Charles Coluzzi
Junior professor in The Biometrics and Evolutionary Biology Laboratory - I’m still fascinated by mobile pieces of DNA
#Plasmids #AMR #Evolution
- Reposted by Charles ColuzziAccurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs
- Reposted by Charles ColuzziI 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...
- Reposted by Charles ColuzziUn 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
- 📢 Recrutement d’un(e) Maître(sses) de conférence en Biochimie générale, spécialité bactériologie moléculaire à MMSB 🔬Recherche *Immunité anti-phages *Réponse au stress, modulation de la croissance bactérienne ✉️ christophe.grangeasse@cnrs.fr 📚Enseignement : Université Lyon I ✉️ patrice.gouet@ibcp.fr
- Reposted by Charles Coluzzi🚨 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...
- Reposted by Charles Coluzzi🚨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 !
- 📢 Recruitment of an Associate Professor (Maître de conférences) in Bacteriology at CIRI and ENS de Lyon. Research at @ciri-lyon.bsky.social @francoisrousset.bsky.social @labxc.bsky.social Anti-phage Immunity, Horizontal gene/ MGE transfer 📚 Teaching at ENS de Lyon within the Department of Biology.
- Reposted by Charles ColuzziHere, 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...
- Reposted by Charles ColuzziBacteria 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...
- Reposted by Charles ColuzziIt 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...
- Reposted by Charles ColuzziBacteriophages 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!
- [1/3] Is your favorite bacterial isolate hiding a surprise lytic virus with a VERY different lifestyle? Finally I can proudly say that our paper on persistent phages is out in Nature Microbiology. rdcu.be/eWJEp. Well done @peterdoug.bsky.social
- Reposted by Charles Coluzzi@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
- Reposted by Charles ColuzziPreprint 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 🧵
- Reposted by Charles ColuzziOur story on plasmid streamlining is now published in PLoS Biology! With @andrewmatthews.bsky.social and @sonjalehtinen.bsky.social #MicroSky #Mevosky journals.plos.org/plosbiology/...
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- Reposted by Charles Coluzzi🚨#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...
- Reposted by Charles ColuzziPlease apply for this, and/or encourage your mentees and peers to do so!
- Every year #ESEB distinguishes a young evolutionary biologist with the John Maynard Smith Prize! Nominations for the 2026 prize are due by January 15th! Find out more here: eseb.org/prizes-fundi...
- Reposted by Charles ColuzziStill 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!)
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- Reposted by Charles Coluzzi@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/...
- Reposted by Charles ColuzziDNA 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
- Reposted by Charles ColuzziJOB 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...
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- Reposted by Charles ColuzziPodcast 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?...
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- Reposted by Charles ColuzziVery excited to share the latest work from our lab, which was published today in Nature! nature.com/articles/s41... PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
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- Reposted by Charles ColuzziCan we exploit past phage infection events (prophages) to decipher the specificity of phage receptor-binding proteins such as depolymerases?🔎 Happy to share our recent work at @natcomms.nature.com 🔽 #microsky #phagesky www.nature.com/articles/s41...
- Reposted by Charles ColuzziIs a healthy microbiome one that is rich in phages? 🦠 Excited to share our paper out in Lancet Microbe with @bkoskella.bsky.social & @dholtappels.bsky.social where we test whether virome diversity can be used a broad signature of microbiome health 📈
- New research article Evaluation of bacteriophages as a signature of #microbiome health: a systematic review and meta-analysis www.thelancet.com/journals/lan... #IDSky #ClinMicro #ViroSky #Phage #OpenAccess #OA
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[Not loaded yet] - Reposted by Charles ColuzziA plasmid and an ICE teaming up... 🤯😱 www.nature.com/articles/s41...
- Reposted by Charles ColuzziNow published in @natcomms.nature.com 🎉 www.nature.com/articles/s41... With Gillian Rodger, @nstoesser.bsky.social, @samlipworth.bsky.social, @stat-sarah.bsky.social, and many others!
- 🚨 New preprint! 🚨 We reveal that blaTEM-1 expression varies across the E. coli phylogeny, driving differences in co-amoxiclav resistance: www.biorxiv.org/content/10.1...
- Reposted by Charles ColuzziDelighted 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
- Reposted by Charles ColuzziNew 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...
- Reposted by Charles ColuzziJob 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.
- Come and work with Nicole Stoesser and I in Oxford with the fantastic team @modmedmicro.bsky.social - great opportunity for a postdoc in microbial genomics to do some creative research with great datasets as part of our HPRU. my.corehr.com/pls/uoxrecru...
- Reposted by Charles Coluzzi🐟💊🦠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
- Reposted by Charles ColuzziMMseqs2-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
- Reposted by Charles ColuzziSuper 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...
- Reposted by Charles Coluzzihey 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!
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- Reposted by Charles ColuzziEt 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...
- Reposted by Charles ColuzziWilling 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...
- 🎓 Applications for Institut Pasteur's PhD programs open Sept 1-Oct 20, 2025 for October 2026 entry. Apply to up to 4 projects across 6 programs: PPU, PPU-IMAGINE @institutimagine.bsky.social, PPU-@ox.ac.uk, PPU-EID @upcite.bsky.social & more 🧬 Register now ✍️ www.pasteur.fr/en/education...
- Reposted by Charles ColuzziJ'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...
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- Reposted by Charles ColuzziDelighted 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👇
- Reposted by Charles ColuzziFor 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...
- Reposted by Charles ColuzziAt 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...
- Reposted by Charles Coluzzi🚨 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...
- Reposted by Charles ColuzziVery 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
- The contribution of natural transformation for the acquisition of novel genes has been notoriously difficult to quantify because it relies on recombination (which is affected by other processes). Here's a first estimate : doi.org/10.1101/2025... (for the very busy: 1-6% of gene gains) #MicroSky
- Reposted by Charles Coluzzi#phagesky I am looking for phages infecting Streptococcus pneumoniae to test a phenotype - does anyone have some and willing to share ? Repost appreciated :)
