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...

New preprint. I've been chewing on why bacteria have pangenomes for years. Most species carry a distributed gene pool far larger than any one genome holds. E. coli has ~163,000 rare genes across the species. Each individual cell carries about 5,000. Why? A 🧵👇

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:...

Fantastic collaboration w/ @dbikard.bsky.social @audeber.bsky.social @rayanchikhi.bsky.social labs led by @jmouradesousa.bsky.social : We assessed the rates of variation of anti-phage systems in P4-like satellites and P2 helper phages. Quick conclusion: Huge variation! We focus on 4 key questions/5

➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔 🧵👇

Rapid modular evolution of antiviral repertoires in P2 phages and their P4 satellites: shuttling, swapping and mixing https://www.biorxiv.org/content/10.64898/2026.02.27.708500v1

🧵 Proud to present a tour de force by postdoc @gregbwhitfield.bsky.social solving the mystery of how bacterial Tad pili can extend and retract with a single motor ATPase. Great collaboration with Lynne Howell, @dr-lori-burrows.bsky.social, @ianyyen.bsky.social www.biorxiv.org/content/10.6...

SNIPE is a widespread bacterial defence system that exploits the spatial organization of phage genome injection to specifically target viral DNA, distinguishing self from non-self in prokaryotic immune systems @nature.com @mitpress.bsky.social www.nature.com/articles/s41...

New preprint on Detectrons from @jihoon-han.bsky.social! These are programmable biosensors for RNA that produce DNA barcodes in the presence of their target RNA. Check out Jihoon's quoted thread and the preprint for more: www.biorxiv.org/content/10.6...

Join us at the 2026 GRC Microbial Stress Response to be held on July 19th-24th at Mount Holyoke College!! Here is the link for more information: www.grc.org/microbial-st...

🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...

Deadline is approaching (Feb 9) to apply for a PI position at Institut Pasteur. Come join us and contribute to an amazing scientific environment!!!

I’m thrilled to share our work on phage triggers of the bacterial immune system in its final form @natmicrobiol.nature.com www.nature.com/articles/s41...

It was a true privilege to co-chair the inaugural GRC meeting on Microbiome Editing together with @jenniferdoudna.bsky.social . The positive energy and quality of the Science presented were truly inspiring. I look forward to the next one chaired by KC Huang and @omalleylab.bsky.social !!!

🦠🧫 Envie d'en savoir plus sur la Microbiologie et de découvrir l'Institut Pasteur ? Rejoignez nous pour conférence scientifique grand public, accompagnée d’une performance artistique le 27 janvier à 18h! Inscrivez-vous :) research.pasteur.fr/fr/event/con...

This is shaping up to be one of the top conferences on microbiome editing!!

Such a privilege to share the Phage Foundry (phagefoundry.org) team’s work at the inaugural GRC meeting on Microbiome Editing 🎉🎊.

@francoisrousset.bsky.social, chercheur en microbiologie au @ciri-lyon.bsky.social est lauréat du Prix Paoletti 2025. 👋 @cnrs-rhoneauvergne.bsky.social buff.ly/o9MCTni

Live microscopy to 'phollow' phage outbreaks 🔬✳️ www.nature.com/articles/s41...

Microbes weaponizing secondary metabolites to make rivals vulnerable to phage attack 🧪🦠 www.nature.com/articles/s41...