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/
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/
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...
In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts.
www.biorxiv.org/content/10.6...
Environment and physiology shape antiphage system expression
Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of anti...
www.biorxiv.org
December 15, 2025 at 9:49 PM
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...
In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts.
www.biorxiv.org/content/10.6...
Reposted by Aude Bernheim
The EMBO Gold Medal 2025 was awarded to Tanmay Bharat and David Bikard: https://www.embo.org/press-releases/embo-gold-medal-2025-awarded-to-tanmay-bharat-and-david-bikard/ 🧪
At #CellBio2025, the EMBO Gold Medal was handed over to David Bikard in recognition of his pioneering work on #GeneEditing.
At #CellBio2025, the EMBO Gold Medal was handed over to David Bikard in recognition of his pioneering work on #GeneEditing.
December 10, 2025 at 1:40 PM
The EMBO Gold Medal 2025 was awarded to Tanmay Bharat and David Bikard: https://www.embo.org/press-releases/embo-gold-medal-2025-awarded-to-tanmay-bharat-and-david-bikard/ 🧪
At #CellBio2025, the EMBO Gold Medal was handed over to David Bikard in recognition of his pioneering work on #GeneEditing.
At #CellBio2025, the EMBO Gold Medal was handed over to David Bikard in recognition of his pioneering work on #GeneEditing.
Reposted by Aude Bernheim
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
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
December 8, 2025 at 3:04 PM
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
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
Reposted by Aude Bernheim
🔬 Call to create junior research groups at the Institut Pasteur
Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies
📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD
Apply now 📝 research.pasteur.fr/en/call/crea...
#JobOpportunity #Research
Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies
📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD
Apply now 📝 research.pasteur.fr/en/call/crea...
#JobOpportunity #Research
Creation of new junior research groups at the Institut Pasteur - Call for applications 2026 - Research
The Institut Pasteur is launching an international call to recruit new junior research group leaders leveraging cutting-edge transdisciplinary approaches to exploring infectious diseases, host-microbe...
research.pasteur.fr
December 8, 2025 at 8:53 AM
🔬 Call to create junior research groups at the Institut Pasteur
Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies
📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD
Apply now 📝 research.pasteur.fr/en/call/crea...
#JobOpportunity #Research
Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies
📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD
Apply now 📝 research.pasteur.fr/en/call/crea...
#JobOpportunity #Research
Reposted by Aude Bernheim
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
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
December 4, 2025 at 1:56 PM
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
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
Reposted by Aude Bernheim
🌍👏 We’re proud to share that @sebbaumgarten.bsky.social, group leader at the Institut Pasteur, has been selected as an EMBO Young Investigator 2025!
This program supports outstanding young scientists building their labs across Europe and beyond.
More : www.embo.org/funding/fell...
@embo.org
This program supports outstanding young scientists building their labs across Europe and beyond.
More : www.embo.org/funding/fell...
@embo.org
December 3, 2025 at 3:12 PM
🌍👏 We’re proud to share that @sebbaumgarten.bsky.social, group leader at the Institut Pasteur, has been selected as an EMBO Young Investigator 2025!
This program supports outstanding young scientists building their labs across Europe and beyond.
More : www.embo.org/funding/fell...
@embo.org
This program supports outstanding young scientists building their labs across Europe and beyond.
More : www.embo.org/funding/fell...
@embo.org
A New-York edition of the Symposium of Immune Sytems of Bacteria.
So looking forward to this. Fantastic science and energy in perspective and well New-York 🤩🧫🗽.
So looking forward to this. Fantastic science and energy in perspective and well New-York 🤩🧫🗽.
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
sisb2026.rockefeller.edu
SISB2026
sisb2026.rockefeller.edu
December 2, 2025 at 7:15 AM
A New-York edition of the Symposium of Immune Sytems of Bacteria.
So looking forward to this. Fantastic science and energy in perspective and well New-York 🤩🧫🗽.
