Rafael Pinilla-Redondo (Rafa)

Take a look at our exciting work into how SauUSI, a type IV REase, degrades methylated DNA. Shredding and fragmenting with only a single 5mC required! @multidefence.bsky.social @alex-hg.bsky.social @oscart32.bsky.social

🚨 New preprint 🚨 We’ve discovered millions of viruses from sequencing data but we don’t always know who they infect. Our new tool, VHAMSTeR generates broad virus host predictions across the tree of life (prokaryote, plant, animal, fungi and protist hosts) A thread 🧵👇 www.biorxiv.org/content/10.6...

1/4 Bacterial immunity with “two-factor authentication”? Our new preprint by @monikajasnauskaite.bsky.social et al. reveals how DRT4 combines DNA synthesis with recognition of a phage protein to activate antiviral defense - a short thread below 🧵 BioRxiv: www.biorxiv.org/content/10.6...

New preprint from my Post-Doc in the Swarts lab How are the guide RNAs generated that direct prokaryotic Argonautes to invading DNA? This has been an open question for >10 years. Our new study reveals that the host housekeeping enzyme RNase E is responsible! A 🧵: 1/14

New preprint studying the environmental drivers of viral diversity in soils. We mined data from a UK-wide monitoring programme for viral sequences (w/colleagues at CEH and Bangor). www.biorxiv.org/content/10.6...

Aminoacylated tRNA tails trigger auxiliary bacterial immunity https://www.biorxiv.org/content/10.64898/2026.10.14.759216v1

New preprint from the Gurney Lab, on bioRxiv: The Phage Time Continuum: Genome Organization Constrains Anti-CRISPR Success. www.biorxiv.org/content/10.6... I think this is one of the cooler things I'll ever do. Work lead by @sczerwinski.bsky.social he coined the term Phage Time Continuum. 1/10

1/1 How does a single methyl group activate bacterial defence? In my PhD work with @matthiaswilmanns.bsky.social and @typaslab.bsky.social, we reveal how this tiny DNA modification triggers retron disassembly and toxin activation. Now on bioRxiv: www.biorxiv.org/content/10.6...

Reverse transcribed ssDNA derepresses translation of a retron antiviral protein: Molecular Cell

Happy to be part of this and to see it out in its final form! 🎉 Don't miss the paper on a fascinating and unexpected biological mechanism!! 👀🔎

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...

Online Now: Reverse transcribed ssDNA derepresses translation of a retron antiviral protein Online now:

3/5 For a deeper dive into the science, check out our original preprint threads below: DRT10 biology and evolution (with @pentamorfico.bsky.social and @rafomics.bsky.social): bsky.app/profile/ster...

Heads up! The Symposium on the Immune System of Bacteria 2027 is now open for registrations! 20-22nd July 2027, Churchill College, University of Cambridge, UK Places are limited, so register soon. Visit the website to see our fantastic line-up of speakers: sisb2027.info #phage

A new preprint 🎉 from phagefoundry.org Mycobacteriophages are candidate therapies for drug-resistant mycobacterial infections, but we still don't know how most of them get into their hosts. Our new preprint tackles this challenge 👉🏽 www.biorxiv.org/content/10.6...

What does it take for a mycobacteriophage to infect M. smegmatis mc² 155? 🦠🗺️ We mapped it for 70 phages using genome-wide CRISPRi. Our new preprint from the Phage Foundry is out! (phagefoundry.org) 🥳🧵 Read the preprint here: www.biorxiv.org/content/10.6...

#plasmidbiology #plasmid Just out! 🚀 Thrilled by our discovery: the function of the C-terminal domain of MOBH1 relaxases! We uncovered this thanks to a fertility inhibitor encoded by a parasitic mobile genetic element. Congrats to Florence on a great piece of work! 👏 academic.oup.com/nar/article/...

Heads-up! I’ll be starting my research group at MedUni Vienna in January 2027, with postdoc and PhD positions available soon. Looking for people interested in bacteria–phage interactions, bacterial defense systems, and phage anti-defense strategies. Please send your CV: anna.lopatina@univie.ac.at

A new plant-bacteria immunological connection in the first preprint of our group at @mpi-bio-fml.bsky.social @plantevolution.bsky.social! Straight from the top of Mt. Olympus ⛰️🦅 Led by Eirik @eiriklag.bsky.social, in collaboration with @geminiteamlab.bsky.social www.biorxiv.org/content/10.6...

1/2 Here we report the activity of Arc, a 50-aa DNA-binding protein encoded within IS605-family transposons. www.biorxiv.org/content/10.6...

