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

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...

Job opportunity for microbial genomicists interested in E. coli and Klebsiella infections and AMR 👀⬇️ - do get in touch if you might be interested! Closing date 7th Oct.

🐟💊🦠Our new study in @natwater.nature.com 🐟💊🦠 "Microbial risks triggered by oral administration of antibiotics in fish aquaculture persist long after the legally mandated antibiotic withdrawal time" www.nature.com/articles/s44... #microsky #amr 1/8

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

Super paper from the mighty Mia Winkler, @genomarit.bsky.social and Iren Lohr. "We have previously shown that there were relatively few strain-sharing events across ecological niches...plasmid-sharing is considerably more common across niches than strain-sharing. " www.biorxiv.org/content/10.1...

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

Hey hey hey! Tomorrow, September 16th at 16:00 UTC, don’t miss the next ISPB virtual seminar! This session will focus on plasmid elimination with great speakers lined up. #Plasmid #ISPB #MGEs

Et bien c'est fait ! Première à l'antenne d'une radio nationale, dans la matinale de France Culture ce matin. Merci à Guillaume Erner de m'avoir accueilli, et à Juliette Devaux pour la préparation de l'émission. www.radiofrance.fr/francecultur...

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...

J'aurai la chance de présenter mes travaux de thèse sur France Culture, dans l'émission "Les Chantiers de la Recherche" ce lundi 15 à 6h45, avec Guillaume Erner. Pour les lève-tard, l'émission sera disponible en podcast. Stay tuned ! www.radiofrance.fr/francecultur...

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.

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👇

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...

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

🚨 New preprint! 🧬 𝐏𝐡𝐚𝐠𝐞-𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 (𝐏-𝐏𝐬) are fascinating elements: both 𝐭𝐞𝐦𝐩𝐞𝐫𝐚𝐭𝐞 𝐩𝐡𝐚𝐠𝐞𝐬 and 𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 ➡️ tricky to detect. We present 𝐭𝐲𝐏𝐏𝐢𝐧𝐠 — the first 𝐢𝐝𝐞𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐜𝐥𝐚𝐬𝐬𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐭𝐨𝐨𝐥 🛠️designed specifically for P-Ps: ✅ Accurate ✅ Sensitive ✅ Easy to use 📖 www.biorxiv.org/content/10.1...

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

#phagesky I am looking for phages infecting Streptococcus pneumoniae to test a phenotype - does anyone have some and willing to share ? Repost appreciated :)

Horton, Cherry, @gretelwaugh.bsky.social @taylorlabgroup.bsky.social et al. combine experimental evolution and bioinformatics in bacteria to characterize a ≥8 bp motif that can increase T:A→G:C mutation rates >1000-fold than the baseline rate. 🔗 doi.org/10.1093/molbev/msaf183 #evobio #molbio

Fluid flow generates bacterial conjugation hot spots by increasing the rate of shear-driven cell–cell encounters #PNAS by Matti Zbinden et al www.pnas.org/doi/abs/10.1...

📝New preprint! We investigated how spatial structure affects cooperation between phages, combining mathematical modelling and experiments. A short thread 🧶

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....

#phagesky www.cell.com/cell-host-mi...

Plasmids link antibiotic resistance genes and phage defense systems in E. coli https://www.biorxiv.org/content/10.1101/2025.07.25.666796v1

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 🤓

The Rare Plasmid Biosphere: A Hidden Reservoir of Genetic Diversity by João Rebelo, Célia Domingues & Francisco Dionisio and co www.biorxiv.org/content/10.1...

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/...

So happy to see this paper finally out! Ridiculous amount of work by Mrudula Sane and Shazia Parveen, showing that reversing baseline transition bias is good, as predicted by models from Lindi Wahl and co. Big thanks to @ncbsbangalore.bsky.social and DBT/WT India Alliance for support.

New paper with @rwheatley8.bsky.social and Cedric Lood Actual title: Chromosomal capture of beneficial genes drives plasmids towards ecological redundancy. Sensationalist title: Plasmids carry useless genes academic.oup.com/ismej/articl...

Mutations generate variation, critical for #evolution, but #MutationBias restricts the choice of mutation type. @deepaagashe.bsky.social &co use #Ecoli strains with different mutation biases to show that changing an old bias should yield more beneficial mutations @plosbiology.org 🧪 plos.io/46LjCRt

#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

Plasmids are small, mobile DNA elements that enable bacteria to exchange genetic material, including genes for antibiotic resistance. We study these genetic vehicles with the aim to uncover how they facilitate the emergence and persistence of antibiotic-resistant pathogens. #AntibioticResistance

Explore the important role of #genomics and data-driven technologies for accelerating advances in #AMRresearch, at our Antimicrobial Resistance meeting! #AMR2026 Discover the latest developments informing a dynamic global response to controlling this crisis. 🗓️ 23–25 March 2026 📎 bit.ly/3SWzJUm

1/6 Excited to share our review 🚀 🧬 CRISPR–Cas therapies targeting bacteria! #MicroSky

Habemus paper! Our story on integron-encoded anti-phage defenses is now out in @science.org! 16 new systems, small versions of known ones, and a lot more in this highly-collaborative study. Many thanks to everyone involved, especially my supervisor @epcrocha.bsky.social bsky.app/profile/bapt...

Preprint: Conjugative transfer inhibition of IncA and IncC plasmids by pervasive SGI1-like elements via relaxosome assembly interference #plasmid #relaxase #bacteria #parasite #MGE #plasmidbiology www.biorxiv.org/content/10.1...

New postdoc position in our lab (2 y+): evolutionary genomics of integrons and MGEs with focus on vibrio-phage interactions. Great environment @pasteur.fr for science, career building. Super collaborators @celineloot.bsky.social @amazeld.bsky.social @fredoleroux.bsky.social 3 weeks to apply!

Great collaboration with @fredoleroux.bsky.social . Kudos for everyone, esp. Charles Bernard & Yannick Labreuche. Thanks to the funders and @pasteur.fr @cnrsbiologie.bsky.social @umontreal.ca @sbroscoff.bsky.social Here's the paper in OA: doi.org/10.1093/isme...

So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu

I was waiting two years to see this out!! The genomic location of bacterial genes is not random!!! Congratulation on the authors (Martin Lercher and Team!). www.science.org/doi/10.1126/...

We are hiring! - Please share We have an open postdoc or PhD position in aquatic ecology with a research focus on fish ecology and the application of molecular tools in ecological research. Join us at @tudresden.bsky.social Institute for Hydrobiology www.verw.tu-dresden.de/StellAus/ste...

Great to see this in its final form: our study showing that antibiotic resistance genes are more often found in families of plasmids that evolve faster than average (in terms of gain/loss of genes, homologous recombination...). Kudos to @charlescoluzzi.bsky.social now Junior Chair Professor @ U Lyon

Phage satellites are now known to be very diverse, numerous and ancient. They pose many evolutionary, ecological and mechanistic questions. Lots of fun in perspective! Great pleasure to write this review to show it, with @jrpenades.bsky.social @dbikard.bsky.social Kim Seed & John Chen.

I'm very happy to share the last paper from my previous postdoc with the amazing @epcrocha.bsky.social! Thanks to the reviewers for their feedback, which improved our work! #Plasmids #AMR #HorizontalGeneTransfer #Evolution

Excited🚨to share our first work on the human gut phageome doi.org/10.1101/2025... Always inspiring to work with @epcrocha.bsky.social , Erick D, Camille d'H and everyone else within this super dynamic consortium @inrae-france.bsky.social[email protected][email protected]! Many thanks for this great journey!🙌