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_...
➡️ 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? 🤔
🧵👇
Congratulations to Sonomi Yamaguchi for her paper at @nature.com. Sonomi discovered Clover defense and explained how nucleotide signals control each step of viral sensing, immune regulation, and viral restriction – named for her beautiful "four-leaf" structures 🍀
www.nature.com/articles/s41...
Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity!
www.nature.com/articles/s41...
🦠🧫 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...
Advancing Fast-Track Genome Engineering in Bacillus subtilis Phages
ACS Synthetic Biology
pubs.acs.org/doi/10.1021/...
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...
🧬🛡️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...
We built GenoPHI: a machine learning workflow that predicts phage-host interactions at strain level. This could help rapidly select phages to treat drug-resistant bacterial infections or for microbiome engineering without exhaustive lab testing.
www.biorxiv.org/content/10.1...
JOB OFFER #PhageSky
We have a postdoc position opening in my group to investigate phage-MGE interactions !
We're based in the very nice city of Lyon, France @mmsb-lyon.bsky.social
Contact me for more info !
>> Apply on the CNRS webpage emploi.cnrs.fr/Offres/CDD/U...
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
Excited to share the work that’s been on my mind for the past 2 years, now on bioRxiv!
Led with Matt Walker, and my first project in the Sternberg Lab .
Check it out ⬇️
tinyurl.com/mshwjd77
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...
🧬 From bacteria to humans: a new study led by @institutcurie.bsky.social, @institutpasteur.bsky.social & @inserm.fr reveals SIRal, a novel human immune protein with ancestral roots. A new path for immunotherapy?
🔗 Read: www.pasteur.fr/en/press-are...
🦠🧍♀️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/...
📢Preprint out!
Excited to share my final work from the @soreklab.bsky.social!
We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery.
Found 3 new families targeting immune signaling!
Le Palais de la Découverte est menacé! Il a contribué à éveiller ma passion pour la science quand j'étais petit. Nous devons tout faire pour protéger ce lieu unique qui a toute sa place au cœur de Paris. Signez la pétition ici: chng.it/BnR9gZvhL2
The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes www.biorxiv.org/content/10.1101/2025.05....
White smoke, we have a new pope and also 16 new anti-phages systems in sedentary integrons (SCIs) !
In collaboration with the Rocha lab, we show in our new paper that cassettes of these large platforms encode many known anti-phage defenses, and uncovered 16 new ones.
www.science.org/doi/10.1126/...
Out in Nature today: A new immune signaling molecule, His-ADPR, is produced by defensive TIR domain proteins in bacteria to protect from phage
Joint work with the Tamulaitienė and Kranzusch labs
www.nature.com/articles/s41...
Congrats Carmel Avraham, Dziugas Sabonis, Renee Chang and co-authors!
It was an honor for my lab and myself to host the meeting on the Immune Systems of Bacteria. Such a high from all the incredible science and sharing with scientists from the whole world the greatness of Paris in the spring.
Vive la science, et vive Paris!
Structural basis for Lamassu-based antiviral immunity and its evolution from DNA repair machinery www.biorxiv.org/content/10.1101/2025.04....
CBASS, CRISPR, and mCpol- oh my! What a satisfying collaboration with @aaronwhiteley.bsky.social 's lab- we uncovered a new cyclic dinucleotide signaling pathway, but it doesn't work how you'd expect! Check out the thread from @aesully98.bsky.social for an overview of the most important findings!
Hello BlueSky! Inaugural post here from the Sternberg Lab. We're excited to share our latest work, in which we teamed up with the @WiedenheftLab to study how DRT9 reverse transcriptases provide antiviral immunity. Here’s what we found: www.biorxiv.org/content/10.1...
New version of DefenseFinder available defensefinder.mdmlab.fr (& cli)
Now encompassing 263 systems (+111 this year..!).
Thanks @ftesson.bsky.social, DefenseFinder grandmaster. Full list of systems here: defense-finder-models/List_system_article.md at master · mdmparis/defense-finder-models
Happy to share our latest piece of work on the PARIS bacterial immune system. We performed a detailed characterization of the AriB Toprim nuclease, the effector of PARIS immunity.
www.biorxiv.org/content/10.1...
Image with text that reads: It's happening now: I know it's totally overwhelming but here are just a handful of things happening in US Science & public health RIGHT NOW. I need you to know, so you can realise how you are being defrauded from a healthy, disease free future, with thriving science. I need you to know, so you can tell others.
Huge thanks to my sister for helping put these together.
I'm thrilled to announce our latest work is now published in Cell! Viruses encode numerous proteins that inhibit host defenses, but identifying immune-modulatory proteins among millions of viral sequences has been nearly impossible - until now! www.cell.com/cell/fulltex...
Phage defence system abundances vary across environments and increase with viral density www.biorxiv.org/content/10.1... #jcampubs
