PHAGE (New Rochelle, N.Y.)Pub Date : 2025-12-03eCollection Date: 2025-12-01DOI: 10.1177/26416549251366991
Alfizah Hanafiah, Asif Sukri, Muhammad Azhari Asmawi, Hamidah Yusoff, Shaliawani Mohd Puzi, Hui-Min Neoh, Bruno S Lopes
{"title":"Recent Advancements in Development and Characterization of Phages Targeting <i>Helicobacter pylori</i>.","authors":"Alfizah Hanafiah, Asif Sukri, Muhammad Azhari Asmawi, Hamidah Yusoff, Shaliawani Mohd Puzi, Hui-Min Neoh, Bruno S Lopes","doi":"10.1177/26416549251366991","DOIUrl":"https://doi.org/10.1177/26416549251366991","url":null,"abstract":"<p><p><i>Helicobacter pylori</i> remains a significant global health concern, with rising antibiotic resistance posing challenges for conventional treatments. Bacteriophages, viruses that specifically target and lyse bacterial cells, present a promising alternative therapeutic approach. This review explores the advancements in phage research related to <i>H. pylori</i>, including the isolation, genomic and proteomic characterization, and therapeutic potential of lytic and lysogenic phages. Novel isolation techniques have identified diverse phages from clinical and environmental sources, such as sewage and wastewater, revealing unique genetic and structural adaptations that enhance their effectiveness in targeting <i>H. pylori</i>. Genomic analysis has highlighted the role of prophages in <i>H. pylori</i> evolution, while proteomic studies have uncovered structural features that enable phages to survive the acidic gastric environment. High-throughput technologies, such as next-generation sequencing, clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) systems, and microfluidic platforms, have revolutionized phage discovery and characterization. Furthermore, the potential for phage-antibiotic synergy offers new avenues for combating antibiotic resistance. Despite these advancements, challenges such as <i>H. pylori</i>'s genetic diversity, its fastidious growth requirements, and the development of robust delivery mechanisms for gastric application persist. This review highlights the need for further research to optimize phage-based therapies as a viable alternative or adjunct to current treatments for <i>H. pylori</i> infections.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 4","pages":"282-291"},"PeriodicalIF":1.8,"publicationDate":"2025-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12892407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146183792","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}
PHAGE (New Rochelle, N.Y.)Pub Date : 2025-12-03eCollection Date: 2025-12-01DOI: 10.1177/26416549251386057
Yulia Rosa Saharman, Nuridha Audinia Safitri, Yustinus Maladan, Ajeng K Pramono, Leli Saptawati, Dewi Anggraini, Iftita Rahmatika, Ruby Setiawan, Dodi Safari, Rosantia Sarassari, Meity Mardiana
{"title":"Morphological and Genomic Analysis of Drulisvirus Targeting Extended-Spectrum β-Lactamase-Producing <i>Klebsiella pneumoniae</i> with K12 and K18 Capsular Types.","authors":"Yulia Rosa Saharman, Nuridha Audinia Safitri, Yustinus Maladan, Ajeng K Pramono, Leli Saptawati, Dewi Anggraini, Iftita Rahmatika, Ruby Setiawan, Dodi Safari, Rosantia Sarassari, Meity Mardiana","doi":"10.1177/26416549251386057","DOIUrl":"https://doi.org/10.1177/26416549251386057","url":null,"abstract":"<p><strong>Background: </strong>The increasing incidence of infections caused by extended-spectrum β-lactamase-producing <i>Klebsiella pneumoniae</i> (ESBL-KP) in Indonesia necessitates the exploration of phage therapy as a potential alternative treatment strategy.</p><p><strong>Materials and methods: </strong>A lytic phage capable of infecting ESBL-KP was isolated from the Cideng River in Jakarta and subsequently characterized morphologically and genomically.</p><p><strong>Results: </strong>A novel lytic phage, designated JKT1, exhibited an icosahedral head (±52 nm diameter), a short tail, and formed large clear plaques with halos on bacterial lawns. JKT1 demonstrated rapid adsorption, a high burst size, and narrow host specificity. JKT1 remained stable at neutral pH and temperatures up to 37°C but lost activity at ≥50°C. Genome analysis revealed a 43,763 bp linear dsDNA genome encoding 57 open reading frames, including a putative depolymerase gene. Phylogenetic and genomic analyses classified JKT1 within the genus Drulisvirus.</p><p><strong>Conclusions: </strong>This study demonstrates JKT1's activity against specific capsular ESBL-KP strains, highlighting its targeted host range and potential for inclusion in phage cocktails for targeting bacterial infections.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 4","pages":"292-301"},"PeriodicalIF":1.8,"publicationDate":"2025-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12929008/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147291915","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}
