New Perspective out co-led with Lisa Pagani! We look at how microbiome ecology and evolution shape AMR across scales, from within-host communities to hospitals and environments, and how mathematical models can help us understand them. @natmicrobiol.nature.com www.nature.com/articles/s41...

Modelling the role of the microbiome in antimicrobial resistance across scales - Nature Microbiology

The microbiome plays a significant yet underexplored role in antimicrobial resistance by influencing ecological and evolutionary processes. This Perspective proposes a framework to integrate microbiom...

nature.com

When is an antiphage mechanism an evolved defence adaptation? This question has been on my mind for so long, because despite the field’s rapid progress there is currently no widely agreed framework in place to answer it. So @brownlab.bsky.social and I wrote this, and I'm happy to share the preprint!

I’ve started my SNSF Ambizione Group Leader position at the University of Zurich 🧬 We will study plasmid evolution, plasmid interactions, and CRISPR-Cas systems to better understand antibiotic resistance spread. Very grateful to everyone who supported me along the way.

New paper out in @pnas.org 🎆! Across healthy humans, the same bacterium encounters markedly different gut microbiomes. How does this shape the ecological interactions it experiences? We explored this focusing on commensal E. coli.
 www.pnas.org/doi/10.1073/... Image: @illuzation.bsky.social

Very proud of this work and all the efforts from my team and collaborators on this! You can now use DGRs for in vivo targeted hypermutagenesis in E. coli. We also included some early proof of concept in Yeast thanks to @seth-shipman.bsky.social !

Raphael Laurenceau@raphael-microb.bsky.social · 4mo ago

🔈Paper out! We turned the most fascinating phage host-switch mechanism, diversity-generating retroelements, into a programmable mutagenesis tool, DGRec. You can perform targeted hypermutation of any 50-200bp sequence directly in vivo in E. coli www.nature.com/articles/s41...

So happy to see this finally published in @plosbiology.org! This is the first chapter of @julielebris.bsky.social PhD thesis demonstrating how capsules are exchanged by plug-and-play dynamics w/ @epcrocha.bsky.social #microsky @klebclub.bsky.social Link below- Check out her 🧵 for more details!

Plug-and-play evolution of the Klebsiella pneumoniae capsule locus enables serotype exchange across genetic backgrounds

How complex multi-gene systems evolve across genetic backgrounds without disruptive epistasis remains unclear, particularly in highly exchangeable loci such as the capsule of Klebsiella pneumoniae. Th...

doi.org

Julie Le Bris@julielebris.bsky.social · 11mo ago

How complex functions, with important physiological and evolutionary impacts get repeatedly and efficiently transferred across genomes? That’s what we explored using one of the fastest-evolving loci in Bacteria: the capsule locus. The paper: www.biorxiv.org/content/10.1... Thread👇

Yesterday our paper "Intra-species competition combats vancomycin-resistant enterococci" was published online. We found an enterococcal strain that can outcompete a VRE strain, but loses its potency when given with other non resistant Enterococci. Here is a high res img from the battle in the gut:

Final version of our last paper is out! www.nature.com/articles/s41...

Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation - Nature Microbiology

Inactivation of chromosomal genes through plasmid-encoded IS elements is an extended mechanism of antimicrobial resistance evolution in bacteria.

nature.com

With @saramitri.bsky.social, @sonjalehtinen.bsky.social and L. Lehmann we’ve launched the UNIL Center for Theory in Ecology and Evolution @unil.bsky.social🇨🇭 To kick things off, we’re offering short visiting fellowships for theorists in ecology & evolution. Apply & pls RP 😀 tinyurl.com/2wem36zz

Fantastic collaboration w/ @dbikard.bsky.social @audeber.bsky.social @rayanchikhi.bsky.social labs led by @jmouradesousa.bsky.social : We assessed the rates of variation of anti-phage systems in P4-like satellites and P2 helper phages. Quick conclusion: Huge variation! We focus on 4 key questions/5

Jorge Moura de Sousa@jmouradesousa.bsky.social · 5mo ago

➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔 🧵👇

➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔 🧵👇

Conjugative plasmids as programmable platforms to combat antibiotic resistance and enable microbiome engineering. such a cool story by Dorado-Morales and team! 💪

Pedro Dorado-Morales@doradomoralesp.bsky.social · 5mo ago

A step toward rationally designed conjugative interventions for AMR containment and microbiome engineering. Feedback very welcome!