1/13 — New pre-print from the Sternberg Lab in collaboration with Leifu Chang's Lab! TnpB nucleases have repeatedly given rise to TldRs, nuclease-dead RNA-guided transcription factors. Here we define the biological role of one TldR clade in its native host. Story: www.biorxiv.org/content/10.6...

Adapting the power of transposon sequencing to phages! Our final paper is out now👇 Our plasmids 🧬 are available on @addgene.bsky.social – try phage Tn-seq on your favorite phage!

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

New from the @multidefence.bsky.social consortium: a deep dive into MANTIS defence. Thanks to @ukri.org for funding. www.biorxiv.org/content/10.6...

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...

What happens when two viruses coinfect the same host? Check out the first publication of my PhD, where we describe two new viruses from an extremophilic system! www.nature.com/articles/s42...

The final version of our manuscript on TnSeq in bacteriophages (“HIDEN-SEQ”) is out today – if you have an interesting phage phenotype and want to know the underlying genetic basis, this one is for you! 1/4

New paper from the lab, out in Nature Microbiology. We ran CRISPRi screens to ask what genes E. coli needs in order to live in a gut and what this can tell us about the gut environment itself. https://doi.org/10.1038/s41564-026-02471-8

New preprint from PhD student Yu Sun. TSR1 is a TIR effector specialised for CRISPR defence. It is an obligate dimer activated by cA3 and degrades its own activator using a ring nuclease domain. Perhaps the first confirmed dimeric TIR effector? www.biorxiv.org/content/10.6...

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 🧵👇

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

Our paper on type II Panoptes is now published at PLOS Biology with new data on phage escapers - quite a step up in microbiology for our lab, led by Sabine Gruschow. Thanks to @erc.europa.eu for funding dx.plos.org/10.1371/jour...

Finally out! 🎉 After 3 years of postdoc in London, here is my main work, now published in Nature Comm. (and as co-corresponding author!) Using a combination of bioinformatic and experimental approaches, we propose a model of plasmid evolution in Staphylococcus. www.nature.com/articles/s41... ⬇️ 1/4

As a wonderful way to wrap up these past few months, I’m deeply honored to receive the Plasmid Biology Prize from the International Society for Plasmid Biology at #ISPB2026 Berlin. 🍾🥳 Many thanks to the Society, and to all the friends, colleagues, and mentors I’m lucky to meet at these meetings.

I'm happy to share one of my favorite projects from the past 4 years. 'Piercing mechanism in the minimal contractile tail of bacteriophage P2'. In this preprint, we applied #cryo-EM, #cryo-ET, TEM, and #computationalbiology to study the #phage P2 virion structure and its contraction mechanism.

It's finally published! What a journey @brownlab.bsky.social and I have been on with this one (ask me about it over a pint 🍻). Super excited to be able to say that it's finally out in Trends (author gift link to follow)! 🦠🧫 #phagesky

Please share! We are looking for a PhD student excited about gene transfer, and tackling Antimicrobial Resistance in Klebsiella pneumoniae. 🧬 More details & applications on funder website by 21st Oct 👇🏻 gw4biomed.ac.uk/developing-c...

New project in the lab - engineering phages to edit mitochondria! We team up with Ian Collinson @ianofbristol.bsky.social + Nicholas Taylor @nmitaylorlab.bsky.social in the ProMit consortium led by Michal Minczuk @mitogene.bsky.social. PostDoc Ruta Prakapaite @rootspr.bsky.social is ready to go! 🪄🧬

We are recruiting a PhD student 🥼🙋 Topic: how germ cells bend gene expression dogmas Fly genetics + proteomics + genomics. Fully funded. Aarhus University 🇩🇰 info on the project and how to apply👇 mbg.au.dk/en/peter-and... I'd really appreciate it if you'd help spread the word. Thanks

Presentation done ✔️ It's already been so nice to catch up with everyone, now for 3 1/2 more days of packed programme! @plasmidsociety.bsky.social #ISPB #ISPB2026

🧬 Postdoc ad is now live: evolutionary genomics of Klebsiella pneumoniae phages. How do prophage depolymerases vs SGNH-esterases shape phage host range? Krakow, Poland. Deadline 21 Sept: mostowylab.com/job-postdoc-...

Identifying #antiphage defense systems can be challenging. This study by @duerkoplab.bsky.social describes a #bioinformatic pipeline that uses a small serine recombinase as a genetic marker to identify novel antiphage defense systems across diverse bacterial phyla. 🧪 #AcademicSky plos.io/4i4ZrUu

We got an ERC StG! 🥳🎉 Huge thank you to all the people who helped us get here. Five years to explore some Qs we’re very excited about! 🧬🔬