PHAGE (New Rochelle, N.Y.)Pub Date : 2025-12-03eCollection Date: 2025-12-01DOI: 10.1177/26416549251386042
Jérémy D R Cherbuin, Jaime Llodrá, Loïc Borcard, Sabine Kaessmeyer, Alban Ramette, Javier Eduardo Fernandez, Theresa Maria Wagner, Sergi Torres-Puig, Peter Kuhnert, Dann Turner, Fabien Labroussaa, Jörg Jores
{"title":"Characterization of Phylogenetically Distinct Temperate Phages from Kenyan <i>Mammaliicoccus sciuri</i>.","authors":"Jérémy D R Cherbuin, Jaime Llodrá, Loïc Borcard, Sabine Kaessmeyer, Alban Ramette, Javier Eduardo Fernandez, Theresa Maria Wagner, Sergi Torres-Puig, Peter Kuhnert, Dann Turner, Fabien Labroussaa, Jörg Jores","doi":"10.1177/26416549251386042","DOIUrl":"https://doi.org/10.1177/26416549251386042","url":null,"abstract":"<p><strong>Background: </strong>Temperate bacteriophages are widespread in bacterial genomes and can play significant roles in bacterial evolution and pathogenicity. Despite their importance, they remain poorly characterized in nonclinical <i>Staphylococcaceae</i>, particularly <i>Mammaliicoccus sciuri</i>.</p><p><strong>Materials and methods: </strong>We analyzed 26 <i>M. sciuri</i> strains isolated from the nasal cavities of East African dogs and camels. Prophages were induced using mitomycin C, and isolated phages were characterized by whole-genome sequencing, phylogenetic analysis, electron microscopy imaging, and host-range determination.</p><p><strong>Results: </strong>Eight novel siphoviruses were isolated. Phylogenomic analysis revealed two new families, each comprising two genera. Notably, phages from one of these families (with genomes >130 kbp) exhibit a broad host range, while the other family is related to previously described phages implicated in horizontal gene transfer.</p><p><strong>Conclusion: </strong>Our findings reveal unexpected diversity of temperate phages in <i>M. sciuri</i>, expanding current knowledge of phage distribution in animal-associated opportunistic pathogens.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 4","pages":"259-271"},"PeriodicalIF":1.8,"publicationDate":"2025-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12929009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147291798","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}
PHAGE (New Rochelle, N.Y.)Pub Date : 2025-12-03eCollection Date: 2025-12-01DOI: 10.1177/26416549251384321
Zahid Ali, Sana Rehman, Saadia Naseem
{"title":"Bacteriophages as Therapeutic and Biotechnological Agents: Host Interactions, Immune Modulation, and Engineering Strategies.","authors":"Zahid Ali, Sana Rehman, Saadia Naseem","doi":"10.1177/26416549251384321","DOIUrl":"https://doi.org/10.1177/26416549251384321","url":null,"abstract":"<p><p>Bacteriophages, viruses that specifically infect bacteria, emerge as precision tools to combat multidrug-resistant infections and modulate host immunity. This review explores the dynamic interactions between bacteriophages and both bacterial and eukaryotic hosts, emphasizing their therapeutic potential and biotechnological applications. We discuss mechanisms of phage entry into mammalian tissues, including traversal of the blood-brain barrier, and their roles in shaping innate and adaptive immune responses. The review also highlights advances in phage engineering, such as non-lytic phagemid systems, clustered regularly interspersed short palindromic repeats (CRISPR)-based antimicrobials, and quorum-sensing disruption strategies. These innovations position bacteriophages as versatile agents in modern microbiology, with implications for personalized medicine, immunotherapy, and synthetic biology.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 4","pages":"272-281"},"PeriodicalIF":1.8,"publicationDate":"2025-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12892408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146183734","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}
PHAGE (New Rochelle, N.Y.)Pub Date : 2025-12-03eCollection Date: 2025-12-01DOI: 10.1177/26416549251384322
Liana Theodoridis, Ferdiye Taner, Aylin Üsküdar Güçlü, Ahmet Başustaoğlu, Tamer Şanlıdağ, Steve Petrovski
