Bacteriophages and microbial interactions

TattleTail: A Pyocin Prediction Tool

TattleTail identifies pyocin-encoding gene clusters in Pseudomonas aeruginosa genomes, distinguishing them from prophages by lacking canonical phage features.

Suppressing Transfer of Antibiotic Resistance by a Small RNA Virus

This paper shows that the ssRNA phage PRR1 inhibits conjugation of the IncP plasmid RP4 by targeting its T4SS pilus, with non-infectious PRR1 particles sufficient for inhibition.

FoundedPBI: Using Genomic Foundation Models to predict Phage-Bacterium Interactions

FoundedPBI uses genomic foundation models and ensemble learning to predict phage-bacterium interactions from DNA sequences, achieving high F1-scores on benchmark datasets.

Viral isolation reveals novel and diverse phages infecting natural stream biofilms

The paper isolates and characterizes novel phages from alpine stream biofilms, revealing their genetic diversity and ecological impact.

Engineered phages evade the complete defense repertoire of highly phage-resistant MRSA clinical isolates

The paper demonstrates engineered phages can evade multiple defense systems in MRSA strains, preventing resistance emergence and offering a strategy for next-generation phage therapy.

A synonymous mutation in MSMEG_4729 occurs at a high frequency in spontaneous D29-resistant mutants of Mycobacterium smegmatis

This study identifies a synonymous mutation in MSMEG_4729 that frequently occurs in D29-resistant mutants of Mycobacterium smegmatis and links it to potential resistance mechanisms involving LOS biosynthesis and m6A modifications.

Prophage induction shifts community composition and functional capacity in a Sargassum-derived multispecies biofilm

This study investigates how prophage induction affects the composition and function of a Sargassum-derived biofilm, showing shifts in community structure and metabolic capacity.

A truncated soil phage catechol 1,2-dioxygenase illustrates how viruses preserve and disseminate auxiliary catalytic functions in the soil microbiome

The paper identifies a truncated viral catechol 1,2-dioxygenase from soil phages that retains catalytic activity and expands host metabolic versatility.

Lipid metabolic pathways determine phage infectivity in Mycobacterium abscessus

This study identifies lipid metabolic pathways as key determinants of phage infectivity in Mycobacterium abscessus by analyzing phage-resistant mutants and their genetic and transcriptional changes.

Identification and Functional Insights into New Phage Tail-Like Bacteriocins (PTLBs) Targeting Pseudomonas aeruginosa as new antimicrobials

This study identifies 34 phage tail-like bacteriocins (PTLBs) in Pseudomonas aeruginosa genomes, with some showing strong antimicrobial activity against bacterial infections.

ApeA cleaves genomic RNA to defend against RNA phage infection

This study identifies ApeA as a non-abortive defense system that cleaves RNA phage genomes to restrict replication without causing cell death.

Bacteriophage host prediction using a genome language model

This paper evaluates a genome language model for predicting bacteriophage hosts using embeddings, finding it effective for narrowing host candidates and capturing broad evolutionary relationships when combined with existing methods.

Infauna selectively enhance DNA virus diversity and activity in marine sediments

The paper investigates how infauna affect DNA and RNA virus communities in marine sediments, finding increased DNA virus abundance and activity under higher infauna conditions.

Structural diversification of phage tail fibres enables recognition of diverse type IV pili

The paper shows how phage tail fibre structure determines their ability to recognize diverse type IV pils despite receptor variation.

Live and let die: lysis time variability and resource limitation shape lytic bacteriophage fitness

This paper uses agent-based simulations to show that lysis time variability in bacteriophages can provide a fitness advantage in competition, even when reducing growth rate in isolation.

Cyclic tri-adenylate signalling by a Panoptes anti-phage guard system with a CARF-TM effector

The paper shows the type II Panoptes system generates cyclic tri-adenylate (cA3) to keep a CARF-TM effector inactive, and its degradation leads to membrane permeabilization and growth arrest.

Large scale antibiotic-phage synergy studies reveal key combinations for urinary tract infection and urosepsis treatments

This study screens phage-antibiotic combinations in clinical isolates to identify synergistic interactions for treating resistant infections.

Pregnancy and Early-Life Gut Virome in the Lifelines NEXT cohort:Origin, Persistence, Influencing Factors and Health Implications

The paper analyzes the gut virome in mother-infant pairs to identify factors influencing its development and persistence, finding that delivery mode and breastmilk shape the infant virome and that viral diversity is linked to food allergies.

Capturing dynamic phage-pathogen coevolution by clinical surveillance

The paper uses clinical surveillance in Bangladesh to study phage-pathogen coevolution in Vibrio cholerae, identifying a parasitic MGE that drives a selective sweep during a major outbreak.

Likely role of promoter reconstitution in Mpr-mediated D29 resistance by Mycobacterium smegmatis

This study identifies promoter reconstitution via IS6120 insertion upstream of mpr as the mechanism behind Mpr overexpression in D29-resistant M. smegmatis mutants.

Genomic Determinants of Phage Activity Against Pseudomonas aeruginosa: Roles of Receptors, Defence Systems, and Anti-Defences

This study identifies genomic features influencing phage activity against Pseudomonas aeruginosa and develops a machine learning classifier to predict phage-host outcomes.

Ionic regulation of Gram-positive phage adsorption governs host range and improves phage isolation efficiency

The paper shows that adjusting ionic conditions improves phage isolation from Gram-positive bacteria and expands their host range.

Semirandom DNA adducts regulate a filamentous defence-associated reverse transcriptase

This study characterizes the DRT1 antiphage defence system, showing it generates semirandom DNA adducts that regulate filament assembly and function through structural changes.

Systematic Scale-Up and Enhanced Purification of Marine Cyanophage P-SSP7

This paper develops a scalable and high-quality method for producing marine cyanophage P-SSP7, enabling efficient structural studies and reducing cryo-EM data collection time.

Nanopore direct RNA sequencing (DRS) of MS2 bacteriophages in E.coli throughout its life cycle reveals a complex transcriptional activity to control and maintain its growth

This study uses Nanopore DRS to analyze MS2 phage transcriptional dynamics in E. coli, revealing complex transcriptional activity and RNA modifications throughout the life cycle.

Structural modeling reveals viral proteins that manipulate host immune signaling

The paper identifies viral proteins that manipulate bacterial immune signaling by analyzing structural and biophysical traits, and develops a computational pipeline to predict such proteins in phage genomes.

Phage protease enzymes activate CBASS antiphage immunity

The paper identifies phage protease activation of CBASS immunity by cleaving CD-NTase activation loops, revealing a conserved mechanism for antiviral defense.

The potential role of viruses controlling phytoplankton community size structure

The paper investigates the role of viruses in shaping phytoplankton community size structure by analyzing gene expression data and finding correlations between cell size, viral-gene diversity, and immune-response genes.

Cryo-EM structure analysis of phage {Phi}Xacm4-11 that infects the phytopathogen Xanthomonas citri

This paper presents the structural and functional analysis of {Phi}Xacm4-11, a phage infecting Xanthomonas citri, revealing its architecture and host recognition mechanisms.

Filament formation is a conserved mechanism of Thoeris SIR2 effector activation

This study shows that 3'cADPR-induced SIR2 filament formation activates ThsA effectors in type I Thoeris systems across bacterial species.