Journal of Microbiology

Review

Recent advances in targeted mutagenesis to expedite the evolution of biological systems: Seungjin Kim, Seungwon Lee, Hyun Gyu Lim; J. Microbiol. 2025;63(3):e2501008. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501008

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Evolution has been systematically exploited to engineer biological systems to obtain improved or novel functionalities by selecting beneficial mutations. Recent innovations in continuous targeted mutagenesis within living cells have emerged to generate large sequence diversities without requiring multiple steps. This review comprehensively introduces recent advancements in this field, categorizing them into three approaches depending on methods to create mutations: orthogonal error-prone DNA polymerases, site-specific base editors, and homologous recombination of mutagenic DNA fragments. Combined with high-throughput screening methods, these advances expedited evolution processes with significant reduction of labor and time. These approaches promise broader industrial and research applications, including enzyme improvement, metabolic engineering, and drug resistance studies.

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

Journal Article

Diversity and composition of microbiota during fermentation of traditional Nuodeng ham: Xiao-mei Zhang , Xi-jun Dang , Yuan-bing Wang , Tao Sun , Yao Wang , Hong Yu , Wu-song Yang; J. Microbiol. 2021;59(1):20-28. Published online December 23, 2020; DOI: https://doi.org/10.1007/s12275-021-0219-4

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Abstract

The microbial community is one of the most important factors in shaping the characteristics of fermented food. Nuodeng ham, traditionally produced and subjected to 1–4 years of fermentation, is a dry fermented food product with cultural and economic significance to locals in southwestern China. In this study, we aimed to characterize the microbiota and physicochemical profiles of Nuodeng ham across different stages of fermentation. Ham samples from each of the four years were analyzed by sequencing bacterial 16S rRNA gene and fungal internal transcribed spacer sequence, in order to characterize the diversity and composition of their microflora. A total of 2,679,483 bacterial and 2,983,234 fungal sequences of high quality were obtained and assigned to 514 and 57 genera, respectively. Among these microbes, Staphylococcus and Candida were the most abundant genera observed in the ham samples, though samples from different years showed differences in their microbial abundance. Results of physicochemical properties (pH, water, amino acid, NaCl, nitrate and nitrite contents, and the composition of volatile compounds) revealed differences among the ham samples in the composition of volatile compounds, especially in the third year samples, in which no nitrite was detected. These results suggest that the structure and diversity of microbial communities significantly differed across different stages of fermentation. Moreover, the third year hams exhibits a unique and balanced microbial community, which might contribute to the special flavor in the green and safe food products. Thus, our study lends insights into the production of high quality Nuodeng ham.

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Metabolite and microbial community composition of normal and sensory defect Nuodeng hams characterized based on metabolomics and high-throughput sequencing
Nannan Zhou, Yaying Zhao, Guiying Wang, Guanghui Chen, Zhijie Zheng, Ruwei Ren, Guozhou Liao
Food Chemistry.2025; 463: 141358. CrossRef
Insight into the Relationship between the Causes of Off-Odour and Microorganism Communities in Xuanwei Ham
Haoyi Wang, Xiaoyu Yin, Lu Zhang, Xuejiao Wang, Jiliang Zhang, Rongxin Wen, Jianxin Cao
Foods.2024; 13(5): 776. CrossRef
Study on the Changes and Correlation of Microorganisms and Flavor in Different Processing Stages of Mianning Ham
Yue Huang, Zhengli Wang, Ling Gan, Jiamin Zhang, Wei Wang, Lili Ji, Lin Chen
Foods.2024; 13(16): 2587. CrossRef
Revealing the correlation between small molecule metabolites, volatile compounds and microbial communities during the ripening of Xuanwei ham
Cong Li, Zhijie Zheng, Guiying Wang, Guanghui Chen, Nannan Zhou, Ruwei Ren, Qiongfang Yang, Wenxi Fu, Bo Li, Guozhou Liao
LWT.2024; 211: 116955. CrossRef
Changes in Physicochemical Characteristics and Microbial Diversity of Traditional Fermented Vinasse Hairtail
Yue Zhang, Chuanhai Tu, Huimin Lin, Yuwei Hu, Junqi Jia, Shanshan Shui, Jiaxing Wang, Yi Hu, Bin Zhang
Fermentation.2023; 9(2): 173. CrossRef
Recent developments in off-odor formation mechanism and the potential regulation by starter cultures in dry-cured ham
Changyu Zhou, Qiang Xia, Lihui Du, Jun He, Yangying Sun, Yali Dang, Fang Geng, Daodong Pan, Jinxuan Cao, Guanghong Zhou
Critical Reviews in Food Science and Nutrition.2023; 63(27): 8781. CrossRef
Role of microbiota and its ecological succession on flavor formation in traditional dry-cured ham: a review
Ping Li, Zhijie Bao, Yang Wang, Xinlian Su, Hui Zhou, Baocai Xu
Critical Reviews in Food Science and Nutrition.2023; : 1. CrossRef
Illumina-Based Analysis Yields New Insights Into the Fungal Contamination Associated With the Processed Products of Crataegi Fructus
Jingsheng Yu, Mengyue Guo, Wenjun Jiang, Yujie Dao, Xiaohui Pang
Frontiers in Nutrition.2022;[Epub] CrossRef
Evaluation of protein degradation and flavor compounds during the processing of Xuan'en ham
Rui Li, Cuizhu Geng, Zhemin Xiong, Yingying Cui, E Liao, Lijuan Peng, Weiping Jin, Haibin Wang
Journal of Food Science.2022; 87(8): 3366. CrossRef
Characterization and correlation of dominant bacteria and volatile compounds in post-fermentation process of Ba-bao Douchi
Yan-Zeng Zhang, Xiang-Na Lin, Yan-Qing Ji, Hong-Jun He, Hong-Zhuan Yang, Xiao-Juan Tang, Yun-Guo Liu
Food Research International.2022; 160: 111688. CrossRef
Microbial community composition and soil metabolism in the coexisting Cordyceps militaris and Ophiocordyceps highlandensis
Xiaorong Xu, Xiaomei Zhang, Zhipu Huang, Yuxiao Xu, Dexiang Tang, Bing Zhang, Ketao Zhang, Chaojin Liu, Hong Yu
Journal of Basic Microbiology.2022; 62(10): 1254. CrossRef
Metagenomic Analysis of Suansun, a Traditional Chinese Unsalted Fermented Food
Yaping Hu, Xiaodong Chen, Jie Zhou, Wenxuan Jing, Qirong Guo
Processes.2021; 9(9): 1669. CrossRef

