Charles Coluzzi
@charlescoluzzi.bsky.social
Junior professor in The Biometrics and Evolutionary Biology Laboratory - I’m still fascinated by mobile pieces of DNA
#Plasmids #AMR #Evolution
#Plasmids #AMR #Evolution
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 !
📖 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.
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.
January 14, 2026 at 5:02 PM
🚨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 !
📖 Une très belle opportunité d'enseigner à des étudiants brillants tout en menant des recherches excitantes !
Reposted by Charles Coluzzi
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...
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 14, 2026 at 11:26 AM
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🧵
Reposted by Charles Coluzzi
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...
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 14, 2026 at 10:14 AM
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...
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
Reposted by Charles Coluzzi
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...
Convergence and global molecular epidemiology of Klebsiella pneumoniae plasmids harbouring the iuc3 virulence locus: a population genomic analysis
Klebsiella pneumoniae is an important pathogen of humans and animals. In the past five years, increasing reports of convergent strains that carry both…
www.sciencedirect.com
January 7, 2026 at 2:13 PM
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...
Reposted by Charles Coluzzi
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!
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
Persistent virulent phages exist across bacterial isolates
Nature Microbiology - The long-term existence of diverse virulent phages within cultures of Escherichia coli and others challenges the virulent–temperate dichotomy and points to non-canonical...
rdcu.be
December 29, 2025 at 3:18 PM
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!
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!
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
🔗 doi.org/10.1093/molbev/msaf312
🖌️ Nishant Asawadekar
#evobio #molbio
December 19, 2025 at 6:53 PM
@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
🔗 doi.org/10.1093/molbev/msaf312
🖌️ Nishant Asawadekar
#evobio #molbio
Reposted by Charles Coluzzi
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
🧵
➡️ 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
🧵
Environment-dependent evolution drives divergent adaptive strategies and parasite dynamics in a minimal community
Prophages, phage genomes integrated into bacterial chromosomes, are widespread, yet, the extent to which these resident parasites contribute to host fitness and shape evolutionary trajectories, partic...
www.biorxiv.org
December 18, 2025 at 2:11 PM
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
🧵
➡️ 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 Coluzzi
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/...
#MicroSky #Mevosky
journals.plos.org/plosbiology/...
Plasmid streamlining drives the extinction of antibiotic resistance plasmids under selection for horizontal transmission
Conjugative plasmids play an important role in the spread of antimicrobial resistance (AMR) genes among pathogenic bacteria. This study shows that AMR loss in evolving populations is associated with t...
journals.plos.org
December 12, 2025 at 12:09 PM
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/...
#MicroSky #Mevosky
journals.plos.org/plosbiology/...
Reposted by Charles Coluzzi
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
Mark your calendars and make sure your best work is ready next September when the call for abstracts opens 🙂
legend2025.sciencesconf.org
February 24, 2025 at 8:58 AM
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
Mark your calendars and make sure your best work is ready next September when the call for abstracts opens 🙂
legend2025.sciencesconf.org
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...
Apply for a 4y funded MRC DiMeN position with me and Jamie Wheeler @livuni-ives.bsky.social www.findaphd.com/phds/project...
MRC DiMeN Doctoral Training Partnership: Resistant zombies: how drug-resistance plasmids manipulate the behaviour of the opportunistic pathogen Pseudomonas aeruginosa at University of Liverpool on Fin...
PhD Project - MRC DiMeN Doctoral Training Partnership: Resistant zombies: how drug-resistance plasmids manipulate the behaviour of the opportunistic pathogen Pseudomonas aeruginosa at University of Li...
www.findaphd.com
November 18, 2025 at 9:38 AM
🚨#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...
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 Coluzzi
Please 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...
Find out more here: eseb.org/prizes-fundi...
November 19, 2025 at 9:21 AM
Please apply for this, and/or encourage your mentees and peers to do so!
Reposted by Charles Coluzzi
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!)
Please RT (or is it RB? not sure how our lingo has changed!)
🚨 15 days left to apply!
Be part of EvoMG-DN and advance your PhD career in evolutionary genomics.
👉 www.evomg-dn.eu
#PhD #DoctoralTraining #ResearchCareers #LifeSciences #BiomedicalResearch #Genomics #EvolutionaryBiology #MSCA #HorizonEurope #EUResearch #ResearchOpportunities #PhDPositions
Be part of EvoMG-DN and advance your PhD career in evolutionary genomics.
👉 www.evomg-dn.eu
#PhD #DoctoralTraining #ResearchCareers #LifeSciences #BiomedicalResearch #Genomics #EvolutionaryBiology #MSCA #HorizonEurope #EUResearch #ResearchOpportunities #PhDPositions
November 14, 2025 at 10:22 AM
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!)
Please RT (or is it RB? not sure how our lingo has changed!)
Reposted by Charles Coluzzi
Reposted by Charles Coluzzi
Join us tomorrow if you like plasmids and clones! @sandrareuter.bsky.social will be talking about a particular intriguing outbreak 🤓. @escmid.bsky.social
We invite you to the joint ESGEM & ESGMAP webinar:
👉 Dr. Sandra Reuter, University of Freiburg
“Tracking clonal and plasmid transmission in carbapenem- and colistin-resistant Klebsiella pneumoniae.”
📅 Date & Time: November 11, 2025, 12:00 PM CEST
🔗 Register here: us06web.zoom.us/webinar/regi...
