How do human cells defend against viruses? @sgfern.bsky.social discovers that human immune proteins named ISGs target ancient features of replication shared between animal and bacterial viruses – opening analysis of human immunity to the power of bacterial genetics www.biorxiv.org/content/10.6...

#microsky #phagesky #phage www.nature.com/articles/s41...

CapK is a bacterial DNA damage-activated kinase that phosphorylates transcriptional repressor CapS to control adjacently-encoded anti-phage immune pathway genes in response to a universal stress signal, DNA damage @kevincorbett.bsky.social and colleagues link.springer.com/article/10.1...

We now present our latest work, now out in @nature.com! A creative new CRISPR-based approach can selectively destroy cells carrying undruggable mutations in cancer. Work led by @jingkunzeng.bsky.social In collaboration with Alan Ashworth, Yang Liu and Ryan Jackson. www.nature.com/articles/s41...

STOP using ipTM for #AlphaFold PPI screens. * Artificially LOW when both full-length proteins have irrelevant, non-binding IDRs/domains. * If one protein is folded & other contains irrelevant IDRs or domains, the score is too HIGH bc of d0. * Use ipSAE or LIS. www.biorxiv.org/content/10.1...

IS110 transposon utilizes two mechanistically distinct RNA-guided transposition pathways: Molecular Cell https://www.cell.com/molecular-cell/fulltext/S1097-2765(26)00315-1?rss=yes

I am delighted to share our latest preprint: doi.org/10.64898/202.... Fantastic work from my past and present lab members @flofournes.bsky.social, Sandra Martin and Nicolas Pellaton. Also many thanks to our precious collaborators @gruberlab.bsky.social and to @snsf.ch for funding this research.

Phage RyR-domain proteins degrade ADPR-based immune signals and fuel NAD synthesis https://www.biorxiv.org/content/10.64898/2026.05.28.727677v1

Out Now! Temperate phages enhance bacterial host fitness via RNA-guided flagellar remodelling #MicroSky

Accelerating scientific discovery with Co-Scientist | Nature https://www.nature.com/articles/s41586-026-10644-y

Tiny Mystery Plasmid Noteworthy — A two-gene plasmid is abundant and highly prevalent in human gut microbiomes.

Happy to share our latest pre-print on the Druantia defense system. We find that Type III Druantia uses a cooperative helicase-nuclease mechanism to sense and degrade replication-associated forked DNA structures. www.biorxiv.org/content/10.6... A🧵

With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...

I’m thrilled to share an update to our work on bacterial NACHT domain containing proteins! In our last preprint, we reported that bNACHT11 is activated by multiple phage proteins. We’ve now expanded this work with structural insight and investigation of programmed cell death following activation.

This one means a lot. Our paper, “Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome,” is out! doi.org/10.1038/s414...

Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome | Nature Communications https://www.nature.com/articles/s41467-026-72671-7

Bacterial immune proteins have repeatedly evolved to become parts of eukaryotic immunity. But how? Our new preprint uncovers a recent horizontal transfer event & shows how eukaryotes co-opted a toxic bacterial immune protein 🦠🧪🧵 1/

Translation-dependent degradation of cas12 mRNA triggered by an anti-CRISPR | Nature https://www.nature.com/articles/s41586-026-10440-8

Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.

Out Now! Nuclease–NTPase antiphage defence systems use conserved molecular features to control bacterial immunity #MicroSky

Transposable elements are driving rapid adaptation of Enterococcus faecium -in @nature.com from Ami Bhatt www.nature.com/articles/s41...

Genome editing of phylogenetically distinct bacteria using cross-species retron-mediated recombineering www.nature.com/articles/s41... #jcampubs

🎉Excited to share our new preprint! TIR domains from diverse animals, including human TLR4, are catalytically active and produce cyclic ADP-ribose (cADPR). This enzymatic activity is widespread in animals and conserved across the tree of life. www.biorxiv.org/content/10.6...

Bacteriophages are in a constant arms race with bacteria 🦠 The Phage ORFeome pooled library from the Aaron Whiteley lab contains phage proteins that activate antiphage defense systems — a tool to dissect the mechanisms of bacterial immunity. Aaron Whiteley

ComEC structure is out!! 😍 Congratulations to the authors! That’s not an easy one. We have been trying for years to get that structure… We failed and gave up.

