Rafal Mostowy
@rafalmostowy.bsky.social
Group leader at Jagiellonian University in Krakow, cofounder of Polonium Foundation. Working on evolution of sex in bugs.
PhD opening in my lab @jagiellonskiuni.bsky.social: using AI to predict how phage enzymes break down bacterial capsules — joint work with ML group GMUM and Zuzanna Drulis-Kawa's phage lab (Wrocław), spanning genomics, AI & evolution. mostowylab.com/job-phd-ai-d... Deadline: 15 August 2026
Klebsiella phages often modify the bacterial capsule instead of degrading it, stripping acetyl groups. Nobody's traced how this evolves. I'm hiring a computational postdoc to find out — Kraków, apply by 21 July. mostowylab.com/job-postdoc-...
#microsky New preprint from the lab! Widespread immune systems protect bacteria against conjugative plasmids www.biorxiv.org/content/10.6... Kudos to the extremely talented lead author Ludovic Poiré! Key contributions by @francoisrousset.bsky.social and also help from C. Lesterlin/TacC lab. 🧵⬇️
Widespread immune systems protect bacteria against conjugative plasmids
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...
biorxiv.org
Loss of O-antigen due to wbbL mutations is common and associated with increased mortality in Escherichia coli bloodstream infections | Science Advances www.science.org/doi/10.1126/...
Loss of O-antigen due to wbbL mutations is common and associated with increased mortality in Escherichia coli bloodstream infections
O-antigen loss in E. coli is not benign—wbbL mutations are associated with increased septic shock and higher mortality.
science.org
Phage therapy via receptor-constrained evolutionary traps: Trends in Microbiology www.cell.com/trends/micro... #phage #phagesky
Phage therapy via receptor-constrained evolutionary traps
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...
cell.com
Phage receptor-binding proteins are known for their LEGO-like modularity, but we still do not fully understand their evolutionary potential and how it shapes phage host range. Our new preprint examines this systematically in Klebsiella phages. 🔗 www.biorxiv.org/content/10.6... Thread 🧵
Mushuvirus is the most widespread phage genus in the human gut. 🌍 Together with other family members, these viruses occur in 89% of humans worldwide, including the Iceman Ötzi! How is it possible that they were hidden in previous metagenomic analyses? [1/7] Read: doi.org/10.64898/202...
Thrilled to share a major milestone from our long-running collaboration with Zuzanna Drulis-Kawa's lab in Wrocław — DepoCatalog, is now out in @natcomms.nature.com: 129 Klebsiella phage depolymerases, 75 capsule types, 5-class structural framework and public database. www.nature.com/articles/s41...
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih
academic.oup.com
Very excited to share our new paper out in Nature. Congrats to Xiaoqian (Annie) Yu and all the coauthors. www.nature.com/articles/s41...
Genome-wide sweeps create ecological units in the human gut microbiome - Nature
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.
nature.com
Master Internships open at Eligo: www.linkedin.com/posts/duport...
#internship #syntheticbiology #genetherapy #microbiometherapeutics #biotechcareers | Xavier Duportet
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...
linkedin.com
Polish phage science meets Polish visual storytelling 🇵🇱🦠 To celebrate our last paper, we collaborated with an artist who previously worked on The Witcher 3 — to create a comic about phages and why understanding them matters in the fight against antibiotic-resistant bacteria. Comic below 👇
Rafal Mostowy@rafalmostowy.bsky.social · 3mo ago🎉 New in @plosbiology.org: Temperate phages of Klebsiella pneumoniae show capsule-driven host tropism — but how? The working assumption was depolymerases: enzymes that chew through the bacterial sugar capsule. Turns out that's not the whole story. 🧵 journals.plos.org/plosbiology/...
J. Craig Venter, Scientist Who Decoded the Human Genome, Dies at 79 A risk-taking outsider, he brought speed, competition and controversy to one of science’s biggest races. #GiftLink Nicholas Wade writes @NYtimes.com www.nytimes.com/2026/04/30/s...
J. Craig Venter, Scientist Who Decoded the Human Genome, Dies at 79
nytimes.com
🎉 New in @plosbiology.org: Temperate phages of Klebsiella pneumoniae show capsule-driven host tropism — but how? The working assumption was depolymerases: enzymes that chew through the bacterial sugar capsule. Turns out that's not the whole story. 🧵 journals.plos.org/plosbiology/...
