Sign in

Aude Bernheim

@audeber.bsky.social
3.4K followers 444 following 216 posts

PI at Institut Pasteur Evolution, immunity, genomics, microbiolgy. Into immunity in bacteria and its conservation in eukaryotes. Advocate for more inclusive sciences mdmlab.fr

PostsRepliesMedia
Reposted by Aude Bernheim
Kranzusch Lab @kranzuschlab.bsky.social · 01/10/2026
Our story with @hobbslabutah.bsky.social discovering CBASS sensing of phage proteases out now in @science.org New data include CBASS recognition of diverse proteases beyond T4, and verifying CD-NTase activation loop cleavage as the trigger for defense in vivo www.science.org/doi/10.1126/...
science.org
Phage proteases activate CBASS antiphage immunity
Cyclic oligonucleotide–based antiphage signaling systems (CBASS) are bacterial immune pathways evolutionarily related to cGAS-STING (cyclic GMP-AMP synthase–stimulator of interferon genes) in humans. ...
08838
Reposted by Aude Bernheim
Hoong Chuin Lim @hclim.bsky.social · 02/10/2026
www.biorxiv.org/content/10.6... New preprint from my lab revealing molecular conflicts between host replication and antiviral defense. RecBCD prevents this conflict by clearing immunogenic DNA ends produced during normal replication termination. #MicroSky #PhageSky
biorxiv.org
RecBCD Prevents Bacterial Autoimmunity by Clearing Self-DNA Ends Produced During Replication Termination
Viral-induced DNA damage triggers both eukaryotic and prokaryotic innate immunity. Here, we report that self-DNA ends generated routinely during normal termination of bacterial replication suffice to ...
12414
Reposted by Aude Bernheim
Nature Reviews Microbiology @natrevmicro.nature.com · 02/10/2026
New online! How bacterial immune systems sense phage infection
dlvr.it
How bacterial immune systems sense phage infection
Nature Reviews Microbiology, Published online: 02 October 2026; doi:10.1038/s41579-026-01376-xBacteria deploy diverse immune systems to counter phage infection, yet how these systems sense invasion remains incompletely understood. This Review categorizes phage-derived triggers and outlines emerging principles that govern immune recognition of phage infection.
04119
Reposted by Aude Bernheim
Philipp Radler @radler92.bsky.social · 01/10/2026
The first paper of my PostDoc in Christa Schlepers group (@archaea-vienna.bsky.social) on the dynamics of Asgard archaea is now out in Nature! www.nature.com/articles/s41... This was a great team effort and I am looking forward to uncover the complex behavior of these cells further!
nature.com
Dynamic protrusions mediate crawling motility in Asgard archaea - Nature
Anoxic live-cell imaging shows actin-dependent crawling motility and dynamic protrusions in Asgard archaea, providing insights into cellular innovations that may have contributed to eukaryotic evoluti...
510239
Reposted by Aude Bernheim
Andrew Santiago-Frangos @asantiagofrangos.bsky.social · 01/10/2026
Our lab's first preprint! The antiphage protein Tiamat is an ATPase and DNase with homologs across the tree of life. What started as undergrad Shirley Yuan's summer project grew into a paper and a collaboration with @jpkbravo.bsky.social's group. Link: www.biorxiv.org/content/10.6...
14924
Reposted by Aude Bernheim
Carl Zimmer @carlzimmer.com · 27/09/2026
Four days ago, a scientist was surprised by the news that Anthropic discovered new virus genes for making DNA. He says he’s been studying them for years—and feeding his data to Anthropic’s AI as part of his own research. Coincidence? Here’s my story. nyti.ms/3VSWayc
nyti.ms
Did Anthropic’s A.I. Really Make a Scientific Discovery on Its Own? (Gift Article)
An expert at the University of Copenhagen said his team had been sharing its research with the company’s A.I. model, Claude, and that its new finding matched their work.
882123874
Aude Bernheim @audeber.bsky.social · 24/09/2026
Really great work !
050
Reposted by Aude Bernheim
Christophe Zimmer @chzimmer.bsky.social · 10/09/2026
Can you tell how an antibiotic kills bacteria just by watching them under a regular microscope — without any dyes ? Yes, it turns out, at least if you are a deep neural net.
