🚨 New preprint from the lab! 🚨 We show that multireplicon plasmids are true AMR "jack-of-all-trades": Widespread, highly mobile, broad host-range, and packed with resistance genes. Far from random, they form co-evolving associations driven & 𝘮𝘢𝘪𝘯𝘵𝘢𝘪𝘯𝘦𝘥 by IS elements. See Nacho's thread below!👇👇

Very proud of this work and all the efforts from my team and collaborators on this! You can now use DGRs for in vivo targeted hypermutagenesis in E. coli. We also included some early proof of concept in Yeast thanks to @seth-shipman.bsky.social !

My main postdoc paper is now out in @natureportfolio.nature.com npj Antimicrobials and Resistance! www.nature.com/articles/s44.... Using flow cytometry, we show that the nucleoside analogues azidothymidine, didanosine, stavudine, and trifluridine reduced transfer of AMR plasmids pCT and pKpQIL (1/3)

En #AGolpeDeBit #RTVE, @sanmillan.bsky.social investigador del #CNB @csic.es habla de este estudio liderado junto a Alfonso Santos López @uam.es y en colaboración con Ayari Fuentes #UNAM_MX centrado en el plásmido pOXA-48 de gran interés clínico 📻 ¡No te lo pierdas! www.rtve.es/play/audios/...

Now out in AEM @asm.org! 🎉🧪 *High school student-isolated mutants 👉🏻 novel genetic causes of biofilm-associated adaptations *We learn how diversity arises quickly and is maintained *EvolvingSTEM enables scalable research in classrooms & promotes scientific literacy journals.asm.org/eprint/FBU9M...

We are pleased to share our last article rdcu.be/fabhM. It offers the most comprehensive analysis so far of Ab+non-Ab resistance genes in human gut microbiome, using an Indigenous population (low industrialization, chronic Hg exposure from gold mining) 6/6👇

Here’s the latest preprint from my work on evolved resistance to Type VI Secretion system (T6SS) weaponry, funded by a @wellcometrust.bsky.social Sir Henry Wellcome Fellowship. So happy to see this out! www.biorxiv.org/content/10.6...

New preprint alert!!! 🚀🤓 We are very happy to finally share this with the world — the result of seven years of work and a new tool to study integrons and discover new functions encoded in these bacterial platforms. If you want to know more, here is a thread 🧵 www.biorxiv.org/content/10.6...

New #AMR pre-print Combining antibiotics with genotoxins can efficiently suppress bacterial in high throughput experimental models. www.biorxiv.org/content/10.6... Fun collaboration with Nassos Typas lab led by @mulkern.bsky.social

Final version of our last paper is out! www.nature.com/articles/s41...

Identifican un nuevo mecanismo utilizado por plásmidos para acelerar la aparición de resistencia a los antibióticos. @sanmillan.bsky.social @uam.es @csic.es  Más info en nuestra web: https://f.mtr.cool/pmappovlkt Artículo en: https://f.mtr.cool/yvxpgzaraz @natureportfolio.nature.com   @erc.europa.eu

New preprint on the limits of detecting higher-order interactions in microbial communities. www.biorxiv.org/content/10.6... We find that the dominance of additive and pairwise interactions on community function may not reflect biological simplicity, but fundamental limits of statistical detection.

Excited to share our latest work! 📝 We measured the fitness effect of 136 AMR genes and found that many are neutral or even beneficial without selection. 🤯🧬 Oxygen availability can flip their fitness and our stochastic model indicates that oxygen fluctuations help maintain them. Learn more 👇🏼

New preprint out on bioRxiv! www.biorxiv.org/content/10.6... Can conjugative plasmids be used to control plasmid and pathogen spread? Follow me down the rabbit hole that led to this story 🧵

Great news!! Really looking forward to starting this collaboration

Now out & nicely formatted in @isme-microbes.bsky.social A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron. A few highlights... 🧵 (1/n) doi.org/10.1093/isme...

So great to finally have such a clear answer to this question!! Well done guys!

Big week: welcomed a new baby boy Harris Lopatkin, AND our PlasAnn paper is finally out: academic.oup.com/nar/article/... (obviously the first more important than the second 🥰). Currently on leave but if anyone has the need to annotate large plasmids, go check it out!

New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story www.pnas.org/doi/10.1073/...

New paper out in @pnas.org, and it made the cover! 👁️ We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve. ‼️Check Paula’s 🧵 and the paper👇 𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿 www.pnas.org/doi/10.1073/...

Novel genes arise from genomic deletions across the bacterial tree of life https://www.biorxiv.org/content/10.64898/2026.01.05.697752v1

Preprint out! By controlling growth, via RNAP, we control the entire cellular machinery, and tune the cellular context into distinct, stable states. See how NOT gates behave! Kudos to @angeles-hg.bsky.social and @mirobueno.bsky.social 🔗https://www.biorxiv.org/content/10.64898/2025.12.19.695408v1

Our story on plasmid streamlining is now published in PLoS Biology! With @andrewmatthews.bsky.social and @sonjalehtinen.bsky.social #MicroSky #Mevosky journals.plos.org/plosbiology/...

