Bacteriophages and microbial interactions

PHI: A Galaxy-based workflow for reproducible prophage-host interaction analysis and standardized viral-genomics reporting

PHI is a Galaxy-based workflow that automates prophage-host interaction analysis and generates standardized reports, detecting 41 prophages across 14 hosts in a mock community.

High Throughput Viral Enumeration of Aquatic Ecosystems via Flow Cytometry

This paper introduces a high throughput flow cytometry method for viral enumeration in aquatic ecosystems, improving speed and reducing contamination compared to traditional methods.

First community challenge for automated virus taxonomy

This paper organizes a community challenge to develop automated virus taxonomy classification tools and evaluates their performance on a combined dataset of expert-curated and metagenomic sequences.

Lytic bacteriophages active in urine against multi-drug resistant clinically derived Klebsiella pneumoniae causing urinary tract infection

The paper isolates and characterizes three lytic bacteriophages active against multi-drug resistant Klebsiella pneumoniae in urine, showing higher lytic activity in human urine than in LB medium.

Predatory bacteria as members of human microbiomes and their impact on gut diversity and homeostasis

This study identifies predatory bacteria (BALOs) in the human gut microbiome, showing they enhance microbial diversity and may contribute to gut homeostasis by controlling harmful bacteria.

Biocontainment of phages inhibits bacterial clearance in micro niches

This study shows that biocontained phages are less effective at clearing bacteria in structured environments compared to wild-type phages.

Host species background, defence systems, and phage tail gene architecture shape phage infectivity in cystic fibrosis-associated Achromobacter

The paper shows bacterial strain identity is the main factor determining phage infectivity in Achromobacter, with lineage and strain identity explaining 90% of variation in infection efficiency.

Bacteriophage genome-wide transposon mutagenesis

This study develops a phage transposon sequencing (TnSeq) platform to identify essential genes in bacteriophages, finding ~110 fitness-conferring genes in a jumbo phage model.

A Minimal Packaging Signal Enables Production of High-Purity Phage-Like Particles for CRISPR-Cas Antimicrobials in Staphylococcus aureus

This paper develops a minimal phagemid packaging signal for producing high-purity CRISPR-Cas antimicrobials in Staphylococcus aureus with high titers and purity.

Mechanism of tandem-repeat DNA synthesis by an antiviral reverse transcriptase

The paper investigates the mechanism of tandem-repeat DNA synthesis by DRT10, revealing a 2:1 RT-ncRNA architecture and how repeat length is controlled by template distance.

Disentangling Production and Persistence of Extracellular Virions in Grassland Soils with SIP-Viromics

This study uses SIP-viromics to distinguish newly produced from persistent virions in soil, revealing that most virions persist without replication, linked to dominant bacterial groups.

Ptolemaea: consensus, comprehensive annotation of antiviral defence systems in bacterial genomes

Ptolemaea harmonizes antiviral defence system annotations across multiple tools to maximize recovery and resolve discrepancies in bacterial genomes.

Sociality changes Gene Essentiality

The paper shows social interactions in phages distort gene essentiality by masking true fitness costs through complementation, and proposes an MOI-based strategy to classify sociality.

The PhageExpressionAtlas reveals shared and unique transcriptional patterns across phage-host interactions

The PhageExpressionAtlas provides a unified resource for time-resolved dual RNA-sequencing data from phage infections, enabling analysis of shared and unique transcriptional patterns across phage-host interactions.

Analysis of a Novel Cluster V Mycobacteriophage EniyanLRS and its Therapeutically Relevant LysB

The paper characterizes a novel mycobacteriophage EniyanLRS and its endolysin LysB, showing LysB's potent antibacterial and antibiofilm activity against mycobacteria.

Antimicrobial-resistance plasmids encode Evangelion, a widespread DUF4062 anti-phage defence family

The paper identifies Evangelion, a new family of anti-phage defence systems encoded in antimicrobial-resistance plasmids, through phenotype-guided analysis of a Staphylococcus aureus plasmid.

Bacteriophage Heteroresistance as a Cause of Treatment Failure in Urinary Tract Infections

The paper investigates phage therapy failure in UTIs by showing that heteroresistance, not traditional resistance, causes rapid treatment failure despite initial susceptibility.

Predictable induction responses of gut prophages

This study identifies and characterizes prophage induction mechanisms in gut bacteria, showing that DNA damage reliably triggers induction of prophages encoding CI-like repressors.

Structural basis of multimodal adsorption and infection initiation by Vibrio phage Peru-2

This study determines the structure of Vibrio phage Peru-2, revealing its multimodal adsorption strategy and infection mechanism involving tailspikes and interactions with bacterial surfaces.

Predatory bacteria impact C. elegans life-history traits by modulating microbiota community dynamics and thereby vitamin B12 availability

This study shows predatory bacteria alter C. elegans microbiota, increasing vitamin B12 availability, which extends lifespan by suppressing a detoxification pathway.

Conformational changes of baseplate regulatingtail contraction of Staphylococcus phage 812

This study uses cryo-EM to show how the baseplate of phage 812 undergoes conformational changes that trigger tail contraction during infection of Gram-positive bacteria.

A humanized Galleria mellonella model reveals prophage-mediated breakdown of colonization resistance against Salmonella

This paper develops a humanized Galleria mellonella model to study prophage-mediated breakdown of colonization resistance against Salmonella, finding that prophages enhance pathogen success through metabolic changes in resident bacteria.

Comprehensive profiling of infant gut virome assembly reveals associations with eczema and wheeze

This study profiles the infant gut virome using dual methods and finds associations with eczema and wheeze.

Discovery, induction, and screening of prophages in clinical Acinetobacter baumannii isolates

The paper identifies and characterizes prophages in A. baumannii isolates using computational analysis and experimental induction, showing their potential as therapeutic agents against antibiotic-resistant strains.

GenomoBase: A comprehensive resource for the family Genomoviridae

GenomoBase is a curated resource integrating genomic, ecological, and bibliographic data for 237 genomovirus species, enabling comparative analyses and metagenome-guided genome recovery.

The co-localizing Zorya II, Druantia III, and ARMADA II defense systems on O-island 172 confer synergistic anti-phage defense in enterohemorrhagic Escherichia coli

This study identifies that the co-localizing Zorya II, Druantia III, and ARMADA II defense systems on O-island 172 in EHEC confer synergistic anti-phage defense, with Druantia III and ARMADA II providing most of the phage resistance.

Optimizing bacteriophage screening and isolation methods for microbial samples derived from different body sites of cattle

This study optimizes bacteriophage screening methods for cattle body sites and isolates 83 lytic phages against commensal bacteria, highlighting their potential for microbiome modulation in cattle.

Bacteriophage replication strategies are associated with organic matter energy content on coral reefs

The paper links bacteriophage replication strategies to dissolved organic matter energy content on coral reefs, showing temperate phages associate with energy-rich compounds.

A global atlas of deep-sea cold seep viruses uncovers extensive genomic novelty and biotechnological potential

The paper constructs a global virome atlas of cold seep ecosystems, revealing novel viral diversity and biotechnological potential.

CBASS limits bacteriophage production while maintaining cell viability in Pseudomonas aeruginosa

The paper shows that CBASS effector CapV limits phage production without reducing cell viability in Pseudomonas aeruginosa by interfering with phage capsid assembly.