Aude Bernheim
@audeber.bsky.social
PI at Institut Pasteur Evolution, immunity, genomics, microbiolgy. Into immunity in bacteria and its conservation in eukaryotes. Advocate for more inclusive sciences https://research.pasteur.fr/en/team/molecular-diversity-of-microbes/
Awesome work! A must-read. What a wonderful tree. Congrats @algao.bsky.social and all the co-authors.
Nature@nature.com · 7d agoNature research paper: Diverse bacterial pattern recognition receptors sense the core phage proteome go.nature.com/45fpXCZ
Come work on exciting AI for biology projects in Paris!! 🇫🇷 Details and application below, deadline sept 1st!
Antigen Evolution & Design Lab@antigenevo.bsky.social · 2w ago🚨 JOB ALERT🚨 We are very excited to be hiring the lab's ✨very first postdoc✨! Work on new AI technologies for decoding antigen protein evolution in a fresh research environment, at the heart of Paris 🇫🇷 Details & link to apply: research.pasteur.fr/en/job/postd... Deadline: Sep 1st
Fantastic work from a brand new lab :)! Amazing to see the same folds being used by pathogens across the tree life! Congrats Jason and all authors.
Jason Nomburg@jnoms.bsky.social · 2w agoHappy to share the first preprint out of the Nomburg lab! Many aspects of cellular immunity are shared across the tree of life. Here, we show that some of these conserved aspects of cellular immunity are mirrored by conserved effectors of immune antagonism. Thread below! 1/15
Happy to share the first preprint out of the Nomburg lab! Many aspects of cellular immunity are shared across the tree of life. Here, we show that some of these conserved aspects of cellular immunity are mirrored by conserved effectors of immune antagonism. Thread below! 1/15
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 2w agoConserved folds enable immune antagonism across the tree of life https://www.biorxiv.org/content/10.64898/2026.07.21.739742v1
Out @cp-cellhostmicrobe.bsky.social, natural products meet bacterial immunity! We used genomics to identify lanthivirins: a family of >2,000 lanthipeptide BGCs that protect Actinobacteria against phages. Led by @hshomar.bsky.social & @mariegllm.bsky.social www.sciencedirect.com/science/arti...
A family of lanthipeptides with anti-phage function
Bacteria produce natural products to adapt to their environments, with phage interactions as major ecological and evolutionary drivers. While some nat…
sciencedirect.com
1/4 Every good defence needs a backup! 🛡️⚔ Out now in @natrevmicro.nature.com our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉 🔗 www.nature.com/articles/s41...
Immune safeguarding as a conserved principle of antiviral defence - Nature Reviews Microbiology
All organisms defend against viral infections through active immunity mechanisms that clear the virus or population-level mechanisms that cause regulated cell death. Recent research increasingly shows...
nature.com
1/10 🚨Preprint! One RING to rule them all (phages)👑💍⚔️ Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇 biorxiv.org/content/10.6...
Excited to share that our Metis story is now published in Science! 🎉 Bacteria can sense phage-induced degradation of their genome and activate immunity. Many thanks to everyone who contributed to this work. 📄 www.science.org/doi/10.1126/... More details in my earlier thread 🧵⬇️
Bacteria sense virus-induced genome degradation via methylated mononucleotides
Phages often degrade the genome of their bacterial host to individual nucleotides. Here we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation. Metis...
science.org
Osterman Ilya@ostermanilya.bsky.social · 9mo agoBacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides. Here’s the story of how we discovered the Metis defense system 👇 www.biorxiv.org/content/10.1...
Gabija restricts phage circularization & DNA replication Gabija prevents phage genome circularization & replication w/out impacting bacterial host. Exposed DNA ends & phage end-binding proteins license DNA targeting while RecBCD protects host from Gabija www.cell.com/cell-host-mi...
Gabija restricts phage circularization and DNA replication
Gabija acts early during phage infection, preventing phage genome circularization and replication. Phage DNA end-binding proteins prevent RecBCD loading onto linear DNA, and the absence of RecBCD lice...
cell.com
Thrilled to share our collab led by Grace Hibshman with the Shipman lab! Type IX retron-Kva2 structure reveals phage detection via an HTH fold, not a primary sequence. We computationally designed triggers that program bacteria cell death, pointing toward designer antimicrobials.
