David Bikard
@dbikard.bsky.social
Bacterial Immunity and Synthetic Biology enthusiast. Head of Lab at Institut Pasteur. Co-Founder of Eligo Bioscience.
Reposted by David Bikard
Reposted by David Bikard
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:26 PM
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
Very interesting strategy to sense infection!
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 7:39 AM
Very interesting strategy to sense infection!
Reposted by David Bikard
Reposted by David Bikard
Reposted by David Bikard
@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Jumbo phage–mediated transduction of genomic islands | PNAS
Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile
genetic elements (MGEs). While plasmids, bacteriophages, and c...
www.pnas.org
October 28, 2025 at 6:36 PM
@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Reposted by David Bikard
🧬🔬🦠🧫🧪@science.org Escherichia coli with a 57-codon genetic code | Science www.science.org/doi/10.1126/...
October 23, 2025 at 9:51 PM
🧬🔬🦠🧫🧪@science.org Escherichia coli with a 57-codon genetic code | Science www.science.org/doi/10.1126/...
Reposted by David Bikard
Happy that the final version of our Lamassu work @yli18smc.bsky.social is now out:
www.nature.com/articles/s41...
Thanks again to our awesome collaborators @mblokesch.bsky.social and David and co and Mark Szczelkun and @steven-shaw.bsky.social and the DCI Lausanne @fbm-unil.bsky.social
www.nature.com/articles/s41...
Thanks again to our awesome collaborators @mblokesch.bsky.social and David and co and Mark Szczelkun and @steven-shaw.bsky.social and the DCI Lausanne @fbm-unil.bsky.social
Glad to share the work of @yli18smc.bsky.social and co on Lamassu, a bacterial defense system related to Rad50/Mre11 (RM). While RM carefully trims DNA ends for repair, Lamassu chops up the host chromosome. Our study reveals how it is regulated to minimize damage, activating only during infection.
October 14, 2025 at 9:28 AM
Happy that the final version of our Lamassu work @yli18smc.bsky.social is now out:
www.nature.com/articles/s41...
Thanks again to our awesome collaborators @mblokesch.bsky.social and David and co and Mark Szczelkun and @steven-shaw.bsky.social and the DCI Lausanne @fbm-unil.bsky.social
www.nature.com/articles/s41...
Thanks again to our awesome collaborators @mblokesch.bsky.social and David and co and Mark Szczelkun and @steven-shaw.bsky.social and the DCI Lausanne @fbm-unil.bsky.social
Reposted by David Bikard
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...
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...
Antiviral reverse transcriptases reveal the evolutionary origin of telomerase
Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...
www.biorxiv.org
October 17, 2025 at 5:22 PM
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...
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...
Reposted by David Bikard
Perfect timing in the field for a beautiful review on NAD+ in bacterial immunity by @hugovaysset.bsky.social and @audeber.bsky.social @cp-molcell.bsky.social
#MicroSky
www.cell.com/molecular-ce...
#MicroSky
www.cell.com/molecular-ce...
October 16, 2025 at 2:58 PM
Perfect timing in the field for a beautiful review on NAD+ in bacterial immunity by @hugovaysset.bsky.social and @audeber.bsky.social @cp-molcell.bsky.social
#MicroSky
www.cell.com/molecular-ce...
#MicroSky
www.cell.com/molecular-ce...
Reposted by David Bikard
Two intensive sampling periods of oyster-associated vibrio and their phage, 4 years apart, and many surprises. Despite being washed by the Atlantic, wide tides, and vibrio (almost?) disappearing most of the year, we can find the exact same virulent phages 4 years later (down to 0 SNP)! preprint👇
October 14, 2025 at 4:08 PM
Two intensive sampling periods of oyster-associated vibrio and their phage, 4 years apart, and many surprises. Despite being washed by the Atlantic, wide tides, and vibrio (almost?) disappearing most of the year, we can find the exact same virulent phages 4 years later (down to 0 SNP)! preprint👇
Reposted by David Bikard
Excited to share our preprint led by Carlos Voogdt et al
We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...