Great fun presenting some of our research @otagomicroimmuno.bsky.social @universityofotago.bsky.social Including transposon mutagenesis of phages. www.biorxiv.org/content/10.6...
High-throughput transposon mutagenesis defines the essential genome of diverse phages
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
biorxiv.org
Asaf Levy@asaflevylab.bsky.social · 5mo agoArabinose isn't only an inducer! @peterfineran.bsky.social gave a talk in our Hebrew Univ. microbiology journal club and mentioned his recent amazing finding that some phages add up to 3 arabinoses (!!) to their DNA to evade bacterial defense. Mahler et al. CHM 2025 www.cell.com/cell-host-mi...
Horizontal gene transfer is often depicted as a process distributing pre-existing functions to novel genetic backgrounds. Yet HGT can also increase the rate of functional innovation after transfer. Here's a brief review on the topic: ecoevorxiv.org/repository/v... #evosky #microsky
From Trading Genes to Crafting New Tricks: How Horizontal Gene Transfer Potentiates the Emergence of Novel Functions
ecoevorxiv.org
With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268
📢 Hiring a Postdoc in Computational Phage Biology (Kraków, Poland) We study the evolution & structural modularity of prophage-encoded glycan-degrading enzymes in Klebsiella pneumoniae — combining genomics and AlphaFold-based analyses. Details in attached PDF 👇
Postdoc Ad
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...
docs.google.com
Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...
Protein structure-informed bacteriophage genome annotation with Phold
Abstract. Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents.
academic.oup.com
George Bouras@gbouras13.bsky.social · 12mo agoStoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...
Can we exploit past phage infection events (prophages) to decipher the specificity of phage receptor-binding proteins such as depolymerases?🔎 Happy to share our recent work at @natcomms.nature.com 🔽 #microsky #phagesky www.nature.com/articles/s41...
Unlocking data in Klebsiella lysogens to predict capsular type-specificity of phage depolymerases - Nature Communications
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.
nature.com
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n
🌟 Exciting news! We’re launching three fully-funded postdoc positions for "New Horizons for Synthetic Phages” Join us in tackling antimicrobial resistance with cutting-edge synthetic biology + AI bioinformatics. Based at Flinders Uni in vibrant Adelaide. 👇 Read on for details! #Phage
What determines who a phage can infect? We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort. 👇 A thread!
I'm looking for a postdoc in computational evolutionary phage genomics, with the goal to better understand how protein innovation arises in viruses, at @jagiellonskiuni.bsky.social in Krakow (Poland). Drop me a line if it sounds cool! Deadline: 20.06. Link here: mcb.uj.edu.pl/documents/15...
We're looking for a PhD student to join us at Vilnius University in Lithuania. We work on RNA virus evolution computationally but we'd like to generate more mosquito RNA virus sequence data. Official ad: www.gmc.vu.lt/en/doctoral-.... Please share & continue reading if interested.
🚀 Follow-up on my recent MANIAC tweet: our new MMseqs2-blased tool is optimised for ANI and alignment fraction (AF) calculation in viral genomes. Unlike many other tools, it excels at ANI ~70%, an important range for viral taxonomy & evolution. Here’s why that matters ➡️ a thread! 🧵
It was a pleasure working with you and Wanangwa on this project and I'm happy to see it published. Congratulations all!
And now with the working link! journals.asm.org/doi/10.1128/...
Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism | mSystems
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...
journals.asm.org
Rafal Mostowy@rafalmostowy.bsky.social · 2y agoOur new paper out in mSystems! journals.asm.org/eprint/ISRAZ... We created a tool called MANIAC to estimate ANI between virus pairs. We found that: 1) MANIAC can reliably estimate ANI ~70%, 2) dsDNA phages exhibit ANI gap around 80%, 3) taxonomic assignment in temperate phages is tricky. Try it!
Our new paper out in mSystems! journals.asm.org/eprint/ISRAZ... We created a tool called MANIAC to estimate ANI between virus pairs. We found that: 1) MANIAC can reliably estimate ANI ~70%, 2) dsDNA phages exhibit ANI gap around 80%, 3) taxonomic assignment in temperate phages is tricky. Try it!
If bacteria can be "good", so can viruses! We made a short clip to explain to the public what phages are and why we should study them. The film also tells how our research on viral mosaicism could be socially and medically revelant. 🎥 Watch the film here: www.youtube.com/watch?v=wXnx...
Bacteriophages, or good viruses: hope in the age of antimicrobial resistance POB
YouTube video by Uniwersytet Jagielloński
youtube.com