I’ve started my SNSF Ambizione Group Leader position at the University of Zurich 🧬 We will study plasmid evolution, plasmid interactions, and CRISPR-Cas systems to better understand antibiotic resistance spread. Very grateful to everyone who supported me along the way.

🔈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...

So happy to see this finally published in @plosbiology.org! This is the first chapter of @julielebris.bsky.social PhD thesis demonstrating how capsules are exchanged by plug-and-play dynamics w/ @epcrocha.bsky.social #microsky @klebclub.bsky.social Link below- Check out her 🧵 for more details!

➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔 🧵👇

🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...

Willing to join us @pasteur.fr for a PhD for a project on how interactions between mobile genetic elements shape bacterial adaptation? Subject to be tailored to candidates with keen interest in evolution, genomics, computational biology, microbiology. Check www.pasteur.fr/en/education...

We're looking for a technician at Institut Pasteur for experimental work on satellite-phage-bacteria interactions, working directly with @jmouradesousa.bsky.social and myself in the lab of @epcrocha.bsky.social ! ANR funded. Link to the job emploi.pasteur.fr/offre-de-emp... Thx for sharing!

Great collaboration with @fredoleroux.bsky.social . Kudos for everyone, esp. Charles Bernard & Yannick Labreuche. Thanks to the funders and @pasteur.fr @cnrsbiologie.bsky.social @umontreal.ca @sbroscoff.bsky.social Here's the paper in OA: doi.org/10.1093/isme...

Phage satellites are now known to be very diverse, numerous and ancient. They pose many evolutionary, ecological and mechanistic questions. Lots of fun in perspective! Great pleasure to write this review to show it, with @jrpenades.bsky.social @dbikard.bsky.social Kim Seed & John Chen.

Our review on recent advances in #PhageTherapy against Klebsiella pneumoniae is out! We analyze KP-phage interactions from an eco-evo perspective, summarize many lab and clinical trials, and discuss novel approaches like genetic engineering & machine learning. #microsky doi.org/10.1371/jour...

🔬 Three fronts in bacterial defense! At EMBO symposium this week in Paris, our PIs showcased: • @mfwhite2.bsky.social: cyclic nucleotide defence signaling • Prof. Stineke Van Houte: prophage warfare in P. aeruginosa • Prof. Tim Blower: autoregulating toxins & phage defence

Mystique is here! When I started my position at @cmdi.bsky.social there were no readily available phage against my A. baumannii focal strain. The solution? Finding my own phage ofc. Mystique is a broad host range Acinetobacter phage, and I'm thrilled to see this work out today #PhageSky 🧪🦠

I'm delighted to announce that the 2025 @microbiologysociety.org meeting on "Understanding and predicting microbial evolutionary dynamics" will be held in Liverpool 26-27 November 2025! Abstract submission will open soon... #microsky 🧪🧫🦠 microbiologysociety.org/event/societ...

@jonaszpatkowski.bsky.social and I pinpointed tail piracy as a new mechanism of horizontal gene transfer and explained the wide spread of cf-PICIs among different bacterial species and viromes.

👋 Hi antiphage defense community, we are soon releasing an update of DefenseFinder. We are doing our best to include all the great discoveries from the community, but with so much going on we might miss things. Please answer wt preprints/papers with new systems or mail/git them to us. 🙏

Happy Hallowe’en! We made a spooky AMR vs bacteriophage comic free to download and use. Take a look and give @andthemicrobes.bsky.social a follow! (There’s even a prequel on plasmids and bacterial diversity!) 🎃🦠🧬👻 bsky.app/profile/andt...

Hi to all my new (and old) followers! So fun to see more people joining us here. I'm currently an independent post-doc and evolutionary microbiologist at Georgia Tech in the US, studying Acinetobacter baumannii – phage dynamics. Welcome! www.biorxiv.org/content/10.1...

Our study on the (huge) variations in transformation rates is now out in OA! Key question: why are so many strains non-transformable if the many recent transitions to non-transformability seem deleterious? doi.org/10.1371/jour...

The view from my new workplace :) Can't possibly be happier to be working on phage satellites with @jmouradesousa.bsky.social , @epcrocha.bsky.social and the team!

My official PhD graduation last month was the closing step of an incredible journey, marking the end of my time in Cornwall!

We have another position advertised 😃 with @taylorlabgroup.bsky.social in Bath to understand the regulation of multi layered defence systems!! You can apply at www.bath.ac.uk/jobs/Vacancy... Applications close on 9th September.

New paper looking at the spread of CRISPR-Cas in bacterial populations. Congratulations to @josie-e.bsky.social on her first, first author paper 🎉! Check out her brilliant thread below. Happy to see this work out in the wild.

Excited to share my 1st paper with @bridgetwatson.bsky.social @taylorlabgroup.bsky.social Edze Westra Sylvain Gandon & David McLeod academic.oup.com/ismej/articl... where we ask “when would using a defence system (CRISPR-Cas) be selectively advantageous over mutations that block phage binding?”1/10

1st foray into T6SS with talented @mermanchester.bsky.social fellow Will Smith: eco-evo models and experimental evolution show how and why producing multiple toxins blocks resistance evolution (even though cross-resistance can evolve under single-toxin attack) www.biorxiv.org/content/10.1...

Hiring a bioinformatician at @uniofexeter.bsky.social to work with the Exeter sequencing facility. Please spread the word! jobs.exeter.ac.uk/hrpr_webrecr...

🆕 I’m looking for a postdoc to join the group! This is for a project as part of the @multidefence.bsky.social consortium, looking at genome defences and horizontal gene transfer in Pseudomonas. Deadline 12th August. 🧵 my.corehr.com/pls/ulivrecr...

