Bacteriophages and microbial interactions

Genomic characterization and therapeutic potential of five broad-spectrum lytic bacteriophages against multidrug-resistant avian pathogenic Escherichia coli (APEC)

This study isolates and characterizes five bacteriophages effective against multidrug-resistant APEC, showing therapeutic potential in a Galleria mellonella model.

Viral genetic diversity and functional potential in polar and subarctic sea ice

The paper analyzes viral diversity and functional potential in polar and subarctic sea ice metagenomes, identifying common auxiliary metabolic genes and host interactions.

Data mining reveals the diversity of prophage endolysins targeting pathogenic enterococci

This study identifies 33 distinct domain architectures of prophage endolysins from enterococci, including a novel cell wall-binding domain, to expand the diversity of potential enzybiotics against multidrug-resistant infections.

Long-term exposure to polyamines leads to bacteriophage resistance in Pseudomonas aeruginosa

This study shows that long-term exposure to putrescine drives phage resistance in Pseudomonas aeruginosa through mutations in type IV pili genes, even without prior phage exposure.

Bacteriophage treatment of Pseudomonas aeruginosa PA14 infection does not alter the native microbiome of Caenorhabditis elegans

This study uses C. elegans to assess how bacteriophage treatment affects the gut microbiome during Pseudomonas aeruginosa infection, finding no significant changes in microbiome composition.

Gut Virome Diversity and Health Status in Rescued Pangolins: Metaviromics Reveals Parvovirus as a Key Virus Associated with Disease

This study characterizes the gut virome of pangolins across health states, finding a shift from phage-dominated to eukaryotic virus-dominated viromes in diseased individuals, with Parvoviridae and Iridoviridae as potential pathogens.

Genomic foundation model embeddings encode higher-order viral genome architecture beyond sequence composition: a benchmark of Evo 2

This paper benchmarks Evo 2's ability to encode viral genome architecture, finding it captures higher-order features beyond sequence composition.

How many phage species remain undiscovered? Species sampling approaches to inform phage discovery

The paper estimates how many new phage species can be discovered based on existing databases and identifies changes in species abundance over time.

Structural mechanism of the type IX Retron-Kva2 anti-phage defense system

This study reveals the structural mechanism of the type IX Retron-Kva2 anti-phage defense system in Klebsiella variicola, showing how it cleaves host RNAs to inhibit phage infection.

Viral lifecycle dynamics and spatial structure explain why accessorygenes are associated with temperate phages

The paper uses a mathematical model to show how phage lifecycle dynamics and spatial structure promote the association of accessory genes with prophages, explaining their evolutionary advantage over plasmids.

Hawaiian Geothermal Fumaroles Contain Diverse and Novel Viruses

This study identifies novel viruses from Hawaiian fumaroles using metagenomics, revealing new viral clades and ecological patterns.

Inferring single-cell heterogeneity of bacteriophage lysis-associated life-history traits from population-scale dynamics

The paper infers single-cell heterogeneity in bacteriophage lysis-associated traits from population-scale dynamics, showing that burst size variability is largely explained by latent period differences.

Diverse but temporally stable virome in a 1.2 km deep karst aquifer accessed via Moab Khotsong mine, South Africa

The paper investigates the virome of a deep karst aquifer, finding diverse, novel viruses with stable communities and lysogenic interactions over five years.

T4-type phages diversity in wetland soils reveals their ubiquity and their likely host-dependent dynamics

The paper examines T4-type phage and bacterial community dynamics in wetland soils, finding their diversity and host-dependent patterns influenced by moisture fluctuations.

A DNA-scaffolded Retron Ring Mediates Antiphage Immunity

This study defines the structure and mechanism of retron type IX, revealing how its DNA-scaffolded ring assembly mediates antiphage immunity through phage-encoded nuclease-triggered activation.

Isolation and characterization of novel filamentous phages from Swiss-type cheeses infecting the Gram-positive bacterium Propionibacterium freudenreichii

This study isolates and characterizes nine new filamentous phages from Swiss-type cheeses infecting Propionibacterium freudenreichii, revealing sequence divergence, host range diversity, and CRISPR spacer targeting.

PEONY: a global reference database of DNA viral (vOTU) sequences from viral size-fractionated metagenomes (viromes)

The paper updates a viral sequence database to include only virus size-fractionated metagenome-derived sequences and presents new data on its utility.

MTB-LysB1: A Novel Endolysin Against Multidrug-resistant Mycobacterium tuberculosis

This paper characterizes MTB-LysB1, a novel endolysin from a mycobacteriophage, showing activity against drug-susceptible and multidrug-resistant M. tuberculosis strains and additive effects with TB drugs.

Higher-order assembly of a type IX retron enables exploitation for designer antimicrobials

This paper determines the cryo-EM structure of retron-Kva2 and designs synthetic triggers to activate its antimicrobial activity.

Phage Endolysin Enables Targeted Manipulation of the Small Intestinal Microbiota and Uncovers Niche Overlap Between Oral and Butyrate-Producing Taxa

This study uses a phage endolysin to target Streptococcus salivarius in the gut, revealing niche overlap with butyrate-producing taxa and potential therapeutic benefits.

Identification and characterization of the antigonococcal prophage-encoded endolysin Phi1gp518

This study identifies and characterizes Phi1gp518, a prophage-encoded endolysin with broad antigonococcal activity and potential therapeutic applications against drug-resistant Neisseria gonorrhoeae.

Phage portal proteins counteract stringent-response-mediated restriction

This study identifies phage portal proteins as factors that counteract bacterial stringent response by inhibiting alarmone synthetases, revealing a conserved viral strategy to overcome host stress physiology.

Lytic bacteriophages against Salmonella Typhi as a potential alternative to antibiotics

This study identifies lytic bacteriophages effective against Salmonella Typhi, showing potential as alternatives to antibiotics in treating enteric fever.

A UG5 reverse transcriptase-nitrilase antiviral module confers phage immunity in the plant symbiont Sinorhizobium meliloti

The paper identifies a UG5 reverse transcriptase-nitrilase antiviral module in Sinorhizobium meliloti that provides immunity against phages.

OLD sentinel: an abortive tRNase surveys phage replication and DNA defects in RecBCD-compromised cells

This paper characterizes OLD, an abortive immunity protein, revealing its structure and activation mechanism in response to phage replication and DNA defects in RecBCD-compromised cells.

Long read and short read whole genome sequencing are equivalent for genomic characterisation of bacteriophage: considerations for high throughput analysis

This study compares long-read and short-read whole genome sequencing for bacteriophage characterization, finding both platforms produce high-quality genomes with comparable completeness.

Perturbations shift the composition of bacterial DNA carried by virus-like particles in the murine gut microbiome

The paper analyzes the murine gut transductome before and after perturbations to identify bacterial families and mobile genetic elements involved in horizontal gene transfer.

Bacteria sense virus-induced genome degradation via methylated mononucleotides

This study identifies a bacterial defense system, Metis, that detects virus-induced genome degradation through methylated mononucleotides, leading to inhibition of phage infection.

High throughput chromatographic ultra-purification of virus-like particles for downstream viromics

This paper introduces an anion exchange chromatography method for purifying virus-like particles (VLPs) that outperforms CsCl in throughput and reproducibility while maintaining similar purity levels.

Phage intervention improves colitis and response to corticosteroids by attenuating virulence of Crohn's disease-associated bacteria

Phage HER259 reduces colitis severity caused by AIEC NRG857c and enhances budesonide efficacy in mice.