12316
Aude Bernheim @audeber.bsky.social · 23/09/2026
Some really cool microbiology!!! Congrats everyone 👏
070
Reposted by Aude Bernheim
David Bikard @dbikard.bsky.social · 21/09/2026
New paper from the lab, out in Nature Microbiology. We ran CRISPRi screens to ask what genes E. coli needs in order to live in a gut and what this can tell us about the gut environment itself. doi.org/10.1038/s41564-026-02471-8
311256
Reposted by Aude Bernheim
Jorge Moura de Sousa @jmouradesousa.bsky.social · 20/09/2026
Happy to see our work on the evolution of antiviral repertoires in P4-like satellites and their P2-like helper phages (check out the 🧵 👇) out in @narjournal.bsky.social 🔗 doi.org/10.1093/nar/... #phagesky #MicroSky #evosky
doi.org
Shuttling, swapping, and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites
Abstract. Interactions between bacteria, bacteriophages, and their satellites are shaped by a myriad of defence and counter-defence mechanisms. Here, we id
25638
Reposted by Aude Bernheim
Tatta Bio @tattabio.bsky.social · 18/09/2026
We're excited to share our new preprint! In collaboration with the @keaslinglab.bsky.social at UC Berkeley, we made gLM2 generative and used it to redesign a chimeric Type I polyketide synthase in the context of the full biosynthetic assembly line. 🧵 Preprint: www.biorxiv.org/content/10.6...
196
Reposted by Aude Bernheim
Malcolm White @mfwhite2.bsky.social · 16/09/2026
Our paper on type II Panoptes is now published at PLOS Biology with new data on phage escapers - quite a step up in microbiology for our lab, led by Sabine Gruschow. Thanks to @erc.europa.eu for funding dx.plos.org/10.1371/jour...
14628
Aude Bernheim @audeber.bsky.social · 14/09/2026
Thanks!
000
Reposted by Aude Bernheim
François Rousset @francoisrousset.bsky.social · 08/09/2026
🚨 We are excited to share the first preprint of our lab ! We discovered an NADase enzymatic domain in bacterial immunity and in the human protein TEP1. www.biorxiv.org/content/10.6...
biorxiv.org
A widespread NADase domain links bacterial immunity with human TEP1
Recent discoveries on bacterial immunity have revealed that several protein domains involved in anti-phage defense are conserved in eukaryotes, such as SIRim, TIR, PNP and gasdermin. Bacterial immune ...
49354
Aude Bernheim @audeber.bsky.social · 04/09/2026
Congeats ++++ so happy about this!!!
120
Aude Bernheim @audeber.bsky.social · 03/09/2026
Congrats!!!!
110
Aude Bernheim @audeber.bsky.social · 03/09/2026
Congrats!
110
Aude Bernheim @audeber.bsky.social · 03/09/2026
Congrats!
010
Reposted by Aude Bernheim
Lucie Etienne @lucievirevolte.bsky.social · 31/08/2026
Insights into longevity & virus-driven adaptation from Myotis bat genomes International & fantastic collab. with @psudmant.bsky.social @denard.bsky.social Labs ! Major credit to the 2 leading scientists: Juan Vazquez & @lauterbur.bsky.social now with their own labs! You 2 rock! (1/n)
nature.com
Insights into longevity and virus-driven adaptation from Myotis bat genomes - Nature
Comparative and functional analyses of Myotis bats uncover unique patterns of adaptation in virus-interacting proteins and longevity-associated pathways, linking two hallmarks of bat biology.
22813
Aude Bernheim @audeber.bsky.social · 31/08/2026
Congrats, great news !
110
Reposted by Aude Bernheim
Tobias Warnecke @tobiaswarnecke.bsky.social · 22/08/2026
Who needs chromatin anyway...? NOT THIS GUY! www.biorxiv.org/content/10.6... 1/n
biorxiv.org
Chromatin is dispensable for bacterial life
Inside cells, DNA is intimately associated with proteins, forming chromatin. The protein constituents of chromatin vary across the tree of life: histones are the principal building blocks of chromatin...
