Conjugative plasmids are a class of mobile genetic elements capable of efficient transfer between bacterial cells. Although they can introduce beneficial traits such as antibiotic resistance to recipi...

O-antigen loss in E. coli is not benign—wbbL mutations are associated with increased septic shock and higher mortality.

Phage therapy often fails when bacteria evolve resistance. We argue that phage selection should begin with receptors whose modification imposes predictable costs, turning resistance into reduced virul...

Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih

Genome-wide selective sweeps commonly occur in the human gut microbiome and can spread across the world within decades to produce epidemic-like population structures.

If "engineer bacteria to fight diseases" is your kind of fun, come build it with us. 4 Master's internships open at Eligo for Fall 2026 to work on real drug projects: engineered phage-particles to del...

Phages are important drivers of bacterial evolution with therapeutic potential as antimicrobials. However, gaps in our understanding of phages and our inability to rapidly engineer them with new genetic cargo hinders progress towards phage-based therapies. To address the lack of unbiased, genome-wide mutational tools for phages, we developed transposon mutagenesis employing CRISPR-anti-CRISPR (Acr)-based selection and deep-sequencing (Phage Tn-seq). Transposon mutagenesis was effective for phages with unmodified or hypermodified genomes and a jumbo phage that protects its DNA within a nucleus. Phage Tn-seq enabled phage gene essentiality assignment consistent with structural proteomics and core gene conservation. Insertion biases allowed prediction of transcriptional direction and early injected phage DNA regions. We exploited the method to rapidly deliver new cargo to phage genomes in just a few days and used an AI-designed Acr to expand the phage transposon toolbox. Phage Tn-seq is a versatile tool to advance our understanding and applications of phages. ### Competing Interest Statement The authors have declared no competing interest. Royal Society Te Apārangi, https://ror.org/04tajb587 Alexander von Humboldt Foundation, https://ror.org/012kf4317 The L’Oréal Groupe Australia University of Otago, https://ror.org/01jmxt844

Postdoctoral Position in Computational Phage Biology Microbial Genomics Group, Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków PL Summary We are seeking a postdoctoral rese...

Abstract. Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents.

Here, the authors exploit the genetic information encoded in Klebsiella prophages to model the interplay between bacteria, prophages, and their depolymerases, using a directed acyclic graph-model and a sequence clustering-based model.

We introduce a novel computational pipeline called MANIAC, designed to accurately assess average nucleotide identity (ANI) and alignment fraction (AF) between diverse viral genomes, scalable to data s...

YouTube video by Uniwersytet Jagielloński

RapidNJ is a really nice program for making neighbour-joining trees from distance matrices or alignment data. If you try and compile on an M1 Mac however, you’ll get errors that look like this: In fil...

AlphaFind is a web-based search engine that provides fast structure-based retrieval in the entire se

Proteins are composed of distinct functional domains, each serving a specific role. Here, Smug et al. show that phages are able to shuffle fragments of their proteins and this predominantly occurs in ...