Charles Coluzzi

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...

🚨#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!)

🥳 congratulations Zam !! Well deserved

High-throughput conjugation reveals strain specific recombination patterns enabling precise trait mapping in Escherichia coli Author summary Escherichia coli demonstrates a remarkable ability to adapt to diverse environments. This adaptability is in part connected to its ability to recombine incoming DNA in its chromosome, a...

#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

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...

@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/...

Napoleon's retreat from Moscow CREDIT Barbieri et al., Current Biology

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...

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...

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...

YouTube video by Milner Centre for Evolution How the Vectors of Antibiotic Resistance Have Evolved - Professor Zamin Iqbal

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?...

"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"

Isolation, engineering and ecology of temperate phages from the human gut - Nature Human host-associated cellular products may act as induction agents for bacteriophages.

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.

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...

Global antibiotic resistance surveillance report 2025
www.who.int/publications...

The time has come for you to listen to the next session of the ISPB Virtual Seminar Series. Tuesday, October 14th, from 07:00–08:00 UTC.
Two new speakers, two great new stories.
Do not miss them!
#ISPB #Plasmid #MGEs

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.

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...

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 📈

Experimental glycopeptide antibiotic EVG7 prevents recurrent Clostridioides difficile infection by sparing members of the Lachnospiraceae family - Nature Communications Treatment of Clostridioides difficile infections (CDI) with vancomycin is associated with high relapse rates. In this study, the experimental glycopeptide antibiotic EVG7 was found to effectively treat CDI without relapse in a murine model of recurrent CDI.

New paper alert! In this work, published in @natcomms.nature.com we show that a new antibiotic is effective against (r)CDI. 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 polymerization and biofilm formation in vivo.

A plasmid and an ICE teaming up... 🤯😱

www.nature.com/articles/s41...

Now 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!

What a Nice thread ! Congratulations Zam !

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.

Microbial risks triggered by oral administration of antibiotics in fish aquaculture persist long after the legally mandated antibiotic withdrawal time - Nature Water Florfenicol treatment substantially increased the abundance and mobility of antibiotic resistance genes (ARGs) in the common carp gut microbiome. The resistome and mobilome profiles failed to return t...

🐟💊🦠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

GPU-accelerated homology search with MMseqs2 - Nature Methods Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

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

A One Health study of Klebsiella pneumoniae species complex plasmids shows a highly diverse and ecologically adaptable plasmidome Plasmids play a pivotal role in the horizontal gene transfer of antimicrobial resistance (AMR) and virulence determinants among bacteria. Members of the Klebsiella pneumoniae species complex (KpSC) ca...

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

Génétique : l’ADN des bactéries comme source de savoirs Un pan de la recherche en génomique se propose d'étudier les bactéries, ces micro-organismes développent des mécanismes de défense particulièrement intéressants.

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...