Benoit Pons

phages.frRéseau Bactériophage FranceBienvenue sur le site du réseau “Phages.fr” Le réseau “Phages.fr” regroupe des scientifiques qui travaillent sur les thématiques incluant les bactériophages dont l’étude des structures, interactions moléculaires & cellulaires, écologie & évolution, thérapie phagique et biocontrôle en santé humaine, végétale & animale et industrie ainsi que des Sciences humaines et sociales. Ces scientifiques appartiennent à différents instituts publics français de recherche tels que CNRS (principal financeur), INRAE, INSERM, ANSES, Institut Pasteur mais aussi de nombreuses universités (Bordeaux, Lyon, Marseille, Montpellier, Nancy, Paris, etc) et hôpitaux, avec aussi la participation de membres d’entreprises.

🧬Phages in Toulouse — November 18–20, 2026! 🦠 We are delighted to announce the next edition of Phages.fr congress, Phages in Toulouse, bringing together the phage research community for 3 days of talks, presentations & scientific discussions! 📍 Toulouse, France 📅 Nov. 18–20

As well as private partners: Greenphage, Inteliphage, Interscience and Phagenix

We have now reached the maximum attendance capacity for the conference, but abstract can still be submitted until Friday 25th September!

phagestoulouse.sciencesconf.orgPhages in Toulouse - Sciencesconf.org Sciencesconf.org

Register & submit your abstract here: phagestoulouse.sciencesconf.org Please share with colleagues interested in phages, phage–host interactions, ecology, applications or the societal aspects of phage research. See you in Toulouse! 🦠🔬

The organisation was made possible thanks to the support from several public institutions: @cbitoulouse.bsky.social, @envt.bsky.social, @sfr-b2s.bsky.social, @spilf.bsky.social @sfmicrobiologie.bsky.social, the FSI of the University of Toulouse, the LMGM and the TULIP Labex

💊 Therapy & Biotechnology with Antonia Scobie from the Royal Free Hospital 🇬🇧 👥 Social Sciences with Sabrina Green @motherofphage.bsky.social .bsky.social from UCLouvain 🇧🇪

📢 Registration & abstract submission are open until September 25! 💶 Registration, including the gala dinner: Students/postdocs/fixed-term researchers: FREE Permanent academics: €50 excl. VAT Industry: €300 excl. VAT

The conference will cover 5 major themes, from the molecular scale to societal issues, each of them being introduced by an international speaker: 🔬 Structure & Assembly — Molecular Scale with Marion Schuller @schullerm.bsky.social from Max Planck Institute of Biochemistry 🇩🇪

@ellinoralseth.bsky.social

🦠 Phage–Host Interactions — Cellular Scale with Franklin Nobrega @fnobrega.bsky.social from the University of Southampton 🇬🇧 🌱 Ecology & Evolution — Population Scale with Anna Dragoš @annadragos.bsky.social from the University of Ljubljana 🇸🇮

Benoit Pons reposted

Ellinor Alseth

11 Sept

It's finally published! What a journey @brownlab.bsky.social and I have been on with this one (ask me about it over a pint 🍻). Super excited to be able to say that it's finally out in Trends (author gift link to follow)! 🦠🧫 #phagesky

Trends in Microbiology@cp-trendsmicrobiol.bsky.social

The bacterial immune system: identifying evolved defense adaptations

dlvr.itThe bacterial immune system: identifying evolved defense adaptationsRecent years have witnessed a rapid expansion in bacterial defense mechanisms. Alongside established defenses against molecular parasites, hundreds of novel mechanisms are being described annually, contributing to an ever-expanding ‘bacterial immune system’. Terms like ‘defense’ and ‘immune’ are often used as shorthand for an observed anti-infection phenotype, but can also imply an evolutionary adaptation with a specific anti-infection function. Despite the field’s growth, no agreed-upon framework exists for identifying defense adaptations. When is a defense mechanism an evolved adaptation? Here, we review prior debates in evolutionary biology and propose a four-part framework to evaluate the case for a defense mechanism being an evolved adaptation. Beyond bacterial immunity, these criteria offer a research roadmap to address functional controversies across microbiology.

