Bacteriophages and microbial interactions

The paper uses AlphaFold 3 and DALI to predict structures and functions of viral genes in cyanophages, identifying 28 new structural homologs including cyanobacteriochrome.

The paper identifies single nucleotide mutations in surface-modifying enzymes that confer phage resistance in Pseudomonas protegens without compromising bacterial fitness.

This study investigates how temperature influences the biogeography of marine giant viruses infecting Micromonas, using modeling and observational data to show temperature drives viral distribution and population dynamics.

The paper identifies Acb4, a viral protein that inhibits bacterial anti-phage defense by sequestering nucleotide signals.

This study shows that spatial structure in bacterial populations affects phage-host coexistence and resistance development in Vibrio anguillarum.

NeoPhAR presents a deep learning model to predict phages for therapeutic use, aiming to simplify and democratize phage therapy for AMR infections.

ProkBERT PhaStyle uses genomic language models to predict phage lifestyles, outperforming existing methods in accuracy and speed.

Sphae is a bioinformatics pipeline that rapidly assesses phage therapeutic potential by analyzing genomic markers for safety and efficacy in under ten minutes.

BEREN is a bioinformatic tool that recovers genomes of giant viruses and related viral groups from metagenomic data, showing improved performance over existing tools.

PHIStruct improves phage-host interaction prediction by using structure-aware embeddings, achieving better precision and recall than sequence-only methods, especially at low sequence similarity.

The paper determines the structure of siphophage T5 tail terminator protein TrP142 and tail completion protein TCPp143 using cryo-EM and Alphafold2, revealing their localization and structural features.

This study analyzes giant virus dynamics using metagenomic data, revealing year-round recovery and distinct population dynamics linked to microdiversity and niche breadth.

The paper analyzes viral metabolic functions in soil viromes, finding that most carbohydrate-active enzymes are related to viral lysis rather than auxiliary metabolism.

This study identifies NAD-jumbo phages, which synthesize and utilize NAD+ for their life cycle, and finds they are widespread in various ecosystems.

This study evaluates the efficacy of bacteriophages and their combination with antibiotics in treating KPC infections in a neutropenic mouse model.

This study shows that temperate phages can synergize with antibiotics to reduce bacterial load in Pseudomonas aeruginosa, but this synergy depends on specific phage-antibiotic and phage-host pairings.

This paper introduces a high-throughput method to quantify phage attachment to bacterial cells using fluorescence microscopy and particle tracking, revealing single-virus dynamics and enabling rapid screening.

This study investigates synergistic interactions between phages and antibiotics in Enterococcus isolates, finding that phage-antibiotic combinations can eradicate vancomycin-resistant strains.

HieVi uses a protein language model to cluster bacteriophages into a hierarchical taxonomy, aligning with ICTV classifications and capturing evolutionary relationships.

The paper determines the high-resolution structure of the neck of SaPI1 virions, revealing interactions between DNA, tail completion protein, and tape measure protein.

This paper introduces a method using fluorescent prey to visualize Bdellovibrio bacteriovorus plaques faster, reducing incubation time from 3 days to 1.5 days.

The paper generates genomic resources for bacterial and viral communities in seagrass ecosystems, revealing potential roles for viruses in carbon cycling.

The paper develops AntiDefenseFinder to detect anti-defense systems in prokaryotes, phages, and MGEs, identifying 47,981 systems and revealing their distribution and evolutionary dynamics.

This study overexpresses 76 genes from mycobacteriophage Amelie and identifies 26 genes that inhibit Mycobacterium smegmatis growth, including eight previously unknown cytotoxic gene families.

The paper shows that increased bacterial motility during range expansion reduces phage spread by spatially sorting infected and uninfected cells, leading to migratory culling of viruses.

The paper identifies three defence islands in Serratia spp. with mixed cargo of anti-phage systems, virulence factors, and anti-bacterial modules, revealing a widespread trend of co-accumulation.

The paper isolates and characterizes bacteriophages targeting carbapenem-resistant Klebsiella pneumoniae, showing ST-specific activity and potential for phage therapy.

The paper characterizes viral communities in four cave pools, finding higher viral abundance than prokaryotes, novel viral sequences, and distinct viral communities in developed vs. undeveloped areas.

This paper develops broad-spectrum bacteriophage therapy cocktails effective against multiple bacterial strains and infections.

TSPDB is a curated database of tailspike proteins from phages, providing 8,099 unique sequences for genomics and metagenomics analysis, with applications in phage research and antimicrobial development.