A step toward rationally designed conjugative interventions for AMR containment and microbiome engineering. Feedback very welcome!

🔬 New work from the Mazel Lab engineers programmable conjugative plasmids to selectively target MDR bacteria and the resistance plasmid pOXA-48, blocking its spread in complex communities. ✍️ @amazeld.bsky.social & coll. @pasteur.fr 📖 shorturl.at/GZdJu #MicroSky #AntibioticResistance #Conjugation

🚨 New preprint 🚨 How promiscuous really are conjugative plasmids, and what does that mean for plasmid co-occurrence? A pleasure to collaborate with @craigmaclean.bsky.social on the first paper of my fellowship! www.biorxiv.org/content/10.6...

Check out our latest preprint from @jnvmartinson.bsky.social and @leosong.bsky.social! 🌟🦠 We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 6mo ago

Plasmids weaponize conjugation to eliminate non-permissive recipients https://www.biorxiv.org/content/10.64898/2026.02.10.705089v1

Big week: welcomed a new baby boy Harris Lopatkin, AND our PlasAnn paper is finally out: academic.oup.com/nar/article/... (obviously the first more important than the second 🥰). Currently on leave but if anyone has the need to annotate large plasmids, go check it out!

PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis

Abstract. Conjugative plasmids are key drivers of bacterial adaptation, enabling the horizontal transfer of accessory genes within and across diverse micro

academic.oup.com

🚨 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...

Postdoctoral position - Synthetic Biology / Bacterial Immunity - Research

The Bikard lab at Institut Pasteur in Paris is seeking to hire postdoctoral researchers. We are investigating bacteria / bacteriophages interactions, and the genetic innovation that happens at this in...

research.pasteur.fr

My team at @cbitoulouse.bsky.social is recruiting a postdoc #bioinformatics with solid experience in metagenomic analyses. Interest in evolution, ecology & MGEs is important. The offer stands until the perfect candidate is found, and it could be you 🫵 🔁 🙏 #microSky #phagesky #UTIsky @cnrs.fr

The 2026 Guarda Summer Course in Evolutionary Biology is now accepting applications. Amazing place, amazing course, amazing opportunity for early grad students. tb.ethz.ch/education/gu...

Summer school:<br> Evolutionary Biology in Guarda

Information about the annual summer school Evolutionary Biology in Guarda

tb.ethz.ch

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/...

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

And now it's going to get cut.

Swiss National Science Foundation (SNSF)@snsf.ch · 8mo ago

What role has the SNSF played in shaping Switzerland's scientific landscape over the past 50 years? 🔍 Our latest #DataStory traces the evolution of research funding since 1975 and the ongoing adaptation of the SNSF’s funding schemes. 👉 buff.ly/MGrQDuq

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

Intracellular competition shapes plasmid population dynamics

From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

science.org

PhD studentship opportunity! Join us at St Andrews to study the factors controlling plasmid transmission in the gut. Competition-funded as part of the EASTBIO DTP, co-supervised with Dr Jaclyn Pearson. Please share & pass on to anyone interested! 🦠🧫 Deadline 15th December👇

🚨#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...

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...

findaphd.com

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...

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.

nature.com

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

Come and be my colleague at the Dunn School! It‘s a brilliant place to work and exciting to be building up our immunology team. Do apply. Do pass on the news 💉🧬🦠🔬🧫

The Dunn School, Oxford@dunnschool.bsky.social · 11mo ago

We're hiring (again)! We are looking for an associate professor in cell and molecular biology, with a particular focus on immunology (defined broadly) If you have a great record and exciting plans, consider joining our thriving and welcoming department www.path.ox.ac.uk/vacancy/asso...

Exciting times ahead! Today marks the first day of the Loeff Lab at Leiden University Medical Center in the Netherlands 🇳🇱. I’m thrilled to begin this new adventure and continue exploring microbial defense mechanisms and their applications through an integrative structural biology approach.

Happy to finally share this! Read here about the best strategy the the persistence of low-copy plasmids. @mariosanter.bsky.social @iwangtoknow.bsky.social doi.org/10.1038/s414...

The combination of active partitioning and toxin-antitoxin systems is most advantageous for low-copy plasmid fitness - Nature Communications

Effe et al. evaluate how specific plasmid traits influence plasmid fitness; they provide mechanistic insight into the persistence of large conjugative plasmids, including those that disseminate antibi...

doi.org