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 PDF

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
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.2025; 65(5): 992. CrossRef
A Snapshot of Microbial Succession and Volatile Component Dynamics of Marselan Wine in Xinjiang During Spontaneous Fermentation
Qingquan Fu, Fangfang Wang, Tiantian Tang, Zimen Liu, Lilin Wang, Qingling Wang, Xuewei Shi, Bin Wang
Foods.2025; 14(6): 994. CrossRef
Impact of Packaging Methods on Physicochemical Properties, Flavor Profile, and Microbial Community in Low-Temperature Stored Mianning Ham
Lin Chen, Mengdie Li, Yiting Song, Wei Wang, Jiamin Zhang, Ting Bai, Ling Gan, Congxia Tang, Lili Ji
Foods.2025; 14(13): 2336. CrossRef
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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
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Jingsheng Yu, Mengyue Guo, Wenjun Jiang, Yujie Dao, Xiaohui Pang
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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
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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 PDF

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.

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Erradicación de Helicobacter pylori con tratamiento de primera línea en un hospital de alta complejidad del suroccidente colombiano
Mauricio Sepúlveda Copete, Nelson Enrique Rojas Rojas, Carlos Julio Vargas Potes, Carolina Agudelo Gutierrez, Heidy Lizeth Benavides Armero, Ana Fernanda Mejía Hurtado, David Alejandro Pantoja Castro, Leidy Johanna Hurtado Bermúdez, Stefania Cruz Calderón
Revista colombiana de Gastroenterología.2024; 39(4): 408. CrossRef
Antimicrobial susceptibility of clinical Helicobacter pylori isolates and its eradication by standard triple therapy: a study in west central region of Colombia
Adalucy Alvarez-Aldana, Paula Andrea Fernandez Uribe, Tatiana Mejía Valencia, Yina Marcela Guaca-Gonzalez, Jorge Javier Santacruz-Ibarra, Brenda Lucia Arturo-Arias, Luis Javier Castañeda-Chavez, Robinson Pacheco-López, Lina María Londoño-Giraldo, José Ign
Microbiology Spectrum.2024;[Epub] CrossRef
The prevalence of clarithromycin-resistant Helicobacter pylori isolates: a systematic review and meta-analysis
Mohammad Sholeh, Saeed Khoshnood, Taher Azimi, Jasem Mohamadi, Vahab Hassan Kaviar, Marzieh Hashemian, Somayeh Karamollahi, Nourkhoda Sadeghifard, Hedayat Heidarizadeh, Mohsen Heidary, Morteza Saki
PeerJ.2023; 11: e15121. CrossRef
Detection of A2143G, A2142C, and A2142G Point Mutations with Real-Time PCR in Stool Specimens from Children Infected with Helicobacter pylori
Nesrin Gareayaghi, Bekir Kocazeybek
Diagnostics.2022; 12(9): 2119. CrossRef
An American lineage of Helicobacter pylori prophages found in Colombia
Angela B Muñoz, Alba A Trespalacios‐Rangel, Filipa F Vale
Helicobacter.2021;[Epub] CrossRef
Genomic Analysis of Antimicrobial Resistance Genotype-to-Phenotype Agreement in Helicobacter pylori
Tal Domanovich-Asor, Yair Motro, Boris Khalfin, Hillary A. Craddock, Avi Peretz, Jacob Moran-Gilad
Microorganisms.2020; 9(1): 2. CrossRef
Descripción de la resistencia de Helicobacter pylori a seis antibióticos de uso frecuente en Colombia
Jose Danilo Atehortua Rendon, Tania Liseth Pérez Cala, Alonso Martínez
Revista Colombiana de Gastroenterología.2020; 35(3): 351. CrossRef
CRHP Finder, a webtool for the detection of clarithromycin resistance in Helicobacter pylori from whole‐genome sequencing data
Melodi Yusibova, Henrik Hasman, Philip Thomas Lanken Conradsen Clausen, Frank Imkamp, Karoline Wagner, Leif Percival Andersen
Helicobacter.2020;[Epub] CrossRef
Genotypic determination of resistance and heteroresistance to clarithromycin in Helicobacter pylori isolates from antrum and corpus of Colombian symptomatic patients
Betsy Verónica Arévalo-Jaimes, Diana F. Rojas-Rengifo, Carlos Alberto Jaramillo, Belén Mendoza de Molano, José Fernando Vera-Chamorro, María del Pilar Delgado
BMC Infectious Diseases.2019;[Epub] CrossRef
Helicobacter pylori: resistencia múltiple en pacientes de Bogotá, Colombia
Azucena Arévalo, William Alberto Otero, Alba Alicia Trespalacios
Biomédica.2019; 39: 125. CrossRef
Mutaciones del gen ARN ribosómico 23S de Helicobacter pylori asociadas con resistencia a claritromicina en pacientes atendidos en una unidad de endoscopia de Medellín, Colombia
Ingrid Johana Roldán, Rodrigo Castaño, María Cristina Navas
Biomédica.2019; 39(Supl. 2): 117. CrossRef
A systematic review and meta‐analysis of genotypic methods for detecting antibiotic resistance in Helicobacter pylori
You‐hua Wang, Zhen Li, Le Wang, Li‐ya Zhu‐ge, Ru‐lin Zhao, Shuang Wu, Ya Wang, Ying An, Yong Xie
Helicobacter.2018;[Epub] CrossRef
Resistance mechanisms ofHelicobacter pyloriand its dual target precise therapy
Yuehua Gong, Yuan Yuan
Critical Reviews in Microbiology.2018; 44(3): 371. CrossRef
Phenotypic and genotypic correlation as expressed in Helicobacter pylori resistance to clarithromycin and fluoroquinolones
Dana Binyamin, Nina Pastukh, Avi On, Maya Paritsky, Avi Peretz
Gut Pathogens.2017;[Epub] CrossRef
Clarithromycin resistance and prevalence of Helicobacter pylori virulent genotypes in patients from Southern México with chronic gastritis
Judit Alarcón-Millán, Gloria Fernández-Tilapa, Enoc Mariano Cortés-Malagón, Carlos Alberto Castañón-Sánchez, José De Sampedro-Reyes, Iván Cruz-del Carmen, Reyes Betancourt-Linares, Adolfo Román-Román
Infection, Genetics and Evolution.2016; 44: 190. CrossRef
Surveillance of Levofloxacin Resistance in Helicobacter pylori Isolates in Bogotá-Colombia (2009-2014)
Alba A. Trespalacios-Rangél, William Otero, Azucena Arévalo-Galvis, Raúl A. Poutou-Piñales, Emiko Rimbara, David Y. Graham, Massimiliano Galdiero
PLOS ONE.2016; 11(7): e0160007. CrossRef
Sequential vs. prolonged 14-day triple therapy forHelicobacter pylorieradication: the meta-analysis may be influenced by ‘geographical weighting’
G. Losurdo, G. Leandro, M. Principi, F. Giorgio, L. Montenegro, C. Sorrentino, E. Ierardi, A. Di Leo
International Journal of Clinical Practice.2015; 69(10): 1112. CrossRef

