PHAGE (New Rochelle, N.Y.)最新文献

{"title":"<i>Escherichia</i> Phage Ge15, NRG-P0073: Genomic Characterization and Host Range Analysis Against the ECOR Reference Library.","authors":"Ranee K Anderson, Shijie Qin, Rachel M Carson, Sam R Nugen","doi":"10.1089/phage.2024.0049","DOIUrl":"10.1089/phage.2024.0049","url":null,"abstract":"<p><strong>Background: </strong>Genomic sequencing and annotation, morphological characterization, and host range analyses of bacteriophage (phage) isolates are crucial to understanding each phage's unique set of properties and how they can be utilized as effective tools in medicine, environmental monitoring, biotechnology, and agriculture. In this study, we present the fully annotated genome of viral isolate <i>Escherichia</i> phage Ge15 (GenBank Accession No. PP359696.1), taxonomically identified as unclassified Tequatrovirus, and deposited into our strain collection as sample NRG-P0073. A host range analysis was performed against all 72 isolates of the <i>E. coli</i> Reference (ECOR) library and a selection of <i>Escherichia coli</i> K-12 single-gene knockouts from the Keio collection in an effort to identify the receptor-binding protein.</p><p><strong>Materials and methods: </strong>Whole genome sequencing, <i>de novo</i> assembly, and evidence-driven annotation using the Center for Phage Technology's Galaxy and Apollo software were performed on NRG-P0073. Double-agar spot tests were performed against the ECOR library and nine <i>E. coli</i> K-12 knockouts from the Keio collection to evaluate both the permissive and adsorptive host ranges of the phage. Transmission electron microscopy was utilized to elucidate the phage morphology.</p><p><strong>Results: </strong>NRG-P0073 was found to have a 170,913 bp genome, coding for 10 tRNAs, 14 terminators, 259 genes, 249 coding sequences, and a GC content of 35.5%. Double-agar spot tests revealed that NRG-P0073 could adsorb 33 of the 72 strains (45.8%), but only 15 of the 72 strains (20.8%) could complete replication to form distinguishable plaques. All nine of the <i>E. coli</i> K-12 single-gene knockout strains (100%) supported complete phage replication, suggesting that none of the nine evaluated receptors are solely responsible for facilitating the attachment of NRG-P0073 to the host surface.</p><p><strong>Conclusions: </strong>This study presents novel and complete genomic data, characterization, and host range analyses for the newly characterized phage NRG-P0073. Further characterization and analysis are required, including the identification of the <i>E. coli</i> receptor-binding protein responsible for initial host recognition. This study provides a foundation for future studies to understand more about NRG-P0073 and provides data that can be utilized for future machine-learning studies of phages and their host interactions.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 2","pages":"81-86"},"PeriodicalIF":0.0,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12172643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144328020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Acknowledgment of Reviewers 2024.","authors":"","doi":"10.1089/phage.2024.25632.revack","DOIUrl":"https://doi.org/10.1089/phage.2024.25632.revack","url":null,"abstract":"","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 1","pages":"48"},"PeriodicalIF":0.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12057296/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144045253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cartoon by Dr. Ellie Jameson, Bangor University.","authors":"","doi":"10.1089/phage.2025.7150","DOIUrl":"https://doi.org/10.1089/phage.2025.7150","url":null,"abstract":"","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 1","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12057295/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144060198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New <i>Morganella morganii</i> Phage vB_Mm5 with Tolerance to Cu²⁺ Ions.","authors":"Rusudan Goliadze, Luka Kamashidze, Natia Karumidze, Sophio Rigvava, Olia Rcheulishvili, Aleksander Rcheulishvili, Marine Goderdzishvili, Ia Kusradze","doi":"10.1089/phage.2024.0036","DOIUrl":"https://doi.org/10.1089/phage.2024.0036","url":null,"abstract":"<p><strong>Background: </strong>Research on phages targeting <i>Morganella morganii</i> is still emerging, with limited studies compared with other phage-host systems. Interest in these phages has increased due to rising antibiotic resistance and their potential for controlling <i>M. morganii</i> spread in the environment.</p><p><strong>Materials and methods: </strong>This study investigates the biology and genetics of the novel <i>M. morganii</i>-infecting myophage <i>vB_Mm5</i> and evaluates its stability under Cu²⁺ exposure.</p><p><strong>Results: </strong>Phage <i>vB_Mm5</i> has a 10-min latent period and a burst size of 30 (±5). It shows high tolerance to elevated temperatures and Cu²⁺. The phage genome, comprising 163,232 bp dsDNA with 229 open reading frames, encodes genes that not only enhance the phage's predatory capabilities but also confer resistance to host defense mechanisms.