Bacteriophages and microbial interactions

Phylogenetic proximity drives temporal succession of marine giant viruses in a five-year metagenomic time-series

The paper analyzes a five-year metagenomic time-series to study temporal dynamics of marine giant viruses, finding that phylogenetic proximity influences their seasonal abundance and ecological interactions.

Phages indirectly maintain plant pathogen defense through regulation of the commensal microbiome

The paper shows that phages enhance plant resistance to pathogens by modulating the microbiome, with allopatric phages providing stronger protection than sympatric ones.

Diversity and evolution of the human anellome

This study expands the known diversity of human anelloviruses by analyzing 829 genomes from microbiome datasets and identifies new clades and recombination patterns.

Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria

The paper uses single-cell genomics to analyze virus-host interactions in freshwater bacteria, revealing differences in infection rates and defense strategies between copiotrophs and oligotrophs.

The bully phage: A Shiga toxin-encoding prophage interferes with the induction of co-hosted prophages

The paper shows that an Stx prophage inhibits the induction of co-hosted prophages in Citrobacter rodentium, revealing a novel competition strategy among prophages.

Unexpected diversity and ecological significance of uncultivable large virus-like particles in aquatic environments

The paper uses flow cytometry and electron microscopy to discover new viral morphotypes and their abundance in aquatic environments, highlighting their ecological role.

AlphaFold 3 proteomic modelling reveals multiple photosystem structural homologs in freshwater cyanophages

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

Single nucleotide switches confer bacteriophage resistance to Pseudomonas protegens

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

Temperature-driven biogeography of marine giant viruses infecting the picoeukaryote Micromonas

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.

A widespread family of viral sponge proteins reveals specific inhibition of nucleotide signals in anti-phage defense

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

Spatial heterogeneity influences phage-host co-existence dynamics and phage resistance development in Vibrio anguillarum

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

NeoPhAR: Next-generation Phage Therapy for Antimicrobial Resistance

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

ProkBERT PhaStyle: Accurate Phage Lifestyle Prediction with Pretrained Genomic Language Models

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

Sphae: An automated toolkit for predicting phage therapy candidates from sequencing data

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

BEREN: A bioinformatic tool for recovering Giant viruses, Polinton-like Viruses, and Virophages in metagenomic data

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: Improving phage-host interaction prediction at low sequence similarity settings using structure-aware protein embeddings

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.

About bacteriophage tail terminator and tail completion proteins: structure of the proximal extremity of siphophage T5 tail

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.

Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity

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

Predominance of viral core functions over auxiliary metabolism among carbohydrate-active enzymes annotated in the global soil virosphere

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

Bacteriophage Treatment against Carbapenem-resistant Klebsiella pneumoniae (KPC) in a Neutropenic Murine Model of Gastrointestinal Translocation and Renal Infection

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

Temperate phage-antibiotic synergy is widespread, but varies by phage, host, and antibiotic pairing

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.

Microscopic Phage Adsorption Assay: High-throughput quantification of virus particle attachment to host bacterial cells

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.

In-vitro resensitization of multidrug resistant clinical isolates of Enterococcus faecium and faecalis through phage-antibiotic synergy

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

HieVi: Protein Large Language Model for proteome-based phage clustering

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

Structure of the Staphylococcus aureus bacteriophage 80a neck shows the interactions between DNA, tail completion protein and tape measure protein

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

An efficient method for visualizing the plaques of Bdellovibrio bacteriovorus

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

A genomic resource for exploring bacterial-viral dynamics in seagrass ecosystems

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

Exploring the diversity of anti-defense systems across prokaryotes, phages, and mobile genetic elements

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.

Genome-wide screen overexpressing mycobacteriophage Amelie genes identifies multiple inhibitors of mycobacterial growth

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

Navigated range expansion promotes migratory culling

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.