Bacteriophages and microbial interactions

A versatile bacterial innate immunity protein directly senses two disparate phage proteins

This study shows that the bacterial immunity protein CapRelSJ46 can sense two distinct phage proteins using the same domain, highlighting its versatility in anti-phage defense.

The vibriophage-encoded inhibitor OrbA abrogates BREX-mediated defense through the ATPase BrxC

This paper identifies how the phage-encoded inhibitor OrbA disrupts the BREX defense system in Vibrio cholerae by directly binding to the BrxC ATPase component.

Systematic annotation of hyper-variability hotspots in phage genomes and plasmids

The paper introduces iLund4u, an algorithm to systematically annotate hyper-variability hotspots in phage genomes and plasmids, identifying 13.7K hotspots and 171K diverse protein families across 873K phage and 696K plasmid sequences.

Systematic, high-throughput characterization of bacteriophage gene essentiality on diverse hosts

This study introduces PhageMaP, a high-throughput method to assess gene essentiality in bacteriophages across diverse hosts and uses it to engineer synthetic phages with enhanced infectivity.

Directional Immobilisation of SpyTag Bacteriophage on PDMS surfaces for Phage based Microfluidics

This paper demonstrates a method to directionally immobilize SpyTagged phages on PDMS surfaces for microfluidic phage-based biosensors.

A Vibrio cholerae Anti-Phage System Depletes Nicotinamide Adenine Dinucleotide to Restrict Virulent Bacteriophages

The paper identifies a Vibrio cholerae anti-phage system, Nezha, that depletes NAD+ to restrict virulent phages, with a phage counteracting this by regenerating NAD+.

Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome

The paper estimates phage population dynamics and lifestyle in the human gut using integrated data, finding a low lysis rate and high genome-to-genome ratio suggesting temperate phage dominance.

Pipolins are bimodular platforms that maintain a reservoir of defense systems exchangeable with various bacterial genetic mobile elements

The paper identifies pipolins as defense islands in bacteria that serve as reservoirs for exchangeable defense genes with mobile genetic elements.

Pathogen genomic surveillance as a scalable framework for precision phage therapy

This paper develops a scalable framework for precision phage therapy by combining genomic surveillance and phage typing to target carbapenem-resistant Acinetobacter baumannii.

A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases.

The paper introduces DefenseFinder, a resource for antiphage defense systems, including a web service, wiki, and databases with structure predictions.

Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequences

Jaeger is a deep-learning tool that accurately and quickly identifies bacteriophage sequences in metagenomic data, achieving high sensitivity and precision.

Structural models predict a significantly higher binding affinity between the NblA protein of cyanophage Ma-LMM01 and the phycocyanin of Microcystis aeruginosa NIES-298 compared to the host homolog

The paper uses structural modeling to show that the viral NblA protein from cyanophage Ma-LMM01 binds more strongly to host phycocyanin than the host's own NblA.

A Cryptic Prophage Transcription Factor Drives Phenotypic Changes via Host Gene Regulation

This study identifies DicC, a cryptic prophage transcription factor in E. coli, and shows it regulates hundreds of host genes, influencing bacterial phenotypes independently of other prophage genes.

Virus-Host Interactions Predictor (VHIP): machine learning approach to resolve microbial virus-host interaction networks

The paper introduces VHIP, a machine learning model that predicts virus-host interactions from genomic data, achieving 87.8% accuracy in predicting interactions at the species level.

Soil redox drives virus-host community dynamics and plant biomass degradation in tropical rainforest soils

This study examines how soil redox conditions influence viral communities and virus-host interactions in tropical rainforest soils, revealing distinct viral populations and their roles in carbon degradation.

Time of day of infection shapes development of a eukaryotic algal-Nucleocytoviricota virocell

This study shows that the time of day a virus infects an algal host affects viral particle production and bloom dynamics.

An archaeal CBASS shows protective activity against both chronic and lytic viruses

This study shows that the archaeal CBASS system H-CBASS2 protects against both lytic and chronic viruses by depleting NAD+, with different kinetics depending on infection type.

Metagenomic analyses of single phages and phage cocktails show instances of contamination with temperate phages and bacterial DNA

The paper reanalyzes published metagenomic sequences of phage cocktails to identify temperate phages and bacterial DNA contamination, highlighting risks for horizontal gene transfer.

Viral diversiy within marine biofilms and their potential roles in microbially influenced corrosion

This study analyzes viral communities in marine biofilms on 8 materials to explore their roles in microbially influenced corrosion, finding viruses influence corrosion through interactions with corrosive microbes.

Diversification of Pseudomonas aeruginosa biofilm populations under repeated phage exposures decreases the efficacy of the treatment

This study shows that repeated phage exposure to P. aeruginosa biofilms reduces phage efficacy due to genetic changes that confer resistance and tolerance.

Genomic Transfer via Membrane Vesicle: A Strategy of Giant Phage phiKZ for Early Infection

The paper describes the EPI vesicle, a structure used by the phiKZ phage to transport viral DNA during early infection, protecting it from bacterial nucleases.

Antibiotic-Induced Morphological Changes Enhance Phage Predation: A Mathematical Model of Plaque Formation in Structured Environments

This paper develops a mathematical model showing that antibiotic-induced morphological changes in bacteria enhance phage predation and plaque size in structured environments.

The world's largest High Arctic lake is dominated by uncharacterized, genetically highly diverse phages

The paper analyzes viral diversity in Lake Hazen, the largest High Arctic lake, using metagenomic and metatranscriptomic data to show unique evolutionary processes and high genetic diversity in High Arctic viruses.

Dynamics and determinants of the gut mobilome in early life

The paper analyzes the gut mobilome in mother-infant dyads, finding increased infant mobilome richness over time, formula feeding effects, and antibiotic resistance gene presence in plasmids.

Machine learning models can identify individuals based on a resident oral bacteriophage family

The paper uses machine learning to identify individuals based on phageprint profiles from oral microbiomes, finding stable and unique phageprints per individual.

New viruses infecting hyperthermophilic bacterium Thermus thermophilus

The paper isolates and analyzes new phages infecting Thermus thermophilus from diverse hot springs, revealing both known relatives and novel phages with unique genetic features.

Bacteriophages Phi 8 and Phi 12 host infection are inhibited by OMVs and LPS purified from P. pseudoalcaligenes strain: East River Isolate A

This study shows that OMVs and LPS from P. pseudoalcaligenes strain ERA inhibit Cystoviridae phages Phi 8 and Phi 12 infection, identifying LPS as the receptor and highlighting differences in LPS composition affecting binding.

Nucleocytoviricota viral factories are transient organelles made by liquid-liquid phase separation

The paper shows that Nucleocytoviricota viral factories are transient organelles formed by liquid-liquid phase separation, using scaffold proteins and client proteins.

Viral adaptations to alternative hosts in the honey bee pathogen Paenibacillus larvae

The paper modifies the Appelmans protocol to evolve phages against Paenibacillus larvae, identifying new lysis patterns and improving phage diversity for honey bee pathogen treatment.

Jumping DNA polymerases in bacteriophages

The paper identifies instances of DNA polymerase (DNAP) swapping among bacteriophages, showing gene replacements between families and subfamilies without altering surrounding gene organization.