Benoit Pons

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.

Flow cytometry graph showing that a subpopulation of CRISPR-immune bacteria is elongated and fluorescent (thus showing a SOS response activation) while surface-based resistant bacteria are homogeneously non-elongated non-fluorescent.

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

Cumulative probability of division curves. Surface-based resistant bacteria are not affected by the presence of phage and the median time between two division is the same for all treatments. CRISPR-resistant bacteria median division time is slightly increased at low phage dose and significantly increased at high phage dose

Microfluidics image displaying bacteria of several different sizes. The one on the right hand side is elongated (8 times longer than a bacteria that just completed division)

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

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.

Survival curves showing that both CRISPR-immune and surface-based resistant bacteria do not die from phage, regardless of the dose used

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.

Typical image from a microfluidics experiment. One large channel at the bottom is linked to several tiny perpendicular channels in which bacteria are growing

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.

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.

Phage provoke growth delays and SOS response induction despite CRISPR-Cas protection | Philosophical Transactions of the Royal Society B: Biological Sciences Bacteria 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...

Phage susceptibility to a minimal, modular synthetic CRISPR-Cas system in Pseudomonas aeruginosa is nutrient dependent | Philosophical Transactions of the Royal Society B: Biological Sciences CRISPR-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...

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...

Lab picture - June 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

Thanks a lot for your insightful presentation! That was great to have you here in Toulouse! You're most welcome to visit us again anytime 😀

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

Presentation of Anne Chevallereau

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 🦠

A screenshot of a paper on bioarxiv illustrating the lack of blue sky share button!

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!

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...

Lovely day @ CBI with our newest team members already working hard in our brand new lab. Check out the incredible #BlueSky in #Toulouse
#MicroSky

I'm recruiting a Research Technician to work on plasmid transmission and antimicrobial resistance in St Andrews, to start in October. Deadline for applications is 19 June. Please share!
www.vacancies.st-andrews.ac.uk/Vacancies/W/...

Just out in The ISME Journal, a paper from my time in the Westra lab. We find that the extent of phage exposure shapes subsequent resistance dynamics over longer timescales (up to 30 days).

And huge thanks to first authors @bridgetwatson.bsky.social and Loris for mammoth experiments!