We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...
October 13, 2025 at 7:48 AM
Excited to share our preprint led by Carlos Voogdt et al
We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...
We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...
Reposted by David Bikard
www.science.org/doi/10.1126/... Another breakthrough work on the fascinating biology of Diversity Generating Retroelements by Jeff Miller’s team
Targeted protein evolution in the gut microbiome by diversity-generating retroelements
Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, su...
www.science.org
October 12, 2025 at 7:34 PM
www.science.org/doi/10.1126/... Another breakthrough work on the fascinating biology of Diversity Generating Retroelements by Jeff Miller’s team
Entretien pour Brut sur la vie Miroir, l'ingénierie génétique et l'éthique de ces recherches: www.brut.media/fr/videos/sc...
Manipulations génétiques, virus créés par l’IA, bactéries miroirs : quelles limites à la recherche scientifique ?
Elles pourraient aider à lutter contre les cancers… mais aussi détruire toute trace de vie sur Terre ! Ce sont les bactéries miroirs. En avez-vous déjà entendu parler ? Et la vie miroir, ça vous dit q...
www.brut.media
October 11, 2025 at 1:30 PM
Entretien pour Brut sur la vie Miroir, l'ingénierie génétique et l'éthique de ces recherches: www.brut.media/fr/videos/sc...
Reposted by David Bikard
Congratulations to Philip J. Kranzusch, Ph.D., Professor of Cancer Immunology and Virology, who was one of three scientists awarded top honors at the 2025 Blavatnik National Awards for Young Scientists.
Watch to learn more about his work: bit.ly/4pZUDkF
Watch to learn more about his work: bit.ly/4pZUDkF
October 8, 2025 at 5:05 PM
Congratulations to Philip J. Kranzusch, Ph.D., Professor of Cancer Immunology and Virology, who was one of three scientists awarded top honors at the 2025 Blavatnik National Awards for Young Scientists.
Watch to learn more about his work: bit.ly/4pZUDkF
Watch to learn more about his work: bit.ly/4pZUDkF
Reposted by David Bikard
Our work on the Panoptes antiphage system is published! Here we find that Panoptes "watches" the cytosol for phage immune evasion proteins–captured in this illustration by Clair Huffine of Insight Illustrations. A beautiful example of the effector triggered immunity paradigm.
October 8, 2025 at 11:14 AM
Our work on the Panoptes antiphage system is published! Here we find that Panoptes "watches" the cytosol for phage immune evasion proteins–captured in this illustration by Clair Huffine of Insight Illustrations. A beautiful example of the effector triggered immunity paradigm.
Reposted by David Bikard
Viral AlphaFold Database (VAD) is live in Science Advances
~27,000 predicted viral protein monomers & homodimers
Conserved folds across bacteria, archaea & eukaryotic viruses
New toxin–antitoxin system KreTA uncovered
Vast “functional darkness” remains uncharted
www.science.org/doi/10.1126/...
~27,000 predicted viral protein monomers & homodimers
Conserved folds across bacteria, archaea & eukaryotic viruses
New toxin–antitoxin system KreTA uncovered
Vast “functional darkness” remains uncharted
www.science.org/doi/10.1126/...
The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes
VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.
www.science.org
October 2, 2025 at 8:48 AM
Viral AlphaFold Database (VAD) is live in Science Advances
~27,000 predicted viral protein monomers & homodimers
Conserved folds across bacteria, archaea & eukaryotic viruses
New toxin–antitoxin system KreTA uncovered
Vast “functional darkness” remains uncharted
www.science.org/doi/10.1126/...
~27,000 predicted viral protein monomers & homodimers
Conserved folds across bacteria, archaea & eukaryotic viruses
New toxin–antitoxin system KreTA uncovered
Vast “functional darkness” remains uncharted
www.science.org/doi/10.1126/...
Je viens de tomber sur ce passage des Frères Karamazov au sujet de la Russie qu'on aurait dit être écrit pour aujourd'hui: "Et il y a longtemps déjà que, dans toute la Russie, on tend les mains et on supplie que soit arrêtée cette course furieuse qui n’épargne rien. ..
