Bacteriophages and microbial interactions

Enhanced multi-omic viral profiling from microbial community sequencing with BAQLaVa

BAQLaVa improves viral profiling from metagenomes and metatranscriptomes, revealing reduced virome diversity in inflammatory bowel diseases and novel phage-host relationships.

Inactivating conditions of therapeutic mycobacteriophages

This study investigates the inactivating conditions of three mycobacteriophages used in compassionate-use NTM treatment to guide their development as therapeutics.

Efficient detection and typing of phage-plasmids

The paper introduces tyPPing, a method for detecting and typing phage-plasmids with high accuracy, outperforming existing tools in sensitivity and scalability.

Bacterial phylogeny explains variation in virulence but not phage efficacy in vivo

This study investigates how bacterial phylogeny influences virulence and phage efficacy in vivo, finding phylogenetic patterns in virulence but not in phage efficacy, and no correlation between in vitro and in vivo phage efficacy.

CRESSENT: a Bioinformatic Toolkit to Explore and Improve ssDNA Virus Annotation

CRESSENT is a bioinformatic toolkit for ssDNA virus annotation that addresses challenges in identification, classification, and decontamination of metagenomic datasets.

Molecular basis for anti-jumbo phage immunity by AVAST Type 5

This study identifies Avs5 systems as a conserved bacterial defense against jumbo phages, revealing their mechanism of recognizing and disrupting phage infection.

Arbitrium systems control lysis/lysogeny through the regulation of small antirepressor proteins

Structural basis of Retron-Eco8-mediated anti-phage defense

This study reveals the structural and functional mechanism of Retron-Eco8, a bacterial defense system that uses a holocomplex to cleave phage DNA and inhibit infection.

Combined Lytic Score as a new metric to quantify phage-host specificity, tested in a screening study on a collection of Salmonella strains.

The paper introduces the Combined Lytic Score (CLS) to quantify phage-host specificity and tests it on Salmonella strains, finding over 65% of strains show high susceptibility.

Chemical inhibition of a bacterial immune system

This study identifies chemical inhibitors that block a bacterial immune system, enhancing phage therapy efficacy against resistant strains.

A dramatic protein fold switch powers a bactericidal nanomachine

The paper describes a protein fold switch in a bactericidal nanomachine that enables membrane puncture and bactericidal activity.

Death & Chemotaxis: Bacterial chemotaxis enables collective escape from phage predation

The paper shows that bacterial chemotaxis allows Escherichia coli to form fronts that escape phage predation without resistance.

Extensive Hidden Prophage Diversity in Enterobacter Species Reveals Host Specificity and Local Distribution

This study identifies extensive prophage diversity in Enterobacter species, revealing host specificity, geographic structuring, and limited cross-species transmission.

Spatio-temporal variability of airborne viruses over sub-Antarctic South Georgia: Influence of sampling methodology and proximity of the ocean

The paper analyzes airborne viral communities in South Georgia using multiple sampling methods, finding that location and ocean proximity influence diversity and that some viruses show adaptations to harsh environments.

Large scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome

The paper uses nanopore sequencing to analyze capsid-packaged DNA in gut microbiomes, finding bacterial DNA encapsidation is widespread and associated with specific bacterial families.

Single-Cell Raman Profiling Enables Rapid Precision Phage Therapy Against Multidrug-Resistant Hypervirulent Klebsiella pneumoniae

This paper uses single-cell Raman spectroscopy and deep learning to rapidly and precisely select lytic phages against multidrug-resistant Klebsiella pneumoniae.

GuFi phages represent the most prevalent viral family-level clusters in the human gut microbiome

The paper identifies GuFi phages as prevalent gut viral families using long-read sequencing and shows their broad host ranges and underappreciated impact on the microbiome.

Deoxydinucleotides activate the bacterial anti-phage defense system ApeA

The paper shows that deoxydinucleotides activate the bacterial anti-phage defense system ApeA by binding to a conserved pocket, enabling broad protection against phage infection.

Phage-Mediated Iron Acquisition by Pseudomonas aeruginosa

This study identifies a novel mechanism by which Pseudomonas aeruginosa acquires iron through a partnership with filamentous phages, enhancing bacterial growth and pathogenesis.

Novel Bacillus altitudinis endolysin (ArtE2) targeting both Gram-positive and Gram-negative bacteria

This study identifies and characterizes endolysins from Bacillus spp., designs a chimeric endolysin ArtE2 with broad antibacterial activity, and validates its effectiveness against Gram-positive and Gram-negative bacteria.

Viral communities in Metania sp. sponge microbiomes with possible effects on CO2 fixation

The paper analyzes viral communities in Metania sp. sponges, identifying their diversity, host interactions, and functional roles, including carbonic anhydrase genes involved in CO2 fixation.

Revealing the pervasive landscape of MGE-host interactions in situ with single-cell genomics

The paper uses single-cell genomics to analyze MGE-host interactions in microbiomes, revealing widespread MGE presence and host range diversity across microbial lineages.

A type II Thoeris anti-phage defense enacts growth arrest independent of NAD depletion

This study characterizes a type II Thoeris system in E. coli that causes growth arrest without NAD+ depletion, revealing functional diversity within Thoeris types.

A {lambda} Phage Platform for Successful Therapeutic Display of Protein Antigens

This paper develops a lambda phage platform for displaying protein antigens and demonstrates its success in antigen selection and immunotherapy in a mouse model.

Limited effect of short- to mid-term storage conditions on an Australian farmland soil RNA virome

This study identifies 1,475 novel RNA viruses in Australian soils and demonstrates that snap-freezing is a viable storage method for at least three months.

Cross-cohort analysis reveals conserved gut virome signatures and phage-encoded auxiliary functions in ulcerative colitis

The paper analyzes the gut virome across cohorts to identify conserved signatures and functional roles of phages in ulcerative colitis.

Lipopolysaccharide truncation and restoration drives a trade-off in resistance to two phages in Pseudomonas aeruginosa

This study isolates a novel phage targeting the LPS inner core of Pseudomonas aeruginosa and shows that LPS modifications create a trade-off in resistance to two phages, suggesting that combining phages targeting different LPS regions can delay resistance.

The Lysis Cassette of Jumbophage phiKZ

The paper identifies a lysis cassette in phiKZ phage essential for temporally regulated host envelope disruption, including a novel cytoplasmic regulator interacting with the holin.

A methylome-derived m6-dAMP trigger assembles a PUA-Cal-HAD immune filament that depletes dNTPs to abort phage infection

The paper identifies a methylome-derived m6-dAMP trigger that forms an immune filament in E. coli to deplete dNTPs and abort phage infection.

Identifying phage proteins that activate the bacterial innate immune system

The paper identifies phage proteins that activate bacterial innate immune systems by screening a plasmid library in diverse E. coli strains and analyzing plasmid depletion.