So looking forward to this. Fantastic science and energy in perspective and well New-York 🤩🧫🗽.
Reposted by Aude Bernheim
How does fever work?
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Avian-origin influenza A viruses tolerate elevated pyrexic temperatures in mammals
Host body temperature can define a virus’s replicative profile—influenza A viruses (IAVs) adapted to 40° to 42°C in birds are less temperature sensitive in vitro compared with human isolates adapted t...
www.science.org
November 27, 2025 at 7:55 PM
How does fever work?
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Reposted by Aude Bernheim
Emergence of a bacterial immune mechanism by incorporating pre-existing cellular machinery. A lesson in the evolution of cell-autonomous defences. Fantastic work by the Bernheim/Patel labs.
🧬🛡️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 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...
November 27, 2025 at 10:28 PM
Emergence of a bacterial immune mechanism by incorporating pre-existing cellular machinery. A lesson in the evolution of cell-autonomous defences. Fantastic work by the Bernheim/Patel labs.
Reposted by Aude Bernheim
The mechanism of Lamassu, an abundant bacterial immune system, is now solved
Lamassu evolved from a DNA repair complex
Beautiful study from the Patel, Bernheim and Sternberg labs
Lamassu evolved from a DNA repair complex
Beautiful study from the Patel, Bernheim and Sternberg labs
🧬🛡️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 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...
November 27, 2025 at 7:08 PM
The mechanism of Lamassu, an abundant bacterial immune system, is now solved
Lamassu evolved from a DNA repair complex
Beautiful study from the Patel, Bernheim and Sternberg labs
Lamassu evolved from a DNA repair complex
Beautiful study from the Patel, Bernheim and Sternberg labs
🧬🛡️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 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...
November 27, 2025 at 9:35 AM
🧬🛡️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 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...
Reposted by Aude Bernheim
🔥 At conferences, who asks the questions shapes who gets seen. Across 24 ID&CM meetings, women were 55% of delegates but asked 36% of questions.
💬 When women moderate or speak first, others follow.
Let’s change the pattern
bit.ly/47VL0eH
🙏 @maudsalmona.bsky.social & MicroID EmpowHERment consortium
💬 When women moderate or speak first, others follow.
Let’s change the pattern
bit.ly/47VL0eH
🙏 @maudsalmona.bsky.social & MicroID EmpowHERment consortium
November 13, 2025 at 9:48 AM
🔥 At conferences, who asks the questions shapes who gets seen. Across 24 ID&CM meetings, women were 55% of delegates but asked 36% of questions.
💬 When women moderate or speak first, others follow.
Let’s change the pattern
bit.ly/47VL0eH
🙏 @maudsalmona.bsky.social & MicroID EmpowHERment consortium
💬 When women moderate or speak first, others follow.
Let’s change the pattern
bit.ly/47VL0eH
🙏 @maudsalmona.bsky.social & MicroID EmpowHERment consortium
Reposted by Aude Bernheim
🚨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
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
November 20, 2025 at 8:40 PM
🚨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
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
Reposted by Aude Bernheim
Bacterial networks #BacNet26 in September 2026 will be chaired by @lalouxlab.bsky.social and co-chaired by @s-lab.bsky.social with @coralietesseur.bsky.social
Sneak peak on invited speakers and preliminary program:
meetings.embo.org/event/26-bac...
Sneak peak on invited speakers and preliminary program:
meetings.embo.org/event/26-bac...
November 20, 2025 at 8:47 AM
Bacterial networks #BacNet26 in September 2026 will be chaired by @lalouxlab.bsky.social and co-chaired by @s-lab.bsky.social with @coralietesseur.bsky.social
Sneak peak on invited speakers and preliminary program:
meetings.embo.org/event/26-bac...
Sneak peak on invited speakers and preliminary program:
meetings.embo.org/event/26-bac...
