Article
Microbiology
Jun Kwon, Sang Wha Kim, Sang Guen Kim, Jeong Woo Kang, Won Joon Jung, Sung Bin Lee, Young Min Lee, Sib Sankar Giri, Cheng Chi, Se Chang Park
Summary: This study isolated and characterized a novel bacteriophage, pPa_SNUABM_DT01, with strong lytic ability against Pseudomonas aeruginosa. Comparative genomic analysis revealed that this phage may belong to a novel genus. The phage showed potential as an alternative to antibiotics for treating antibiotic-resistant infections.
Article
Virology
Xiaoyao Cai, Fengjuan Tian, Li Teng, Hongmei Liu, Yigang Tong, Shuai Le, Tingting Zhang
Summary: This study identified a novel mutualistic parasitic dsRNA phage, phiNY, which suggests that dsRNA phages with nonlytic lifestyles might be common in nature and deserve more investigations. Using different virus isolation methods could help identify phages with nonlytic lifestyles beyond strictly lytic ones.
JOURNAL OF VIROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Samuel Coulbourn Flores, Michal Maly, Dominik Hrebik, Pavel Plevka, Jiri Cerny
Summary: The revolution in cryo-electron microscopy has provided unprecedented capabilities in deciphering large macromolecular complexes, including viruses. However, methods for studying nucleic acids lag behind. This study presents a method that utilizes the spiral winding patterns of DNA in viral capsids to quickly generate DNA shells and explain density. The findings suggest rules for DNA turns that determine the capsid inner diameter.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Roman B. Gorodnichev, Maria A. Kornienko, Maja V. Malakhova, Dmitry A. Bespiatykh, Valentin A. Manuvera, Oksana V. Selezneva, Vladimir A. Veselovsky, Dmitry V. Bagrov, Marina V. Zaychikova, Veronika A. Osnach, Anna V. Shabalina, Oleg V. Goloshchapov, Julia A. Bespyatykh, Anna S. Dolgova, Egor A. Shitikov
Summary: To address the crisis of Klebsiella pneumoniae infections caused by drug-resistant strains, new approaches to antimicrobial therapy, such as using phages or phage derivatives, need to be developed. This study describes the first K. pneumoniae phage from the Zobellviridae family, which was isolated from river water and demonstrates lytic activity against K. pneumoniae strains with the KL20 capsule type. The phage's receptor-binding protein was identified as a polysaccharide depolymerase, showing promise for using depolymerases in antimicrobial therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Yuanyuan Niu, Xiaobo Yang, Shang Wang, Yutong Yang, Hongrui Zhou, Chenyu Li, Bin Xue, Xi Zhang, Chen Zhao, Zhiqiang Shen, Jingfeng Wang, Yun Ling, Pingfeng Yu, Zhigang Qiu
Summary: In this study, two phages PPAT and PPAY that infect Pseudomonas aeruginosa PAO1 were isolated and characterized. These phages showed growth inhibitory effects on bacteria and can be used for research and clinical purposes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Milan Gerovac, Laura Wicke, Kotaro Chihara, Cornelius Schneider, Rob Lavigne, Joerg Vogel
Summary: The study utilized Grad-seq to identify stable RNA-protein complexes in Pseudomonas aeruginosa, revealing important noncoding RNAs and RNA-binding proteins. Changes in cellular RNA/protein complexes were observed after bacteriophage infection.
Article
Virology
Wang Liu, Xiaowei Zheng, Xin Dai, Zhenfeng Zhang, Wenyan Zhang, Tian Xiao, Li Huang
Summary: Viruses are more abundant in the marine ecosystem than cellular microorganisms, and yet there is a lack of knowledge about viruses isolated from marine sediments, particularly hydrothermal vent sediments. This study reports the isolation and characterization of a temperate bacteriophage called PVJ1, which infects Psychrobacillus from a hydrothermal vent field. The phage possesses a linear dsDNA genome with multiple encoding regions for various functions. The integration of the phage genome into the host chromosome does not disrupt the host gene function. Additionally, similar phages to PVJ1 are found in diverse environments and primarily infect Firmicutes. This research contributes valuable insights into the biology and interactions of bacterial viruses in the ocean bottom.
Article
Multidisciplinary Sciences
Jaclyn G. McCutcheon, Andrea Lin, Jonathan J. Dennis
Summary: This study characterizes the bacteriophage AXL1, which was isolated from soil and has the ability to selectively kill multiple pathogenic bacteria. It also demonstrates the presence of antibiotic resistance in the phage. Additionally, the study reveals the mechanism of AXL1 using the type IV pilus as its host receptor for infection.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Soo Khim Chan, Zhongchao Zhao, Samuel Penziner, Ethan Khong, David Pride, Robert T. Schooley, Nicole F. Steinmetz
Summary: Antimicrobial resistance is a global health threat exacerbated by the misuse of antibiotics in medicine and agriculture. Phage therapy, as an alternative antimicrobial treatment, involves using bacteriophages to destroy bacterial pathogens. This study aimed to develop versatile tools for tracking and imaging phages by screening and isolating peptides that bind to specific phages.