{"title":"Isolation of <i>Pseudomonas aeruginosa</i> Phages vB_Psu_NEU2023 and vB_Psu_NEU2024 Leads to the Establishment of a New Genus, <i>Alasiavirus</i>.","authors":"Liana Theodoridis, Ferdiye Taner, Aylin Üsküdar Güçlü, Ahmet Başustaoğlu, Tamer Şanlıdağ, Steve Petrovski","doi":"10.1177/26416549251384322","DOIUrl":"https://doi.org/10.1177/26416549251384322","url":null,"abstract":"<p><strong>Introduction: </strong><i>Pseudomonas aeruginosa</i> is an opportunistic pathogen responsible for severe infections, particularly in immunocompromised patients. The rise of multidrug-resistant <i>P. aeruginosa</i> has become a significant global health concern, highlighting the need for alternative strategies to combat infection.</p><p><strong>Methods: </strong>Two <i>Pseudomonas</i> phages, vB_Psu_NEU2023 and vB_Psu_NEU2024, were isolated from hospital wastewater using plaque assays. Phages were imaged using transmission electron microscopy. DNA was extracted and sequenced using nanopore technology, and bioinformatic analysis uncovered the phage taxonomy.</p><p><strong>Results: </strong>Phages vB_Psu_NEU2023 and vB_Psu_NEU2024 have inovirus and siphovirus morphology, respectively. Whole-genome analysis showed vB_Psu_NEU2023 to belong to a novel genus, here named <i>Alasiavirus</i>, within the <i>Inoviridae</i> family, while vB_Psu_NEU2024 displayed a close relationship to <i>Yuavirus</i> phages within the <i>Mesyanzhinovviridae</i> family. Both phages showed lytic activity against clinical multidrug-resistant <i>P. aeruginosa</i> strains. vB_Psu_NEU2024 genome annotation saw an absence of genes associated with lysogeny and toxin production.</p><p><strong>Conclusions: </strong>This study underscores the importance of hospital wastewater as a valuable reservoir for novel phages with potential clinical applications against multidrug-resistant pathogens.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 4","pages":"302-312"},"PeriodicalIF":1.8,"publicationDate":"2025-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12929007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147313344","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}
PHAGE (New Rochelle, N.Y.)Pub Date : 2025-12-03eCollection Date: 2025-12-01DOI: 10.1177/26416549251376357
Ole Hylling, Laura M Forero-Junco, Lea Ellegaard-Jensen, Peter C Dedon, Liang Cui, Tue K Nielsen, Martin Hansen, Horst Neve, Anders Johansen, Witold Kot
{"title":"Novel Modification Sites of dPreQ<sub>0</sub> in <i>Aminobacter niigataensis</i> Phage Erebus Provide New Insights into the Role of 7-Deazaguanine Modifications in Bacteriophages.","authors":"Ole Hylling, Laura M Forero-Junco, Lea Ellegaard-Jensen, Peter C Dedon, Liang Cui, Tue K Nielsen, Martin Hansen, Horst Neve, Anders Johansen, Witold Kot","doi":"10.1177/26416549251376357","DOIUrl":"https://doi.org/10.1177/26416549251376357","url":null,"abstract":"<p><strong>Background: </strong>Bacteriophages protect themselves against host-encoded defense systems through DNA modifications. This study introduces Erebus, a newly identified phage infecting <i>Aminobacter niigataensis</i>, a bacterium capable of mineralizing 2,6-dichlorobenzamide- a common pesticide metabolite. The use of such bacterial degraders has been proposed for the bioremediation of contaminated groundwater. However, the presence of bacteriophages targeting these degraders poses a potential challenge to the success of such strategies.</p><p><strong>Materials and methods: </strong>The Erebus phage was isolated and subjected to whole-genome sequencing. Phylogenetic analysis was performed to determine its taxonomic placement and genomic synteny. DNA modifications were identified using a combination of liquid chromatography-mass spectrometry (LC-MS) and Oxford Nanopore Technologies sequencing. Transmission electron microscopy was used to determine the phage morphology.</p><p><strong>Results: </strong>Phylogenetic analysis revealed that Erebus belongs to an unclassified genus, showing high synteny with Rhizobium phages of the <i>Kleczkowskaviridae</i> family. The phage possesses a double-stranded DNA genome of 52,229 base pairs, which includes a functional 7-deazaguanine DNA-modification system. Nanopore sequencing and LC-MS analysis confirmed the presence of PreQ<sub>0</sub> modifications at novel GG and AG motifs, conferring resistance against multiple restriction endonucleases.</p><p><strong>Conclusions: </strong>This is the first report of a phage infecting the genus <i>Aminobacter</i>, highlighting the potential impact of bacteriophages on microbial biodegradation strategies. The findings underscore the importance of considering phage-host interactions when deploying bacterial degraders for environmental remediation.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 4","pages":"250-258"},"PeriodicalIF":1.8,"publicationDate":"2025-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12929006/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147313326","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}
