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Leah Smith

@leahmsmith.bsky.social
52 followers 53 following 5 posts

Research Fellow at University of Otago NZ interested in phages, biofilms, genomics, CRISPR & phage therapy

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Reposted by Leah Smith
Dorentina Humolli @humollidorentina.bsky.social · 25/09/2026
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...
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Vivek Mutalik @vivekmutalik.bsky.social · 29/09/2026
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
Machine learning workflow for GenoPHI platform
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Leah Smith @leahmsmith.bsky.social · 28/09/2026
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!
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Anna Olina @annaolina.bsky.social · 22/09/2026
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...
biorxiv.org
Engineering the Pseudomonas aeruginosa virus-isolation host viPAO1 reveals how host genetic barriers shape recoverable phage diversity
Cultured phage collections provide essential access to viral biology, but they capture only a small and biased fraction of natural phage diversity. Key barriers to diverse phage isolation are likely t...
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Vivek Mutalik @vivekmutalik.bsky.social · 19/09/2026
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 🧵👇
Schematics of how single strand RNA and DNA phages infect bacteria with F-pilus
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Emily Goodall @emgoodall.bsky.social · 14/09/2026
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...
microbiologyresearch.org
Applications of transposon-insertion sequencing for understanding bacterial physiology
Transposon-insertion sequencing (Tn-seq) couples transposon mutagenesis with next-generation sequencing to identify the transposon insertion site for thousands of mutants in parallel. It is a powerful...
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Reposted by Leah Smith
Yuping Li @yuping-li.bsky.social · 03/09/2026
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.
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Noah Houpt @noahhoupt.bsky.social · 25/08/2026
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...
academic.oup.com
Mutations in filamentous bacteriophages spark eco-evolutionary feedbacks in Pseudomonas aeruginosa
Abstract. Microbial populations strongly shape their environment, which can re-route adaptation toward organism-generated fitness optima. However, the cond
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Vivek Mutalik @vivekmutalik.bsky.social · 14/08/2026
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.
Phage art
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Rafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 21/07/2026
1/4 Every good defence needs a backup! 🛡️⚔ Out now in @natrevmicro.nature.com our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉 🔗 www.nature.com/articles/s41...
nature.com
Immune safeguarding as a conserved principle of antiviral defence - Nature Reviews Microbiology
All organisms defend against viral infections through active immunity mechanisms that clear the virus or population-level mechanisms that cause regulated cell death. Recent research increasingly shows...
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Rafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 02/06/2026
Phages invented sgRNAs before humans!! 🧬 Obviously, for mischief… 😈 Loved seeing this story unfold!
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Vivek Mutalik @vivekmutalik.bsky.social · 19/05/2026
Revised story Systematic receptor mapping in acapsular Klebsiella www.biorxiv.org/content/10.6...
biorxiv.org
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Enea Maffei @phagemuffin.bsky.social · 18/05/2026
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.
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Peter Fineran @peterfineran.bsky.social · 04/03/2026
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.
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Zamin Iqbal @zaminiqbal.bsky.social · 17/02/2026
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...
ebi.ac.uk
AlphaFold Database welcomes community datasets
Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities
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Malcolm White @mfwhite2.bsky.social · 14/01/2026
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
portlandpress.com
Biochemical Journal | Portland Press
Exploring the molecular mechanisms that underpin key biological processes, the Biochemical Journal is a leading bioscience journal publishing high-impact scientific research papers and reviews in the ...
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Nature Portfolio @natureportfolio.nature.com · 06/01/2026
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 🧪
This is figure 4, which shows proteomic differences between LC and CC groups in the 2020–2021 cohort.
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Jack Bravo @jpkbravo.bsky.social · 02/12/2025
📢 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
phd.pages.ista.ac.at
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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 02/12/2025
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
quinlanlab.org
Intro to Bedder – The Quinlan Lab
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Sean Meaden @seanmeaden.bsky.social · 27/11/2025
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
tiny.cc
A Farewell to Arms: The Trade-off Between Growth and Defence in Bacteria (York YBDTP Project) at University of York on FindAPhD.com
PhD Project - A Farewell to Arms: The Trade-off Between Growth and Defence in Bacteria (York YBDTP Project) at University of York, listed on FindAPhD.com
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Nature Microbiology @natmicrobiol.nature.com · 11/11/2025
#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...
nature.com
A phage-encoded anti-CRISPR protein co-opts host enolase to prevent type III CRISPR immunity - Nature Microbiology
Streptococcus thermophilus phages circumvent host CRISPR defences via AcrIIIA2, which complexes with enolase, a highly abundant glycolysis enzyme, to block phage RNA binding.
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Ben Adler @benadler.bsky.social · 01/10/2025
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...
nature.com
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
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Leah Smith @leahmsmith.bsky.social · 15/09/2025
Nice write up by Kalani Gast and Rodolphe Barrangou previewing our latest paper 🧫 ✂️ 🧬 out now in @cp-cellhostmicrobe.bsky.social
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Reposted by Leah Smith
Paul Gardner @ppgardne.bsky.social · 06/09/2025
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.
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Josie Elliott @josie-e.bsky.social · 04/09/2025
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...
doi.org
Phage susceptibility to a minimal, modular synthetic CRISPR-Cas system in Pseudomonas aeruginosa is nutrient dependent | Philosophical Transactions of the Royal Society B: Biological Sciences
CRISPR-Cas systems can provide adaptive, heritable immunity to their prokaryotic hosts against invading genetic material such as phages. It is clear that the importance of acquiring CRISPR-Cas immunit...
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George Bouras @gbouras13.bsky.social · 08/08/2025
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...
biorxiv.org
Protein Structure Informed Bacteriophage Genome Annotation with Phold
Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...
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Leah Smith @leahmsmith.bsky.social · 20/08/2025
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...
sciencedirect.com
Type I CRISPR-Cas immunity primes type III spacer acquisition
CRISPR-Cas systems are diverse, with microbes harboring multiple classes and subtypes. Type I DNA-targeting and type III RNA-targeting systems often c…
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Siân Owen @sianowen.bsky.social · 26/07/2025
Still open for applications! We are looking for prospective new faculty doing exciting research in virology or any vector borne diseases
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David Sünderhauf @davvi36.bsky.social · 22/07/2025
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
Conference flyer, all info is on link too
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Hannelore Longin @hannelorelongin.bsky.social · 21/07/2025
📣 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...
doi.org
Fold first, ask later: structure-informed function annotation of Pseudomonas phage proteins
Phages, the viruses of bacteria, harbor an incredibly diverse repertoire of proteins capable of manipulating their bacterial hosts, inspiring many medical and biotechnological applications. However, t...
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Malcolm White @mfwhite2.bsky.social · 18/07/2025
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...
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Leah Smith @leahmsmith.bsky.social · 26/06/2025
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
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