Phage homing endonuclease amplifies anti-defense genes to evade bacterial immunity - Nature Communications Phages employ diverse counter-defense strategies to overcome bacterial immune systems. Here, the authors reveal that the phage homing nuclease SegB facilitates immune evasion by promoting the segmenta...

Happy to share our new work on how phages escape bacterial immunity.

We show that a phage homing endonuclease drives segmental amplification of anti-defense genes, pointing to a versatile and rapid mode of adaptation.

www.nature.com/articles/s41...

#PhageSky #MicroSky

Very proud of this work and all the efforts from my team and collaborators on this! You can now use DGRs for in vivo targeted hypermutagenesis in E. coli. We also included some early proof of concept in Yeast thanks to @seth-shipman.bsky.social !

I am so excited to share our new findings with you! We provide the structural evidence for a direct protein-to-DNA information pathway, showing how a bacterial enzyme 'reads' its own structure to 'write' DNA. www.science.org/doi/10.1126/...

A bacterial CARD–NLR-like immune system controls the release of gene transfer agents - Nature Microbiology An immunity-like system functions as a lysis control hub to promote gene transfer agent particle release from host bacterial cells, suggesting that bacterial immune systems may be co-opted to promote ...

Delighted to share our latest work on gene transfer agents (GTAs). We found a lysis control hub which allows GTAs to escape their bacterial host cells and transfer DNA 🧬 between bacteria. Thanks to @tunglejic.bsky.social, all co-authors, and our amazing collaborators!
www.nature.com/articles/s41...

Diversity-generating retroelements for programmable targeted hypermutagenesis - Nature Biotechnology Diversity-generating retroelements are engineered for directed evolution in E.coli.

Diversity-generating retroelements for programmable targeted hypermutagenesis | Nature Biotechnology https://www.nature.com/articles/s41587-026-03078-4

Very cool, congratulations Melanie!

Excited to share our new paper out today in @science.org 🎉

We show that HGT via natural competence drives diversification of chromosomal integrons in V. cholerae 🤩

Below a 🧵 on key findings incl. background on natural competence in V. cholerae 1/
#microsky #phagesky
www.science.org/doi/10.1126/...

PostDoc position available!
(links in post below)

Feel free to share!

‼️Please share‼️

Nemudryi lab is looking for postdocs to join our team and study:

🦠 Bacterial phage defense mechanisms

🧬 RNA repair & CRISPR-based RNA editing

Excited about RNA, host-virus interactions & mechanistic biology?

Let's talk!

Apply: explore.jobs.ufl.edu/en-us/job/53...

‘Treasure trove’ of antiviral proteins could inspire powerful molecular tools Two research teams mined genomic data from bacteria to create databases containing thousands of antiviral defence proteins that could inspire powerful biotechnologies.

Bacteria have been fighting off viruses using a huge arsenal of molecular weaponry that scientists did not know about — until now. Researchers have identified proteins that could lead to virus-fighting drugs and technologies.

go.nature.com/4dqQnXI

Congratulations Peter! Very exciting work and glad to see this out!

Excited to see our work out in Science today! Using machine learning to identify prokaryotic immune systems www.science.org/doi/10.1126/...

Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here

📣Huge preprint 🔔
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.

Very cool work Aude and team! Congratulations!!

How diverse is bacterial immunity ?

We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems.
👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie...

Explore them here defensefinder.mdmlab.fr/wiki/refseq_...

Phages communicate across species to shape microbial ecosystems Gallego-del-Sol et al. show that arbitrium-coding phages can sense non-cognate peptide signals from other phages to regulate lysis-lysogeny decisions. This crosstalk affects lysis-lysogeny outcomes of...

This paper started as an idea @albertomarina.bsky.social had many years ago… which of course means he was right all along 😄. Some of us just needed a few years (and a lot of experiments) to catch up.
Grateful (and slightly humbled) to be part of this. Thanks Alberto!
www.cell.com/cell/fulltex...

