🎉 4 Institut Pasteur scientists elected as Fellows of the European Academy of Microbiology (EAM) 2026! David Bikard, Arianne Briegel, Ivo Gomperts Boneca & Eduardo Rocha honored for excellence in microbiology. Joining 95 new global members.

Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.

A new family of rolling-circle replication endonucleases widespread in archaeal viruses and plasmids. This family is unrelated to the HUH superfamily Reps, but distantly related to the bacterial Rep_trans enzymes. @narjournal.bsky.social academic.oup.com/nar/article/...

So yes—stewardship works. But biology (and ecology) doesn’t move at policy speed. Full paper: www.nature.com/articles/s44... #AMR #OneHealth #microbiome #veterinary #metagenomics

New in @science.org ‼️ In the most comprehensive study to date, we show that wildlife trade is driving animal-to-human zoonotic spillover at a planetary scale, with +1 spillover per host every 10 years. Live animal markets and illegal trade pose even greater risks. 🔓 www.science.org/doi/10.1126/...

www.biorxiv.org/content/10.6... Cool new anti conjugation mechanism

Our ms on re-sampling 4 years apart vibrio phage in natural environments is now out with some improvements. First, clearer evidence of cryptic population dynamics between phage and vibrio, presumably because of genetic diversity. www.nature.com/articles/s41...

Big update for #gbdraw! - Multi-record circular plots: Genomes with multiple replicons can now be displayed in a single view! - Advanced linear plots: Focus on regions of interest with granular control over feature selection and color-coding! Try now: gbdraw.app #microbiology #bioinformatics

How diverse is bacterial immunity ? We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems. 👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie... Explore them here defensefinder.mdmlab.fr/wiki/refseq_...

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!

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

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

Capturing dynamic phage–pathogen coevolution by clinical surveillance "we capture the acquisition of a parasitic anti-phage mobile genetic element, PLE11, that initiated a selective sweep coinciding with the largest cholera outbreak in recent records. " www.nature.com/articles/s41...

🚨 New paper! Very excited to have been part of this collaborative work looking at the effect of antibiotics on the gut microbiota even years after prescription. Amazing effort led by Gabriel @tovefall.bsky.social and many others published today in Nature Medicine! 🔗 www.nature.com/articles/s41...

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 👇🏼

Fantastic collaboration w/ @dbikard.bsky.social @audeber.bsky.social @rayanchikhi.bsky.social labs led by @jmouradesousa.bsky.social : We assessed the rates of variation of anti-phage systems in P4-like satellites and P2 helper phages. Quick conclusion: Huge variation! We focus on 4 key questions/5

➡️ 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? 🤔 🧵👇

📢 Opportunity to apply for a PhD fellowship to join our group and work on MGE-MGE interactions and phage defence systems! @mmsb-lyon.bsky.social See informations about eligibility and research project on this web page: graduate-plus.fr/immunology-v... Contact me if you are interested !

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 🧵

Up to what degree of interspecific genetic distance is it possible to form viable and fertile hybrids? A strange species of paramecium breaks the record: www.biorxiv.org/content/10.6...

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 preprint 🚨 How promiscuous really are conjugative plasmids, and what does that mean for plasmid co-occurrence? A pleasure to collaborate with @craigmaclean.bsky.social on the first paper of my fellowship! www.biorxiv.org/content/10.6...

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!

A new paper shows that less than 2 months of exposure to Twitter’s algorithmic feed significantly shifts people’s political views to the right. Moving from chronological feed to the algorithmic feed also increases engagement. This is one of the most concerning papers I’ve read in awhile.

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...

Check out our latest preprint from @jnvmartinson.bsky.social and @leosong.bsky.social! 🌟🦠 We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵

Plasmids weaponize conjugation to eliminate non-permissive recipients https://www.biorxiv.org/content/10.64898/2026.02.10.705089v1

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs

I couldn’t agree more! Help support Wikipedia. It has been a pillar of high-quality knowledge sharing since the early web, and it’s more relevant than ever in the fuzzy age of AI www.nature.com/articles/d41...

