Article
Biochemistry & Molecular Biology
Jens A. Hammerl, Andrea Barac, Philipp Erben, Julius Fuhrmann, Ashish Gadicherla, Franziska Kumsteller, Anne Lauckner, Felix Mueller, Stefan Hertwig
Summary: Researchers isolated and characterized two phages from game animals, which showed a broad host range and effectively lysed various serotypes of Yersinia enterocolitica. These phages also demonstrated lytic activity against different strains of Yersinia pseudotuberculosis under specific conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Lanlan Cai, Yuan Tian, Ziqiang Li, Yunlan Yang, Chunxiang Ai, Rui Zhang
Summary: In this study, a lytic bacteriophage, named vB_VhaS-R18L (R18L), was isolated from coastal seawater in Dongshan Island, China. R18L was characterized as a stable bacteriophage with broad lytic activity against multiple Vibrio species, making it a potential candidate for phage therapy in controlling vibriosis in aquaculture systems.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Virology
Jose Gil, John Paulson, Matthew Brown, Henriett Zahn, Minh M. Nguyen, Marcia Eisenberg, Stephen Erickson
Summary: Host range is crucial for the industrial utility of bacteriophages. Manipulating receptor-binding proteins can improve host range and detection specificity for Salmonella.
Article
Biochemistry & Molecular Biology
Jens Andre Hammerl, Sabrin El-Mustapha, Michelle Boelcke, Hannah Trampert, Andrea Barac, Claudia Jaeckel, Ashish K. Gadicherla, Stefan Hertwig
Summary: The study identified three groups of temperate phages in pathogenic Y. enterocolitica strains, each with different lytic activity against different strains.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Syeda Zainab Ilyas, Hafsa Tariq, Abdul Basit, Hamza Tahir, Zulquernain Haider, Shafiq Ur Rehman
Summary: This study reports the first lysogenic phage, SGP-C, against Salmonella gallinarum, a poultry restricted-pathogen causing fowl-typhoid disease. SGP-C phage showed infection ability in multiple field strains of S. gallinarum and exhibited moderate virulence. The genome of SGP-C contains 63 ORFs and is likely to exist as a prophage. This study provides important insights into the understanding of Salmonella gallinarum and lysogenic phage.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Danitza Xiomara Romero-Calle, Francisnei Pedrosa-Silva, Luiz Marcelo Ribeiro Tome, Vagner Fonseca, Raquel Guimaraes Benevides, Leila Thaise Santana de Oliveira Santos, Tulio de Oliveira, Mateus Matiuzzi da Costa, Luiz Carlos Junior Alcantara, Vasco Ariston de Carvalho Azevedo, Bertram Brenig, Thiago M. Venancio, Craig Billington, Aristoteles Goes-Neto
Summary: Despite the use of new treatments, antimicrobial resistance is still increasing, calling for novel strategies. Bacteriophages have the potential to control bacterial pathogens like Salmonella. A Salmonella phage, Wara, was isolated from water samples in the Subae River Basin in Brazil. Its genome was sequenced using Oxford Nanopore Technologies and Illumina HiSeq, and assembly was carried out using Racon and Unicycler. Wara was found to be a member of the Tequintavirus genus and has therapeutic and biocontrol potential against Salmonella in healthcare and agriculture.
Article
Microbiology
Tingting Feng, Sebastian Leptihn, Ke Dong, Belinda Loh, Yan Zhang, Melanie I. Stefan, Mingyue Li, Xiaokui Guo, Zelin Cui
Summary: Phage therapy is a potential treatment option for infections caused by multidrug-resistant bacteria, and the phage JD419 has a broad host range and can be modified through gene engineering to prevent potential lysogeny.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biology
Sriram Srikant, Chantal K. Guegler, Michael T. Laub
Summary: This study reveals the mechanism by which phages overcome bacterial defense systems through experimental evolution. The emergence of one counter-defense mechanism can lead to the loss of other mechanisms, thus constraining the host range of phages.
Article
Gastroenterology & Hepatology
Meiying Yan, Yongming Zhou, Yang Cao, Zhenpeng Li, Xin Lu, Bo Pang, Shukun Wang, Biao Kan
Summary: This study discovered a new serovar of Salmonella (S. enterica subsp. II serovar 4,5,12:a:-) and demonstrated its ability to infect humans and cause clusters of cases. Whole-genome sequencing detection and surveillance of Salmonella can accurately define Salmonella classification and clonality, improve diagnosis, facilitate outbreak detection, and aid in the source tracing of salmonellosis epidemics.