PHAGE (New Rochelle, N.Y.)Pub Date : 2025-11-21eCollection Date: 2026-03-01DOI: 10.1177/26416549251395012
Zahra Nasiri Shoeibi, Farzaneh Kianian, Behnaz Jahanbin, Hamidreza Abtahi, Mohammad Mehdi Feizabadi
{"title":"Phage-Encoded Lysis Proteins (Holins and Spanins): Mechanisms and Emerging Applications.","authors":"Zahra Nasiri Shoeibi, Farzaneh Kianian, Behnaz Jahanbin, Hamidreza Abtahi, Mohammad Mehdi Feizabadi","doi":"10.1177/26416549251395012","DOIUrl":"10.1177/26416549251395012","url":null,"abstract":"<p><p>Holins and spanins are bacteriophage-encoded enzymes that control the onset and efficiency of bacterial cell lysis in the late stage of the bacteriophage life cycle. Their ability to compromise bacterial membranes has attracted attention in various domains. With rise in antimicrobial resistance surpassing the development of new antimicrobials, phage-encoded lysis proteins, especially holins and spanin, have now become prospective for implementation of next-generation therapeutics because of their specific activity and low impact on the host. Furthermore, understanding their complex regulation, structural diversity, and controlled lytic activity has led to the expansion of their potential in fields such as vaccine development, drug delivery, bioprocessing, and other medical or industrial applications. This review highlights recent insights into holin and spanin biology, focusing on how these lethal, membrane-disrupting proteins function, and discusses their potential use in a wide range of applications.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"7 1","pages":"62-79"},"PeriodicalIF":1.8,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13089268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147936051","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}
PHAGE (New Rochelle, N.Y.)Pub Date : 2025-11-12eCollection Date: 2026-03-01DOI: 10.1177/26416549251394921
Prasanth Manohar, Ry Young
{"title":"The Lysis Genes of the Paradigm Phage SP6.","authors":"Prasanth Manohar, Ry Young","doi":"10.1177/26416549251394921","DOIUrl":"10.1177/26416549251394921","url":null,"abstract":"<p><strong>Background: </strong>The Salmonella podophage SP6 has been extensively studied as a divergent relative of T7 and as a prototype for therapeutic applications. Two decades ago, it underwent two comprehensive genomic investigations and was among the first phage GenBank files converted into RefSeq entries. Recent experimental and genomic research has shown that the annotation of the lysis genes in the SP6 genome and, consequently, in the large SP6-like phage family, is outdated.</p><p><strong>Materials and methods: </strong>We employed bioinformatic analysis to identify the lysis genes within the SP6 genome. The anticipated genes were subsequently evaluated with the λ complementation method to verify the lysis characteristics.</p><p><strong>Results: </strong>Our functional study identifies SP6_gp39 as holin, SP6_gp46 as an endolysin, and SP6_gp47 and gp56 as i-spanin and o-spanin, respectively.</p><p><strong>Conclusion: </strong>Here, we present a revised whole-genome analysis and a set of experiments that identify the components of the Multi-Gene Lysis genes for this paradigm phage.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"7 1","pages":"43-50"},"PeriodicalIF":1.8,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13089288/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147936054","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}
PHAGE (New Rochelle, N.Y.)Pub Date : 2025-11-12eCollection Date: 2026-03-01DOI: 10.1177/26416549251395011
Siddharth Singh Tomar, Krishna Khairnar