3231104
Reposted by Aude Bernheim
Tara Bartolec @tarabartolec.bsky.social · 20/08/2026
So happy to share that this work is finally out, now in @nature.com! Lots of new goodies since preprint so plz check it out (old thread below). Giant thank you to everybody involved + all @savitski-lab.bsky.social and @typaslab.bsky.social lab members 🙏🙏🙏 @embl.org nature.com/articles/s41...
nature.com
Pervasive phosphorylation by phage T7 kinase disarms bacterial defences - Nature
The T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection.
36725
Reposted by Aude Bernheim
Ben Morehouse @benmorehouse.bsky.social · 12/08/2026
Today we are excited to introduce you to PanDA 🐼🐼🐼, a newly uncovered antiphage system!! Attendees at @SISB2026 would have heard a little about this from graduate student Ali Nabhani back in May, but we are now out here in preprint form and delighted to share more of the details. (Thread below)
biorxiv.org
Minimal diadenylate cyclases have been co-opted to detect phage immune evasion
Many bacterial immune defenses transmit recognition of phage infection via the generation of diverse cyclic nucleotide second messengers. Phage have evolved to subvert this kind of immunity by sequest...
15323
Reposted by Aude Bernheim
Ady Ragucci @aragucci.bsky.social · 12/08/2026
Excited to share our story on diadenylate cyclases in bacterial immunity! Building on the discovery of Panoptes, we present Panoptoo: a DAC operon that uses cUA to guard against phage infection. Grateful to @daniellehaley.bsky.social and @kranzuschlab.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
Bacterial diadenylate cyclase domains synthesize diverse nucleotide signals in anti-phage defense
Bacterial diadenylate cyclase (DAC) enzymes synthesize the nucleotide signal 3′3′ cyclic di-AMP (3′3′-c-di-AMP) to control osmoregulation, cell-wall homeostasis, and DNA-damage responses. Here we disc...
13720
Reposted by Aude Bernheim
Kranzusch Lab @kranzuschlab.bsky.social · 12/08/2026
The shared principles of human and bacterial antiviral immunity An honor to highlight remarkable discoveries from many labs over the past 12 years that unite previously disparate fields of how animal cells and prokaryotes defend against viruses. www.nature.com/articles/s41... rdcu.be/fzwyB
nature.com
Shared principles of human and bacterial antiviral immunity - Nature
The Review describes shared ancient, conserved mechanisms between human antiviral immunity and bacterial anti-phage systems, outlining universal principles of pathogen sensing, signalling and effector...
513161
Reposted by Aude Bernheim
Landon Getz @landongetz.bsky.social · 06/08/2026
DNA glycosylases are repair enzymes, essential to all cellular life. They find chemically damaged bases and remove them so DNA can be repaired. Today in Nature Microbiology, we show bacteria have repeatedly repurposed them into antiviral immune systems 🧵 www.nature.com/articles/s41...
nature.com
Antiviral defence is a conserved function of diverse bacterial DNA glycosylases - Nature Microbiology
DNA glycosylases, typically used for DNA repair, can also protect bacteria against phages that would otherwise evade host immunity by incorporating modified bases into their genomes.
38139
Aude Bernheim @audeber.bsky.social · 29/07/2026
Awesome work! A must-read. What a wonderful tree. Congrats @algao.bsky.social and all the co-authors.
0162
Reposted by Aude Bernheim
Spyros Lytras @spyroslytras.bsky.social · 23/07/2026
Come work on exciting AI for biology projects in Paris!! 🇫🇷 Details and application below, deadline sept 1st!
02727
Aude Bernheim @audeber.bsky.social · 22/07/2026
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.
160
Reposted by Aude Bernheim
Jason Nomburg @jnoms.bsky.social · 22/07/2026
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
38249
Aude Bernheim @audeber.bsky.social · 21/07/2026
A huge collaborative effort led by Helena Shomar @hshomar.bsky.social and Marie Guillaume @mariegllm.bsky.social, special thanks to our Leiden collaborators. And Special thanks to Science à la Pelle citizen science project participants who helped build the phage collection!
