Bacteriophages and microbial interactions

The paper shows that dairy practices have selected for thermostable endolysins in phages infecting Streptococcus thermophilus, reducing endolysin diversity.

The paper investigates viral horizontal gene transfer (vHGT) among nucleocytoviruses and finds it accounts for 28% to 42% of gene gain events in each viral order.

The paper identifies prophages in Burkholderia spp. genomes that show lytic activity against conspecific and heterospecific isolates, suggesting their potential for phage therapy.

The paper models and experiments on how bacterial interactions influence bacteriophage diet breadth, finding that competition favors generalists while mutualism favors specialists.

This study identifies host susceptibility and resistance factors for Salmonella enterica infected by bacteriophages SPLA1a and SPLA5b, showing that their combination reduces phage resistance emergence.

The paper benchmarks 63 viral identification rulesets on mock metagenomes and aquatic samples, finding that combining rules increases recall but also false positives, with some combinations achieving high accuracy.

This study evaluates the ability of predatory bacteria to limit intraocular growth of resistant Gram-negative bacteria in a rabbit model, finding that active predation, not antimicrobial effects, is responsible for inhibiting Pseudomonas aeruginosa.

The paper shows multicellular bacteria use DGRs to diversify antigen sensors, enhancing adaptive immunity and supporting the evolution of multicellularity.

The paper identifies extensive RNA virus diversity in Australian soils and sediments, revealing novel viral clades and highlighting environmental factors influencing viral abundance and diversity.

The paper evaluates virus-host prediction tools on a dataset of 1,046 pairs and applies the best-performing tools to a metagenomic dataset from the Cuatro Cienegas Basin, finding that alignment-free and alignment-based methods agree best when analyzing diverse viral communities.

The paper identifies a hybrid receptor binding protein in phage F341 that enables infection of Campylobacter by binding to flagella and lipooligosaccharides, revealing potential for phage resistance mechanisms.

This paper develops a synthetic biology method to construct and reboot clinically-relevant Pseudomonas aeruginosa phages, demonstrating successful cloning, assembly, and rebooting in different bacterial strains.

The paper identifies an ultraconserved bacteriophage genome in 1300-year-old human faeces, showing 97.7% identity to its modern counterpart and reconstructs 297 other ancient phage genomes.

The paper develops a stochastic model to evaluate CRISPR-Cas plasmid-based anti-phage protection, showing it is robust except under specific parameter conditions where segregation loss enables phage outbreaks.

The paper identifies PICMI, a new family of phage satellites in marine bacteria, showing they spread via virulent phages and confer host protection.

The paper identifies 59 gene families co-evolving with GTA genes in alphaproteobacteria, suggesting they are involved in stress response, DNA repair, and biofilm formation, supporting a model for GTA persistence in microbial populations.

This paper analyzes the genetic contexts of HicA toxin domains in prokaryotes, revealing their diversity and potential roles in anti-phage defense through bioinformatics and structural modeling.

This study identifies SieA as the key P22 phage protein that blocks DNA injection by P22-like phages and shows that mutations in ejection proteins can overcome this block.

The paper identifies two new groups of RNA viruses associated with thermoacidophilic bacteria in acidic hot springs and other environments.

The paper isolates and characterizes 28 unique bacteriophages against ESBL/AmpC E. coli, showing they can form broad host range cocktails effective in inhibiting bacterial growth in vitro.

The paper assesses how genome topology and viral selection affect biological interpretation in the human gut virome, highlighting the need for standardized reporting of circular-to-linear genome ratios and dereplication thresholds.

The paper investigates viral communities in proglacial streams, finding high host specificity and shared auxiliary metabolic genes among phages infecting microdiverse bacterial clades.

The paper identifies and characterizes two RNA polymerases in a thermophilic virus, showing their structural and functional differences and evolutionary origin.

This study uses a new single-virus sequencing platform to identify diverse viral genomes in river water, revealing novel species and gene transfer patterns.

The paper identifies viral chronotypes from time-series metagenomic data, revealing seasonal patterns and environmental influences on viral dynamics.

The paper analyzes viral diversity in seamount sediments, identifying 78,069 vOTUs and 16 vAMGs, suggesting ecological roles in biogeochemical cycles.

IPEV identifies and classifies prokaryotic and eukaryotic virus-derived sequences in viromes using deep learning, achieving higher precision and efficiency than existing methods.

The paper introduces a method to recover high-quality viral genomes from coral samples, builds a global virome database, and identifies key phage functions in coral holobiont interactions.

The paper identifies widespread polintovirus integrations in stony coral genomes, revealing their role in shaping lineage-specific genome dynamics and potential impacts on coral health.

The paper investigates how Enterococcus faecalis protease GelE affects phage infection, finding that its reduction increases phage susceptibility and alters biofilm formation.