David Bikard

Very nice discovery from the Jackson, Bravo and Basel labs. Cleaved tRNA ends, loaded with an amino acid, activate a form of bacterial immunity

Want to run targeted hypermutation in E. coli? You can now order our DGRec plasmids from Addgene: www.addgene.org/browse/artic... We recommend using them in a strain with sbcB and recJ deletions such as this one: www.addgene.org/220588/

How does a single methyl group activate bacterial defence? Our new preprint, led by @pspatharas.bsky.social in collaboration with the group of @matthiaswilmanns.bsky.social, explains how a single DNA methylation event activates large retron assemblies. www.biorxiv.org/content/10.6...

1. CRISPR came from basic research on bacteria. 2. Optogenetics started with a discovery in algae. 3. The GFP protein comes from jellyfish. The biggest breakthroughs all trace to scientists following their curiosity, and this is one huge reason why we must keep funding basic research!

New @science.org A breakthrough in understanding why do we get fever and an inflammation response to vaccines. The gut microbiome chronic production of flagellin Paves the way to potentially prevent these acute phase side-effects in the future www.science.org/doi/10.1126/...

Very happy that this work found a good home at @pnas.org Thanks to the reviewers for their constructive comments. www.pnas.org/doi/10.1073/...

Out Now! Defining the essential genome of diverse phages with phage Tn-seq #MicroSky

Very happy to share that HIDEN-SEQ is now out in @natmicrobiol.nature.com! Using this technique, we recapitulated decades of established phage genetics and uncovered new gene functions, including previously unknown anti-defense factors against several defense systems. www.nature.com/articles/s41...

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.

Interested in #archaea, #methane, #cell-envelopes? New paper out @nature.com ! We discovered an enzyme that specifically cleaves the cell wall of methanogens, revealing a new chemical structure of archaeal peptidoglycan, 50 yrs after its first description www.nature.com/articles/s41... #MicroSky 🧵👇

Amandine is looking for a postdoc position. Get her if you can!!!

ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...

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

Some of the smallest 😎 viruses on Earth are all around us. Three or four genes 😍 each, in nearly every environment. We keep finding thousands by sequencing, yet don't know who they infect, can't easily isolate them, or even how the few we have infect a cell. Our new preprint takes this on 🧵👇

Out now in Science: Two papers from our lab reveal VIPR, an RNA-guided DNA-targeting system in bacteriophages, providing clues to the origins of CRISPR www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... Congrats to Peter Yoon, @kenjmloi.bsky.social @terryzzy.bsky.social, T.Docter & team

I wrote about what came before CRISPR 4 billion years ago: a war among viruses. Gift link: nyti.ms/3TBq4q0

Microbial intergenic regions encode much of the regulatory and functional logic of the genome, but they remain systematically difficult to discover and annotate. We trained a sparse autoencoder on gLM2 to identify recurring patterns across hundreds of millions of microbial intergenic regions... 🧵

Out Now! Prophage-encoding engineered bacteria enable prophylactic lytic phage therapy for enteric infection in mice #MicroSky

Ten years ago Tami, Roy, and I released a movie we made of antibiotic resistance evolving in real time. I thought maybe a couple thousand people tops would see it. I couldn't have imagined it would be seen millions of times, and be taught from middle school through the graduate level worldwide

Antiviral defence is a conserved function of diverse bacterial DNA glycosylases www.nature.com/articles/s41...

Foldseek-Interface enables fast search/clustering of the protein interface universe! We clustered 3.1M PDB dimers into 77,167 groups and found new interfaces keep appearing even as fold discovery plateaus. 🧵 📄 www.biorxiv.org/content/10.6... 🔎 search.foldseek.com/interface 🌐 interface.foldseek.com

Very happy that our paper Obligate cross-feeding of metabolites is common in soil microbial communities just came out in Nature Microbiology. See here 👇 Paywalled version: www.nature.com/articles/s41... Free read-only version: rdcu.be/fBHAb

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...

We are PUBLISHED!!! Our mechanistic work on how CRISPR-Cas ancestors unwind DNA and how this can be used to engineer hypercompact plant editors can now be found on Mol Cell- if you are interested in what defines a good genome editor, this read is for you 😎 🔗 www.sciencedirect.com/science/arti...

Out Now! Phage hijacks host phosphorothioate DNA modification machinery to circumvent bacterial Ssp defences #MicroSky

“Resistance did not arise from mutation accumulation or strain displacement. Instead, it occurred because plasmid-borne resistance genes were transferred to the previously sensitive pathogens inside patients’ lungs”. Cool (sobering) study #AMR #MicroSky #IDSKy #CysticFibrosis

Come work on exciting AI for biology projects in Paris!! 🇫🇷 Details and application below, deadline sept 1st!

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...

Stunning pre-print from @artemisaev.bsky.social @dbikard.bsky.social and the Wang lab answering long-standing questions about OLD phage defense and extending the concept of "protein complex disassembly" controlling activation of bacterial immunity: www.biorxiv.org/content/10.6...

🚨 We're hiring! My new lab at EMBL Hamburg is looking for a Research Technician. I'm looking for someone excited by phages, metabolism, enzymes, structural biology and bacterial immunity—if you know the right person, please share this post!🧵⬇️ Apply here: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Thrilled to share! We present the structure of a prototypical P2 OLD and reveal that its tRNAse activity is triggered by ssDNA hairpins in phage origins or unresolved termini in RecBCD-deficient cells. Great team effort with Wang, Bikard & Nudler labs. www.biorxiv.org/content/10.6...

Our paper out in Science today: The Metis defense system senses molecular byproducts released when a phage degrades the bacterial genome, and then prevents replication of the phage in the infected cell Congratulations @ostermanilya.bsky.social and co-authors!

Si les nouvelles règles de l'éligibilité de l'ANR sont bien réelles, alors je ne comprends pas quelle est la logique sous jacente. Au vu de la pyramide des ages, forcer une collaboration avec chercheurs(ses) <10 ans post thèse va de facto exclure 80% des candidats.

Les nouvelles règles d'éligibilité de l'AAPG 2027 de @agencerecherche.bsky.social sont une catastrophe. Comment se fait-il qu'il n'y ait pas plus de réactions dans la communauté ? Sommes-nous à ce point résignés, ou individualistes ? #ESR

Functional divergence and conservation in the QueC protein family (PF06508): from tRNA modification to anti-phage defense 🦠 portlandpress.com/biochemj/art...

Very cool findings!

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

Organisers @lisamaierlab.bsky.social @kiranrpatil.bsky.social @robdfinn.bsky.social @embl.org @events.embl.org Speakers Ami Bhatt @dbikard.bsky.social Xiang Gao kc-huang.bsky.social @jhcepas.bsky.social @microbegrrl.bsky.social @keyfm.bsky.social @microbiome.bsky.social Elisabeth Lowe ...

1/4 Excited to share our new preprint on phage genome editing: Targeted DNA nicking enables efficient, single-step and counterselection-free editing of bacteriophage genomes Preprint: lnkd.in/dv4g5kW6

Finally published. Many thanks to a wonderful collaborative team and scientific platforms!!! And thanks to editors and reviewers for enthusiasm and a great review. www.nature.com/articles/s41...

Back to the age of emperors and gladiator shows to please the crowd!