👉 Dr. Sandra Reuter, University of Freiburg
“Tracking clonal and plasmid transmission in carbapenem- and colistin-resistant Klebsiella pneumoniae.”
📅 Date & Time: November 11, 2025, 12:00 PM CEST
🔗 Register here: us06web.zoom.us/webinar/regi...
Welcome! You are invited to join a webinar: ESGEM & ESGMAP: Tracking clonal and plasmid transmission in carbapenem- and colistin-resistant Klebsiella pneumoniae. After registering, you will receive a ...
Chairs: Natacha Couto & Elisabeth Grohmann
Speaker: Sandra Reuter
us06web.zoom.us
November 10, 2025 at 2:54 PM
Join us tomorrow if you like plasmids and clones! @sandrareuter.bsky.social will be talking about a particular intriguing outbreak 🤓. @escmid.bsky.social
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/...
www.pnas.org/doi/10.1073/...
Jumbo phage–mediated transduction of genomic islands | PNAS
Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile
genetic elements (MGEs). While plasmids, bacteriophages, and c...
www.pnas.org
October 28, 2025 at 6:36 PM
@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/...
www.pnas.org/doi/10.1073/...
Reposted by Charles Coluzzi
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
Nicolás Rascovan & colleagues
@currentbiology.bsky.social
October 24, 2025 at 3:00 PM
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
Nicolás Rascovan & colleagues
@currentbiology.bsky.social
Reposted by Charles Coluzzi
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...
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...
Portail Emploi CNRS - Offre d'emploi - Postdoctoral researcher Microbiology (M/F)
emploi.cnrs.fr
October 22, 2025 at 9:35 AM
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...
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...
Reposted by Charles Coluzzi
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...
The assembly of a hybrid type IV secretion system by a Crohn’s disease-associated Escherichia coli strain.
www.nature.com/articles/s41...
The assembly of a hybrid type IV secretion system by a Crohn’s disease-associated Escherichia coli strain - Nature Communications
Adherent-invasive strains of E. coli are commonly isolated from patients with Crohn’s disease. Here, the authors show that an AIEC harbours a hybrid Type IV secretion system (T4SS) that mediates pilin...
www.nature.com
October 20, 2025 at 6:38 PM
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...
The assembly of a hybrid type IV secretion system by a Crohn’s disease-associated Escherichia coli strain.
www.nature.com/articles/s41...
Reposted by Charles Coluzzi
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?...
youtu.be/Mzr3TD4ijs0?...
How the Vectors of Antibiotic Resistance Have Evolved - Professor Zamin Iqbal
YouTube video by Milner Centre for Evolution
youtu.be
October 17, 2025 at 11:48 AM
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?...
youtu.be/Mzr3TD4ijs0?...
Reposted by Charles Coluzzi
"Comment l'IA révolutionne la biologie ?", une conférence grand public animée par Bastien Boussau dans le cadre de la Fête de la Science.
Inscription ici : tinyurl.com/3pe9wzcc
📆 Samedi 11 octobre, 15h00.
📍Campus de la Doua - arrêt Tram T1 et T4 "La Doua-Gaston Berger"
Inscription ici : tinyurl.com/3pe9wzcc
📆 Samedi 11 octobre, 15h00.
📍Campus de la Doua - arrêt Tram T1 et T4 "La Doua-Gaston Berger"
October 4, 2025 at 10:39 AM
"Comment l'IA révolutionne la biologie ?", une conférence grand public animée par Bastien Boussau dans le cadre de la Fête de la Science.
Inscription ici : tinyurl.com/3pe9wzcc
📆 Samedi 11 octobre, 15h00.
📍Campus de la Doua - arrêt Tram T1 et T4 "La Doua-Gaston Berger"
Inscription ici : tinyurl.com/3pe9wzcc
📆 Samedi 11 octobre, 15h00.
📍Campus de la Doua - arrêt Tram T1 et T4 "La Doua-Gaston Berger"
Reposted by Charles Coluzzi
Very 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.
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.
Isolation, engineering and ecology of temperate phages from the human gut - Nature
Human host-associated cellular products may act as induction agents for bacteriophages.
nature.com
October 15, 2025 at 9:41 PM
Very 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.
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.
Reposted by Charles Coluzzi
Global antibiotic resistance surveillance report 2025
www.who.int/publications...
www.who.int/publications...
Global antibiotic resistance surveillance report 2025
This new WHO report presents a global analysis of antibiotic resistance prevalence and trends, drawing on more than 23 million bacteriologically confirmed cases of bloodstream infections, urinary trac...
www.who.int
October 14, 2025 at 11:12 AM
Global antibiotic resistance surveillance report 2025
www.who.int/publications...
www.who.int/publications...
Reposted by Charles Coluzzi
Can 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...
www.nature.com/articles/s41...
Unlocking data in Klebsiella lysogens to predict capsular type-specificity of phage depolymerases - Nature Communications
Here, the authors exploit the genetic information encoded in Klebsiella prophages to model the interplay between bacteria, prophages, and their depolymerases, using a directed acyclic graph-model and a sequence clustering-based model.
www.nature.com
October 8, 2025 at 8:59 AM
Can 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...
www.nature.com/articles/s41...
Reposted by Charles Coluzzi
Is 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
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
October 10, 2025 at 1:12 PM
Is 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 📈