Months (years ?) spent on species-wide screens, over 3.000 PCR reactions and an unbelievable amount of 10-uL tips : I'm glad to introduce the novel TAR family of anti-plasmid defenses ! The war between bacteria and their MGEs is far more complex than we expected ⚔️ Read Xavier's 🧵 for more details !

We're excited to share our work on how prophages influence the evolution of resistance against DNA-damaging antibiotics! This has been a fun project with @sianowen.bsky.social, @baym.lol, @theshreyaspai.bsky.social, @kepatitis-c.bsky.social, & @fernpizza.bsky.social biorxiv.org/content/10.6... 1/

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

Shoutout to this amazing piece of work! Do you want to know how chronic gut inflammation affects bacterial and MGEs evolution? Give this thread a read, it is fire 🔥! (ba-dum-tss)

New paper out! 🔈 Genomic Characterization of the RyC collection: 50 Multidrug Resistant Clinical Isolates of Escherichia coli and Klebsiella spp. 50 MDR gut isolates, 2 sequencing platforms, 4 “omes,” and 1 mission: provide a resource to decode AMR and MGE dynamics www.biorxiv.org/content/10.6...

What if multireplicon plasmids are not an oddity, but an evolutionary strategy? We found that they are common, more mobile, broader-host-range, and enriched in AMR. Even more interesting: their assembly doesn’t look random. 👀 Paper preprint: www.biorxiv.org/content/10.6... Thread below!🧵👇

Excited to share our new paper out today in @science.org 🎉 We show that HGT via natural competence drives diversification of chromosomal integrons in V. cholerae 🤩 Below a 🧵 on key findings incl. background on natural competence in V. cholerae 1/ #microsky #phagesky www.science.org/doi/10.1126/...

I am excited to share our latest paper, Uniform bacterial genetic diversity along the gut, now out in Nature Communications! www.nature.com/articles/s41.... (1/n)

This year's GIMM fest is all about microbial evo-evo and health&disease 🧫 Two days speaking about microbes by the lovely Lisbon coast, need I say more?

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!

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...

Horizontal gene transfer is often depicted as a process distributing pre-existing functions to novel genetic backgrounds. Yet HGT can also increase the rate of functional innovation after transfer. Here's a brief review on the topic: ecoevorxiv.org/repository/v... #evosky #microsky

Glad to see our latest work out in Nature Microbiology!! Extremely grateful to everyone involved in the project. Check it out!! 👇🏻👇🏻

With @saramitri.bsky.social, @sonjalehtinen.bsky.social and L. Lehmann we’ve launched the UNIL Center for Theory in Ecology and Evolution @unil.bsky.social🇨🇭 To kick things off, we’re offering short visiting fellowships for theorists in ecology & evolution. Apply & pls RP 😀 tinyurl.com/2wem36zz

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 👇🏼

I’m very happy to have joined the Evolutionary Biology lab in @gimminstitute.bsky.social as a postdoc, headed by @isabelgordo.bsky.social. After 10 years living abroad, I am finally back home! 2.6km away from where I grew up, to be exact! Here is to new adventures and amazing science by the ocean! 🥳

➡️ 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? 🤔 🧵👇

🔬 New work from the Mazel Lab engineers programmable conjugative plasmids to selectively target MDR bacteria and the resistance plasmid pOXA-48, blocking its spread in complex communities. ✍️ @amazeld.bsky.social & coll. @pasteur.fr 📖 shorturl.at/GZdJu #MicroSky #AntibioticResistance #Conjugation

Amazing piece of work I had the great luck to be a part of!

Out now in @plosbiology.org : our big joint effort on the role of #CRISPR in plasmid competition. Read on for a really fun (I’m biased ok) analysis of how a defence system has new selective pressures when it’s mobile journals.plos.org/plosbiology/... 1/6

New pre-print with @wtmatlock.bsky.social!!! www.biorxiv.org/content/10.6... What shapes the distribution of plasmids across bacteria? Our paper shows that conjugative plasmids actually have a very narrow distribution compared to mobilizable plasmids. Conjugative systems restrict plasmid transfer!

How does treatment induced antibiotic resistance happen in real-world infections? We analysed 25k Pseudomonas isolates from 180 patients in a clinical trial to find out! TLDR: The ecological and evolutionary paths are surprisingly diverse & complex even in patients receiving identical treatment…

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

Today is my last day working in the PBE lab @cnb-csic.bsky.social. Goodbyes are always bittersweet. These walls have seen me grow a lot as a scientist and a person, and I have all these lovely people to thank for it. I will carry you with me to my next adventure 🥰

#NatMicroPicks E. coli can be engineered to secrete a glue consisting of an adhesive protein and a healing factor, inducible in response to gastrointestinal bleeding, to treat colitis in a mouse model @natbiotech.nature.com www.nature.com/articles/s41...