Review
Biochemistry & Molecular Biology
Jarin Taslem Mourosi, Ayobami Awe, Wenzheng Guo, Himanshu Batra, Harrish Ganesh, Xiaorong Wu, Jingen Zhu
Summary: Bacteriophages are being rediscovered as natural antibacterial agents due to the increasing threat of drug-resistant bacterial pathogens. Understanding the structure and function of phage tail fibers is crucial for reprogramming phages' host range and improving phage therapy. Design strategies, including machine-learning-assisted engineering, are being developed based on the vast amount of phage genetic information available.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
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
Guillermo Uceda-Campos, Oseias R. Feitosa-Junior, Caio R. N. Santiago, Paulo M. Pierry, Paulo A. Zaini, Wesley O. de Santana, Joaquim Martins, Deibs Barbosa, Luciano A. Digiampietri, Joao C. Setubal, Aline M. da Silva
Summary: This study comprehensively analyzed X.fastidiosa strains from different plant hosts and geographic regions. The core-genome phylogeny showed that the strains were mainly classified based on geographic region rather than plant hosts. However, no strong candidate host-specificity determinants were found through the comparative analysis of orthologous genes. Additionally, the study revealed the rich and diverse accessory genome of X.fastidiosa.
Article
Microbiology
Sam Ford, Sara Moeskjaer, Peter Young, Rosa I. Santamaria, Ellie Harrison
Summary: Temperate phages in rhizobia, including a novel group identified in this study, have the potential to impact the ecological dynamics of bacterial communities. Genome comparisons among these phages revealed a high degree of gene conservation with a region of hypervariability containing hypothetical genes. These phages exhibit a history of active mobilization within and between Rhizobium species, as indicated by phylogenetic discordance between prophage and host phylogenies.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Suzanne Humphrey, Alfred Fillol-Salom, Nuria Quiles-Puchalt, Rodrigo Ibarra-Chavez, Andreas F. Haag, John Chen, Jose R. Penades
Summary: It is commonly thought that horizontal transfer of most bacterial chromosomal genes is limited, in comparison with the frequent transfer of mobile genetic elements. Humphrey et al. show that, actually, phage-mediated lateral transduction of core chromosomal genes can be more efficient than the transfer of mobile genetic elements via conjugation or generalized transduction.
NATURE COMMUNICATIONS
(2021)
Review
Microbiology
Dominique Holtappels, Poliane Alfenas-Zerbini, Britt Koskella
Summary: Bacteriophages, as obligate parasites, have a broad range of hosts and their diversity is influenced by various factors. The understanding of phage host range is crucial for predicting their impacts, therapeutic applications, and evolutionary changes. This article explores the drivers of phage infection and host range, evaluates the importance of different factors, and discusses their implications in phage-based therapeutics.
FEMS MICROBIOLOGY REVIEWS
(2023)
Article
Multidisciplinary Sciences
Vivek K. Mutalik, Pavel S. Novichkov, Morgan N. Price, Trenton K. Owens, Mark Callaghan, Sean Carim, Adam M. Deutschbauer, Adam P. Arkin
NATURE COMMUNICATIONS
(2019)
Article
Biochemistry & Molecular Biology
Robert G. Egbert, Harneet S. Rishi, Benjamin A. Adler, Dylan M. McCormick, Esteban Toro, Ryan T. Gill, Adam P. Arkin
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biology
Gavin J. Knott, Brady F. Cress, Jun-Jie Liu, Brittney W. Thornton, Rachel J. Lew, Basem Al-Shayeb, Daniel J. Rosenberg, Michel Hammel, Benjamin A. Adler, Marco J. Lobba, Michael Xu, Adam P. Arkin, Christof Fellmann, Jennifer A. Doudna
Article
Biochemistry & Molecular Biology
Vivek K. Mutalik, Benjamin A. Adler, Harneet S. Rishi, Denish Piya, Crystal Zhong, Britt Koskella, Elizabeth M. Kutter, Richard Calendar, Pavel S. Novichkov, Morgan N. Price, Adam M. Deutschbauer, Adam P. Arkin
Article
Ecology
Sean Carim, Ashley L. Azadeh, Alexey E. Kazakov, Morgan N. Price, Peter J. Walian, Lauren M. Lui, Torben N. Nielsen, Romy Chakraborty, Adam M. Deutschbauer, Vivek K. Mutalik, Adam P. Arkin
Summary: Tailocins are bactericidal protein complexes produced by various bacteria with high specificity, making them potential precision antibacterial agents. Research indicates that O-antigen composition and display are crucial factors defining sensitivity to Tailocins, while LPS thinning can increase sensitivity of resistant strains to Tailocins.