{"title":"Disruption in the Host-Phage Dynamics and Altered Microbial Diversity in the Upper Respiratory Tract of SARS-CoV-2-Infected Individuals.","authors":"Siddharth Singh Tomar, Krishna Khairnar","doi":"10.1177/26416549251395011","DOIUrl":"10.1177/26416549251395011","url":null,"abstract":"<p><strong>Background: </strong>The upper respiratory tract (URT) is an important site for the predisposition and multiplication of the SARS-CoV-2 virus. Therefore, URT is a critical site for investigating the changes in the microbiome caused by the SARS-CoV-2 infection. This study aims to compare phageome diversity and investigate the correlation of the phageome profiles with the sample type (SARS-CoV-2 or control) to determine the nature of phage-host interactions in the human URT microbiome and to assess the effect of SARS-CoV-2 viral load on host and phage abundance.</p><p><strong>Materials and methods: </strong>In this study, we have used the whole-genome shotgun metagenomic approach to investigate URT swab samples (<i>n</i> = 96) collected from SARS-CoV-2-positive individuals (<i>n</i> = 48) (nonhospitalized but symptomatic) and healthy controls (<i>n</i> = 48) belonging to five districts of central India.</p><p><strong>Results: </strong>The results revealed distinct phageome profiles among the groups; <i>Detrevirus</i> dominated the composition in the control samples, while <i>Maxrubnervirus</i> was dominant in SARS-CoV-2 samples. Microbial diversity analysis showed significantly higher richness in the SARS-CoV-2 group compared to controls for both bacteria (Chao1: 886.00 vs. 351.00, <i>p</i> < 0.0001) and phages (Chao1: 39.00 vs. 16.00, <i>p</i> = 0.0002). Bacterial diversity (Simpson index) was lower in the SARS-CoV-2 group (0.88 vs. 0.93, <i>p</i> = 0.0024), whereas phage diversity was higher in the SARS-CoV-2 group (0.86 vs. 0.79, <i>p</i> = 0.0384). Viral load, as reflected by cycle threshold (Ct) values, significantly influenced both bacteria (<i>H</i> = 6.69, <i>p</i> = 0.035) and phage (<i>H</i> = 8.97, <i>p</i> = 0.011) abundances. Host-phage interaction networks appeared disrupted in SARS-CoV-2 samples, with a weaker logistic model fit (<i>R</i> <sup>2</sup> = 0.7425) than controls (<i>R</i> <sup>2</sup> = 0.9265).</p><p><strong>Conclusion: </strong>SARS-CoV-2 infection alters URT microbiome composition, increasing microbial diversity but disrupting host-phage dynamics. SARS-CoV-2 Viral load correlates with the shifts in microbial abundance, indicating infection-driven shifts in microbiome stability compared to healthy controls.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"7 1","pages":"9-20"},"PeriodicalIF":1.8,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13089279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147936000","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}
Rachel M Carson, Ranee K Anderson, Shijie Qin, Brenda Werner, Sam R Nugen
{"title":"NRG-P0074 Viral Sample RU1 from Unclassified <i>Mosigvirus</i> Genomic Characterization and Host Range Analysis.","authors":"Rachel M Carson, Ranee K Anderson, Shijie Qin, Brenda Werner, Sam R Nugen","doi":"10.1089/phage.2025.0003","DOIUrl":"10.1089/phage.2025.0003","url":null,"abstract":"<p><strong>Background: </strong>Machine learning models for phage-host range prediction and design require comprehensive training data on phage genomes and host ranges to predict phage-host interactions effectively.</p><p><strong>Materials and methods: </strong>This study characterizes phage sample NRG-P0074 viral sample RU1 from unclassified <i>Mosigvirus</i>, originally isolated by the Betty Kutter. The complete genome of NRG-P0074 was sequenced, annotated, and analyzed using various bioinformatic tools. Host range analysis was conducted using the <i>Escherichia coli</i> Reference (ECOR) Library and nine <i>Escherichia coli (E. coli)</i> K12 strains (Keio Knockout Collection) with single nonessential gene deletions.</p><p><strong>Results: </strong>The genome of NRG-P0074 spans 168,357 base pairs with a guanine-cytosine (GC) content of 37.5%. NRG-P0074 exhibited permissiveness in 15.28% of the ECOR isolates and all 9 Keio knockout strains. Comparative genomic analysis revealed that NRG-P0074 is closely related to <i>E. coli</i> phage a20. Its genome is comprised of 270 coding sequences, 153 known genes, 16 terminators, 3 ribosomal-binding sites, 0 tRNAs, and 117 hypothetical proteins.</p><p><strong>Conclusions: </strong>This research provides valuable data for developing machine learning models to predict phage-host interactions, aiding the development of targeted phage therapies against antibiotic-resistant bacteria.</p>","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"6 3","pages":"235-240"},"PeriodicalIF":1.8,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12570860/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145411167","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}