October 5, 2025 at 8:29 AM
Je viens de tomber sur ce passage des Frères Karamazov au sujet de la Russie qu'on aurait dit être écrit pour aujourd'hui: "Et il y a longtemps déjà que, dans toute la Russie, on tend les mains et on supplie que soit arrêtée cette course furieuse qui n’épargne rien. ..
Reposted by David Bikard
Finally out, such an awesome piece of work, very proud of this one: www.cell.com/cell-systems... #MicroSky
October 4, 2025 at 8:48 AM
Finally out, such an awesome piece of work, very proud of this one: www.cell.com/cell-systems... #MicroSky
Reposted by David Bikard
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...
Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
www.nature.com
October 1, 2025 at 5:57 PM
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...
Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...
Reposted by David Bikard
For decades, human genome editing has been limited to small, localized modifications.
Today, in a new paper published in @science.org , researchers from Arc's Hsu lab show that bridge recombinase technology is capable of large-scale genomic rearrangements in human cells.
Today, in a new paper published in @science.org , researchers from Arc's Hsu lab show that bridge recombinase technology is capable of large-scale genomic rearrangements in human cells.
September 25, 2025 at 6:27 PM
For decades, human genome editing has been limited to small, localized modifications.
Today, in a new paper published in @science.org , researchers from Arc's Hsu lab show that bridge recombinase technology is capable of large-scale genomic rearrangements in human cells.
Today, in a new paper published in @science.org , researchers from Arc's Hsu lab show that bridge recombinase technology is capable of large-scale genomic rearrangements in human cells.
Reposted by David Bikard
Recent paper from the lab studying predictors of phage cocktail efficacy against complex clinical Pseudomonas populations
royalsocietypublishing.org/doi/epdf/10....
Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska
royalsocietypublishing.org/doi/epdf/10....
Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska
Bacteria–phage infection network structure and genomic defence system content predict efficacy of a phage therapy cocktail against Pseudomonas aeruginosa from chronic lung infections
royalsocietypublishing.org
September 25, 2025 at 1:55 PM
Recent paper from the lab studying predictors of phage cocktail efficacy against complex clinical Pseudomonas populations
royalsocietypublishing.org/doi/epdf/10....
Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska
royalsocietypublishing.org/doi/epdf/10....
Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska
Reposted by David Bikard
Reposted by David Bikard
Delighted to share our recently published work!
Ever wondered how Klebsiella (and others) deals with capsule production’s costs ?
The paper: journals.asm.org/doi/10.1128/...
Thread👇
Ever wondered how Klebsiella (and others) deals with capsule production’s costs ?
The paper: journals.asm.org/doi/10.1128/...
Thread👇
Phenotypic heterogeneity of capsule production across opportunistic pathogens | mBio
The polysaccharidic capsule is present in ~50% of species across the bacterial phylogeny, including all ESKAPE microorganisms, the six most significant multidrug-resistant (MDR) nosocomial pathogens. It is also an important virulence factor and a major ...
journals.asm.org
September 5, 2025 at 1:49 PM
Delighted to share our recently published work!
Ever wondered how Klebsiella (and others) deals with capsule production’s costs ?
The paper: journals.asm.org/doi/10.1128/...
Thread👇
Ever wondered how Klebsiella (and others) deals with capsule production’s costs ?
The paper: journals.asm.org/doi/10.1128/...
Thread👇
Reposted by David Bikard
De novo design of All-atom biomolecular interactions with RFdiffusion3 www.biorxiv.org/content/10.1...
De novo Design of All-atom Biomolecular Interactions with RFdiffusion3
Deep learning has accelerated protein design, but most existing methods are restricted to generating protein backbone coordinates and often neglect interactions with other biomolecules. We present RFd...
www.biorxiv.org
September 19, 2025 at 10:32 AM
De novo design of All-atom biomolecular interactions with RFdiffusion3 www.biorxiv.org/content/10.1...