Thrilled to share! We present the structure of a prototypical P2 OLD and reveal that its tRNAse activity is triggered by ssDNA hairpins in phage origins or unresolved termini in RecBCD-deficient cells. Great team effort with Wang, Bikard & Nudler labs. www.biorxiv.org/content/10.6...

Our paper out in Science today: The Metis defense system senses molecular byproducts released when a phage degrades the bacterial genome, and then prevents replication of the phage in the infected cell Congratulations @ostermanilya.bsky.social and co-authors!

Si les nouvelles règles de l'éligibilité de l'ANR sont bien réelles, alors je ne comprends pas quelle est la logique sous jacente. Au vu de la pyramide des ages, forcer une collaboration avec chercheurs(ses) <10 ans post thèse va de facto exclure 80% des candidats.

Les nouvelles règles d'éligibilité de l'AAPG 2027 de @agencerecherche.bsky.social sont une catastrophe. Comment se fait-il qu'il n'y ait pas plus de réactions dans la communauté ? Sommes-nous à ce point résignés, ou individualistes ? #ESR

Functional divergence and conservation in the QueC protein family (PF06508): from tRNA modification to anti-phage defense 🦠 portlandpress.com/biochemj/art...

Very cool findings!

Congratulations to Aude Bernheim (@audeber.bsky.social), elected EMBO Member 2026 🎉 Her work on bacterial immunity is reshaping how we understand immune systems across all life forms — from bacteria to humans. @embo.org

Organisers @lisamaierlab.bsky.social @kiranrpatil.bsky.social @robdfinn.bsky.social @embl.org @events.embl.org Speakers Ami Bhatt @dbikard.bsky.social Xiang Gao kc-huang.bsky.social @jhcepas.bsky.social @microbegrrl.bsky.social @keyfm.bsky.social @microbiome.bsky.social Elisabeth Lowe ...

1/4 Excited to share our new preprint on phage genome editing: Targeted DNA nicking enables efficient, single-step and counterselection-free editing of bacteriophage genomes Preprint: lnkd.in/dv4g5kW6

Finally published. Many thanks to a wonderful collaborative team and scientific platforms!!! And thanks to editors and reviewers for enthusiasm and a great review. www.nature.com/articles/s41...

Back to the age of emperors and gladiator shows to please the crowd!

Very happy that this piece of research finally sees the daylight! Super nice collaboration between Nanjing, York and Helsinki. Fun fact: we started this work over 10 years ago when I was working as a fellow at Imperial College. Sometimes good things come to those who wait.

AI + publish-or-perish -> huge increase in publications Publication volume becomes meaningless as a metric. Might academia adapt to produce fewer, better papers? substack.com/@journalolog... Or will output continue to increase and we just accept that the only readers are AI agents...? 1/2

How do human cells defend against viruses? @sgfern.bsky.social discovers that human immune proteins named ISGs target ancient features of replication shared between animal and bacterial viruses – opening analysis of human immunity to the power of bacterial genetics www.biorxiv.org/content/10.6...

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 🧵

Our paper is out in Nature Microbiology: functional analysis of 80 phage sponges, revealing new sponges that inhibit bac immunity by binding the immune signals cCMP, cUMP and N7-cADPR Thanks to all coauthors and our collaborators at the Kranzusch Lab. Congrats Romi! www.nature.com/articles/s41...

Now at the mic: David BIKARD from @pasteur.fr / Eligo Bioscience. He's showing how engineered phage vectors and CRISPR can be used to selectively perturb gut bacteria. The future of AMR treatment? #CRISPR #Phage @dbikard.bsky.social @ibeidlabex.bsky.social

Phage-encoded single-guide RNAs subvert CRISPR-Cas9 immunity https://www.biorxiv.org/content/10.64898/2026.06.01.729453v1

A nice piece at @science.org covers the exploding field of bacterial immunity, and how it led to the understanding that components of the human immune system evolved from bacterial defenses against phage www.science.org/content/arti...

Like a prophage being awakened from its slumber, the phage field has seen a lot of renewed activity during the last decade. Check out our new @natrevmicro.nature.com review on the temperate phage life cycle here to stay up-to-date 🧫🦠 www.nature.com/articles/s41...

