Bacteriophages and microbial interactions

The paper constructs virtual viruses within a spatial minimal cell to model viral development and host interactions.

This paper introduces ESMCapsid, a protein language model that detects viral capsids and infers their architecture from sequences, revealing hidden structural patterns in metagenomic data.

The paper isolates and characterizes four novel Vibrio coralliilyticus phages, proposing two new genera based on genomic and morphological analyses.

This study identifies host factors critical for ssRNA and ssDNA phage infection in E. coli, revealing conserved dependencies and lineage-specific requirements.

This study identifies and characterizes bacteriophages in Ottawa's municipal wastewater that can infect clinically relevant E. coli and K. pneumoniae strains, showing high similarity to European phages but with genetic divergence.

The paper shows that removing genetic barriers from Pseudomonas aeruginosa hosts increases the diversity of recoverable phages, leading to the isolation of 69 new phages from clinical isolates.

The paper quantifies antiviral defenses in marine prokaryoplankton using single-amplified genomes to show taxon-specific defense repertoires and lateral transfer of defense systems.

DepoCat is a database of experimentally verified phage depolymerases that enables sequence and structure-based classification and specificity prediction.

This study identifies eight cytotoxic genes in a Pseudomonas putida phage through genome-wide overexpression, revealing metabolic remodeling and conserved proteins across diverse phages.

This paper identifies gp48, a mycobacteriophage protein that inhibits the host enzyme Mpg, essential for cell wall biosynthesis, by disrupting its dimer formation.

The paper investigates how different chemical stressors induce prophage replication in Acinetobacter baumannii strains, revealing differential induction patterns across host backgrounds.

The paper identifies an antibacterial peptide from a phage that inhibits E. coli growth by disrupting Mre-dependent peptidoglycan synthesis.

The paper uses CRISPR spacer analysis to identify 790 myxophages across 3,229 myxobacterial genomes, revealing six new viral lineages and their functional roles in host interactions.

This study shows that multispecies biofilm structure and matrix composition influence phage susceptibility, with V. anguillarum protecting E. coli and K. cryocrescens from lytic phages.

This study uses cryo-EM and tomography to reveal the structural changes in bacteriophage P2 during tail contraction and host infection, identifying new architectural features and mechanisms of genome translocation.

The paper identifies a new viral order, Skiavirales, in marine protists through long-read sequencing and shows gene exchange between viruses and host genomes.

This study shows H-NS silences bacterial antiviral immunity by compacting chromatin, and its deletion enhances phage defense in E. coli.

This study characterizes a bacteriophage and its endolysin against antibiotic-resistant uropathogenic E. coli, showing lytic activity and potential as antimicrobial tools.

The study identifies surface glycan layers as primary or optional recognition substrates for phage infection in E. coli O157:H7, revealing their role in receptor access and infection outcomes.

The paper identifies capsular polysaccharides as a mechanism that stabilizes prophage-bacterium symbiosis by preventing collateral viral attack and enhancing transmission.

The paper determines the in vivo structures of P22 infection intermediates and explains how gp10 templates the sequential assembly of three proteins into a trans-envelope channel for genome translocation.

The paper examines GI activity in a microbial consortium under stress, finding increased excision and expression compared to monocultures, and highlights the importance of community context in GI dynamics.

This study develops GVHoP, a machine learning tool that predicts eukaryotic hosts for giant viruses using genomic data, achieving high accuracy and revealing novel host associations across environments.

The paper identifies a conserved NADase domain, NIR, in bacterial immunity and eukaryotic proteins like human TEP1, linking bacterial defense mechanisms to eukaryotic functions.

The paper identifies novel enzybiotic candidates targeting human bacterial pathogens by analyzing viral-host associations in a large viral genome database.

The paper identifies a novel phage resistance mechanism in Pseudomonas putida through experimental evolution, revealing a secreted protein Psh that confers broad-spectrum phage resistance without fitness costs.

PhageTAILor uses LightGBM on 74 detector features to flag prophages and bacterial phage tail-like elements (tailocins, T6SS, eCIS), recovering 12 of 13 validated tailocins under leave-one-genus-out.

The paper reports crystal structures of LlaI components, revealing nucleotide specificity evolution and DNA binding mechanisms in McrBC restriction complexes.

The paper determines the cryo-EM structure of Jabs, a bacteriophage infecting Mycobacterium abscessus, revealing unique capsid assembly and adhesion features.