Benoit Pons reposted

Tuta

@tuta.com

31 Aug

If you have a Gmail account, you need to read this. Google's AI now scans your emails and attachments, bank statements, tax files, medical letters, all of it. It turned on by default, and there's a class-action lawsuit over how. Here are 5 moves to shut it off, the switch is hidden in two places:

Benoit Pons reposted

1 June

🌟 Very proud of the newest Dr. in the team , Dr. @julielebris.bsky.social 👩‍🎓! She brilliantly defended her PhD last Friday @pasteur.fr Excellent thesis in terms of output & quality! Thanks to the jury @lucyweinert.bsky.social @sylvainbrisse.bsky.social @edfeil.bsky.social Maria Halima Laaberki

Benoit Pons reposted

@ellinoralseth.bsky.social

19 May

🔬🦠 Comment #Klebsiella parvient-elle à changer de capsule aussi fréquemment pour mieux s’adapter à son environnement ? Les travaux de @julielebris.bsky.social mis à la une par @cnrsbiologie.bsky.social 👏 -avec @epcrocha.bsky.social #MicroSky @cbitoulouse.bsky.social

CNRS Biologie@cnrsbiologie.bsky.social

#ResultatScientifique🔎| Une bactérie capable de changer de « bouclier » pour mieux s’adapter à son environnement : une stratégie étonnante de Klebsiella pneumoniae qui éclaire ses capacités d’évolution et de résistance. ✍️ @olayarendueles.bsky.social @julielebris.bsky.social ▶️ buff.ly/q8AKHo1

Benoit Pons reposted

Ellinor Alseth

13 May

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!

ecoevorxiv.orgThe bacterial immune system: identifying evolved defense adaptations

Benoit Pons reposted

doi.orgPlug-and-play evolution of the Klebsiella pneumoniae capsule locus enables serotype exchange across genetic backgroundsHow 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...

26 Mar

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!

Julie Le Bris@julielebris.bsky.social

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👇

biorxiv.orgSerotype swapping in Klebsiella spp. by plug-and-playUnderstanding how complex, multi-gene systems evolve and function across genetic backgrounds is a central question in molecular evolution. While such systems often impose costs through epistatic inter...

Benoit Pons reposted

3 Feb

Today we were thrilled to host @tatianadimitriu.bsky.social at @cbitoulouse.bsky.social @cnrsbiologie.bsky.social She discussed factors contributing to plasmid spread (defense systems, environmental factors…) - with @benoitjpons.bsky.social

Benoit Pons reposted

15 Jan

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

Benoit Pons reposted

biorxiv.orgEnvironment-dependent evolution drives divergent adaptive strategies and parasite dynamics in a minimal communityProphages, 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...

18 Dec 2025

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 🧵

doi.orgPhage provoke growth delays and SOS response induction despite CRISPR-Cas protection | Philosophical Transactions of the Royal Society B: Biological SciencesBacteria evolve resistance against their phage foes with a wide range of resistance strategies whose costs and benefits depend on the level of protection they confer and on the costs for maintainance....

How do bacteria choose what type of defences to use against phages? We explored that question in the last paper I worked on as a postdoc at the Uni of Exeter @uniofexeteresi.bsky.social with Stineke van Houte, Stefano Pagliara and Edze Westra (not on Bluesky) doi.org/10.1098/rstb...

Finally, we used flux cytometry to confirm that the elongated phenotype was linked with SOS response induction.

Overall, we conclude that while CRISPR-immunity prevents bacteria from dying at high phage doses, a subpopulation undergoes SOS-response mediated growth defects and elongation. Conversely, surface-based resistant bacteria do not, thus favouring this type of resistance at high phage dose.

We then tested our second hypothesis, that CRISPR-immune bacteria were displayed growth defects compared to surface-based resistant bacteria at high phage doses. We did not observe a significant difference in growth rate at the whole population level.

