Phage papers

Prophage border curation reveals horizontal transfer of lysogeny-related elements between filamentous and double jelly-roll phages - PubMed While tailed bacteriophages dominate contemporary models of phage biology, non-tailed phages-particularly filamentous inoviruses and double jelly-roll (DJR) capsid phages-remain poorly understood, despite their environmental ubiquity and ecological importance. Here, we identify 515 inoviruses and 25 …

Prophage border curation reveals horizontal transfer of lysogeny-related elements between filamentous and double jelly-roll phages.

DOI: 10.1038/s42003-025-09276-1

https://pubmed.ncbi.nlm.nih.gov/41413665/

Metagenomic analysis of bacteriome and phageome of wastewater from a ceramic factory in Türkiye - PubMed Bacteriophages are major determinants of bacterial community dynamics. Industrial wastewaters constitute distinctive microbe-phage ecosystems shaped by heavy-metal and chemical stressors, yet they remain sparsely characterized by metagenomics. Most existing studies focus on municipal or hospital was …

Metagenomic analysis of bacteriome and phageome of wastewater from a ceramic factory in Türkiye.

DOI: 10.1007/s10123-025-00753-5

https://pubmed.ncbi.nlm.nih.gov/41258374/

Identification and analysis of the crucial holin domain and sites and the bactericidal activity of a holin-endolysin lysis cassette from phage PZL-Ah152 against Aeromonas hydrophila - PubMed With the increasing prevalence of antibiotic-resistant bacteria, phage therapy has garnered significant attention. Holin and lysin play essential roles in the phage-induced lysis of bacteria. This study investigated the functions of the holin protein Hol 46 and the lysozyme protein Lys 17 from the p …

Identification and analysis of the crucial holin domain and sites and the bactericidal activity of a holin-endolysin lysis cassette from phage PZL-Ah152 against Aeromonas hydrophila.

DOI: 10.1128/jvi.00832-25

https://pubmed.ncbi.nlm.nih.gov/41395932/

Direct electron microscopy study on the morphological diversity of bacteriophage populations in lake plusssee - PubMed Direct electron microscopy of bacteriophages adsorbed to a carbon film without prior enrichment by specific host strains or concentration by physical or chemical methods was used to study the morphological diversity of natural bacteriophage assemblages in a North German lake. All samples contained a …

Direct electron microscopy study on the morphological diversity of bacteriophage populations in lake plusssee.

https://pubmed.ncbi.nlm.nih.gov/16349070/

Genomic Analysis of 96 Paenibacillus larvae Bacteriophages Including 26 from Aotearoa, New Zealand - PubMed The bacterium <i>Paenibacillus larvae</i> is responsible for the devastating honey bee (<i>Apis mellifera</i>) disease American Foulbrood. Research into bacteriophages that infect <i>P. larvae</i> is growing rapidly due to increasing antibiotic resistance and restrictions on antibiotic use in beehiv …

Genomic Analysis of 96 Paenibacillus larvae Bacteriophages Including 26 from Aotearoa, New Zealand.

DOI: 10.3390/v17020137

https://pubmed.ncbi.nlm.nih.gov/40006892/

Prophage-DB: a comprehensive database to explore diversity, distribution, and ecology of prophages - PubMed Given that prophages are particularly overlooked and merit increased attention due to their vital implications for microbiomes and their hosts, we created Prophage-DB to advance our understanding of prophages in microbiomes through a comprehensive characterization of prophages in publicly available …

Prophage-DB: a comprehensive database to explore diversity, distribution, and ecology of prophages.

DOI: 10.1186/s40793-024-00659-1

https://pubmed.ncbi.nlm.nih.gov/39806487/

Screening of Oligopeptides that Recognize Inorganic Crystalline Facets of Metal Nanoparticles - PubMed Peptides that possess specific affinity to distinct crystal facets have been reported previously. However, their adsorption behavior in terms of the crystal sizes and shapes is less exploited. Herein, we isolate several phage clones that show the strong affinity to {100} of Pd at a neutral pH from t …

Screening of Oligopeptides that Recognize Inorganic Crystalline Facets of Metal Nanoparticles.