Article
Microbiology
Xiao Wang, Jingjing Tang, Wen Dang, Zhen Xie, Fuhua Zhang, Xinwei Hao, Sihuai Sun, Xuan Liu, Yi Luo, Mengyuan Li, Yanchao Gu, Yao Wang, Qiwei Chen, Xihui Shen, Lei Xu
Summary: In this study, three bacteriophages capable of infecting Pseudomonas aeruginosa were isolated and their biological characteristics were investigated. The experiment showed that these phages were stable in different environments and could reduce P. aeruginosa biofilms, suggesting their potential as candidates for treating P. aeruginosa infections.
MICROBIOLOGY SPECTRUM
(2023)
Article
Virology
Bahareh Lashtoo Aghaee, Mohammadali Khan Mirzaei, Mohammad Yousef Alikhani, Ali Mojtahedi, Corinne F. Maurice
Summary: Antibiotic resistance is a significant global threat, and using a combination of phages and antibiotics may be an effective strategy for treating multidrug-resistant Pseudomonas aeruginosa infections.
Review
Infectious Diseases
Guillermo Santamaria-Corral, Abrar Senhaji-Kacha, Antonio Broncano-Lavado, Jaime Esteban, Meritxell Garcia-Quintanilla
Summary: Phage therapy is an alternative therapy used as a last resort against multidrug-resistant bacteria infections. Pseudomonas aeruginosa, a pathogen that commonly infects immunocompromised individuals, can be effectively treated using bacteriophages alone or in combination with antibiotics. This review summarizes recent studies highlighting the synergistic effects of phage-antibiotic combinations and successful treatments.
Article
Microbiology
Samuel Namonyo, Gilda Carvalho, Jianhua Guo, Karen D. Weynberg
Summary: This study isolated and characterized four novel phages against multi-drug resistant Pseudomonas aeruginosa clinical strains from Australia, and proposed their potential use as phage therapy candidates.
Article
Virology
Tom P. Pielhop, Carolin Popp, Dennis Knierim, Paolo Margaria, Edgar Maiss
Summary: In this study, a new mycovirus IpCV1 was identified, which infects the fungus Ilyonectria pseudodestructans. IpCV1 has a tripartite dsRNA genome encoding three viral proteins. This study provides a basis for further investigation of the impact of IpCV1 on its host and the etiology of ARD.
ARCHIVES OF VIROLOGY
(2022)
Article
Virology
WeiJie Gong, Hong Liu, XiaoFei Zhu, ShiYun Zhao, JiaLe Cheng, Hongjian Zhu, Jie Zhong, Qian Zhou
Summary: A novel mycovirus, named Alternaria solani fusarivirus 1 (AsFV1), was discovered in Alternaria solani with a genome of 6845 nucleotides. AsFV1 contains three ORFs and a poly(A) tail, and could be a new member of the Fusariviridae family based on sequence alignment and phylogenetic analysis. This is the first report of a fusarivirus infecting Alternaria solani with its full-length nucleotide sequence.
ARCHIVES OF VIROLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Mengyu Shen, Yuhui Yang, Wei Shen, Lujia Cen, Jeffrey S. McLean, Wenyuan Shi, Shuai Le, Xuesong He
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2018)
Article
Microbiology
Yuhui Yang, Shuai Le, Wei Shen, Qian Chen, Youying Huang, Shuguang Lu, Yinling Tan, Ming Li, Fuquan Hu, Yang Li
FRONTIERS IN MICROBIOLOGY
(2018)
Article
Microbiology
Yuhui Yang, Wei Shen, Qiu Zhong, Qian Chen, Xuesong He, Jonathon L. Baker, Kun Xiong, Xiaoling Jin, Jing Wang, Fuquan Hui, Shuai Le
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Multidisciplinary Sciences
Qiu Zhong, Lan Yang, Linlin Li, Wei Shen, Yang Li, Huan Xu, Zhuojun Zhong, Ming Chen, Shuai Le
Article
Immunology
Nannan Wu, Jia Dai, Mingquan Guo, Jianhui Li, Xin Zhou, Feng Li, Yuan Gao, Hongping Qu, Hongzhou Lu, Jing Jin, Tao Li, Lei Shi, Qingguo Wu, Ruoming Tan, Mingli Zhu, Lan Yang, Yun Ling, Shunpeng Xing, Jianzhong Zhang, Bangxin Yao, Shuai Le, Jingmin Gu, Jinhong Qin, Jie Li, Mengjun Cheng, Demeng Tan, Linlin Li, Yiyuan Zhang, Zhaoqin Zhu, Jinfeng Cai, Zhigang Song, Xiaokui Guo, Li-Kuang Chen, Tongyu Zhu
Summary: This study investigated the efficacy of phage therapy in treating secondary bacterial infections in COVID-19 patients. The results showed that phages were able to reduce the burden of CRAB infections, indicating their potential in responding to secondary outbreaks in COVID-19 patients.