Open Positions -

Open postdoc position in my lab on HGT and interbacterial competition. We seek candidates with a PhD in microbiology (or related fields)+ strong 1st-author publications.
Curious, highly motivated, and dedicated team players ready to contribute fully are encouraged to apply. Details: tiny.cc/cz01101

Cryo-electron microscopy scientist Join our team to contribute to the operation and innovation of state-of-the-art cryo-electron microscopes and empower groundbreaking research.

The newly established NeCEN Utrecht is looking for a #cryoEM scientist!

www.uu.nl/en/organisat...

Work with a new Krios 5 + pFIB and support cutting-edge life science research.

📍 Utrecht | 🗓 Apply by 30 April

Please share with your network!

Bacterial 2′,3′-cGAMP activates a SAVED effector to form membrane-disrupting filaments and restrict phage replication Tak et al. discover that bacteria use 2′,3′-cGAMP, the same signaling molecule employed by mammalian cGAS-STING, for phage defense. In response to phage, 2′,3′-cGAMP activates filament formation of Ca...

Happy to share the final version of my postdoc work on bacterial CBASS immunity with @aaronwhiteley.bsky.social published in @cp-cellhostmicrobe.bsky.social

www.cell.com/cell-host-mi...

Excited to share the first preprint from the lab! We show that ApeA defends against RNA phage infection by cleaving the phage genome:

www.biorxiv.org/content/10.6...

Proper organelle regulation during mitosis is a must, but how do membrane-less condensates like PML bodies behave during cell division? In work led by Eric Aird, we found the balance of speckled proteins SP110 & SP100 to be the key. doi.org/10.1038/s415...

New preprint: Cyclic tri-adenylate signalling by a Panoptes anti-phage guard system with a CARF-TM effector. Great work led by Sabine Grüschow
www.biorxiv.org/content/10.6...

Bacterial Schlafen proteins mediate phage defence - Nature Microbiology This study highlights that Schlafens are ancient, mechanistically conserved immune effectors that mediate antiviral immunity in organisms ranging from humans to bacteria.

Bacterial Schlafen proteins mediate phage defence

(new work from @anemudraia.bsky.social and @artemnemudryi.bsky.social labs)

www.nature.com/articles/s41...

Schlafens are an ancient, mechanistically conserved family of tRNA-targeting immune effectors.

Conditional activation of Cas13 enforces lysogeny in a native type VI-A CRISPR host Nature Microbiology, Published online: 10 March 2026; doi:10.1038/s41564-026-02288-5RNA-targeting CRISPR in Listeria seeligeri restricts the lytic cycle of temperate phages but tolerates prophage acquisition while also preventing induction—a system that enables acquisition of beneficial prophages while mitigating the risks of lysis.

Out Now! Conditional activation of Cas13 enforces lysogeny in a native type VI-A CRISPR host #MicroSky

Bacterial Schlafen proteins mediate phage defence Nature Microbiology, Published online: 09 March 2026; doi:10.1038/s41564-026-02277-8This study highlights that Schlafens are ancient, mechanistically conserved immune effectors that mediate antiviral immunity in organisms ranging from humans to bacteria.

Out Now! Bacterial Schlafen proteins mediate phage defence #MicroSky

Excited to see this in print! Congratulations @artemnemudryi.bsky.social and @anemudraia.bsky.social!!

Congratulations Sam, very cool story!

CBASS is a cyclic nucleotide-based antiviral system in bacteria that is related to cGAS-STING signaling in animals. One of the big questions is how CBASS is activated during phage infection? We made some progress on this during my final year in the Kranzusch lab.
www.biorxiv.org/content/10.6...

Out today: We discovered new viral proteins that target immune signaling molecules, solely based on their AlphaFold-predicted shapes

www.science.org/doi/10.1126/...

Congrats Nitzan Tal and coauthors! Thank you Kranzusch lab for the fun collaboration!

Linking below previous thread on our findings

@nitzantal.bsky.social @romihadary.bsky.social @soreklab.bsky.social use structure prediction and in silico binding site analysis to discover viral immune evasion proteins! Exciting for our lab @reneechang.bsky.social @riveralopz.bsky.social to help with this project.
www.science.org/doi/10.1126/...