However, we noticed some heterogeneity in the population, with some CRISPR-immune bacteria stalling and suffering from elongation, particularly at high phage doses, which is consistent with this second hypothesis

While CRISPR-Cas system inability to fully prevent phage gene expression seemed to play a role, it was still unclear what was causing the apparent CRISPR-Cas fitness cost at high phage doses. Here we investigated two hypotheses by using a microfluidics set-up to follow single bacteria in microscopy.

Our first hypothesis was that at high phage dose, surface-based resistance offered more protection than CRISPR-immunity. However, we showed that both types of defences offer a similar, almost perfect protection against phages regardless of the phage dose.

Pseudomonas aeruginosa can choose between CRISPR-Cas immunity and resistance through surface receptor mutation to evade their phages foes. Previous work from the lab had shown that the choice depends on the strength of phage selection pressure, with CRISPR-immunity being favoured at low phage dose.

Benoit Pons reposted

Josie Elliott

@josie-e.bsky.social

doi.orgPhage susceptibility to a minimal, modular synthetic CRISPR-Cas system in Pseudomonas aeruginosa is nutrient dependent | Philosophical Transactions of the Royal Society B: Biological SciencesCRISPR-Cas systems can provide adaptive, heritable immunity to their prokaryotic hosts against invading genetic material such as phages. It is clear that the importance of acquiring CRISPR-Cas immunit...

Can CRISPR-Cas systems target any phage? Yes, no, it depends? What does it depend on? The second paper from my PhD came out today in a special issue of Phil Trans B on the ecology and evolution of bacterial immune systems doi.org/10.1098/rstb...

Benoit Pons reposted

David Sünderhauf

@davvi36.bsky.social

2 Sept 2025

PhD opportunity, please share: We are looking for a prospective PhD student to start in October 2026 who is excited about bacteria (Klebsiella pneumoniae), how they interact, and how they exchange DNA. All details can be found on the funder website 👉 gw4biomed.ac.uk/developing-c...

gw4biomed.ac.ukDeveloping CRISPR-Cas antimicrobials to tackle antibiotic resistance spread in Klebsiella pneumoniae - GW4 BioMed MRC DTPProject Code MRCIIAR26Ex van Houte Project Type Wet lab Research Theme Infection, Immunity, Antimicrobial Resistance and Repair Project Summary Download Summary Antimicrobial resistance (AMR) poses a ...

Benoit Pons reposted

@annechevallereau.bsky.social

18 July 2025

The team is growing fast! 🎉 Congratulations to Léa Masson on receiving a PhD fellowship from the BSB doctoral school @universitetoulouse.bsky.social 👏 The PhD will be co-supervised by @benoitjpons.bsky.social and myself - @cbitoulouse.bsky.social #PhD #Microbiology #Klebsiella

Benoit Pons reposted

Anne Chevallereau

9 May 2025

Had an amazing time at @cbitoulouse.bsky.social! Stimulating discussions, insightful questions, and always a joy to reconnect with old friends and colleagues! Thanks for the invitation @benoitjpons.bsky.social @olayarendueles.bsky.social

Olaya Rendueles@olayarendueles.bsky.social

Great talk today @cbitoulouse.bsky.social from @annechevallereau.bsky.social- on the importance of surface receptors in phage adsorption and of intracellular phage defense mechanisms - and the relative importance of each of them in shaping phage host range &productive phage infection 🦠

Benoit Pons reposted

Benoit Pons reposted

Would you like to see @biorxivpreprint.bsky.social add a share to blue sky button?! I know I would! Share this post to let @richardsever.bsky.social @erictopol.bsky.social and others at bioarxiv know!

Benoit Pons reposted

Sean Meaden

@seanmeaden.bsky.social

26 Nov 2024

Looking for a PhD in phage ecology, metagenomics and defence systems? We have a fully funded PhD opportunity to join us at the University of York with great collaborators. See here for more info: www.findaphd.com/phds/project...

Benoit Pons reposted