Bacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed. In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts. www.biorxiv.org/content/10.6...

Happy to share that I’m opening my lab at the Weizmann Institute of Science! We’ll study systems-level regulation of bacterial defense, driven by RNA-protein interactions shaping cell fate. Now recruiting PhD students & postdocs tinyurl.com/4yfa55vd Please reach out and share!

Exciting pre-print on new variants of anti-phage defense systems including CBASS, Pycsar, and Gabija! www.biorxiv.org/content/10.6...

✨New preprint! 🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al! Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬 🔗👇

Phages are full of genes of unknown function that are likely adaptive in specific conditions. New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out tinyurl.com/bdcfrejh

Preprint: Systematic discovery of TIR-based immune signaling systems in bacteria Conservation of TIR-derived signals accross the tree of life! We found bacterial TIR immune systems that signal via canonical cADPR (like in humans) and 2'cADPR (a plant immune signal). Documented 11 Thoeris types

I’m happy to share our new preprint! We uncovered the full diversity of bacterial TIR-based antiviral immune signaling, massively expanded the known diversity of Thoeris systems, and revealed conservation of TIR-derived immune signals across the tree of life. www.biorxiv.org/content/10.6...

Check this out for the 2026 SISB (phage defense) meeting in NYC. Mark your calendar! (and note the Zoom option, if needed) sisb2026.rockefeller.edu

🧬🛡️How are new immune mechanisms created? We show how Lamassu antiphage system, originated from a DNA-repair complex and evolved into a compact and modular immune machine, wt Dinshaw Patel lab in @pnas.org. 👏 @matthieu-haudiquet.bsky.social, Arpita Chakravarti & all authors! doi.org/10.1073/pnas...

The hinge bypass gate paper is finally out! doi.org/10.1038/s414... We show how loop-extruding SMC complexes can maintain DNA entrapment while bypassing obstacles on DNA — including transcription machinery & potentially other SMCs. A lucky convergence of 3 projects lead to the initial discovery!

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages. Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms. A thread 1/8

Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️ www.science.org/doi/10.1126/...

1/9 Metagenomics lets us read microbiomes in nature without cultivation, but writing (editing) them in their native context is still a major challenge. Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...

Our nuclease-protease story is out! We explored a fascinating case of coevolution and modularity in prokaryotic immune systems: www.science.org/doi/10.1126/... Thanks to wonderful coauthors/collaborators/friends, the whole @doudna-lab.bsky.social and everyone at @innovativegenomics.bsky.social

Gluing a bulky host protein onto an immune surveillance complex is a wild mechanism of viral immune evasion! @natmicrobiol.nature.com #phagesky #phage #microsky www.nature.com/articles/s41...

Cool work by the @soreklab.bsky.social laboratory. Metis detects host-genome degradation by sensing the accumulation of methylated deoxy-adenosines. Subsequently, triggering its immune response. Very elegant mechanism! Congrats to all involved!

Huge news for the Dutch structural biology community! NWO is investing €33 million to modernize the national cryo-EM infrastructure (EMPower). Exciting times ahead! www.nwo.nl/en/news/nati...

Last year it was discovered that a single bacterial NLR-like protein can recognize multiple, structurally unrelated phage proteins (Béchon et al, Kibby et al) Now, a new study shows the same for a plant NLR. Another example how principles of immunity remain conserved from bacteria to eukaryotes

On that note: hello world! My new lab on genetics of proteome remodeling is starting at the incredible MPI-CBG. We have big plans and open positions for PhD students and an RA. Apply now (!) at imprs.mpi-cbg.de and tinyurl.com/2vywj6f6 respectively.

Glad to share our paper out today @NatureEcoEvo: “Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor”. www.nature.com/articles/s41... #microsky #archaeasky

1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from? Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria. www.biorxiv.org/content/10.1...

One week left to apply!!

How do SMC complexes load onto DNA to get ready for loop extrusion? @roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸‍♂️🤸‍♂️🤸‍♂️. Check out the new paper: www.cell.com/molecular-ce...

Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems. Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here: www.nature.com/articles/s41...

Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...

Hiring! 🧬🔬 Ever wondered how bacteria fight off viruses? We’re looking for a PhD student to dive into the molecular basis of newly discovered microbial immune systems, an area of biology where much remains to be uncovered. RT/share to help us find our next team member! www.lumc.nl/en/about-lum...

You’ve heard of ubiquitination, meet deazaguanylation: Doug Wassarman in our lab discovered phage defense pathways have co-opted Q nucleobase biosynthetic enzymes to catalyze a new form of protein conjugation chemistry @science.org www.science.org/doi/10.1126/...