111
Aude Bernheim @audeber.bsky.social · 21/07/2026
Whie exact chemistry and molecular mechanism remain to be resolved, this work connects two fields: bacterial immunity and natural products. It shows that BGCs can encode intracellular antiphage defenses and points to a much larger antiviral chemical space that remains to be explored.
100
Aude Bernheim @audeber.bsky.social · 21/07/2026
Our current model is that the matured lanthivirin interacts with a phage-encoded GNAT and the phage DNA primase, and may act as a molecular glue that could lock them in a non-productive complex, thereby blocking phage DNA replication.
120
Aude Bernheim @audeber.bsky.social · 21/07/2026
7/10 15 independent escapers, isolated from 4 phages, carried mutations in homologs of the same phage-encoded GNAT acetyltransferase. Interaction experiments further connected lanthivirin precursor with phage GNAT and DNA primase. The GNAT therefore appears central to lanthivirin sensitivity.
110
Aude Bernheim @audeber.bsky.social · 21/07/2026
How do they work? Lanthivirins do not detectably harm the host, trigger cell death, or block phage adsorption. They act after entry: phage DNA accumulation drops early, followed by reduced phage transcripts, proteins, and particle production.
100
Aude Bernheim @audeber.bsky.social · 21/07/2026
The biosynthetic chemistry is essential for the antiviral activity. Deleting the LanB-like dehydratase or LanC-like cyclase abolished defense. So did mutations in conserved residues predicted to form the lanthionine rings. Lanthivirin maturation is required for antiviral activity.
100
Aude Bernheim @audeber.bsky.social · 21/07/2026
Genomics gave us candidates; then came a lot of Streptomyces work, thx to a lot of collaborators for helping us with that! Six diverse lanthivirin systems protected against phages in heterologous hosts. In S. coelicolor, activating cryptic lanthivirin cluster reduced phage titers by 10^4.
100
Aude Bernheim @audeber.bsky.social · 21/07/2026
3/10 We combined antiSMASH and DefenseFinder predictions across 29,401 actinobacterial genomes. One clade of class I lanthipeptide clusters was strongly enriched near known defense systems. It contains >2,000 systems across diverse Actinobacteria. We named them lanthivirins
100
Aude Bernheim @audeber.bsky.social · 21/07/2026
How many more are out there ? To answer this, we needed a scalable method. Of course, we turned to genomics 💻❤️ Our starting idea was simple: antiphage systems cluster in defense islands. Could biosynthetic gene clusters found in the same genomic regions also contribute to bacterial immunity?
100
Aude Bernheim @audeber.bsky.social · 21/07/2026
2/10 The biological roles of most bacterial natural products remain unknown. A few were shown to provide antiphage phenotypes, as early as 1945 by Doris Jones and more recently by the @themaxwelllab.bsky.social and @frunzkelab.bsky.social labs. Ex: www.nature.com/articles/s41...
131
Aude Bernheim @audeber.bsky.social · 21/07/2026
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...
sciencedirect.com
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…
18444
Reposted by Aude Bernheim
Rafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 21/07/2026
1/4 Every good defence needs a backup! 🛡️⚔ Out now in @natrevmicro.nature.com our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉 🔗 www.nature.com/articles/s41...
nature.com
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...
17145
Reposted by Aude Bernheim
Rafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 16/07/2026
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...
411858
Reposted by Aude Bernheim
Osterman Ilya @ostermanilya.bsky.social · 09/07/2026
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 🧵⬇️
science.org
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...
48230
Reposted by Aude Bernheim
Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 17/07/2026
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...
cell.com
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...
03116
Reposted by Aude Bernheim
Nogales Lab @nogaleslab.bsky.social · 20/07/2026
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.
15921
Reposted by Aude Bernheim
Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 20/07/2026
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...
cell.com
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...
03724
Reposted by Aude Bernheim
Institut Pasteur | 130 years of biomedical research @pasteur.fr · 07/07/2026
🔬 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-...
pasteur.fr
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...
1247
Aude Bernheim @audeber.bsky.social · 07/07/2026
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.
1184