DOI: 10.1002/ijch.201400151

https://pubmed.ncbi.nlm.nih.gov/31666749/

Transmission mechanisms and risk tracing of antibiotic resistance genes in rivers driven by wastewater inputs - PubMed Aquatic environments are critical for ARG dissemination, yet contributions from different wastewater sources, dominant HGT mechanisms, and residual risks in natural waters remain unclear. Based on 863 metagenomic samples across China, we systematically analyzed wastewater inputs, HGT mechanisms, and …

Transmission mechanisms and risk tracing of antibiotic resistance genes in rivers driven by wastewater inputs.

DOI: 10.1016/j.jhazmat.2025.140523

https://pubmed.ncbi.nlm.nih.gov/41259914/

Technological advancements in antibody-based therapeutics for treatment of diseases - PubMed Monoclonal antibodies (mAbs) represent a major class of therapeutics with widespread clinical applications in oncology, immunology, hematology, neurology and infectious disease. Since the introduction of hybridoma technology in 1975, the field has been advanced by a succession of innovations includi …

Technological advancements in antibody-based therapeutics for treatment of diseases.

DOI: 10.1186/s12929-025-01190-2

https://pubmed.ncbi.nlm.nih.gov/41219972/

The infectome framework: linking polymicrobial ecology and biofilm dynamics to precision diagnostic approaches - PubMed Chronic infections are a persistent global health problem and are frequently sustained by polymicrobial communities rather than by a single pathogen. This review brings together current evidence for the infectome concept, defined as the dynamic set of pathogenic or pathobiont taxa in the host, their …

The infectome framework: linking polymicrobial ecology and biofilm dynamics to precision diagnostic approaches.

DOI: 10.1007/s15010-025-02687-6

https://pubmed.ncbi.nlm.nih.gov/41201733/

Resolution of acute rejection in a bilateral double-lung transplanted cystic fibrosis patient following phage intervention - PubMed This case underscores the potential of phage therapy to complement traditional treatments in managing chronic bacterial infections in CF patients, though further studies are needed to optimize treatment protocols and understand the role of phages in modulating the bacterial population.

Resolution of acute rejection in a bilateral double-lung transplanted cystic fibrosis patient following phage intervention.

DOI: 10.1128/asmcr.00058-24

https://pubmed.ncbi.nlm.nih.gov/41244966/

Harnessing droplet microfluidics and morphology-based deep learning for the label-free study of polymicrobial-phage interactions - PubMed Evaluating the impact of bacteriophages on bacterial communities is required to assess the future utility of phage therapy. Methods able to study bacterial polycultures in the presence of phages are useful to mimic evolutionary pressures found in natural environments and recapitulate complex ecologi …

Harnessing droplet microfluidics and morphology-based deep learning for the label-free study of polymicrobial-phage interactions.

DOI: 10.1038/s42003-025-08925-9

https://pubmed.ncbi.nlm.nih.gov/41225150/

Bathing seawater and sand as reservoirs of clinically relevant and antimicrobial resistant Klebsiella pneumoniae strains - PubMed Klebsiella pneumoniae is included in the ESKAPE list of bacteria, which are currently considered the greatest threat to human health. It is widely distributed in the environment, including waters, soils, and plants. According to the One Health concept, it is essential to enhance our understanding of …

Bathing seawater and sand as reservoirs of clinically relevant and antimicrobial resistant Klebsiella pneumoniae strains.

DOI: 10.1016/j.scitotenv.2025.180930

https://pubmed.ncbi.nlm.nih.gov/41237617/

Disarming Salmonella virulence with 32H-hilE anti-virulence bacteriophage - PubMed As the development of new antibiotics struggles with the continuous emergence of drug-resistant bacteria, targeting bacterial virulence factors instead of viability has been proposed as one of the alternative approaches to combat the pathogens. Here, we genetically engineered the temperate phage SPC …

Disarming Salmonella virulence with 32H-hilE anti-virulence bacteriophage.

DOI: 10.1016/j.micres.2025.128396

https://pubmed.ncbi.nlm.nih.gov/41240734/

Identification of internalizing ScFvs for EGFR inhibition and apoptosis induction in cholangiocarcinoma cells - PubMed Cholangiocarcinoma (CCA) is an aggressive malignancy with limited treatment options. EGFR overexpression is associated with tumor recurrence and poor prognosis, yet current EGFR-targeted therapies show limited efficacy. To identify alternative therapeutic candidates, we performed subtractive bio-pan …

Identification of internalizing ScFvs for EGFR inhibition and apoptosis induction in cholangiocarcinoma cells.

