A recipient-based anti-conjugation factor triggers an abortive mechanism by targeting the Type IV secretion system https://www.biorxiv.org/content/10.64898/2026.03.10.710775v1

Capturing dynamic phage–pathogen coevolution by clinical surveillance @nature.com @ucberkeleyofficial.bsky.social
www.nature.com/articles/s41...

Semirandom DNA adducts regulate a filamentous defence-associated reverse transcriptase https://www.biorxiv.org/content/10.64898/2026.03.07.710306v1

Structural and mechanistic insights into the dual-nuclease defense protein Upx as an anti-phage system | Nature Communications https://www.nature.com/articles/s41467-026-70435-x

Our work on bacterial Schlafens in phage defense is out today @natmicrobiol.nature.com!

Check out the final version here:
rdcu.be/e7Bmz

We are looking for postdocs and students to expand our team! Official postings are coming soon.

Please reach out if you're interested!
#phage #phagesky #microsky

CBASS is a cyclic nucleotide-based antiviral system in bacteria that is related to cGAS-STING signaling in animals. One of the big questions is how CBASS is activated during phage infection? We made some progress on this during my final year in the Kranzusch lab.
www.biorxiv.org/content/10.6...

With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268

Elegant study from @erinhuiting.bsky.social @jbdsf.bsky.social on CBASS phage inhibition without loss of cell viability. Especially interesting to see this phenotype with a CapV membrane-targeting effector and evidence for 3'3'-cGAMP transport!

www.biorxiv.org/content/10.6...

1/5
Happy by a recent biorxiv pre-print about DARNA (PD-T7-3) anti-phage defense system. This system is activated by binding to ssDNA, presented by phage SSB, to cleave tRNA in the anti-codon loop.
www.biorxiv.org/content/10.6...

New preprint on Detectrons from @jihoon-han.bsky.social! These are programmable biosensors for RNA that produce DNA barcodes in the presence of their target RNA. Check out Jihoon's quoted thread and the preprint for more:
www.biorxiv.org/content/10.6...

We found a new mode by which bacteria deplete NAD+ to protect from phages. And then we found how phages overcome this defense

Discovered by talented biochemist Dr Ilya Osterman, read the preprint: tinyurl.com/Narp-ap

A thread 🧵

Preprint out: We characterise PUA-Cal-HAD, a widespread bacterial antiphage defence family. An infection cue switches a preassembled complex into an immune filament that drains dNTPs via a coupled two-enzyme cascade, and phage DNA mimics can block filament assembly (anti-polymerisation).

Most plasmids described in E. coli are small compared to the megaplasmids we identified here! Check out the preprint if you want to learn about these mysterious large elements and their potential functions 🧬. I’m very grateful to have had the opportunity to work on this in @banfieldlab.bsky.social

RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity - Nature Cas12a3 nucleases constitute a distinct clade of type V CRISPR–Cas bacterial immune systems that preferentially cleave the 3′ tails of tRNAs after recognition of target RNA to induce growth arres...

Our paper is out! Hiding in plain sight among Cas12a nucleases, Cas12a3 cleaves not its RNA target but the 3′ ends of tRNA. Huge thanks to all who made this possible, especially the Beisel lab, Biao & Dirk for the structure, & @sebastianglatt.bsky.social for all things tRNA. doi.org/10.1038/s415...

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.

Structural basis of Retron-Eco8-mediated anti-phage defense https://www.biorxiv.org/content/10.64898/2025.12.04.692459v1

The Ppl protein senses 3′-hydroxyl DNA overhangs and NTP depletion to halt phage infection Xu et al. reveal that the Ppl defense system protects bacteria from phages by acting as a “double-check” security system. It requires two simultaneous phage-induced stresses to activate, a sophisticated mechanism that ensures effective immunity while preventing premature abortive infection.

Online Now: The Ppl protein senses 3′-hydroxyl DNA overhangs and NTP depletion to halt phage infection Online now:

Structural mechanism of the Retron-Eco7 anti-phage defense system - Nature Communications The Retron-Eco7 is a genetic element involved in anti-phage defense that encodes two effector proteins (PtuA and PtuB) and cleaves the host tRNA. Here, the authors solved the Retron-Eco7 complex struc...

www.nature.com/articles/s41...

Structural mechanism of the Retron-Eco7 anti-phage defense system

⭐ NAR Breakthrough! ⭐
🦠 New study shows phage X1 hijacks Yersinia's enterocolitica flagellum to inject its DNA directly into the cytosol. Yersinia, though, strikes back!
🦠 A fascinating look at the #dualrole of #flagella in #viralentry and #bacterialimmunity.
🧬 Read more: doi.org/10.1093/nar/...

Bacteriophage genome-wide transposon mutagenesis https://www.biorxiv.org/content/10.1101/2025.11.23.690004v1

🚨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

Systematic mapping of bacteriophage gene essentiality with HIDEN‑SEQ The constant arms race of bacteriophages and their bacterial hosts has inspired major breakthroughs in biotechnology and shaped phages as fierce predators with great clinical potential to fight multid...

First the link to the preprint: www.biorxiv.org/content/10.1...

I’m excited to share my recent postdoc work. Here, we interrogate how different phage infection outcomes (productive vs. restrictive) affect the expression of phage defense systems. We find that a restricted infection not only inhibits the phage but also induces increased immune protein abundance.

Surviving phage attack dynamically regulates bacterial immunity to defeat counterdefenses https://www.biorxiv.org/content/10.1101/2025.11.13.688357v1

Cap1 forms a cyclic tetra-adenylate-induced membrane pore during the type III-A CRISPR-Cas immune response https://www.biorxiv.org/content/10.1101/2025.11.13.688252v1

Scalable and systematic hierarchical virus taxonomy with vConTACT3 Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...

🚨vConTACT3 preprint live!🚨(Peer Review soon...!)

vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.

🔗 Read the preprint: doi.org/10.1101/2025...

Improvements details below 👇

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...

A membrane-bound nuclease directly cleaves phage DNA during genome injection https://www.biorxiv.org/content/10.1101/2025.11.03.685801v1

Phage SSB detection by retron Eco8 msDNA unleashes nuclease-mediated immunity The cryo-EM structure of the retron Eco8 system reveals an autoinhibited 4:4:4 complex of RT, msDNA, and OLD nuclease. Phage SSB binding to msdDNA unleashes non-specific nuclease activity to restrict ...

I’m thrilled to share our Retron Eco8 paper published in Molecular Cell today. Thanks all Fu lab members and our collaborators.
👉Phage SSB detection by retron Eco8 msDNA unleashes nuclease-mediated immunity. www.cell.com/molecular-ce...

Been working on a really strange retron bacterial immune system, here's the preprint: www.biorxiv.org/content/10.1...
Type VI retrons are unlike any other. Phage infection triggers reverse transcription of a DNA fragment that activates translation of a toxin to kill the infected cell.