prakash Kulkarni, David Horne, Aritro Nath, Ravi Salgia, Sharad S. Singhal
Biochimica et Biophysica Acta (BBA) - Reviews on Cancer.2025; 1880(1): 189233. CrossRef
From nanotechnology to AI: The next generation of CRISPR-based smart biosensors for infectious disease detection
Irkham, Abdullahi Umar Ibrahim, Chidi Wilson Nwekwo, Pwadubashiyi Coston Pwavodi, Salma Nur Zakiyyah, Mehmet Ozsoz, Yeni Wahyuni Hartati
Microchemical Journal.2025; 208: 112577. CrossRef
Trends in Aptasensing and the Enhancement of Diagnostic Efficiency and Accuracy
Mohd Afaque Ansari, Damini Verma, Mohd-Akmal Hamizan, Maumita Das Mukherjee, Noor Faizah Mohd-Naim, Minhaz Uddin Ahmed
ACS Synthetic Biology.2025; 14(1): 21. CrossRef
Comprehensive approaches to heavy metal bioremediation: Integrating microbial insights and genetic innovations
Mehran khan, Mir Muhammad Nizamani, Muhammad Asif, Ali Kamran, Guandi He, Xiangyang Li, Sanwei Yang, Xin Xie
Journal of Environmental Management.2025; 374: 123969. CrossRef
Cell-free systems: A synthetic biology tool for rapid prototyping in metabolic engineering
Kumyoung Jeung, Minsun Kim, Eunsoo Jang, Yang Jun Shon, Gyoo Yeol Jung
Biotechnology Advances.2025; 79: 108522. CrossRef
Synthetic biology and parasite genomics: engineering parasite-resistant human microbiomes for sustainable disease prevention
Esam S. Al-Malki
Beni-Suef University Journal of Basic and Applied Sciences.2025;[Epub] CrossRef
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Amankeldi K. Sadanov, Baiken B. Baimakhanova, Saltanat E. Orasymbet, Irina A. Ratnikova, Zere Z. Turlybaeva, Gul B. Baimakhanova, Aigul A. Amitova, Anel A. Omirbekova, Gulzat S. Aitkaliyeva, Bekzhan D. Kossalbayev, Ayaz M. Belkozhayev
Microorganisms.2025; 13(3): 599. CrossRef
AlPaCas: allele-specific CRISPR gene editing through a protospacer-adjacent-motif (PAM) approach
Serena Rosignoli, Elisa Lustrino, Alessio Conci, Alessandra Fabrizi, Serena Rinaldo, Maria Carmela Latella, Elena Enzo, Gianni Prosseda, Laura De Rosa, Michele De Luca, Alessandro Paiardini
Nucleic Acids Research.2024; 52(W1): W29. CrossRef
Use of paired Cas9-NG nickase and truncated sgRNAs for single-nucleotide microbial genome editing
Song Hee Jeong, Ho Joung Lee, Sang Jun Lee
Frontiers in Genome Editing.2024;[Epub] CrossRef
Developing pioneering pharmacological strategies with CRISPR/Cas9 library screening to overcome cancer drug resistance
Yu He, Huan Li, Xueming Ju, Bo Gong
Biochimica et Biophysica Acta (BBA) - Reviews on Cancer.2024; 1879(6): 189212. CrossRef
Efficient CRISPR-Cas12f1-Mediated Multiplex Bacterial Genome Editing via Low-Temperature Recovery
Se Ra Lim, Hyun Ju Kim, Sang Jun Lee
Journal of Microbiology and Biotechnology.2024; 34(7): 1522. CrossRef
CRISPR-based biosensor for the detection of Marburg and Ebola virus
Irkham Irkham, Abdullahi Umar Ibrahim, Pwadubashiyi Coston Pwavodi, Chidi Wilson Nwekwo, Yeni Wahyuni Hartati
Sensing and Bio-Sensing Research.2024; 43: 100601. CrossRef
Advancements in Synthetic Biology for Enhancing Cyanobacterial Capabilities in Sustainable Plastic Production: A Green Horizon Perspective
Taufiq Nawaz, Liping Gu, Zhong Hu, Shah Fahad, Shah Saud, Ruanbao Zhou
Fuels.2024; 5(3): 394. CrossRef
Genetic Engineering in Bacteria, Fungi, and Oomycetes, Taking Advantage of CRISPR
Piao Yang, Abraham Condrich, Ling Lu, Sean Scranton, Camina Hebner, Mohsen Sheykhhasan, Muhammad Azam Ali
DNA.2024; 4(4): 427. CrossRef
Perspective Evaluation of Synthetic Biology Approaches for Effective Mitigation of Heavy Metal Pollution
Sandhya Mishra, Anju Patel, Pankaj Bhatt, Shaohua Chen, Pankaj Kumar Srivastava
Reviews of Environmental Contamination and Toxicology.2024;[Epub] CrossRef
Advancing microbiota therapeutics: the role of synthetic biology in engineering microbial communities for precision medicine
Asiya Nazir, Fathima Hasnain Nadeem Hussain, Afsheen Raza
Frontiers in Bioengineering and Biotechnology.2024;[Epub] CrossRef
Multifaceted Applications of Synthetic Microbial Communities: Advances in Biomedicine, Bioremediation, and Industry
Edgar Adrian Contreras-Salgado, Ana Georgina Sánchez-Morán, Sergio Yair Rodríguez-Preciado, Sonia Sifuentes-Franco, Rogelio Rodríguez-Rodríguez, José Macías-Barragán, Mariana Díaz-Zaragoza
Microbiology Research.2024; 15(3): 1709. CrossRef
Prospects for synthetic biology in 21st Century agriculture
Xingyan Ye, Kezhen Qin, Alisdair R. Fernie, Youjun Zhang
Journal of Genetics and Genomics.2024;[Epub] CrossRef
Biotechnological production of omega-3 fatty acids: current status and future perspectives
Jiansong Qin, Elif Kurt, Tyler LBassi, Lucas Sa, Dongming Xie
Frontiers in Microbiology.2023;[Epub] CrossRef
Emerging Technologies in Industrial Microbiology: From Bioengineering to CRISPR-Cas Systems
Umar Farooq, Malathi Hanumanthayya, Izharul Haq
Salud, Ciencia y Tecnología.2023; 3: 406. CrossRef
Optimized Linear DNA Recombineering for CRISPR-Cpf1 System in Corynebacterium glutamicum
Ting Wang, Xiaowan Jiang, Shufang Lv, Linfeng Hu, Shuangcheng Gao, Qingyang Xu, Junhui Zhang, Dianyun Hou
Fermentation.2023; 10(1): 31. CrossRef