EMERGING MICROBES & INFECTIONS
(2021)
Article
Biochemistry & Molecular Biology
Wei Shen, Hong Ren
Summary: This article introduces TaxonKit, a command-line toolkit for comprehensive and efficient manipulation of NCBI Taxonomy data, which includes seven core subcommands providing various practical functions, competitive processing performance, scalability, and good accessibility.
JOURNAL OF GENETICS AND GENOMICS
(2021)
Article
Virology
Xiaoyao Cai, Fengjuan Tian, Li Teng, Hongmei Liu, Yigang Tong, Shuai Le, Tingting Zhang
Summary: This study identified a novel mutualistic parasitic dsRNA phage, phiNY, which suggests that dsRNA phages with nonlytic lifestyles might be common in nature and deserve more investigations. Using different virus isolation methods could help identify phages with nonlytic lifestyles beyond strictly lytic ones.
JOURNAL OF VIROLOGY
(2021)
Article
Gastroenterology & Hepatology
Taiyu He, Yingzhi Zhou, Pan Xu, Ning Ling, Min Chen, Tianquan Huang, Biqiong Zhang, Ziqiao Yang, Ling Ao, Hu Li, Zhiwei Chen, Dazhi Zhang, Xiaofeng Shi, Yu Lei, Zhiyi Wang, Weiqun Zeng, Peng Hu, Yinghua Lan, Zhi Zhou, Juan Kang, Ying Huang, Tongdong Shi, Qingbo Pan, Qian Zhu, Xiping Ran, Yingzhi Zhang, Rui Song, Dejuan Xiang, Shuang Xiao, Gaoli Zhang, Wei Shen, Mingli Peng, Dachuan Cai, Hong Ren
Summary: This study investigated the safety and antibody responses of COVID-19 vaccination in patients with chronic hepatitis B (CHB) virus infection. The results showed that the vaccine was well tolerated and induced effective antibody responses in CHB patients.
LIVER INTERNATIONAL
(2022)
Letter
Infectious Diseases
Shiying Li, Jin Tong, Yi Liu, Wei Shen, Peng Hu
JOURNAL OF INFECTION
(2022)
Article
Virology
Lujia Cen, Yunjie Chang, Joseph K. Bedree, Yansong Ma, Qiu Zhong, Daniel R. Utter, Pu-Ting Dong, Renate Lux, Batbileg Bor, Jun Liu, Jeffrey S. McLean, Shuai Le, Xuesong He
Summary: Bacteriophages are an important component of the human oral microbiome, with specific phages like LC001 showing remarkable host specificity targeting Schaalia odontolytica. The study suggests that LC001 may exploit the host bacterium-encoded lytic transglycosylase function to access the receptor, facilitating infection.
JOURNAL OF VIROLOGY
(2022)
Article
Microbiology
Gang Li, Wei Shen, Yali Gong, Ming Li, Xiaocai Rao, Qian Liu, Yanlan Yu, Jing Zhou, Keting Zhu, Mengmeng Yuan, Weilong Shang, Yi Yang, Shuguang Lu, Jing Wang, Yan Zhao
Summary: This study investigated the prevalence and role of co-infectious microbes on the pathogenesis and fitness essentiality of Staphylococcus aureus (S. aureus). A high incidence of co-infection between S. aureus and Acinetobacter baumannii was observed. The study identified a core set of genes essential for S. aureus infection and tissue colonization. Co-infection with A. baumannii altered the fitness requirements of S. aureus, and a greater number of genes were essential during co-infection compared to mono-infection. The study provided new insights into the development of antimicrobial regimens to control co-infections.
Article
Biochemical Research Methods
Wei Shen, Hongyan Xiang, Tianquan Huang, Hui Tang, Mingli Peng, Dachuan Cai, Peng Hu, Hong Ren
Summary: This study developed a K-mer-based metagenomic profiling tool, KMCP, which utilizes genome coverage information and a modified Compact Bit-Sliced Signature Index for fast alignment-free sequence searching. Experimental results demonstrate that KMCP allows accurate taxonomic profiling of prokaryotic and viral populations and provides more reliable pathogen detection in low-depth clinical samples.
Letter
Immunology
Juan Bao, Nannan Wu, Yigang Zeng, Liguang Chen, Linlin Li, Lan Yang, Yiyuan Zhang, Mingquan Guo, Lisha Li, Jie Li, Demeng Tan, Mengjun Cheng, Jingmin Gu, Jinghong Qin, Jiazheng Liu, Shiru Li, Guangqiang Pan, Xin Jin, Bangxin Yao, Xiaokui Guo, Tongyu Zhu, Shuai Le
EMERGING MICROBES & INFECTIONS
(2020)