I am so proud to be part of this work, that we initiated Fernando de la Cruz and I, when he was on sabbatical in my lab in 2009... it took so much time for this achievement, 1000 thanks to Raúl Fernández-López! this brought me back to my PhD on cyanobacteria genetics. www.pnas.org/doi/10.1073/...

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

Really excited to share our latest paper led by @simonaube.bsky.social. Fascinating results examining whether regulatory mutations can lead to adaptation as fast as coding mutations do. #mevosky #evobio #evoSky www.biorxiv.org/content/10.1...

Delighted to share our recently published work! Ever wondered how Klebsiella (and others) deals with capsule production’s costs ? The paper: journals.asm.org/doi/10.1128/... Thread👇

Check out @julielebris.bsky.social’s thread on our latest manuscript describing phenotypic heterogeneity in capsule production in Klebsiella & Acinetobacter @klebclub.bsky.social This work started when I was still in @pasteur.fr & got finished in @cbitoulouse.bsky.social #microsky #phagesky

We are hiring a PhD student! Are you fascinated by microbes and evolution? Come join us in Barcelona!

How complex functions, with important physiological and evolutionary impacts get repeatedly and efficiently transferred across genomes? That’s what we explored using one of the fastest-evolving loci in Bacteria: the capsule locus. The paper: www.biorxiv.org/content/10.1... Thread👇

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny www.biorxiv.org/content/10.1... github.com/iqbal-lab-or...

El grupo de Álvaro San Millán revela el coste de mantener la resistencia en enterobacterias El trabajo traza un mapa funcional del plásmido pOXA-48, con potencial para guiar nuevas terapias contra resistencias bit.ly/4p0fCmY @sanmillan.bsky.social @aliciapcv.bsky.social @jorgesastred.bsky.social

Extremely glad to see this out!! Wonderful work by all the lab, especially @aliciapcv.bsky.social. Don't miss her thread!!

Our new manuscript is out! A bit of everything cool: Plasmids ✅ Insertion Sequences ✅ AMR Evolution ✅ Microbial Communities ✅ Databases analyses ✅ Mathematical modeling ✅ See the scientific thread below of Jorge Sastre, who has brilliantly led this work with @palomarodera.bsky.social

If you ever find yourself needing evidence for ‘Plasmids are just as common in microbes without resistance genes,’ we’ve got you covered! Check our new paper, out today: www.microbiologyresearch.org/content/jour...

New paper in collaboration with the @asantoslopez.bsky.social lab! www.biorxiv.org/content/10.1...

New paper out! 🔈🔈📣📣 Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation. Combining experimental and computational approaches, we unveil how two of the most prevalent bacterial MGE accelerate the evolution of AMR. 🧵👇🏻 www.biorxiv.org/content/10.1...

Do plasmids evolve faster 🐇, slower 🐢, or just like chromosomes 🧬? In our new paper, we tackled this question using theory, simulations, bioinformatics, and experiments! 👇 Check out all the details in Paula’s thread! Hint: 🐇 (most of the time)

New paper alert! 🚨 Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate. We combine theory, simulations, experimental evolution, and bioinformatics to demonstrate that mutation rates scale with plasmid copy number. Let's dive in! 🧵👇

New pre-print from my lab! Plasmids link antibiotic resistance and phage defense. E.coli plasmids are hotspots for both antibiotic resistance and phage defense. Phage therapy has the potential to accidentally select for antibiotic resistance!!! #microsky#AMR#phage www.biorxiv.org/content/10.1....

🦠 Nuestro #articulodelmes habla sobre cómo los integrones móviles codifican sistemas de defensa contra fagos de la mano del grupo investigador liderado por el Dr. José Antonio Escudero 📄https://f.mtr.cool/qxwueostwp

I am very happy to share our latest study on ciprofloxacin resistance instability in P. aeruginosa during periods of drug restriction. A fantastic collaboration @pablolaborda.bsky.social, RuggeroLaRosa, JLMartínez, SørenMolin & HelleJohansen 🥳 @cnb-csic.bsky.social www.nature.com/articles/s41...

#Bacteria use weapons to outdo rivals, but what happens if they're transferred? @prokaryota.bsky.social @jdpal.bsky.social &co show that HGT of toxin #plasmids is rare but recipients can thrive under relaxed nutrient competition, reshaping bacterial warfare @plosbiology.org 🧪 plos.io/43vC3X7

New opinion paper from the lab! www.cell.com/trends/micro...

Our updated lab website is live! We’ve kicked off a new project and a new look with it. Take a look and let us know what you think! 👉 plasmidlab.es

Our opinion piece on transmission timing in phages and plasmids graces the cover of @cp-trendsmicrobiol.bsky.social this month. Featuring the work of talented master student Andrina Bernhard, the illustration showcases cues that MGEs use to switch between horizontal and vertical transmission.

What a milestone!!! I’m really glad I got to add my two cents to the growing knowledge about integrons — this paper is totally worth checking out!

🧪 Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉 Short 🧵 www.science.org/doi/10.1126/...