Article
Multidisciplinary Sciences
Vivek K. Mutalik, Adam P. Arkin
Summary: At the current rate, the rise of antimicrobial-resistant infections is expected to have severe consequences. With limited new antibiotics in development, alternative solutions are needed. Bacteriophages offer a powerful alternative approach to combat bacterial infections. However, further development and systematic implementation of phage therapies are required. The proposed Phage Foundry framework aims to address knowledge and technological gaps in phage therapeutics and promote rational exploitation of phages for treatment.
Article
Microbiology
Benjamin A. Adler, Tomas Hessler, Brady F. Cress, Arushi Lahiri, Vivek K. Mutalik, Rodolphe Barrangou, Jillian Banfield, Jennifer A. Doudna
Summary: In this study, the defensive capabilities of LbuCas13a protein were analyzed, and it was found to have robust antiviral activity against a wide range of phages. By leveraging LbuCas13a targeting, successful genome editing of multiple phages was achieved, demonstrating the versatility and potency of Cas13a as a generalizable tool for editing diverse biological entities.
NATURE MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Steffanie A. Strathdee, Graham F. Hatfull, Vivek K. Mutalik, Robert T. Schooley
Summary: Increasing antimicrobial resistance rates have prompted a resurgence in bacteriophage research as an alternative therapy. The ideal therapeutic phage should possess lytic properties, efficiently kill the bacterial host, and be well-characterized to ensure safety. This article reviews the current state of phage therapy, including biological mechanisms, clinical applications, challenges, and future directions involving naturally occurring and genetically modified or synthetic phages.
Article
Biochemistry & Molecular Biology
Enbo Ma, Kai Chen, Honglue Shi, Elizabeth C. Stahl, Ben Adler, Marena Trinidad, Junjie Liu, Kaihong Zhou, Jinjuan Ye, Jennifer A. Doudna
Summary: In this study, CRISPR-Cas12a was engineered and evolved to improve its genome editing efficiency and ability to induce homology-directed repair (HDR) editing. This strategy can be applied to other CRISPR-Cas enzymes to enhance the efficacy of genome editing proteins.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Benjamin A. Adler, Karthik Chamakura, Heloise Carion, Jonathan Krog, Adam M. Deutschbauer, Ry Young, Vivek K. Mutalik, Adam P. Arkin
Summary: This study used a high-throughput genetic screen to identify genome-wide host suppressors of diverse single-gene lysis factors (Sgls). In addition to validating known mechanisms, the researchers discovered that the Sgl of PP7, a Pseudomonas aeruginosa ssRNA phage, targets MurJ, the flippase responsible for lipid II export, which was previously shown to be the target of the Sgl of coliphage M. These unrelated Sgls, which are predicted to have opposite membrane topology, represent a case of convergent evolution. Furthermore, the genetic screens revealed a common set of multicopy suppressors for uncharacterized Sgls, suggesting a shared or similar mechanism of action.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Benjamin A. Adler, Marena Trinidad, Daniel Bellieny-Rabelo, Elaine Zhang, Hannah M. Karp, Petr Skopintsev, Brittney W. Thornton, Rachel F. Weissman, Peter H. Yoon, Linxing Chen, Tomas Hessler, Amy R. Eggers, David Colognori, Ron Boger, Erin E. Doherty, Connor A. Tsuchida, Ryan Tran, Laura Hofman, Honglue Shi, Kevin M. Wasko, Zehan Zhou, Chenglong Xia, Muntathar J. Al-Shimary, Jaymin R. Patel, Vienna C. J. X. Thomas, Rithu Pattali, Matthew J. Kan, Anna Vardapetyan, Alana Yang, Arushi Lahiri, Michaela F. Maxwell, Andrew G. Murdock, Glenn C. Ramit, Hope R. Henderson, Roland W. Calvert, Rebecca S. Bamert, Gavin J. Knott, Audrone Lapinaite, Patrick Pausch, Joshua C. Cofsky, Erik J. Sontheimer, Blake Wiedenheft, Peter C. Fineran, Stan J. J. Brouns, Dipali G. Sashital, Brian C. Thomas, Christopher T. Brown, Daniela S. A. Goltsman, Rodolphe Barrangou, Virginius Siksnys, Jillian F. Banfield, David F. Savage, Jennifer A. Doudna
Summary: CRISPR-Cas enzymes play a crucial role in bacterial immunity and genome editing. CasPEDIA is a comprehensive database that summarizes the enzymatic properties of Cas enzymes, providing valuable resources for researchers.
NUCLEIC ACIDS RESEARCH
(2023)