Reposted by Aude Bernheim
Are you looking for female speakers in CryoEM for seminars and conferences? Are you a woman in CryoEM and not yet on the ‚woman in CryoEM‘ list? Find your speakers and add/update name and affiliation! docs.google.com/spreadsheets...
November 18, 2025 at 10:18 AM
Are you looking for female speakers in CryoEM for seminars and conferences? Are you a woman in CryoEM and not yet on the ‚woman in CryoEM‘ list? Find your speakers and add/update name and affiliation! docs.google.com/spreadsheets...
Akin to bacterial SIR2 antiphage proteins, human SIRal, also known as FAM118b, forms filaments that are essential for its NAD processing activity.
Awesome to see structures of these filaments that differ from bacterial ones.
Congrats to the authors on this beautiful study.
Awesome to see structures of these filaments that differ from bacterial ones.
Congrats to the authors on this beautiful study.
Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.
Filament formation and NAD processing by noncanonical human FAM118 sirtuins
Nature Structural & Molecular Biology - Baretić and Missoury et al. identify vertebrate proteins FAM118B and FAM118A as sirtuins similar to bacterial antiphage enzymes and show that...
rdcu.be
November 17, 2025 at 4:52 PM
Akin to bacterial SIR2 antiphage proteins, human SIRal, also known as FAM118b, forms filaments that are essential for its NAD processing activity.
Awesome to see structures of these filaments that differ from bacterial ones.
Congrats to the authors on this beautiful study.
Awesome to see structures of these filaments that differ from bacterial ones.
Congrats to the authors on this beautiful study.
Reposted by Aude Bernheim
Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.
Filament formation and NAD processing by noncanonical human FAM118 sirtuins
Nature Structural & Molecular Biology - Baretić and Missoury et al. identify vertebrate proteins FAM118B and FAM118A as sirtuins similar to bacterial antiphage enzymes and show that...
rdcu.be
November 17, 2025 at 11:37 AM
Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.
Reposted by Aude Bernheim
Are you passionate about the mathematics of data science, computational geometry and topology and want to apply your skills to a beautiful biological question?
Come do a PhD with us!
You will help us understand of how boundaries are established and maintained in early heart development.
Come do a PhD with us!
You will help us understand of how boundaries are established and maintained in early heart development.
November 15, 2025 at 3:42 PM
Are you passionate about the mathematics of data science, computational geometry and topology and want to apply your skills to a beautiful biological question?
Come do a PhD with us!
You will help us understand of how boundaries are established and maintained in early heart development.
Come do a PhD with us!
You will help us understand of how boundaries are established and maintained in early heart development.
Reposted by Aude Bernheim
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
Thanks to wonderful coauthors/collaborators/friends, the whole @doudna-lab.bsky.social and everyone at @innovativegenomics.bsky.social
Recurrent acquisition of nuclease-protease pairs in antiviral immunity
Antiviral immune systems diversify by integrating new genes into existing pathways, creating new mechanisms of viral resistance. We identified genes encoding a predicted nuclease paired with a trypsin...
www.science.org
November 13, 2025 at 10:15 PM
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
Thanks to wonderful coauthors/collaborators/friends, the whole @doudna-lab.bsky.social and everyone at @innovativegenomics.bsky.social
An incredible honor for an incredible scientist!
Congratulations Nitzan 💫👏
Congratulations Nitzan 💫👏
Congratulations to Sorek lab alumnus Nitzan Tal, who won the prestigious 2025 Science & SciLifeLab prize for the best PhD thesis in Systems Biology! 💫
Read her Prize Assay, published in the journal Science today
www.science.org/doi/10.1126/...
@nitzantal.bsky.social
Read her Prize Assay, published in the journal Science today
www.science.org/doi/10.1126/...
@nitzantal.bsky.social
November 14, 2025 at 9:55 PM
An incredible honor for an incredible scientist!