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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Abstract PDF

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.

Citations

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Mutations in rpoB and katG genes and the inhA operon in multidrug-resistant Mycobacterium tuberculosis isolates from Zambia
Eddie S. Solo, Chie Nakajima, Trevor Kaile, Precious Bwalya, Grace Mbulo, Yukari Fukushima, Sylvia Chila, Nanthan Kapata, Yogendra Shah, Yasuhiko Suzuki
Journal of Global Antimicrobial Resistance.2020; 22: 302. CrossRef
Mutations of rpoB, katG, inhA and ahp genes in rifampicin and isoniazid-resistant Mycobacterium tuberculosis in Kyrgyz Republic
Jainagul Isakova, Nurmira Sovkhozova, Denis Vinnikov, Zoy Goncharova, Elnura Talaibekova, Nazira Aldasheva, Almaz Aldashev
BMC Microbiology.2018;[Epub] CrossRef
Genotyping and molecular detection of multidrug-resistant Mycobacterium tuberculosis among tuberculosis lymphadenitis cases in Addis Ababa, Ethiopia
O. Zewdie, A. Mihret, T. Abebe, A. Kebede, K. Desta, A. Worku, G. Ameni
New Microbes and New Infections.2018; 21: 36. CrossRef
Evaluation of the GenoType MTBDRplus assay for detection of rifampicin- and isoniazid-resistant Mycobacterium tuberculosis isolates in central Ethiopia
Zufan Bedewi Omer, Yalemtsehay Mekonnen, Adane Worku, Aboma Zewde, Girmay Medhin, Temesgen Mohammed, Rembert Pieper, Gobena Ameni
International Journal of Mycobacteriology.2016; 5(4): 475. CrossRef
Resistance to Isoniazid and Ethionamide in Mycobacterium tuberculosis : Genes, Mutations, and Causalities
Catherine Vilchèze, William R. Jacobs JR., Graham F. Hatfull, William R. Jacobs Jr.
Microbiology Spectrum.2014;[Epub] CrossRef

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