Coming up next week: the third Dutch Structural Biology meeting! Now in Delft, on Sept 26. See program here: nvbmb.kncv.nl/biology-2025 with #teamtomo #cryoEM #nmrchat simulations and more (looks like) Organized by the #NVBMB (associated with KNCV)

Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data. @ruoshiz.bsky.social @milot.bsky.social www.nature.com/articles/s41...

🚀 New publication alert! 🚀 We just published in @natbiotech.nature.com: 👉 Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes doi.org/10.1038/s415...

Excited to share my latest review, now published in the Royal Society theme issue on ‘The ecology and evolution of bacterial immune systems' (available OA): Defence systems encoded by core genomic islands of seventh pandemic Vibrio cholerae royalsocietypublishing.org/doi/10.1098/...

How can we understand the earliest events in evolution of eukaryotic immunity? @yao-li.bsky.social reports incredible molecular fossils of complete bacterial-like operons in eukaryotes that illuminate how animal immunity was first acquired from anti-phage defense www.biorxiv.org/content/10.1...

Our Wadjet-II paper by @roisnehamelinf.bsky.social is out in polished form: www.cell.com/structure/fu... With a great preview by @kevincorbett.bsky.social & @amardeeep.bsky.social highlighting the potential of Wadjets: Wadjet—Keeping a watchful eye on circular DNA. www.cell.com/structure/fu...

Preprint: De-novo design of proteins that inhibit bacterial defenses Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications Congrats Jeremy Garb! tinyurl.com/Syttt 🧵

📢 New preprint alert! We designed synthetic proteins that can block bacterial immune systems, allowing phages + plasmids to overcome natural defenses. This could transform phage therapy + genetic engineering. Here’s what we found 🧵 Preprint🔗: www.biorxiv.org/content/10.1...

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

Great opportunity to join the Leiden University Medical Center as a Junior Principal Investigator! Congratulations to this year's awardees (Marieke Barnhoorn, Edouard Fu, Lydiane Hirschler, @lloeff.bsky.social and Rajagopal Murugan)! Applications are possible for 2026: www.lumc.nl/en/news/2025...

Preprint: We discovered phage proteins that sequester diverse immune signaling molecules, including cUMP, cCMP, and N7-cADPR The first viral sponges to inhibit Pycsar and type IV Thoeris Congrats to talented leading author Romi Hadary! Read her thread to learn more about our findings

Extremely excited to share that I’m joining Columbia University @columbiauniversity.bsky.social as an Assistant Professor! We will explore how the mobile genome works—how transposons shape us, our DNA and how they can be harnessed to build useful technologies. #NewPI #RNAsky #TEsky thawanilab.org

Ever wondered why some bacteria have multiple CRISPR-Cas systems? Our new study led by Leah Smith shows how type I CRISPR systems can promote the acquisition and retention of new spacers into a co-occuring type III system. www.sciencedirect.com/science/arti...

Exciting times ahead! Today marks the first day of the Loeff Lab at Leiden University Medical Center in the Netherlands 🇳🇱. I’m thrilled to begin this new adventure and continue exploring microbial defense mechanisms and their applications through an integrative structural biology approach.

WORK! I currently have 5 (!) open positions for postdocs/PhD students in our CDlab for projects: - Nanopore protein sequencing - Archaeal CDV cell division - Microfluidics for synthetic cells - Nuclear Pore Complex - Origami mimics of peroxisomes Please apply! ceesdekkerlab.nl/come-join-us/ RT=👍

Check it out for yourself: 🔗 alphafold.ebi.ac.uk

We wrote a review on the free nucleotide pool as a central playground in human, bacterial, and plant immunity – now out in Nature Reviews in Immunology www.nature.com/articles/s41... Was fun to write this piece with Dina Hochhauser! Here is a thread to explain the premises 1/

Excited to finally share this work! We noticed a pair of genes - a nuclease and a protease - shuffles between antiviral systems. We show how proteolysis activates the nuclease, triggering defense in known and unknown immune contexts. tinyurl.com/2uwwy4ty

Thrilled to see our Kiwa story out today! A membrane-associated supercomplex that senses infection and blocks replication and transcription. www.cell.com/cell/fulltex... Huge congratulations to Yi and Zhiying for bringing it home, to Thomas for starting us off, and to all the collaborators.

🦠🧍‍♀️From bacterial to human immunity. We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity. Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social www.science.org/doi/10.1126/...

First preprint from the Nemudryi Lab! 🍾 In this work, we link antiviral immunity in bacteria and humans by showing that homologs of human Schlafen nucleases protect bacteria from phages. www.biorxiv.org/content/10.1...

Exciting work from the Nemudryi lab! Bacterial Schlafen proteins mediate antiviral immunity, just like their human homologs!