Un poste de Maître de Conférence est ouvert pour rejoindre notre unité à Lyon ! Possibilité de rejoindre mon équipe pour travailler sur: - caractérisation des mécanismes de défense anti-phage - transfert horizontal et interactions entre éléments génétiques mobiles N'hésitez pas à me contacter

🚨 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...

🚨L'ENS de Lyon recrute un.e maître de conférence qui rejoindra le CIRI pour développer ses recherches sur l'immunité bactérienne, les transferts horizontaux et les MGE. 📖 Une très belle opportunité d'enseigner à des étudiants brillants tout en menant des recherches excitantes !

Here, we find that many Genomic islands have origins of transfer (oriT) mobilisable by conjugation, incl. known Pathogenicity & defense islands. iOriT use only an oriT for transfer by hitching on conjugative elements: they make abundant, diverse, ancient families of mobile genetic elements. See🧵

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...

It has been a long road, but our paper on Klebsiella plasmids is finally out in Lancet Microbe. Thanks to all co authors but especially Marjorie Gibbon and Natacha Couto www.sciencedirect.com/science/arti...

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!

@laasya2.bsky.social @deepaagashe.bsky.social et al. quantified the growth cost of mistranslation rates and exposure to antibiotics in E. coli, finding that altered translation accuracy can shape adaptive outcomes. 🔗 doi.org/10.1093/molbev/msaf312 🖌️ Nishant Asawadekar #evobio #molbio

Preprint alert📢! 
Ever wondered how much bacterial parasites influence evolutionary outcomes of their host? ➡️ We co-evolved two bacterial strains in conditions in which the costs and benefits of prophage carriage varied Here is what we found. 
www.biorxiv.org/content/10.6... 
#MicroSky #PhageSky 🧵

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/...

The next LEGEND conference on machine learning for evolutionary genomics will be in Aussois (French Alps) between December 8th and 12th. Mark your calendars and make sure your best work is ready next September when the call for abstracts opens 🙂 legend2025.sciencesconf.org

🚨#PhD studentship opportunity! Plasmids provide bacteria with antimicrobial resistance, but do they have more fundamental effects on behaviour? 🧫🦠💫🧟‍♂️ Apply for a 4y funded MRC DiMeN position with me and Jamie Wheeler @livuni-ives.bsky.social www.findaphd.com/phds/project...

Please apply for this, and/or encourage your mentees and peers to do so!

Still looking for our perfect doctoral candidate as part of @evomg-dn.bsky.social - come and join us to work on the evolutionary pressures that shape gene expression and disease in the uterus! Please RT (or is it RB? not sure how our lingo has changed!)

#microsky 😮 journals.plos.org/plosgenetics...

Join us tomorrow if you like plasmids and clones! @sandrareuter.bsky.social will be talking about a particular intriguing outbreak 🤓. @escmid.bsky.social

@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎 www.pnas.org/doi/10.1073/...

DNA from Napoleon’s 1812 army identifies the pathogens likely responsible for the army’s demise during their Russian retreat. www.cell.com/current-biol... Nicolás Rascovan & colleagues @currentbiology.bsky.social

JOB OFFER #PhageSky We have a postdoc position opening in my group to investigate phage-MGE interactions ! We're based in the very nice city of Lyon, France @mmsb-lyon.bsky.social Contact me for more info ! >> Apply on the CNRS webpage emploi.cnrs.fr/Offres/CDD/U...

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...

Podcast with me and @turiking.bsky.social for the @milnerevolution.bsky.social series, on plasmid evolution over the last 100 years, talking about our ( @cazares-adr.bsky.social , Nick Thomson, @sarah1alexander.bsky.social & co) recent paper www.science.org/doi/10.1126/... youtu.be/Mzr3TD4ijs0?...