DOI: 10.1038/s41598-025-24324-w

https://pubmed.ncbi.nlm.nih.gov/41257876/

Exploring diversity and distribution patterns of chicken gut bacteriophage community - PubMed The online version contains supplementary material available at 10.1186/s42523-025-00484-y.

Exploring diversity and distribution patterns of chicken gut bacteriophage community.

DOI: 10.1186/s42523-025-00484-y

https://pubmed.ncbi.nlm.nih.gov/41239428/

Complete genome sequence of lytic Pseudomonas aeruginosa phage vB_PaeS_Tums_P6 - PubMed The online version contains supplementary material available at 10.1007/s13205-025-04528-7.

Complete genome sequence of lytic Pseudomonas aeruginosa phage vB_PaeS_Tums_P6.

DOI: 10.1007/s13205-025-04528-7

https://pubmed.ncbi.nlm.nih.gov/41255842/

Conserved tripartite tail proteins mediate virophage-host interactions through Synechococcus lipopolysaccharide binding - PubMed This study significantly advances our understanding of virophage biology by elucidating key molecular mechanisms underlying their host interactions. The discovery of a conserved heterotrimeric tail complex in Dishui Lake Virophage 2, evolutionarily related to tail proteins of <i>Synechococcus</i> ph …

Conserved tripartite tail proteins mediate virophage-host interactions through Synechococcus lipopolysaccharide binding.

DOI: 10.1128/jvi.01082-25

https://pubmed.ncbi.nlm.nih.gov/41251349/

Identification of internalizing ScFvs for EGFR inhibition and apoptosis induction in cholangiocarcinoma cells - PubMed Cholangiocarcinoma (CCA) is an aggressive malignancy with limited treatment options. EGFR overexpression is associated with tumor recurrence and poor prognosis, yet current EGFR-targeted therapies show limited efficacy. To identify alternative therapeutic candidates, we performed subtractive bio-pan …

Identification of internalizing ScFvs for EGFR inhibition and apoptosis induction in cholangiocarcinoma cells.

DOI: 10.1038/s41598-025-24324-w

https://pubmed.ncbi.nlm.nih.gov/41257876/

KlebPhaCol: a community-driven resource for Klebsiella research identified a novel phage family - PubMed The growing threat of multidrug-resistant Klebsiella pneumoniae, coupled with its role in gut colonisation, has intensified the search for new treatments, including bacteriophage therapy. Despite increasing documentation of Klebsiella-targeting phages, clinical applications remain limited, with key …

KlebPhaCol: a community-driven resource for Klebsiella research identified a novel phage family.

DOI: 10.1093/nar/gkaf1122

https://pubmed.ncbi.nlm.nih.gov/41261852/

Genomic characterization of an Anticarsia gemmatalis multiple nucleopolyhedrovirus isolate from the cotton leafworm, Alabama argillacea with cross-species infectivity potential for pest management - PubMed The cotton leafworm Alabama argillacea is an important pest of cotton in South America, traditionally controlled using chemical insecticides, which reinforces the demand for environmentally safe alternatives. Baculoviruses are widely used in microbial pest control due to their efficacy and biosafety …

Genomic characterization of an Anticarsia gemmatalis multiple nucleopolyhedrovirus isolate from the cotton leafworm, Alabama argillacea with cross-species infectivity potential for pest management.

DOI: 10.1016/j.virol.2025.110740

https://pubmed.ncbi.nlm.nih.gov/41248595/

Antivirulence drugs against Acinetobacter baumannii: where do they stand? - PubMed Acinetobacter baumannii is a nosocomial Gram-negative pathogen of multi- and extensive-drug resistance phenotypes. In certain regions, multi-drug resistance rates can soar as high as 80-90%. Accordingly, reports by the World Health Organization and the Centers for Disease Control and Prevention unde …

Antivirulence drugs against Acinetobacter baumannii: where do they stand?

DOI: 10.1007/s11274-025-04593-3

https://pubmed.ncbi.nlm.nih.gov/41165876/

Inactivating conditions of therapeutic mycobacteriophages - PubMed There is a need for new therapies to treat drug resistant nontuberculous mycobacteria (NTM) disease. Bacteriophages (phages), which are viruses that infect and kill bacteria, are actively being explored as an alternative approach for treating mycobacterial diseases. Several compassionate-use cases o …

Inactivating conditions of therapeutic mycobacteriophages.