</p><p><strong>Conclusions: </strong><i>vB_Mm5</i> is highly distinct from other sequenced <i>M. morganii</i> phages, does not contain any known virulence genes, and holds potential as a therapeutic agent against <i>M. morganii</i> infections.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 1","pages":"41-47"},"PeriodicalIF":0.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12060847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144051677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phage-Encoded Antimicrobial Peptide gp28 Demonstrates LL-37-Like Antimicrobial Activity Against Multidrug-Resistant <i>Pseudomonas aeruginosa</i>.","authors":"Rachael C Wilkinson, Nerissa E Thomas, Amita Bhatti, Matthew R Burton, Naomi Joyce, Rowena E Jenkins","doi":"10.1089/phage.2024.0009","DOIUrl":"https://doi.org/10.1089/phage.2024.0009","url":null,"abstract":"<p><strong>Background: </strong><i>Pseudomonas aeruginosa</i> (<i>P. aeruginosa</i>) is a gram-negative bacterial pathogen commonly associated with nosocomial infections. Treatment of <i>P. aeruginosa</i> infections is notoriously difficult due to biofilm formation and antibiotic resistance. Antimicrobial peptides (AMPs) are thought to be promising new antimicrobials. Gp28, a phage-derived AMP, is a novel class of characterized phage AMPs with activity against <i>Escherichia coli</i> in a manner similar to the human peptide LL-37. LL-37 exhibits strong antimicrobial activity against <i>P. aeruginosa</i> as well as biofilm disruption and synergy with certain antibiotics posing the question whether gp28 could act similarly.</p><p><strong>Methods: </strong>Antibacterial activity of gp28 against <i>P. aeruginosa</i> was established using growth inhibition assays, with minimum inhibitory concentration calculated. Biofilm disruption was assessed using crystal violet staining and scanning electron microscopy. Combined treatment of gp28 with tobramycin against <i>P. aeruginosa</i> was measured using a modified time-kill assay at sublethal concentrations.</p><p><strong>Results: </strong>Gp28 inhibits <i>P. aeruginosa</i> planktonic growth, with a minimum inhibitory concentration of 109 μg mL^-1 and disrupts established biofilms. We demonstrate that gp28 increases the susceptibility of <i>P. aeruginosa</i> to tobramycin.</p><p><strong>Conclusions: </strong>Gp28 demonstrates potential for development as a putative therapeutic agent against a clinically resistant <i>P. aeruginosa</i> strain either alone or in combination with the frontline antibiotic tobramycin.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 1","pages":"12-19"},"PeriodicalIF":0.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12063199/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144054861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Semantics Count in the Description of the Interactions Between Bacteria and Bacteriophage.","authors":"Brandon A Berryhill, Bruce R Levin","doi":"10.1089/phage.2024.0063","DOIUrl":"https://doi.org/10.1089/phage.2024.0063","url":null,"abstract":"","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 1","pages":"3-4"},"PeriodicalIF":0.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12022465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143999625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"taxMyPhage: Automated Taxonomy of dsDNA Phage Genomes at the Genus and Species Level.","authors":"Andrew Millard, Rémi Denise, Maria Lestido, Moi Taiga Thomas, Deven Webster, Dann Turner, Thomas Sicheritz-Pontén","doi":"10.1089/phage.2024.0050","DOIUrl":"https://doi.org/10.1089/phage.2024.0050","url":null,"abstract":"<p><strong>Background: </strong>Bacteriophages are classified into genera and species based on genomic similarity, a process regulated by the International Committee on the Taxonomy of Viruses. With the rapid increase in phage genomic data there is a growing need for automated classification systems that can handle large-scale genome analyses and place phages into new or existing genera and species.</p><p><strong>Materials and methods: </strong>We developed <i>taxMyPhage</i>, a tool system for the rapid automated classification of dsDNA bacteriophage genomes. The system integrates a MASH database, built from ICTV-classified phage genomes to identify closely related phages, followed by BLASTn to calculate intergenomic similarity, conforming to ICTV guidelines for genus and species classification. taxMyPhage is available as a git repository at https://github.com/amillard/tax_myPHAGE, a conda package, a pip-installable tool, and a web service at https://phagecompass.ku.dk.</p><p><strong>Results: </strong><i>taxMyPhage</i> enables rapid classification of bacteriophages to the genus and species level. Benchmarking on 705 genomes pending ICTV classification showed a 96.7% accuracy at the genus level and 97.9% accuracy at the species level. The system also detected inconsistencies in current ICTV classifications, identifying cases where genera did not adhere to ICTV's 70% average nucleotide identity (ANI) threshold for genus classification or 95% ANI for species. The command line version classified 705 genomes within 48 h, demonstrating its scalability for large datasets.