Research Support, Non-U.S. Gov't

Phenotypic and Genotypic Analysis of Clarithromycin-Resistant Helicobacter pylori from Bogotá D.C., Colombia: Alba A. Trespalacios , William Otero , Jorge E. Caminos , Marcela M. Mercado , Jenny Ávila , Liliana E. Rosero , Azucena Arévalo , Raúl A. Poutou-Piñales , David Y. Graham; J. Microbiol. 2013;51(4):448-452. Published online August 30, 2013; DOI: https://doi.org/10.1007/s12275-013-2465-6

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Abstract: Resistance of Helicobacter pylori to clarithromycin is the most common cause of treatment failure in patients with H. pylori infections. This study describes the MICs and the presence of 23S rRNA mutations of H. pylori isolates from Bogotá, D.C., Colombia. H. pylori were isolated from gastric biopsies from patients with functional dyspepsia. Clarithromycin susceptibility was investigated by agar dilution and strains were considered resistant if the MIC was ≥1 μg/ml. DNA sequences of the 23S rRNA gene of strains resistant and sensitive to clarithromycin were determined to identify specific point mutations. Clarithromycin resistance was present in 13.6% of patients by agar dilution. The A2143G, A2142G and A2142C mutations were found in 90.5, 7.1, and 2.4% of H. pylori strains with resistance genotype.The resistant phenotype was associated with 23S rRNA resistance genotype in 85.7% of isolates. The point mutations in 23S rRNA were well correlated with MICs values for clarithromycin.

Journal Article

Genotypic and Phenotypic Characteristics of Tunisian Isoniazid-Resistant Mycobacterium tuberculosis Strains: Alya Soudani , Meriem Zribi , Feriel Messaadi , Taieb Messaoud , Afef Masmoudi , Mohamed Zribi , Chedlia Fendri; J. Microbiol. 2011;49(3):413-417. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-0268-1

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9 Scopus

Abstract: Forty three isoniazid (INH)-resistant Mycobacterium tuberculosis isolates were characterized on the basis of the most common INH associated mutations, katG315 and mabA -15C→T, and phenotypic properties (i.e. MIC of INH, resistance associated pattern, and catalase activity). Typing for resistance mutations was performed by Multiplex Allele-Specific PCR and sequencing reaction. Mutations at either codon were detected in 67.5% of isolates: katG315 in 37.2, mabA -15C→T in 27.9 and both of them in 2.4%, respectively. katG sequencing showed a G insertion at codon 325 detected in 2 strains and leading to amino acid change T326D which has not been previously reported. Distribution of each mutation, among the investigated strains, showed that katG S315T was associated with multiple-drug profile, high-level INH resistance and loss or decreased catalase activity; whereas the mabA -15C→T was more prevalent in mono-INH resistant isolates, but it was not only associated with a low-level INH resistance. It seems that determination of catalase activity aids in the detection of isolates for which MICs are high and could, in conjunction with molecular methods, provide rapid detection of most clinical INH-resistant strains.

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