Journal Article

Salicibibacter halophilus sp. nov., a moderately halophilic bacterium isolated from kimchi: Young Joon Oh , Joon Yong Kim , Hyo Kyeong Park , Ja-Young Jang , Seul Ki Lim , Min-Sung Kwon , Hak-Jong Choi; J. Microbiol. 2019;57(11):997-1002. Published online October 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9421-z

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Abstract

A Gram-stain-positive, rod-shaped, alkalitolerant, and halophilic bacterium–designated as strain NKC3-5T–was isolated from kimchi that was collected from the Geumsan area in the Republic of Korea. Cells of isolated strain NKC3-5T were 0.5–0.7􍾘μm wide and 1.4–2.8 μm long. The strain NKC3-5T could grow at up to 20.0% (w/v) NaCl (optimum 10%), pH 6.5–10.0 (optimum pH 9.0), and 25–40°C (optimum 35°C). The cells were able to reduce nitrate under aerobic conditions, which is the first report in the genus Salicibibacter. The genome size and genomic G + C content of strain NKC3-5T were 3,754,174 bp and 45.9 mol%, respectively; it contained 3,630 coding sequences, 16S rRNA genes (six 16S, five 5S, and five 23S), and 59 tRNA genes. Phylogenetic analysis based on 16S rRNA showed that strain NKC- 3-5T clustered with bacterium Salicibibacter kimchii NKC1-1T, with a similarity of 96.2–97.6%, but formed a distinct branch with other published species of the family Bacillaceae. In addition, OrthoANI value between strain NKC3-5T and Salicibibacter kimchii NKC1-1T was far lower than the species demarcation threshold. Using functional genome annotation, the result found that carbohydrate, amino acid, and vitamin metabolism related genes were highly distributed in the genome of strain NKC3-5T. Comparative genomic analysis revealed that strain NKC3-5T had 716 pan-genome orthologous groups (POGs), dominated with carbohydrate metabolism. Phylogenomic analysis based on the concatenated core POGs revealed that strain NKC3-5T was closely related to Salicibibacter kimchii. The predominant polar lipids were phosphatidylglycerol and two unidentified lipids. Anteiso- C15:0, iso-C17:0, anteiso-C17:0, and iso-C15:0 were the major cellular fatty acids, and menaquinone-7 was the major isoprenoid quinone present in strain NKC3-5T. Cell wall peptidoglycan analysis of strain NKC3-5T showed that meso-diaminopimelic acid was the diagnostic diamino acid. The phenotypic, genomic, phylogenetic, and chemotaxonomic properties reveal that the strain represents a novel species of the genus Salicibibacter, for which the name Salicibibacter halophilus sp. nov. is proposed, with the type strain NKC3-5T (= KACC 21230T = JCM 33437T).

Citations

Citations to this article as recorded by

Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi
Young Joon Oh, Joon Yong Kim, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
Journal of Microbiology.2021; 59(5): 460. CrossRef
The Methods of Digging for “Gold” within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools
Jakub Lach, Paulina Jęcz, Dominik Strapagiel, Agnieszka Matera-Witkiewicz, Paweł Stączek
Genes.2021; 12(11): 1756. CrossRef
List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef

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