Fabienne Benz

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...

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 💉🧬🦠🔬🧫

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.

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...

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...

Do plasmids evolve faster 🐇, slower 🐢, or just like chromosomes 🧬?

In our new paper, we tackled this question using theory, simulations, bioinformatics, and experiments!

👇 Check out all the details in Paula’s thread!

Hint: 🐇 (most of the time)

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 🤓

Due to some server issues, some applications have been lost, particularly the ones submitted within 12h of the announcement, if that’s your case, it’s better to resubmit, sorry everyone 🙏🏻

graphical abstract of the article the extended mobility of plasmids

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/...

Universal rules govern plasmid copy number - Nature Communications Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

🚨🚨New paper out in @natcomms.nature.com!!

Come for the first large-scale analysis of plasmid copy number across species,
stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬

👉 www.nature.com/articles/s41...

I created a list of researchers working at the @institutpasteur.bsky.social

DM me if you'd like to be added to it.

bsky.app/profile/did:...

Project manager: Genomic taxonomy of bacterial strains, epidemiological surveillance and antimicrobial resistance - Research We are looking for a project manager to develop our activities around the genomic taxonomy of bacterial strains and the corresponding platform at https://bigsdb.pasteur.fr/. The project manager’s main...

The BIGSdb-Pasteur project, running under my supervision since 20 years, is looking for a project manager - great opportunity to contribute to this high-profile international resource in the field of reference strain taxonomies, genomic epidemiology and antimicrobial resistance surveillance

‼️ Great Postdoc opportunity ‼️
In pathogen interactions with Rolf Kümmerli at the University of Zurich

Working on #klebsiella genomes? ✅
Want to collaborate globally to advance Klebs genomic epi? ✅

Please join us via the KlebNET-GSP Epidemiology consortium ⬇️

#microsky #AMR

I will be recruiting new postdocs with start dates end 2025 - early 2026. If you'd like to work at the Pasteur Institute in the heart of Paris surrounded by amazing scientists, reach out to discuss possible projects on SynBio / Bacterial Immunity!

Very happy to have this comprehensive review published. Well done Fabienne for leading the charge on this 👏

Massive effort lead by the amazing @fabbenz.bsky.social to discuss the present and future of CRISPR-based antimicrobials ⚡

… I had to read it immediately and it is great! Congrats for this important piece of work Laura and Alvaro!

Plasmid–bacteria associations in the clinical context Antimicrobial resistance (AMR) is one of the most pressing global health problems, with plasmids playing a central role in its evolution and dissemination. Over the past decades, many studies have inv...

New opinion paper from the lab!

www.cell.com/trends/micro...

An excellent and insightful review! Congratulations to all authors!

6/6
🙏 Huge thanks to co-authors
@beatrizbeamud.bsky.social
@raphael-microb.bsky.social
@amandinemaire.bsky.social
@adecrulle.bsky.social
XavierDuportet
@dbikard.bsky.social

5/6 – Clinical opportunities
👩‍⚕️ First-in-human trials already show safety and efficacy—proof CRISPR therapeutics can work in humans!

4/6 – The big hurdles
🛡️ Bacterial defences — restriction–modification systems, anti-CRISPRs and mutational escape — and how to bypass them

3/6 – In-situ delivery
🚚 Engineered phages, conjugative plasmids & more — pros, cons, host range, cargo size and manufacturability. No one-size-fits-all!

2/6 – CRISPR-Cas strategies
🧰 Toolbox & design considerations to eliminate bacteria or their plasmids — and to engineer microbes in situ

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

Heey! ✋
If you missed the live session of the ISPB Virtual Seminar Series, there's still time to catch up and enjoy the great work of Zhengqing Zhou and Alicia Calvo Villamañán.
Huge thanks to the speakers and the organizers!! 🫂

Mobile integrons encode phage defense systems Integrons are bacterial genetic elements that capture, stockpile, and modulate the expression of genes encoded in integron cassettes. Mobile integrons (MIs) are borne on plasmids, acting as a vehicle ...

#NatureMicroPicks

Microbial integrons in focus 🦠🧬

Two studies showing microbial integrons encoding phage defense systems

#MicroSky

www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...

Conjugative transfer inhibition of IncA and IncC plasmids by pervasive SGI1-like elements via relaxosome assembly interference Broad-host-range IncA and IncC conjugative plasmids propagate multidrug resistance in bacteria and mobilize chromosomal resistance islands, including Salmonella Genomic Island 1 (SGI1) across genera. ...

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!