Last week, we hosted the XXXIII CNB Scientific Workshop. We are delighted to announce this year’s award winners: 🏆 Best Postdoctoral Talk: Alicia Calvo-Villamañán 🏆 Best PhD Talk: Silvia López Borrego 🏆 Best Poster: Jorge Sastre Domínguez Congratulations to all! #CNB_CSIC

A pleasure and an honour to have received this prestigious grant with my admired colleagues and friends @sanmillan.bsky.social and @asanchezlab.bsky.social . More about AMR under plasmid lens!. My sincere gratitude to @caixaresearch.bsky.social @microryc.bsky.social @esgem-sg.bsky.social

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

👏 Dos proyectos del #CNB seleccionados en la convocatoria de Investigación en Salud 2025 de la @caixaresearch.bsky.social Ambos abordan un gran reto global: la resistencia a los antimicrobianos. #HealthResearch #FundaciónlaCaixa @sanmillan.bsky.social @jaescudero.bsky.social f.mtr.cool/jejatlbssz

1/ Antibiotic resistance causes ➕ than 1 M deaths each year and understanding why this happens is key to stopping it. With #HealthResearch support, @sanmillan.bsky.social#HealthResearchis investigating how different plasmids (DNA fragments) coexist in bacteria and confer resistance. https://tinyurl.com/3bysv6cr

So happy to share this! Bacteriocins were first discovered over 100 years ago, but what do they actually do? We look at >1000 bacteriocin plasmids and find links to virulence and antimicrobial resistance, and frequent bacteriocin sharing in Enterobacteriaceae. www.nature.com/articles/s41...

New preprint out! 📣🚨 We found that loss-of-function mutations in the carbapenem entry porin OprD of Pseudomonas aeruginosa do more than confer #AntibioticResistance: they reshape the bacterial membrane and interaction with the host, enhancing epithelial colonization capacity 🦠 #Microsky

One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential. www.biorxiv.org/content/10.1...

✨New paper from @jrpenades.bsky.social and @sanmillan.bsky.social labs. We found that non-conjugative plasmids 🧬 tend to have low mobility to promote functional diversity ⚔️💊 in bacterial communities🦠🦠. Brilliant work by Akshay, @asantoslopez.bsky.social and others. www.cell.com/cell-reports...

New paper with my (amazing) friend and mentor @jrpenades.bsky.social Really looking forward to see what plasmid aficionados think of this one!! With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others www.cell.com/cell-reports...

New paper just out from #OurImperial @tcostalab.bsky.social The assembly of a hybrid type IV secretion system by a Crohn’s disease-associated Escherichia coli strain. www.nature.com/articles/s41...

Dissecting the fitness effects of a carbapenem resistance plasmid in clinical Enterobacterales using plasmid-wide CRISPRi screens @aliciapcv.bsky.social @jorgesastred.bsky.social @sanmillan.bsky.social @cnb-csic.bsky.social #bacteria #plasmids

DYK most P. aeruginosa carry filamentous phage(s) that don't need to kill the cell to reproduce? We 👉🏻@nanamikubota.bsky.social show that these Pf phages can go ROGUE. "Filamentous cheater phages drive bacterial and phage populations to lower fitness" 🔗 authors.elsevier.com/c/1lt5I3QW8S...

Nuestro compañero Álvaro San Millán (@sanmillan.bsky.social), investigador en el #CNB_CSIC ha recibido el Premio María Moliner, que reconoce la labor de quienes se inician en la dirección de tesis doctorales, destacando su compromiso en el acompañamiento del talento emergente. ¡Enhorabuena!👏

New pre-print www.biorxiv.org/content/10.1... Plasmid-dependent phage (PDPs) are ubiquitous, but the selective pressures that they impose on plasmids are not well understood. Project led by Daniel Cazares in collaboration with @brockhurstlab.bsky.social! #phagesky#microsky

El proyecto "Descubrir actividades de resistencia antimicrobiana más allá de la resistencia" de @sanmillan.bsky.social (#CNB, @csic.es) y @jaescudero.bsky.social (@ucm.es) recibe una ayuda del Programa #Fundamentos de Fundación BBVA. ℹ️Lee la noticia aquí👇 bit.ly/48cvkp1

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

Recent paper from the lab studying predictors of phage cocktail efficacy against complex clinical Pseudomonas populations royalsocietypublishing.org/doi/epdf/10.... Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska

New ERC funded computational postdoc position in my lab! We are looking for someone who will study the genomics of bacterial evolution using samples from experimental evolution and clinical trials. Lots of opportunities for interesting and fun collaboration! my.corehr.com/pls/uoxrecru...

Excited to share our new Perspective in npj Antimicrobials & Resistance: "Towards the integration of antibiotic resistance gene mobility into environmental surveillance and risk assessment.” www.nature.com/articles/s44... 1/3 #AMR #microsky

How do loci for bacterial capsules (Klebsiella) manage to get swapped around despite their outstanding phenotypes? They just plug and play, having little impact on the rest of the genome. Kudos to @julielebris.bsky.social , check her thread below

Continuing work on our exhibition #microbes 🎨 Honored by a talk from Prof. Itzik Hen, director of The Institute for Advanced Studies Jerusalem and a researcher, followed by a food tour at Mahane Yehuda Market, and a recital by Ido Grinshpan and Shelly Jonathan.🎻 Stay tuned for #exhibition details! 🦠

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...

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

Thrilled to share our two latest papers with the @tcostalab.bsky.social lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species. @imperialcollegeldn.bsky.social www.cell.com/cell/fulltex...

Our second paper with @tcostalab.bsky.social and GoogleDeepMind reports our experience with Google’s co-scientist: remarkably, the AI independently recapitulated our experimental discovery on cf-PICIs, showcasing AI’s potential to accelerate biology. www.cell.com/cell/fulltex...

Antimicrobial Resistance (AMR) could cause 10 million deaths by 2050. At PLAS-FIGHTER, we are working to change this! 🔎 We study how plasmids spread resistance to open up new avenues for future containment and diagnostic strategies. Find out more 👇 plasmidlab.es/project/ #AntibioticResistance