</p><p><strong>Conclusions: </strong><i>taxMyPhage</i> significantly enhances the speed and accuracy of bacteriophage genome classification at the genus and species levels, making it compatible with current sequencing outputs. The tool facilitates the integration of bacteriophage classification into standard workflows, thereby accelerating research and ensuring consistent taxonomy.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 1","pages":"5-11"},"PeriodicalIF":0.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12060842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144054876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Degradation of Preformed Gram-Positive and Gram-Negative Bacterial Biofilms Using Disintegrated and Intact Phages.","authors":"Sahd Ali, Abdulkerim Karaynir, Hanife Salih Doğan, Ramesh Nachimuthu, Kingsley Badu, Bülent Bozdoğan","doi":"10.1089/phage.2024.0029","DOIUrl":"https://doi.org/10.1089/phage.2024.0029","url":null,"abstract":"<p><strong>Introduction: </strong>Biofilm is a major challenge across several sectors and contributes to serious risks to public health. This study aimed to evaluate the antibiofilm efficacy of disintegrated phages, whose lytic activities have been eliminated, against bacterial biofilms.</p><p><strong>Methods: </strong>A total of seven lytic phages were disintegrated by sonication and confirmed to have completely lost their lytic activities by the spot test. Subsequently, both the disintegrated and intact phages were tested on the biofilms produced by five different biofilm-producing bacteria. The effects of heat and proteinase K on the ability of disintegrated phages to disrupt biofilms were determined. Moreover, the structural proteins released after the disintegration of phages were screened for their presence of lipase, amylase, protease, and DNase activities. Genome analysis of all the seven phages were screened for the presence of genes encoding proteins with enzymatic activities.</p><p><strong>Results: </strong>The disintegrated phages showed more effectiveness in degrading the bacterial biofilm when compared with intact phages. The amylase test results were positive for all the seven disintegrated phages tested, confirming the presence of starch-degrading enzymes. Genomic analysis of five phages revealed the presence of genes encoding transglycosylases, amidases, and glycosaminidases, which could contribute to biofilm degradation. However, only four of these proteins were also structural proteins of phages.</p><p><strong>Conclusions: </strong>Our study demonstrated that disintegrated phages without lytic effects can still possess biofilm degrading ability, probably associated with the enzymatic activities of their structural proteins. This study showed that phages may have activities beyond lytic phage activities exhibited by their structural enzymes.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 1","pages":"20-31"},"PeriodicalIF":0.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12059619/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144044465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling and Classifying the Hidden Potential of Bacteriophages.","authors":"Martha R J Clokie, Thomas Sicheritz-Pontén","doi":"10.1089/phage.2025.7130","DOIUrl":"https://doi.org/10.1089/phage.2025.7130","url":null,"abstract":"","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12057294/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144058821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Six Novel <i>Pseudomonas aeruginosa</i> Phages: Genomic Insights and Therapeutic Potential.","authors":"Amit Rimon, Ortal Yerushalmy, Jonathan Belin, Sivan Alkalay-Oren, Lilach Gavish, Shunit Coppenhagen-Glazer, Ronen Hazan","doi":"10.1089/phage.2024.0037","DOIUrl":"https://doi.org/10.1089/phage.2024.0037","url":null,"abstract":"<p><strong>Introduction: </strong><i>Pseudomonas aeruginosa</i> is an opportunistic pathogen that causes health care-associated infections. The rise of antibiotic-resistant bacterial strains necessitates alternative treatment strategies, with bacteriophage therapy being a promising approach.</p><p><strong>Methods: </strong>Six bacteriophages were isolated from sewage samples. Phage isolation involved centrifugation, filtration, and plaque assays. The morphology of each sample was examined using transmission electron microscopy (TEM). Genomic DNA was sequenced and compared among the isolates. The phages' lytic activities were assessed using growth curve analysis.</p><p><strong>Results: </strong>The phages displayed distinct genomic characteristics, grouping into three genomic clusters. No known virulence or antibiotic resistance genes were detected, indicating their safety for therapeutic use. Taxonomic analysis identified the phages as belonging to the genera <i>Pbunavirus</i>, <i>Nipunavirus</i>, <i>Abidjanvirus</i>, and a novel genus. TEM analysis revealed their diverse morphologies. Temperate phages showed less effective lytic activities.</p><p><strong>Conclusion: </strong>Several of the isolated bacteriophages show potential as candidates for phage therapy research and could be effective against <i>P. aeruginosa</i> infections.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 1","pages":"32-40"},"PeriodicalIF":0.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12060848/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144030803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}