Google reminds me that it's been 2 years since this picture and the Workshop on plasmids as vehicles of AMR spread. We did our best to reorganize it this year but we couldn't get any funding . We haven't given up on the workshop and at some point we will organize another edition!

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n 📄 www.nature.com/articles/s41... 💿 mmseqs.com

My first Bluesky post - it's been a time coming, but I have decided to only review for journals that are associated with academic societies. I will also focus my publication efforts in those journals as well. Our APCs should go back into the subject.

You like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range. @rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social www.nature.com/articles/s41...

Really glad to announce a new preprint from our lab: Global distribution of quinones in Bacteria! We here combine comparative genomics and text mining to leverage information on quinones distribution from thousands of articles describing new species and from dozens of thousands of genomes! 1/5

Exclusion systems, far from slowing down plasmid spread, are in fact essential to preserve host cell viability and thereby ensure the successful dissemination of conjugative plasmids and antibiotic resistance genes. @nfrk92.bsky.social @narjournal.bsky.social academic.oup.com/nar/article/...

Open postdoc position in in my lab in Berlin @mpiib-berlin.mpg.de. Join us to push the frontier in ancient microbial genomics. Please apply until Oct 17th. Reach out in case you have any questions. www.mpiib-berlin.mpg.de/2193291/job_...

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!

🚀 Applications for the PPU International PhD Program are open until October 20, 2025! We invite you to discover 2 projects on Structural Biology & 3 Research & Technology projects 👇 📍 Program starts: October 2026 Discover all the projects & apply now: www.pasteur.fr/en/education...

No Genetics? Try ASOs – A non-genetic approach to silence genes at the phage-host interface. We use it to study jumbo phage biology and anti-phage defence. @jorg-vogel-lab.bsky.social @helmholtz-hiri.bsky.social @uni-wuerzburg.de @helmholtzhzi.bsky.social published now in @nature.com

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

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...

About 10 years ago, we set up lots of experimental beetle populations, censused monthly. Expecting extinction, I said the workload would drop soon. But they all rescued themselves! 😱 So Vrinda & co kept counting. Many hundreds of thousands of beetles later, we have some neat outcomes. Enjoy!

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...

We are welcoming applications for a full professorship on Molecular and Evolutionary Zoology at Kiel Univerdity, Northern Germany, with fantastic facilities and infrastructure! @uni-kiel.de @crc1182.bsky.social @transevo.bsky.social www.nature.com/naturecareer...

So excited our antibiotic potentiation story is out 🤩 Led by the extraordinary @manonlang.bsky.social with @fox-science.bsky.social & @amazeld.bsky.social +amazing collaborators @immunobladder.bsky.social @imaneelmeouche.bsky.social 🦠 We believe it can make a difference in #AMR infections!

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...

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

Lots of heterogeneity in capsule production in Klebsiella and Acinetobacter. Given the pleiotropic impact of capsules, this provides opportunities for multiple types of phenotypical heterogeneity. Check @julielebris.bsky.social thread on our recent publication.

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...

A new theme issue of #PhilTransB examines the evolutionary history of bacterial immune systems, their modes of action, and the patterns how different bacterial immune systems are distributed across different ecosystems. Read: buff.ly/Z4qdxY1

The ecology and evolution of microbial immune systems: a look on the wild vibrio side Phil. Trans. R. Soc. B by @fredoleroux.bsky.social royalsocietypublishing.org/doi/10.1098/...

Happy to see our paper out! Functional assessment of anti-phage defence systems in their native clinical E. coli host royalsocietypublishing.org/doi/10.1098/... Thread in previous post 👇

We have a position for an Assist Prof in Microbial Genomics in our School of III. Hod Joan Geoghegan will be happy to field questions if you are interested. No specific area of microbial genomics preferred so please do consider it www.jobs.ac.uk/job/DOO184/a...

