Review
Microbiology
Aisylu Shaidullina, Alexander Harms
Summary: Bacteriophages are important predators in ecosystems with potential applications in biotechnology and bacterial infection treatment. Advances in sequencing and genome-wide screens allow for systematic study of phage-host interactions, paving the way for future applications and research expansion.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Article
Microbiology
Vidar Sorum, Emma L. Oynes, Anna S. Moller, Klaus Harms, Orjan Samuelsen, Nicole L. Podnecky, Pal J. Johnsen
Summary: This study investigates the stability of collateral networks in ciprofloxacin-resistant Escherichia coli strains. The results show that the collateral effects caused by resistance development are not stable, complicating the general applicability and clinical implementation of collateral effects in treatment strategies.
Article
Spectroscopy
Saba Bashir, Haq Nawaz, Muhammad Irfan Majeed, Mashkoor Mohsin, Ali Nawaz, Nosheen Rashid, Fatima Batool, Saba Akbar, Muhammad Abubakar, Shamsheer Ahmad, Saqib Ali, Muhammad Kashif
Summary: This study aimed to identify and differentiate tigecycline-resistant E. coli (TREC) from tigecycline-sensitive E. coli (TSEC) using Surface-enhanced Raman Spectroscopy (SERS). Statistical analyses including PCA, HCA, and PLS-DA were employed to assess the diagnostic potential of SERS. Qualitative identification and differentiation between resistant and sensitive strains were efficiently done using PCA and HCA. PLS-DA successfully discriminated among TREC and TSEC at the strain level with 98% area under the ROC curve, 100% sensitivity, 98.7% specificity, and 100% accuracy.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Immunology
Mengting Guo, Ya Gao, Yibing Xue, Yuanping Liu, Xiaoyan Zeng, Yuqiang Cheng, Jingjiao Ma, Hengan Wang, Jianhe Sun, Zhaofei Wang, Yaxian Yan
Summary: The study isolated three lytic phages from sewage of dairy farm, showing broad host range and high efficiency against E. coli. Phage cocktail significantly reduced bacterial number, somatic cells, and inflammatory factors in a mastitis infected cow model, achieving the same effect as antibiotic treatment. Overall, phage cocktail may be a promising alternative therapy against mastitis caused by drug resistant E. coli.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Microbiology
Yinfeng Wang, Guanhua Xuan, Houqi Ning, Jiuna Kong, Hong Lin, Jingxue Wang
Summary: A high-throughput method combining Tn5 transposon mutation and phage screening was successfully used to obtain phage-resistant strains of Escherichia coli BL21 (DE3). Mutant strains PR281-7, PR338-8, PR339-3, PR340-8, and PR347-9 were obtained, which effectively resisted phage infection and maintained the capability of producing recombinant proteins. Comparative genomics analysis revealed mutated genes in ecpE, nohD, nrdR, and livM in these phage-resistant strains.
JOURNAL OF MICROBIOLOGY
(2023)
Article
Veterinary Sciences
Liming Jiang, Yaxian Jiang, Wen Liu, Rui Zheng, Chenghua Li
Summary: Escherichia coli, a gram-negative bacterium, is widely distributed and poses a threat to human and animal health. This study identified two phages with good antibiofilm effects against E. coli, which can be potential candidates for phage therapy.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Medicine, Research & Experimental
Ahmed A. Abdelaziz, Amal M. Abo Kamer, Ahmed M. Nosair, Lamiaa A. Al-Madboly
Summary: The aim of this study was to isolate, characterize, and assess the potential efficacy of a bacteriophage in the treatment of an induced gastrointestinal tract infection caused by extensively drug-resistant Escherichia coli. The results showed that the phage phPE42 demonstrated broad coverage activity against E. coli and exhibited favorable growth kinetics and stability under challenging conditions. Phage therapy effectively eradicated bacterial burden and reduced tissue damage and inflammatory markers in a rat model.