Congratulations Nitzan 💫👏
Congratulations Nitzan 💫👏
Such an elegant mechanism. Perfect to make November more fun.
Also, we wrote a review about NAD+ and bacterial immunity, that came out last month. Thanks Ilya for making it outdated already :).
Congrats to everyone for a beautiful discovery!
Also, we wrote a review about NAD+ and bacterial immunity, that came out last month. Thanks Ilya for making it outdated already :).
Congrats to everyone for a beautiful discovery!
Bacteria 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...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
November 6, 2025 at 8:50 AM
Such an elegant mechanism. Perfect to make November more fun.
Also, we wrote a review about NAD+ and bacterial immunity, that came out last month. Thanks Ilya for making it outdated already :).
Congrats to everyone for a beautiful discovery!
Also, we wrote a review about NAD+ and bacterial immunity, that came out last month. Thanks Ilya for making it outdated already :).
Congrats to everyone for a beautiful discovery!
Reposted by Aude Bernheim
Bacteria 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...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:00 AM
Bacteria 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...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Hi everyone, a few years ago, we started a list of labs studying bacterial immunty for students, editors, conference organizers... (currently n=79).
Update time ! Send me a message to 1) add your lab or others 2) Correct info
docs.google.com/spreadsheets...
#Phagesky #Microsky
Update time ! Send me a message to 1) add your lab or others 2) Correct info
docs.google.com/spreadsheets...
#Phagesky #Microsky
Labs in bacterial immunity
docs.google.com
November 4, 2025 at 3:06 PM
Hi everyone, a few years ago, we started a list of labs studying bacterial immunty for students, editors, conference organizers... (currently n=79).
Update time ! Send me a message to 1) add your lab or others 2) Correct info
docs.google.com/spreadsheets...
#Phagesky #Microsky
Update time ! Send me a message to 1) add your lab or others 2) Correct info
docs.google.com/spreadsheets...
#Phagesky #Microsky
Reposted by Aude Bernheim
Exciting day for the lab: our 1rst paper is officially out in @currentbiology.bsky.social 🥳 Wonderful collaboration wt @gautamdey.bsky.social showing how Cryo-ExM achieves consistent immunostaining in diverse diatoms, from the lab and the natural environment 1/n
#ProtistsOnSky
tinyurl.com/2zxaund7
#ProtistsOnSky
tinyurl.com/2zxaund7
October 31, 2025 at 3:27 PM
Exciting day for the lab: our 1rst paper is officially out in @currentbiology.bsky.social 🥳 Wonderful collaboration wt @gautamdey.bsky.social showing how Cryo-ExM achieves consistent immunostaining in diverse diatoms, from the lab and the natural environment 1/n
#ProtistsOnSky
tinyurl.com/2zxaund7
#ProtistsOnSky
tinyurl.com/2zxaund7
Reposted by Aude Bernheim
NAD+ is a central molecule in bacterial immunity. An excellent and timely review by Hugo Vausset and Aude Bernheim
Many antiphage systems use NAD+, in many ways.
@hugovaysset.bsky.social reviewed them all!
Read to know more about all their molecular mechanisms, how phages counteract them, their distribution in bacteria and their conservation in eukaryotic immunity!
www.cell.com/molecular-ce...
@hugovaysset.bsky.social reviewed them all!
Read to know more about all their molecular mechanisms, how phages counteract them, their distribution in bacteria and their conservation in eukaryotic immunity!
www.cell.com/molecular-ce...
The multifaceted roles of NAD+ in bacterial immunity
In this review, Vaysset and Bernheim examine how nicotinamide adenine dinucleotide
(NAD+) is a key player in diverse and widespread bacterial antiphage defense systems
and phage counterdefense. The au...
www.cell.com
October 18, 2025 at 2:56 PM
NAD+ is a central molecule in bacterial immunity. An excellent and timely review by Hugo Vausset and Aude Bernheim