At last ! A tool specifically for phage-plasmid hunters. Check tyPPing by @karinailchenko.bsky.social and @eugenpfeifer.bsky.social

New paper from our lab up on Biorxiv, showing how a toxin targets replication to induce competence. 👇

Amazing resource to query the whole genomics sequence data by @rayanchikhi.bsky.social

The SMBE 2026 Annual Meeting in Copenhagen is open for symposium proposals from Sept 1 to Oct 15, 2025. Details at https://smbe2026.org/symposia/. Looking forward to your submissions! #conference

Preprint: De-novo design of proteins that inhibit bacterial defenses Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications Congrats Jeremy Garb! tinyurl.com/Syttt 🧵

Out of China? Macrolide-resistant #pertussis in France in 2024: Our epi-genomic study suggesting this scenario is out today in @cmijournal.bsky.social thanks to all colleagues, not least @noemielefrancq.bsky.social #EURLdiphtheriaPertussis ‬https://doi.org/10.1016/j.cmi.2025.06.025

Three postdoc positions are now open for applications! Live and work on Kaurna land (Adelaide) in sunny South Australia. We have beach views, wineries, kangaroos, and koalas. Develop new synthetic biology to engineer and understand #phage, and computational tools for #phage and #microbiome analysis

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

Beautiful work from @claudiaalcar.bsky.social, congrats! Piecing Together the History of Protein Folds From a Fragmented Evolutionary Record academic.oup.com/gbe/article/...

Third Era of Phylogenetics! 1️⃣ Era 1: Morphology 🦴 2️⃣ Era 2: Sequences 🧬 3️⃣ Era 3: 3D Structures ⚛️ Solving deep evolutionary puzzles like never before. Our new review in GBE explores what's next in #phylogenetics academic.oup.com/gbe/article/... #structuralbiology #evolution #AlphaFold #SciSky

Manuscript accepted just in time for #ESEB2025 @eseb2025.bsky.social @julielebris.bsky.social will present phenotypic heterogeneity in some #ESKAPE pathogens 🧫 ! S34.01 - Mechanisms of adaptation to changing conditions in microorganisms Those not going to Barcelona, stay tuned for details!

@swstkm.bsky.social & @martinlercher.bsky.social evaluate HGT inference methods, showing that those analyzing gene family presence/absence patterns across species trees outperform approaches based on gene tree-species tree reconciliation. 🔗 doi.org/10.1093/molbev/msaf166 #evobio #molbio #HGT

Excited 🥳 to share our latest work on gut phages! Big thanks to @epcrocha.bsky.social, Erick D, Camille d'H, @fplazaonate.bsky.social, Quentin LB, and all others involved for support and contributions! 🙌 Out in Cell Reports @cp-cellreports.bsky.social doi.org/10.1016/j.ce... Here's what we found 🤓

A 2-year postdoc position in my lab, under the supervision of P-Alex Kaminski, on Z-DNA phages and the benefit given by ZTGC DNA and the replication machinery, with attempt to create a Z based minireplicon research.pasteur.fr/en/job/a-two...

After many years in the making, here is our host range #phage paper with #ecology, #evolution and #biocontrol perspectives published in Molecular Ecology! @phimresearch.bsky.social‬ @inrae-pv.bsky.social‬ #PVBMT #JulianGarneau onlinelibrary.wiley.com/doi/10.1111/... These are our key findings:

The preprint of my first article is available on bioRxiv! We use a transposon ecology framework to analyze the distribution of insertion sequences within prokaryotic genomes. We characterize their ecological niche and show evidence of niche construction 🧪🧬💻 www.biorxiv.org/content/10.1...

Great to see this out. The impact of antibiotics on the gut phages and what it tells us of the disruption associated with antibiotics . www.cell.com/cell-reports... Check @eugenpfeifer.bsky.social thread

Unwelcome guests: characterizing the ecological niche of insertion sequences within prokaryotic genomes https://www.biorxiv.org/content/10.1101/2025.07.22.666184v1

🦠🧍‍♀️From bacterial to human immunity. We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity. Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social www.science.org/doi/10.1126/...

The #ESEB2025 meeting in Barcelona is getting closer, there are still places available but time for registration is running up. Are you going to miss the main evolutionary biology event in Europe this year? 👇 eseb2025.com/registration/

Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...

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 online! Viromics approaches for the study of viral diversity and ecology in microbiomes

A new preprint led by Sonomi Yamaguchi in our lab describes a bacterial anti-phage defense system named Clover that uses nucleotide signals to both activate and inhibit host immunity. www.biorxiv.org/content/10.1...

Heads up! 📢 The 5th Session of the ISPB Virtual Seminars is tomorrow, from 8:00 to 9:00 UTC. Hope to see you there virtually! #Plasmid #ISPB #VirtualSeminar

#Joboffer #CNRS CPJ computational biology in our unit. Deadline for submitting your application is July 14. See details below. Come to join us! @univparissaclay.bsky.social @cea.fr @genopole.bsky.social