#NatMicroPicks Baby-to-baby strain transmission shapes the developing gut microbiome - out now in Nature! 👶🦠👶 #microsky #microbiome @nature.com @cibiocm.bsky.social www.nature.com/articles/s41...

Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive. Here we explore the conjugative capacity of these mysterious Genomic Islands. www.biorxiv.org/content/10.6...

Bacteriophages are normally classified as either virulent or temperate. Reality is, of course, more complicated! Here we show many bacterial isolates contain non-temperate phages that can persist through restreaking. Thanks to all co-authors for such a great collaboration!

The EMBO Gold Medal 2025 was awarded to Tanmay Bharat and David Bikard: https://www.embo.org/press-releases/embo-gold-medal-2025-awarded-to-tanmay-bharat-and-david-bikard/ 🧪 At #CellBio2025, the EMBO Gold Medal was handed over to David Bikard in recognition of his pioneering work on #GeneEditing.

On the plane after a fantastic few days in Liverpool at #MicroEvo25 organised by the @microbiologysociety.org. The science, the people, and the city were all way above expectations. I’m definitely coming back. Had an absolute blast!

Very happy to be at #microevo25 in Liverpool! Here’s to two days of micro-awesomeness and Beatles’ references!

Our new paper is out in @narjournal.bsky.social We show that natural transformation enables bacteria to shuffle integron cassettes, boosting their phenotypic diversity. academic.oup.com/nar/article/... 1/5

#microsky #phagesky CRISPR-cas galore www.nature.com/articles/s41...

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 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

New paper online at @nature.com from co-leads @erinedoherty.bsky.social + @benadler.bsky.social !

🔬PPU 2025 Call for Candidates - Discover the PhD projects Today's featured projects: 4 Cell Biology & Infection projects and 2 Parasites & Insect Vectors projects 🗓 Applications deadline: October 20, 2025 📍Program starts: October 2026 Discover all projects & apply now: bit.ly/4nlPz8x

Very happy to see this one out: doi.org/10.1093/molbev/msaf192 Here, we assessed the contribution of natural transformation to the acquisition of novel genes. See preprint thread. @molbioevol.bsky.social #microsky #evobio

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

Have you ever wondered what increasing environmental stress will do to microbial communities? In our new preprint, @martinadalbello.bsky.social, Jeff Gore and I studied the impact of salinity on microbial community composition and function. 🧵 (1/5) www.biorxiv.org/content/10.1...

#NatMicroPicks AI Designs Next-Gen Antibiotics! 💊🤖 Generative deep learning and genetic algorithms created structurally novel antibiotics that effectively target drug-resistant bacteria, offering a powerful new tool to combat drug resistance. #MicroSky #AMR www.cell.com/cell/abstrac...

Our paper “Genetic determinants of pOXA-48 plasmid maintenance and propagation in Escherichia coli” is now online in @natcomms.nature.com ✨ 👉 www.nature.com/articles/s41... @cnrs-rhoneauvergne.bsky.social @mmsb-lyon.bsky.social

🚨🚨New paper out in @natcomms.nature.com!! Come for the first large-scale analysis of plasmid copy number across species, stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬 👉 www.nature.com/articles/s41...

For those who love bacterial replicons, The ultimate review, from our lab, signed by the master of their evolution. ‪@val-meve.bsky.social‬ www.sciencedirect.com/science/arti...

This work is finally published! 🥳🧬 Plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by @jorgesastred.bsky.social, @sanmillan.bsky.social and myself! 1/14

#NewResearch Prion-like proteins in Escherichia coli trigger an abortive infection mechanism in response to phage infection—a process similar to amyloid-mediated immune signalling in fungi and animals. #MicroSky 🦠 www.nature.com/articles/s41...

Very happy to be a (small) part of this story! The role of plasmid-encoded ISs in the acceleration of AMR evolution, through inactivation of different bacterial genes.

White smoke, we have a new pope and also 16 new anti-phages systems in sedentary integrons (SCIs) ! In collaboration with the Rocha lab, we show in our new paper that cassettes of these large platforms encode many known anti-phage defenses, and uncovered 16 new ones. www.science.org/doi/10.1126/...