A family of lanthipeptides with anti-phage function Discovery of 2,000+ lanthipeptide biosynthetic gene clusters with anti-phage potential. Lanthivirins inhibit phage replication by targeting phage proteins & interfering with phage DNA replication. www.cell.com/cell-host-mi...
A family of lanthipeptides with anti-phage function
Shomar, Guillaume, et al. report the genomics-driven discovery of a family of more than 2,000 lanthipeptide biosynthetic gene clusters with anti-phage potential. They experimentally demonstrate anti-p...
cell.com
🔬 Meet Spyros Lytras, one of our new G5 group leaders! Using AI to predict viral protein evolution, he's designing vaccines for strains that don't yet exist. No more waiting for threats to emerge—be ready ahead of time. The future of pandemic preparedness. 🧬 📖 www.pasteur.fr/en/research-...
Predicting viral evolution with AI
Spyros Lytras is one of four young scientists selected in 2025 to lead new research groups at the Institut Pasteur. He has headed the “Antigen Evolution & Design laboratory” 5-year Group (G5) since Ju...
pasteur.fr
Fantastic study tackling a new aspect of bacterial immunity: defense against conjugation ! Added bonus: Mesopotamian deities are fascinating, a good reason to dive again into this civilisation.
Xavier Charpentier@labxc.bsky.social · 4w ago#microsky New preprint from the lab! Widespread immune systems protect bacteria against conjugative plasmids www.biorxiv.org/content/10.6... Kudos to the extremely talented lead author Ludovic Poiré! Key contributions by @francoisrousset.bsky.social and also help from C. Lesterlin/TacC lab. 🧵⬇️
Humans and bacteria share strategies to defend against viruses. We wondered: could they use each other's genes? Yes, both can! Bacteria can use human immune genes to defend against phages AND Human cells can use bacterial genes for viral defense. www.biorxiv.org/content/10.6...
Bacterial and human exonucleases mediate interkingdom antiviral immunity
All kingdoms of life have developed strategies to limit viral infection. In humans, interferons induce a suite of antiviral factors that collectively provide immunity. Some human immune genes are homo...
biorxiv.org
Very honored by this. Deeply grateful to all lab members and collaborators for the joy of doing science together. I hope that joy is reflected in the science we produce.
Institut Pasteur | 130 years of biomedical research@pasteur.fr · last mo.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
Preprint: Plant pathogens cleave 2’cADPR to suppress TIR immune signaling Inspired by knowledge on how phages inhibit bacterial immunity, we now show that disease-causing bacteria inhibit plant immunity in a similar way. A 🧵 www.biorxiv.org/content/10.6...
Plant pathogens cleave 2'cADPR to suppress TIR immune signaling
Small molecules produced by TIR (Toll-interleukin-1 receptor) domains are essential for plant immune signaling. A central TIR-derived signal is 2'cADPR, a cyclic ADP-ribose (ADPR) molecule that is gen...
biorxiv.org
New paper alert!! We just discovered a new filament system that is widespread exclusively within CPR bacteria! www.biorxiv.org/content/10.6.... Short thread below. 🦠🔬🚀
A Novel Pilus System in Candidate Phyla Radiation Bacteria
The Candidate Phyla Radiation (CPR) represents a bacterial superphylum estimated to include between 15–50% of all bacterial species, yet CPR bacteria remain challenging to culture and have been primar...
biorxiv.org
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...
Our paper on the YprA family of helicases and their roles in bacterial defence is now out! We describe ARMADA, a defence system synergise with Druantia and show that both systems spread horizontally on a novel type of mobile genetic element that we call SPIDERs www.sciencedirect.com/science/arti...
YprA-family helicases provide the missing link between diverse prokaryotic immune systems
Bacteria and archaea possess an enormous variety of antiviral immune systems that often share homologous proteins and domains. YprA-family helicases a…
sciencedirect.com
Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity @natmicrobiol.nature.com from Michael Laub & Abel Garcia-Pino www.nature.com/articles/s41...
Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity - Nature Microbiology
The activation of an antiphage defence system relies on host factors targeted by phages, a mechanism analogous to the way that eukaryotic innate immune systems detect pathogen-induced perturbations of...
nature.com
CapK is a bacterial DNA damage-activated kinase that phosphorylates transcriptional repressor CapS to control adjacently-encoded anti-phage immune pathway genes in response to a universal stress signal, DNA damage @kevincorbett.bsky.social and colleagues link.springer.com/article/10.1...
