Leah Smith

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!

Cover image alert 🎨🚨👇🏼 - check out the amazing drawing of Sophia Zimmermann from our group in Nature Microbiology @natmicrobiol.nature.com ! Fun fact: Sophia initially drew it as a present to Dorentina @humollidorentina.bsky.social when we celebrated her recent paper on TnSeq with phages 🥂😊.

Great to see phage Tn-seq & HIDEN-SEQ featured on the cover of this month’s issue of @natmicrobiol.nature.com! Lovely cover art by Sophia Zimmermann! 👏 🦠 🧬 🔦

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...

Happy to share that @averynoonan.bsky.social paper “Phylogeny-agnostic strain-level prediction of phage–host interactions from genomes using machine learning” is now published in @natmicrobiol.nature.com 🎉🎊 👉🏽 rdcu.be/nR2NizD7H5va

Excited to share this part of my research as a part of @multidefence.bsky.social: meet viPAO1 - the very best Pseudomonas strain for phage research😉 Also check out our temperate phage collection featuring PAnicatthedisco, PAthetic and some other new fun names🎉 www.biorxiv.org/content/10.6...

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 🧵👇

Our opinion piece on what you can do with tradis [tn-seq]. It's a shortish read, aimed at fellow daydreamers. Thank you @microbiologysociety.org for the invite and opportunity, this was surprisingly pleasant to research and write! www.microbiologyresearch.org/content/jour...

We are thrilled and grateful that our project is funded by #ERCStG via @erc.europa.eu . This will allow us to uncover how the widespread jumbophage killer sensor recognizes the invasion of phiKZ-like jumbophages, which form fascinating vesicle & nucleus compartments during infection.

Thrilled to see this project officially published in ISMEJ! We showed that filamentous prophages frequently acquired repressor mutations causing hyperactivity which, in turn, drove the evolution of phage resistance with pleiotropic consequences. academic.oup.com/ismej/advanc...

Newest preprint 🎉 from phagefoundry.org Here we built one of the most comprehensive K. pneumoniae phage–host interaction datasets to date, an atlas of 8,484 interactions testing 84 taxonomically diverse phages vs 101 globally sourced clinical strains, including some of the most resistant kinds.

1/4 Every good defence needs a backup! 🛡️⚔ Out now in @natrevmicro.nature.com our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉 🔗 www.nature.com/articles/s41...

Phages invented sgRNAs before humans!! 🧬 Obviously, for mischief… 😈 Loved seeing this story unfold!

Revised story Systematic receptor mapping in acapsular Klebsiella www.biorxiv.org/content/10.6...

1/6 👻 Something strange in your liquid agar? Who you gonna call? Thermophile hunters. Our new @asm.org #MRA paper reports the complete genome sequence of Geobacillus stearothermophilus strain CS7089 isolated from a commercial agar preparation.

New post-doctoral research position in my phage-host interactions (Phi) laboratory in @otagomicroimmuno.bsky.social at @universityofotago.bsky.social New Zealand. The project is focused on defences against jumbo phages. Please share and if interested apply using the link in the comments.

Delighted to see over 17 million new protein structure predictions from novel proteins in AllTheBacteria are now integrated into the AlphaFold Database at @ebi.embl.org ! Huge work from @gbouras13.bsky.social @oschwengers.bsky.social and friends to generate these. www.ebi.ac.uk/about/news/u...

Pleased to announce that I've joined the editorial board of the Biochemical Journal portlandpress.com/biochemj as an associate editor. I'd love to receive manuscripts focussed on CRISPR, anti-viral defence, archaean biochemistry and nucleic acid processing enzymes. @biochemsoc.bsky.social

A study in Nature Immunology shows that Long COVID is characterized by persistent activation of chronic inflammatory pathways and T cell exhaustion. The findings suggest new therapeutic targets and potential biomarkers of disease. go.nature.com/4oU0kib #immunosky #medsky 🧪

📢 We have multiple open PhD positions to study bacterial immune systems using cutting-edge cryo-EM, microbiology, and biochemistry in our group! Join us and uncover how bacterial defenses eliminate predators and engineer next-gen biotech tools. 🔥 Apply by Jan 8, 2026 Details: phd.pages.ista.ac.at

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

Two fully-funded PhD openings in my research group at the University of York. If you’re excited about viromes, phage biology, Nanopore sequencing, soils and the odd bit of alpine or agricultural field sampling, we’d love to hear from you! 🌱🦠🏔️ tiny.cc/c4pv001 tiny.cc/e4pv001

#NewResearch Streptococcus thermophilus phages circumvent host CRISPR defences via AcrIIIA2, which complexes with enolase, a highly abundant glycolysis enzyme, to block phage RNA binding #MicroSky #CRISPR 🦠 www.nature.com/articles/s41...

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...

Nice write up by Kalani Gast and Rodolphe Barrangou previewing our latest paper 🧫 ✂️ 🧬 out now in @cp-cellhostmicrobe.bsky.social

Applied research is digging for gold, basic research is figuring out where to dig. Marsden used to fund it all. Each grant is rigorously assessed in 2 rounds by a panel of local & international experts. It is risky research, with potentially high rewards.

Can CRISPR-Cas systems target any phage? Yes, no, it depends? What does it depend on? The second paper from my PhD came out today in a special issue of Phil Trans B on the ecology and evolution of bacterial immune systems doi.org/10.1098/rstb...

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

In a multi-CRISPR-Cas system host, @peterfineran.bsky.social & I found that type I priming promotes spacer 🧬 uptake & maintenance by a type III system & that multiple systems minimize phage escape ⬇️ @cp-cellhostmicrobe.bsky.social @otagomicroimmuno.bsky.social www.sciencedirect.com/science/arti...

Still open for applications! We are looking for prospective new faculty doing exciting research in virology or any vector borne diseases

Please share! 🦠 Workshop on Phage Therapy in Liverpool on 25th November organised by Stineke van Houte, @jojofoth.bsky.social, @brockhurstlab.bsky.social, & Edze Westra. Limited FREE tickets & more info here: sites.exeter.ac.uk/vanhoutelab/... #MicroSky

📣 New preprint alert! Happy to share the first results from our effort to reannotate Pseudomonas #phage proteins of unknown function, using structural bioinformatics. 📄 doi.org/10.1101/2025...

Next up from our lab - a ring nuclease with a novel fold which cleaves all cOA species involved in Type III CRISPR defence. It's also found in plasmid and phage genomes, where it presumably functions as an anti-CRISPR. www.biorxiv.org/content/10.1...

Great to see this comprehensive work on phage DNA arabinosylation & defense finally out! 🧬🚫✂️ A major collaborative effort & stellar PhD work by Marina Mahler, whom I had the pleasure of co-supervising at Otago 👩🏻‍🔬 @peterfineran.bsky.social @universityofotago.bsky.social @cellpress.bsky.social #mm