Article
Food Science & Technology
Khashayar Shahin, Hongduo Bao, Shujiao Zhu, Abbas Soleimani-Delfan, Tao He, Mojtaba Mansoorianfar, Ran Wang
Summary: This study identified and characterized three highly effective antibacterial phages with stable bacteriolytic activity under different conditions. These phages exhibited extensive lytic effects on a wide range of E. coli strains, including pathogenic and antibiotic-resistant ones. Food testing confirmed that the phage cocktail was able to completely inhibit the growth of E. coli in food matrices, making them ideal candidates for further development as bio-control agents for E. coli in food production.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Infectious Diseases
Mingju Hao, Jessica Schuyler, Haifang Zhang, Elena Shashkina, Hong Du, Derrick E. Fouts, Michael Satlin, Barry N. Kreiswirth, Liang Chen
Summary: A study on CRKp isolates from New York and New Jersey revealed low in vitro activity of apramycin and a high resistance rate, mainly among the K. pneumoniae ST258 strains. The study identified the presence of a novel cointegrate plasmid, p59494-RX116.1, demonstrating the potential spread of apramycin resistance through plasmids.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2021)
Article
Environmental Sciences
Xinjun Hu, Yingying Chen, Hao Xu, Jie Qiao, Haoyu Ge, Ruishan Liu, Beiwen Zheng
Summary: This study conducted a prospective investigation in six farms in China and found MCRPEC strains in different samples, with ST10 being the dominant sequence type and the potential for clonal transmission. The results indicated the possibility of interspecies and cross-regional transmission between farms. Therefore, further surveillance and research on non-clinical MCRPEC strains are necessary to reduce their threat.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Microbiology
Dongyang Gao, Hongyue Ji, Xin Li, Xiquan Ke, Xiangmin Li, Pin Chen, Ping Qian
Summary: In this study, a polyvalent broad-spectrum phage, GSP044, was isolated from pig farm sewage, which showed the ability to simultaneously lyse multiple serotypes of Salmonella and E. coli. GSP044 has a short latent period, high stability, and good tolerance to chloroform. Genome sequencing analysis revealed that GSP044 belongs to the Demerecviridae family, Epseptimavirus genus, and does not contain any lysogenicity-related, virulence-related, or antibiotic resistance-related genes. The initial application of phage GSP044 showed promising results in reducing biofilm formation, degrading mature biofilm, and decreasing the number of colonized S. Enteritidis in vitro and in vivo.
MICROBIOLOGICAL RESEARCH
(2023)
Article
Microbiology
Naveen Chaudhary, Ravi Kumar Maurya, Dharminder Singh, Balvinder Mohan, Neelam Taneja
Summary: Urinary tract infections (UTIs) are common bacterial infections in humans. A lytic phage 590B has been discovered to effectively disrupt bacterial biofilms and can be used as an alternative to antibiotics in the treatment of multidrug-resistant UTIs.
Article
Microbiology
Yan D. Niu, Hui Liu, Hechao Du, Ruiqiang Meng, El Sayed Mahmoud, Guihua Wang, Tim A. McAllister, Kim Stanford
Summary: In this study, the efficacy of different bacteriophages against E. coli O157 was evaluated, revealing that the combination of phages did not always follow the individual phage activity. Factors such as temperature, exposure time, and phage strains influenced the interactions among phages, with some combinations showing facilitation while others demonstrated antagonistic effects. The development of phage cocktails should consider confirming lack of antagonism and preferably facilitation or synergistic effects among constituent phages.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Rene Dofini Magnini, Francois Pedinielli, Julia Vergalli, Noufou Ouedraogo, Simon Remy, Adama Hilou, Jean-Michel Brunel, Jean-Marie Pages, Anne Davin-Regli
Summary: The emergence of bacterial resistance has changed the effectiveness of different antibiotic families, and research into alternative therapeutic molecules from medicinal plants is needed. This study used molecular networking and MS/MS data to characterize active molecules in natural extracts from A. senegal. The activities of different combinations of fractions and antibiotics were tested using the chessboard test. Bio-guided fractionation identified fractions with chloramphenicol activity, and LC-MS/MS analysis revealed that these fractions contained Budmunchiamines, which are macrocyclic alkaloids. This study provides a potential source of bioactive secondary metabolites related to Budmunchiamines that can restore chloramphenicol activity in enterobacterial-resistant strains with AcrB efflux pumps.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Environmental Sciences