A DNA damage-activated kinase phosphorylates a transcriptional repressor to control bacterial immune pathway expression - The EMBO Journal
Bacteria encode numerous stress-response pathways that protect their hosts against both internal and external threats. A key question is how these pathways are regulated, especially anti-phage immune ...
link.springer.com
Excited to see our work out in @natmicrobiol.nature.com! We uncovered broad functional diversity within phage sponge families🧽. Huge thanks to all coauthors and brilliant collaborators @kranzuschlab.bsky.social @reneechang.bsky.social ! www.nature.com/articles/s41...
Functional diversity of phage sponge proteins that sequester host immune signals - Nature Microbiology
A functional screen reveals phage sponge proteins that bind Pycsar, Thoeris and CBASS signalling molecules to inhibit bacterial immunity.
nature.com
Romi Hadary@romihadary.bsky.social · 12mo ago📢 Preprint out! Together with @reneechang.bsky.social @kranzuschlab.bsky.social and the amazing @soreklab.bsky.social, we explored viral sponges to map their diversity and function. Discovered huge diversity, including sponges that inhibit Pycsar & Type IV Thoeris! www.biorxiv.org/content/10.1...
Our aRES story is finally out 😀 Beyond what was reported in the preprint, we found that aRES is activated by direct binding of the phage DNA polymerase. Another NAD-degrading defense system — and multiple phage strategies to overcome it. www.sciencedirect.com/science/arti...
Bacterial defense via RES-mediated NAD+ depletion is countered by phage phosphatases
Many bacterial defense systems restrict phage infection by breaking down the molecule nicotinamide (Nam) adenine dinucleotide (NAD+) into adenosine di…
sciencedirect.com
Osterman Ilya@ostermanilya.bsky.social · 6mo ago🧬 Metabolic arms race continues! We discovered a new NAD⁺-depleting bacterial immune system aRES and phage enzymes that overcome it. Our preprint is out: www.biorxiv.org/content/10.6...
(1/6) Thrilled to share this story! In our preprint from my PhD in the @kranzuschlab.bsky.social, with help from the Hatfull lab and @soreklab.bsky.social, we discover RyDEP, a phage-encoded RyR-domain glycosidase that allows phages to evade Thoeris defense. Highlights below! doi.org/10.64898/202...
❤️this Perspective from @jennifergarrison.bsky.social strongly advocating that: 🥚 ovarian biology has systemic effects in women ❌has been neglected long enough thank you very much 👩🦳 ovarian aging should be at the center of female geroscience Hear her roar indeed (Blsky profile)! plos.io/4dOqcZw 🧪
PLOS Biology@plosbiology.org · 2mo agoClassifying ovaries solely as #reproductive organs has obscured their role as systemic regulators of female physiology. @jennifergarrison.bsky.social contends that ovarian #aging is a primary determinant of healthspan and belongs at the center of geroscience. 🧪
One of my favorite scientist in the field is opening his lab in Europe 🥳🇪🇺🧬. So happy about this and excited about the science that will come out of this lab!
Osterman Ilya@ostermanilya.bsky.social · 2mo ago🚨After 4 fantastic years in the Sorek lab @soreklab.bsky.social, I’ll be starting my own group at EMBL @embl.org bl.org Hamburg. www.embl.org/groups/oster... Metabolism-driven immunity: phages, metabolites, and discovery of new enzymes, molecules, and pathways 🦠🧬
Great piece and cover @science.org about how our field is uncovering the evolutionary and mechanistic connections between bacterial and eukaryotic immunity ! www.science.org/content/article/ancient-wars-between-microbes-gave-us-key-immune-defenses
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...
Revisiting the life cycle of temperate phages - Nature Reviews Microbiology
The life cycle of temperate bacteriophages involves lytic or lysogenic cycles and has historically served as a model for studying genetic regulation. This Review provides an updated overview of these ...
nature.com
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🧵
biorxiv.org
That's a wrap on three days of incredible science at #SISB2026! Special thanks to @rockefeller.edu for hosting us on their beautiful campus, to our speakers and poster presenters, and most of all to this community that never fails to inspire. Can't wait for #SISB2027 🫶
