Bacteriophages and microbial interactions

Unprecedented Microviridae phages isolated from equine uteri

The paper identifies novel Microviridae phages from horse uteri and suggests similar viruses may exist in related animals' uterine microbiomes.

The hidden prevalence and unique protein folds of huge phages

The paper curates a comprehensive database of huge phage genomes and protein structures, revealing a prevalent clade and unique protein folds with potential applications in microbiome research and biotechnology.

"Paraxenoviridae", a putative family of ubiquitous marine bacteriophages with double-stranded RNA genomes

The paper identifies a new family of marine bacteriophages with double-stranded RNA genomes, named Paraxenoviridae, based on genomic and structural analyses.

A prophage-encoded anti-phage defense system that prevents phage DNA packaging by targeting the terminase complex

The paper identifies a prophage-encoded anti-phage defense system in Listeria monocytogenes that prevents phage DNA packaging by targeting the terminase complex, without halting the lytic cycle.

Strain-level and phenotypic stability contrasts with plasmid and phage variability in water kefir communities

This study examines microbial community stability and variability in water kefir, finding species-level stability but plasmid and phage diversity across generations and households.

Mammalian Uteri Contain a Diverse Virome: Insights from Healthy Mares

This study identifies a diverse virome in the equine uterus, revealing novel viral species and antibiotic resistance genes, and highlights potential applications for phage therapy.

Insights into Diversity, Host-Range, and Temporal Stability of Bacteroides and Phocaeicola Prophages

This study characterizes prophages in Bacteroides and Phocaeicola using bioinformatic tools, revealing their diversity, broad host range, and temporal stability in the human gut.

Reduced prevalence of phage defense systems in Pseudomonas aeruginosa strains from Cystic Fibrosis Patients

This study compares phage defense systems in Pseudomonas aeruginosa strains from cystic fibrosis and non-cystic fibrosis patients, finding fewer defenses in CF strains.

Metagenomics reveals potential interactions between CPR bacteria and their phages in groundwater ecosystems

This study identifies phage-CPR interactions in groundwater ecosystems, revealing lysogenic infection strategies and auxiliary metabolic genes that enhance CPR bacteria's metabolic potential and symbiotic lifestyle.

taxmyPHAGE: Automated taxonomy of dsDNA phage genomes at the genus and species

TaxmyPHAGE automates the classification of dsDNA phage genomes into genera and species using MASH and BLASTn, enabling rapid and accurate taxonomic assignment at scale.

A phage nucleus-associated protein from the jumbophage Churi inhibits bacterial growth through protein translation interference

The paper identifies gp335, a phage protein from Churi, which inhibits Pseudomonas aeruginosa growth by interfering with protein translation through ribosome association.

When Not to Kill Your Host in Competitive Bust-Boom Environments

This study investigates how temperate phages balance lysogeny and lytic cycles in competitive environments, finding that stable lysogens outcompete others and that dispersal between fluctuating sub-systems reduces their survival against virulent phages.

Phage interactions may contribute to the population structure and dynamics of hydrothermal vent microbial symbionts

The paper examines phage interactions with chemosynthetic symbionts of hydrothermal vent snails and mussels, finding species-specific phages influence strain-level diversity and population dynamics.

Complete Genome Sequence of Six Pseudomonas aeruginosa Bacteriophages aim for research and treatments

The paper isolates and characterizes six Pseudomonas aeruginosa bacteriophages, finding they have distinct genomic clusters and morphologies, with some showing lytic activity suitable for phage therapy.

PharaCon: A new framework for identifying bacteriophages via conditional representation learning

PharaCon uses a conditional BERT framework to improve phage identification in metagenomic data by incorporating label constraints during pre-training.

Metagenomic mining reveals novel viral histones in dsDNA viruses

This study identifies over 1,500 viral histones and histone-fold proteins in dsDNA viruses, revealing their structural and functional diversity beyond nucleocytoplasmic large DNA viruses.

Molecular basis of foreign DNA recognition by BREX anti-phage immunity system

This study elucidates the molecular mechanism of BREX anti-phage immunity by showing how BrxX methyltransferase recognizes DNA and forms an immune complex to protect against phage infection.

Genomic and structural insights into Jyvaskylavirus, the first giant virus isolated from Finland

The paper isolates and characterizes Jyvaskylavirus, a new giant virus from Finland, revealing its structural features and genomic similarities to other marseilleviruses.

Base-modified nucleotides mediate immune signaling in bacteria

The paper identifies a bacterial anti-phage system that uses nucleobase modification to generate immune messengers, leading to population-level defense through infected cell death.

Deciphering the dynamics of Cyanobacteria-Phage in a natural lake: Insights from a decade-long investigation

This study investigates phage-cyanobacteria interactions in Lake Champlain over a decade, finding that phages share environmental niches with bacteria but exhibit distinct dynamics and co-variation patterns.

Comparative analysis of novel Pseudobdellovibrionaceae genera and species yields insights into the genomics and evolution of bacterial predation mode

The paper characterizes new Pseudobdellovibrionaceae strains, revealing genomic features and evolutionary insights into bacterial predation modes.

Phages carry orphan antitoxin-like enzymes to neutralize the DarTG1 toxin-antitoxin defense system

The paper identifies an orphan antitoxin-like enzyme in phages that neutralizes the bacterial DarTG1 toxin-antitoxin defense system by removing ADP-ribose modifications from phage DNA.

Prophages are Infrequently Associated With Antibiotic Resistance in Pseudomonas aeruginosa Clinical Isolates

This study analyzes 186 Pseudomonas aeruginosa clinical isolates to assess the association between prophage presence and antibiotic resistance, finding few significant links.

PhageDPO: Phage Depolymerase Finder

PhageDPO is a machine learning tool that predicts depolymerases in bacteriophage genomes to aid in discovering novel antibacterial agents.

Synthetic community Hi-C benchmarking provides a baseline for virus-host inferences

The paper benchmarks Hi-C for virus-host linkage detection using synthetic communities and applies optimized protocols to soil samples, revealing new interactions and establishing performance metrics.

Lysogen formation governs colonies while lytic infection is more prevalent in single cells of the bloom-forming cyanobacterium, Microcystis

This study examines how colony formation in Microcystis affects viral infection strategies, finding that colonies favor lysogeny while single cells experience more lytic infection.

Functional and evolutionary characterization of potential auxiliary metabolic genes (AMGs) of the global RNA virome

This study identifies and characterizes 274 auxiliary metabolic genes (AMGs) encoded by RNA viruses from global virome datasets, revealing their functional diversity and potential horizontal gene transfer from non-host organisms.

A novel virus vB_PshM_Y4 with low similarity to both cultured and uncultured viruses

This study isolates and characterizes a novel virus, vB_PshM_Y4, showing it is not detectable by high-throughput sequencing and belongs to an unknown viral family.

VirMake: a flexible and user-friendly pipeline for viral taxonomic and functional characterisation from shotgun metagenomic sequencing data

VirMake processes shotgun metagenomic data to identify and characterize viral taxa and functions, showing variability in viral genome richness and taxonomy across environments and protocols.

Whole-body Bacteriophage Distribution Characterized by a Physiologically based Pharmacokinetic Model

This paper develops a physiologically based pharmacokinetic model to characterize the whole-body distribution of bacteriophages in mice, finding rapid elimination and the need for multi-dose regimens.