Sudhakar Padmesh, Aditi Singh, Sidharth Chopra, Manodeep Sen, Saman Habib, Deepti Shrivastava, Parul Johri
Summary: This study isolated 31 bacteriophages from urban sewage treatment plants and analyzed their physico-chemical properties. Two bacteriophages (ASEC2201 and ASEC2202) were able to survive at different temperatures and pH values, as well as effectively combat multidrug-resistant Escherichia coli. Morphological characterization through transmission electron microscopy revealed that both phages were tailed phages, and genomic analysis confirmed that they belonged to the Escherichia phage family Drexlerviridae of Caudovirales.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Editorial Material
Microbiology
Yeah-Ji Ahn, Jong An Lee, Kyeong Rok Choi, Junho Bang, Sang Yup Lee
Summary: This article introduces the advantages of microbe-based carbon capture, sequestration, and utilization (CCSU) technologies over physicochemical and plant-based methods, and describes the role of microorganisms in the global carbon cycle. Strategies to enhance microbe performance and the use of microbes in addressing environmental crises are provided. Finally, the challenges and future prospects of microbe-based CCSU technologies are discussed.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Editorial Material
Biotechnology & Applied Microbiology
Woo Dae Jang, Gi Bae Kim, Sang Yup Lee
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Jong An Lee, Jung Ho Ahn, Gi Bae Kim, Sol Choi, Ji Yeon Kim, Sang Yup Lee
Summary: Mannheimia succiniciproducens, a rumen bacterium, was engineered to produce a high yield of malic acid through pathway reconstruction, respiration system reconstruction, and cell membrane engineering. The strategies used in this study for systems metabolic engineering could be valuable for developing anaerobic bioprocesses for the production of various industrially important chemicals.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Review
Biotechnology & Applied Microbiology
Gi Bae Kim, So Young Choi, In Jin Cho, Da-Hee Ahn, Sang Yup Lee
Summary: Bio-based production of chemicals and materials has gained attention for its role in establishing sustainability and improving human health. Metabolic engineering (ME) allows deliberate modification of cellular metabolic, regulatory, and signaling networks to enhance chemical production and degrade harmful substances. Over the past 30 years, ME has advanced significantly through the integration of synthetic biology, systems biology, evolutionary engineering, and data science aided by artificial intelligence. This review provides an overview of the field, highlighting its contributions to sustainable production, health, and the environment through representative examples. Future challenges and perspectives are also discussed.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Baodong Hu, Haibo Yu, Jingwen Zhou, Jianghua Li, Jian Chen, Guocheng Du, Sang Yup Lee, Xinrui Zhao
Summary: By exploiting versatile P450 enzymes, whole-cell biocatalysis can be performed to synthesize valuable compounds in Escherichia coli. However, the insufficient supply of heme limits the whole-cell P450 biocatalytic activity. This study reports a strategy for improving intracellular heme biosynthesis to enhance the catalytic efficiencies of P450s. The strategy involves optimizing intracellular heme biosynthesis through the integrated expression of necessary synthetic genes and the fine-tuning of heme levels using mutated biosensors and regulatory RNA systems.
Article
Chemistry, Multidisciplinary
Ji Yeon Kim, Yeah-Ji Ahn, Jong An Lee, Sang Yup Lee
Summary: Due to the climate crisis and environmental problems caused by reliance on fossil resources, many efforts have been made to establish biorefinery platforms for the bio-based production of chemicals. Systems metabolic engineering has enabled efficient engineering of microorganisms to produce platform chemicals. This paper reviews recent advances and future prospects in the bio-based production of representative platform chemicals, accompanied by a table summarizing their titer, yield, and productivity.
CURRENT OPINION IN GREEN AND SUSTAINABLE CHEMISTRY
(2023)
Article
Biochemical Research Methods
Hannah Chung, Jiyong Kim, Yong Jae Lee, Kyeong Rok Choi, Ki Jun Jeong, Geun-Joong Kim, Sang Yup Lee
Summary: A strategy to enhance mRNA stability and improve recombinant protein production in E. coli was developed by knocking down the expression level of RnpA. This strategy successfully allowed the overexpression of 23 different recombinant proteins, including difficult-to-produce proteins, such as Cas9 protein and spider silk protein. This study has broad application potential for the production of recombinant proteins.
BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
Jae Sung Cho, Dongsoo Yang, Cindy Pricilia Surya Prabowo, Mohammad Rifqi Ghiffary, Taehee Han, Kyeong Rok Choi, Cheon Woo Moon, Hengrui Zhou, Jae Yong Ryu, Hyun Uk Kim, Sang Yup Lee
Summary: Researchers have developed a synthetic sRNA platform that can be used in a wide range of bacteria, allowing knockdown of target genes and reducing virulence-associated phenotypes in pathogens. It can also be used for metabolic engineering to produce specific chemicals. The platform has been successfully tested in 16 bacterial species.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Liuyan Gu, Xinxin Xiao, Ge Zhao, Paul Kempen, Shuangqing Zhao, Jianming Liu, Sang Yup Lee, Christian Solem
Summary: This study demonstrates for the first time that Lactococcus lactis, a lactic acid bacterium, can use ferricyanide as an alternative electron acceptor to support growth. By analyzing mutants and conducting electrochemical analysis, the essential role of NADH dehydrogenase and 2-amino-3-carboxy-1,4-naphtoquinone in extracellular electron transfer is identified and the underlying pathway is systematically uncovered. The study also reveals the unexpected effects of ferricyanide respiration on L. lactis, including changes in morphology and increased acid resistance.
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Linxia Liu, Jinlong Li, Yuanming Gai, Zhizhong Tian, Yanyan Wang, Tenghe Wang, Pi Liu, Qianqian Yuan, Hongwu Ma, Sang Yup Lee, Dawei Zhang
Summary: Vitamin B6 is a vital nutrient widely used in medicine, food, animal feed, and cosmetics industries. Researchers have developed an engineered strain of Escherichia coli to produce vitamin B6 more efficiently and affordably. By optimizing the metabolic pathway and enzyme efficiency, the final strain achieved a high productivity of 1.4 g/L of vitamin B6 through fed-batch fermentation. These strategies are valuable for developing microbial strains for producing vitamins and other bioproducts with low metabolic fluxes.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Qian Kang, Huan Fang, Mengjie Xiang, Kaixing Xiao, Pingtao Jiang, Chun You, Sang Yup Lee, Dawei Zhang
Summary: This study reports a method for the synthesis of adenosylcobalamin (AdoCbl) using a cell-free reaction system, which overcomes technical challenges and achieves efficient synthesis. The strategies described here for coordinating synthetic modules in a complex cell-free system will be useful for developing platforms to produce complex natural compounds with long and complicated biosynthetic pathways.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Christopher M. Whitford, Tetiana Gren, Emilia Palazzotto, Sang Yup Lee, Yaojun Tong, Tilmann Weber
Summary: CRISPRtools, specifically Cas9n-sgRNA guided cytidine deaminase base editors like CRISPR-BEST, have greatly simplified genetic manipulation of streptomycetes. The possibility for multiplexed experiments in genomically instable species is a major advantage of CRISPR base editing technology. This study demonstrates the scalability of Csy4 based multiplexed genome editing using CRISPR-mcBEST in Streptomyces coelicolor and provides important insights into its performance and potential applications.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Won Jun Kim, Youngjoon Lee, Hyun Uk Kim, Jae Yong Ryu, Jung Eun Yang, Sang Yup Lee
Summary: In metabolic engineering, predicting gene overexpression targets is challenging. The iBridge method identifies positive and negative metabolites that impact product formation and identifies bridgereactions as overexpression and downregulation targets. It can be used to optimize the production of numerous chemicals.
Article
Multidisciplinary Sciences
Gi Bae Kim, Ji Yeon Kim, Jong An Lee, Charles J. Norsigian, Bernhard O. Palsson, Sang Yup Lee
Summary: The functional annotation of open reading frames in microbial genomes is still incomplete. In this study, a deep learning model called DeepECtransformer was developed to predict specific catalytic functions for un-annotated genes. Experimental validation confirmed the accuracy of the predicted enzymatic activities for three proteins and revealed that the neural network relies on functional motifs of enzymes to predict EC numbers.
NATURE COMMUNICATIONS
(2023)
Review
Biochemical Research Methods
Taehee Han, Alisher Nazarbekov, Xuan Zou, Sang Yup Lee
Summary: Systems metabolic engineering has revolutionized sustainable production through the integration of metabolic engineering with systems biology, synthetic biology, and evolutionary engineering. This article reviews the latest tools and strategies and highlights trends and challenges in the field.
CURRENT OPINION IN BIOTECHNOLOGY
(2023)