DOI: 10.1101/2025.09.30.679648

https://pubmed.ncbi.nlm.nih.gov/41256447/

Resolution of acute rejection in a bilateral double-lung transplanted cystic fibrosis patient following phage intervention - PubMed This case underscores the potential of phage therapy to complement traditional treatments in managing chronic bacterial infections in CF patients, though further studies are needed to optimize treatment protocols and understand the role of phages in modulating the bacterial population.

Resolution of acute rejection in a bilateral double-lung transplanted cystic fibrosis patient following phage intervention.

DOI: 10.1128/asmcr.00058-24

https://pubmed.ncbi.nlm.nih.gov/41244966/

Isolation, Identification and Typing of Nine Strains of Brucella in Arun Banner - PubMed People involved in raising and trafficking sheep constitute a high-risk group for brucellosis. The strains isolated were B. melitensis, with ST8 as the predominant type identified by MLST typing. Attention should also be given to the discovery of new alleles.

Isolation, Identification and Typing of Nine Strains of Brucella in Arun Banner.

DOI: 10.1002/vms3.70694

https://pubmed.ncbi.nlm.nih.gov/41251272/

Polyvalent phage GSP004 recognizes O-antigen polysaccharide receptors in Salmonella and Escherichia coli through tail fiber protein ORF208 - PubMed The majority of phages are capable of lysing only specific bacterial strains within a single species, and polyvalent phages with cross-genus lytic capability are relatively rare. In this study, we isolated a polyvalent phage, GSP004, from swine farm wastewater, which exhibited cross-genus lytic acti …

Polyvalent phage GSP004 recognizes O-antigen polysaccharide receptors in Salmonella and Escherichia coli through tail fiber protein ORF208.

DOI: 10.1128/jvi.00810-25

https://pubmed.ncbi.nlm.nih.gov/41251352/

Hypervirulent Klebsiella pneumoniae causing aortitis retains its capsule and mucoviscosity and remains genotypically and phenotypically stable over time - PubMed Aortitis due to hypervirulent Klebsiella pneumoniae (hvKp) in a Belarusian male from central New York is described. Isolates at the time of diagnosis (Kp031824-1, Kp031824-2) and after 12 weeks of antimicrobial therapy (Kp070124) were characterized. Kp070124 was genomically and phenotypically unchan …

Hypervirulent Klebsiella pneumoniae causing aortitis retains its capsule and mucoviscosity and remains genotypically and phenotypically stable over time.

DOI: 10.1038/s41598-025-23563-1

https://pubmed.ncbi.nlm.nih.gov/41233465/

Bacteriophage density influences the rate of resistance evolution - PubMed The antagonistic relationship between bacteria and bacteriophages (phages) drives genetic changes that result in phage resistance. Phage resistance mutations arise in natural microbial communities and during the treatment of diseases with phages (phage therapy), making it important to understand the …

Bacteriophage density influences the rate of resistance evolution.

DOI: 10.1101/2025.10.05.680490

https://pubmed.ncbi.nlm.nih.gov/41256655/

Structural basis for Lamassu-based antiviral immunity and its evolution from DNA repair machinery - PubMed Bacterial immune systems exhibit remarkable diversity and modularity, as a consequence of the continuous selective pressures imposed by phage predation. Despite recent mechanistic advances, the evolutionary origins of many antiphage immune systems remain elusive, especially for those that encode hom …

Structural basis for Lamassu-based antiviral immunity and its evolution from DNA repair machinery.

DOI: 10.1073/pnas.2519643122

https://pubmed.ncbi.nlm.nih.gov/41252147/

A novel long-acting C5a-blocking cyclic peptide prevents sepsis-induced organ dysfunction via effective blockade of the inflammatory cascade - PubMed Sepsis is a life-threatening syndrome characterized by dysregulated host responses to infection, leading to severe organ dysfunction and a high mortality rate. Reducing the incidence of sepsis is of paramount importance. Given that sepsis-associated drugs largely fail in clinical trials, in this pro …

A novel long-acting C5a-blocking cyclic peptide prevents sepsis-induced organ dysfunction via effective blockade of the inflammatory cascade.

DOI: 10.1038/s41392-025-02457-8

https://pubmed.ncbi.nlm.nih.gov/41188260/