Happy to share our new work on how phages escape bacterial immunity. We show that a phage homing endonuclease drives segmental amplification of anti-defense genes, pointing to a versatile and rapid mode of adaptation. www.nature.com/articles/s41... #PhageSky #MicroSky

I am so excited to share our new findings with you! We provide the structural evidence for a direct protein-to-DNA information pathway, showing how a bacterial enzyme 'reads' its own structure to 'write' DNA. www.science.org/doi/10.1126/...

🔈Paper out! We turned the most fascinating phage host-switch mechanism, diversity-generating retroelements, into a programmable mutagenesis tool, DGRec. You can perform targeted hypermutation of any 50-200bp sequence directly in vivo in E. coli www.nature.com/articles/s41...

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...

Diversity-generating retroelements for programmable targeted hypermutagenesis | Nature Biotechnology https://www.nature.com/articles/s41587-026-03078-4

Excited to share our new paper out today in @science.org 🎉 We show that HGT via natural competence drives diversification of chromosomal integrons in V. cholerae 🤩 Below a 🧵 on key findings incl. background on natural competence in V. cholerae 1/ #microsky #phagesky www.science.org/doi/10.1126/...

www.biorxiv.org/content/10.6... Cool new anti conjugation mechanism

‼️Please share‼️ Nemudryi lab is looking for postdocs to join our team and study: 🦠 Bacterial phage defense mechanisms 🧬 RNA repair & CRISPR-based RNA editing Excited about RNA, host-virus interactions & mechanistic biology? Let's talk! Apply: explore.jobs.ufl.edu/en-us/job/53...

PostDoc position available! (links in post below) Feel free to share!

Molecular kinetics dictate population dynamics in CRISPR-based plasmid defense | PNAS https://www.pnas.org/doi/10.1073/pnas.2525424123

Huge work! Joint effort over four years of EPC Rocha & Fred Le Roux Labs sampling in the wild for 4 years! www.nature.com/articles/s41... @epcrocha.bsky.social @fredoleroux.bsky.social

Nucleoid-associated proteins sense phage-induced genome damage to elicit abortive infection https://www.biorxiv.org/content/10.64898/2026.04.06.716658v1

Excited to see our work out in Science today! Using machine learning to identify prokaryotic immune systems www.science.org/doi/10.1126/...

And the preprint is out! www.biorxiv.org/content/10.6... We compared plasmid conjugation in liquid and on solid across 13 AMR plasmids with different types of conjugative pili.

How diverse is bacterial immunity ? We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems. 👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie... Explore them here defensefinder.mdmlab.fr/wiki/refseq_...

Hey #Phagesky [Ph]ans! My first work with the Penadés lab is out! Come read how arbitrium-coding phages sense non-cognate Arbitrium signals from other phages to influence their lysis-lysogeny decisions. www.cell.com/cell/fulltex...

Open postdoc position in my lab on HGT and interbacterial competition. We seek candidates with a PhD in microbiology (or related fields)+ strong 1st-author publications. Curious, highly motivated, and dedicated team players ready to contribute fully are encouraged to apply. Details: tiny.cc/cz01101

What if plant immunity doesn’t stop bacteria from arriving - but from staying? Excited to share our new Dangl Lab paper (doi.org/10.1073/pnas.2535583123), asking a fundamental co-evolutionary question: which flagellar function is targeted by plant immunity? #Coevolution #Plant-Microbiome #PNAS 🧵1/8

Nature research paper: Immune evasive DNA donors and recombinases license kilobase-scale writing go.nature.com/4b3e0E2

AlphaFold 3-powered discovery of phage proteins that inhibit bacterial transcription initiation: Cell Reports https://www.cell.com/cell-reports/fulltext/S2211-1247(26)00160-9?rss=yes

Final version of our last paper is out! www.nature.com/articles/s41...

Capturing dynamic phage–pathogen coevolution by clinical surveillance "we capture the acquisition of a parasitic anti-phage mobile genetic element, PLE11, that initiated a selective sweep coinciding with the largest cholera outbreak in recent records. " www.nature.com/articles/s41...

This is so cool: www.biorxiv.org/content/10.6... Discovery of a Genetic Toxin-Antidote System in Vertebrates hat tip to @asaflevylab.bsky.social

Out Now! Conditional activation of Cas13 enforces lysogeny in a native type VI-A CRISPR host #MicroSky