Happy to share our latest pre-print on the Druantia defense system. We find that Type III Druantia uses a cooperative helicase-nuclease mechanism to sense and degrade replication-associated forked DNA structures. www.biorxiv.org/content/10.6... A🧵

With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...

What if multireplicon plasmids are not an oddity, but an evolutionary strategy? We found that they are common, more mobile, broader-host-range, and enriched in AMR. Even more interesting: their assembly doesn’t look random. 👀 Paper preprint: www.biorxiv.org/content/10.6... Thread below!🧵👇

Master Internships open at Eligo: www.linkedin.com/posts/duport...

I’m thrilled to share an update to our work on bacterial NACHT domain containing proteins! In our last preprint, we reported that bNACHT11 is activated by multiple phage proteins. We’ve now expanded this work with structural insight and investigation of programmed cell death following activation.

This one means a lot. Our paper, “Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome,” is out! doi.org/10.1038/s414...

Bacterial immune proteins have repeatedly evolved to become parts of eukaryotic immunity. But how? Our new preprint uncovers a recent horizontal transfer event & shows how eukaryotes co-opted a toxic bacterial immune protein 🦠🧪🧵 1/

Interrogating the Escherichia coli epitranscriptome via CRISPR interference and Nanopore native RNA sequencing www.biorxiv.org/content/10.6...

Host exonuclease SbcB and a phage-encoded SSB-like protein control activation of the DRT10 reverse transcriptase defense system | bioRxiv https://www.biorxiv.org/content/10.64898/2026.04.29.721553v1?rss=1

Our lab is proud to present our latest work harnessing Bridge Recombinase for genome-scale editing in diverse bacteria, microbiome editing, and programmable horizontal gene transfer.

🎉 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/...

#Bacteriophages infecting #Klebsiella show capsule specificity that strongly shapes host range. @rafalmostowy.bsky.social &co reveal diverse prophage-encoded receptor-binding enzymes, including esterases, that drive capsule tropism @plosbiology.org 🧪 plos.io/48z4DdE

Out Now! Nuclease–NTPase antiphage defence systems use conserved molecular features to control bacterial immunity #MicroSky

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

Genome editing of phylogenetically distinct bacteria using cross-species retron-mediated recombineering - @seth-shipman.bsky.social @gladstoneinst.bsky.social go.nature.com/4tZluOU

Diversity-generating retroelements for programmable targeted hypermutagenesis - @dbikard.bsky.social @institutpasteur.bsky.social go.nature.com/3OG2nKN

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 !

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/...

Bravo Karen!

A big advance in the field of bacterial immunity, from the Bernheim and Laub labs

📣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.

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_...

How do you kill a MRSA superbug armed with 15 different anti-phage defense systems? You make a smarter phage. Check out our latest preprint on overcoming bacterial immunity using defense-guided engineering to build durable therapeutic phage cocktails! Led by Sarah Voss. doi.org/10.64898/202...

Meet Molly Ingersoll, microbiologist & immunologist. Her work shows how women and men can respond very differently to infections, and why sex-specific treatments are urgently needed. She also speaks up about the invisible hurdles women face in science. Follow her here @immunobladder.bsky.social

Today we report single-cell APEX-seq (scAPEX-seq)—a method for unbiased mapping of subcellular transcriptomes at single-cell resolution. It reveals cell states invisible to standard scRNA-seq and identifies regulators of CAR T function that improve solid tumor killing. tinyurl.com/32pf6b8p

We are recruiting! If you are passionate about technology development, protein engineering, computational design, directed evolution, chemical biology - please reach out! (The setting is pretty nice too…)

How can we tap into the enormous functional diversity of microbes on this planet? Join us at EMBL Heidelberg (8–10 Dec 2026) to learn about ongoing efforts to decode gene function and organisation in human gut microbes, and present your science.

Genome modelling and design across all domains of life - Evo2 A biological foundation model trained on 9 trillion DNA base pairs to predict the functional impacts of genetic variation www.nature.com/articles/s41...

Out now! In collaboration with Leifu Chang, we uncover the molecular and structural underpinnings of CRISPR-Cas12f-like RNA-guided transcription systems! Links to the published articles: tinyurl.com/55kpavet tinyurl.com/sk6djwx3 Previous thread for the preprint: bsky.app/profile/did:...