Researchers in #ScienceAdvances have discovered a genetic footprint that helps explain herding dogs’ mental acuity and keen social skills. scim.ag/3RO3RRd

Do people in the same household share strains when they have the same species? How many cells transmit when a strain is shared? Can strain composition be dynamic when species composition is stable? We answer these and related questions for the facial skin microbiome in our latest paper. 🧵[1/10]

This meeting will be great! Abstract submission open now See you 26-27 Nov in Liverpool microbiologysociety.org/event/societ...

Excited to share the first manuscript from my PhD in which we leveraged ultra-long Nanopore sequencing, D. melanogaster inbred lines, and a ton of manual validation to investigate the effects of long-read length on population-level structural variant (SV) calling accuracy! doi.org/10.1101/2025...

Do restriction-modification systems shape plasmid sequence composition? A group of plasmid-aficionados, led by Liam Shaw, started to explore this during the 2023 @embo.org Workshop on Plasmids in Trieste. Happy to have contributed to this work and be part of such a great team!

Our new preprint by @nanamikubota.bsky.social shows that P. aeruginosa, and likely many other bacteria carrying filamentous prophages (like V. parahaemolyticus), risk being exploited by these phages in a runaway process that reduces fitness of both host and virus. www.biorxiv.org/content/10.1... 🧵

Preprint out! Bacteria w/ hyper-replicative filamentous phage lead to overnight emergence of cheater phages. Bacteria w/ both phages can outcompete wildtype, then rapidly lose phage via a phage Tragedy of the Commons @shellyscrib.bsky.social @vscooper.micropopbio.org www.biorxiv.org/content/10.1...

🚨 Seminar at ETH this Thursday! 🚨 Join Dr. Jerónimo Rodríguez-Beltrán (@jerorb.bsky.social) for a talk on how plasmids shape antibiotic resistance. Plasmid evolution: a (copy) numbers game 🗓 April 3rd | 🕙 10:00–11:00 📍 CHN F42, ETH Zurich evodynamicslab.com

Preprint below has been a long time coming, here just in time for #microbio25 ! (if the train wifi lets me) With @andrewmatthews.bsky.social #MicroSky 🧵

Excited to see review with @asherleeks.bsky.social out today in Nature Antimicrobials and Resistance. We compare application of social evolution to treatment of infection in bacteria and viruses: very different stories! rdcu.be/eftKw @biology.ox.ac.uk @erc.europa.eu @naturerevmicro.bsky.social

Can we use social evolution to fight pathogens? @asgriffin.bsky.social and I review the evidence for 'cheat therapy' in bacteria and viruses... 🧪🦠 #socialviruses #evosky #virosky 1/3

New online! Genetics, ecology and evolution of phage satellites

If you are interested in phage satellites, we hope you'll enjoy this. Fun collaboration with the Rocha, Seed, Bikard, and Chen labs! rdcu.be/efkvG

... and finally the paper is out on microbial genomics! www.microbiologyresearch.org/content/jour...

1/35 New paper out! @jamesTstroud and I dive into why long-term studies are crucial for understanding evolution. They reveal processes impossible to detect in short timescales and capture rare events that transform our understanding of evolutionary dynamics. www.nature.com/articles/s41...

Join us in at #ESEB2025 Barcelona for our symposium on microbial adaptation to changing conditions. Organised by @mtoll8.bsky.social @javierdelafuente.bsky.social and me. Amazing invited speakers @saramitri.bsky.social and Itzik Mizrahi!! @eseb2025.bsky.social

www.nature.com/articles/s41... In collaboration with Andrew Lang and Alison Buchan, we just published a review on the complex and sometimes convoluted interactions and evolutionary relationships among bacterial mobile genetic elements. #phage #plasmid #evolution #bacteria #plasmidbiology #MGE

The International Society for Plasmid Biology and other Mobile Genetic Elements are finally in Bluesky!! 😎😎😎

Legitmately thrilled to share our latest work, in which @fernpizza.bsky.social solved an experimental challenge in plasmid biology as old as the field: measuring how plasmids compete and evolve within individual cells!

We are recruiting! We are looking for a PhD student to study rapid adaptation to stress in bacteria (shorturl.at/sr0Mj). Come join us in Barcelona!

Experimental evolution of evolvability | Science www.science.org/doi/10.1126/...

With @CostaT_Lab, we challenged AI co-scientist to generate scientific hypotheses. It correctly predicted how cf-PICIs spread between bacterial species, matching our unpublished, experimentally confirmed mechanism! 🤯 @imperialcollegeldn.bsky.social www.biorxiv.org/content/10.1...

Valuable contribution to the issue of how we ight look at data that have evolved in a hierarchical manner: www.nature.com/articles/s41...

New mechanism of gene transfer! With @tcostalab.bsky.social @imperialcollegeldn.bsky.social, we discovered that cf-PICIs form tail-less elements that, once released, spread among different bacterial species by hijacking tails from various phages. More exciting news soon! shorturl.at/kRJqE

A University of Basel study shows that antibiotic failure is due to nutrient-starved Salmonella, not persister bacteria, as traditional methods underestimate surviving bacteria. Researchers suggest focusing on nutrient-related resilience to improve treatments. #AMR www.nature.com/articles/s41...