I'm so happy to see the main part of my PhD work published in Cell Host & Microbe! We discover and characterise MADS (Methylation Associated Defense System) in its native host, a clinical isolate of 𝘗𝘴𝘦𝘶𝘥𝘰𝘮𝘰𝘯𝘢𝘴 𝘢𝘦𝘳𝘶𝘨𝘪𝘯𝘰𝘴𝘢 strain SMC4386 www.cell.com/cell-host-mi...

7 yrs ago, I got very lucky when I got my permanent researcher position @cnrs.bsky.social Now, even more so. I just got promoted to director of research (associate professor?) Thx to all who contributed closely or loosely & special thx to PhD student julie for a wonderful & unexpected gift!

While struggling to isolate a phage at all, we also discovered that other phages in our collection actually *can* infect AB5075... but only in liquid culture. In other words, phages that do not plaque on a bacterial lawn may still be able to infect in liquid!

Going from PhD to independent postdoc has been hard, and switching bacteria didn't make it easier. Especially when I found out that my A. baumannii (5075) has/had no available phage. But, that meant I had a gap to fill! And that's resulted in this work here: www.biorxiv.org/content/10.1...

Sharing our latest paper as my first post here 🔵 💙 Plasmids encode Type IV CRISPR-Cas to fight other plasmids💥⚔️ Now out in Cell Host & Microbe www.sciencedirect.com/science/arti...

Nice paper from Tim Cooper from earlier this year showing variation in AMR plasmid cost across E. coli strains explained by a genetic conflict with a resident prophage #microsky journals.asm.org/doi/full/10....

🧪Any time you think you understand viruses, they get weirder. Meet Jingmen tick virus (JMTV), the 1st multipartite virus of primates discovered. What's weird about it? Imagine a group of people who travel everywhere together, but in different cars. That's the JMTV genome.

I've got a fully funded, 4-year PhD position available to work on virus-bacteria interactions in soils. Part of the GenerationResearch scheme at York aimed at widening access to postgrad research. Please share! generationresearch.ac.uk/phd_proposal...

New paper from the lab, the mysteries involving the genetic elements that move by being mobilized by other MGEs. Hitcher Genetic Elements are distinctive, ancient and diverse. ecoevorxiv.org/repository/v...

New job offer: we search a postdoc (bioinformatics) to work on mobile genetic elements and gene flow in bacteria, with a focus on antibiotic resistance within a consortium including bioinformatics, synthetic biology, epidemiology & biochemistry. See research.pasteur.fr/en/job/postd... #MicroSky

Using phage therapy to resensitize P aeruginosa to antibiotics in murine lung infection, featuring @mermanchester.bsky.social’s Rosanna Wright, led by Jo Fothergill www.nature.com/articles/s41...

BBSRC 2-year PDRA position to work on ecology & evolution of phage therapy with synthetically engineered phages. Part of an exciting multi-university consortium & UK’s Engineering Biology priority. Synthetic genomics; experimental evolution; AMR. www.jobs.manchester.ac.uk/Job/JobDetai... #microsky

🎊 First post here 🎊 I am happy to announce that I will join the MMSB lab in Lyon in September to start my own group to study the evolution of phage-bacteria interactions 🦠 🔬🧫 Postdoc position available 🧬🧪 More details below 👇 emploi.cnrs.fr/Offres/CDD/U...

Very nice to see published our first sLola article! Working with every single member of this consortium is really great:)

First paper from the MultiDefence consortium reviewing what we know about multi-layered genome defences in bacteria. Supported by BBSRC sLoLa led by Edze Westra. Aleksei Agapov did a great job pulling it all together! www.sciencedirect.com/science/arti...

Just out in The ISME Journal, a paper from my time in the Westra lab. We find that the extent of phage exposure shapes subsequent resistance dynamics over longer timescales (up to 30 days). And huge thanks to first authors @bridgetwatson.bsky.social and Loris for mammoth experiments!

Congratulations to our MEEhubs2024 Oxford Poster Award winner @josie-e.bsky.social! 🎉🏆 Prize generously sponsored by the Microbiology Society UK

With a small pinch in my ❤️, I leave Institu Pasteur for the 3rd time. More than 12 years of scientific endeavors, challenges, collaborations & friends in genomes genetics & microbio dpt IP Thanks to @epcrocha.bsky.social for the last 8 yrs, 14 papers, 2 national grants, 2 prizes. OFF to the ☀️

Job alert. We’re looking for head of dept in ecology, evolution and behaviour at UoLiverpool. Fantastic group of colleagues and a chance to provide leadership in addressing climate change. my.corehr.com/pls/ulivrecr...

I was very happy to write a spotlight article with J. Horton & @matthewjshepherd.bsky.social on excellent recent work from A. Wong's lab, led by Nicole Filipow on the adaptive trajectory of 17 strains of P. aeruginosa to SCFM. 🧪https://www.sciencedirect.com/science/article/pii/S0966842X23003372

New postdoc position in our lab for a project led by Marie Touchon (bioinformatics) and with O Tenaillon (experiments) on the evolution and dynamics of microbial genomes to understand their diversification by gene flow. Check research.pasteur.fr/en/job/postd...

Job opportunity in microbiomes at Liverpool. Initially short term but likely to be extended. Jo Fothergill and myself www.jobs.ac.uk/job/DEL318/p...

Microbe of the month: Pseudomonas aeruginosa in Trends Microbiol www.cell.com/trends/micro...

I am passionate about both doing and communicating evolutionary research effectively. If you are too, do check out this #PhD opportunity with me and Prof L Hurst. Deadline 11th Feb, Start Sept 2024, Funding available for home students (Sorry). #scicomm *Pls RP* www.findaphd.com/phds/project...