José R Penadés

PS Simon’s tail fibre protein structure models showing the variants causing altered surface receptor binding specificity are Lovell-y

5-years in the making this paper has been a real journey!

Also, a fun collaboration with @frimanscience.bsky.social @jofoth.bsky.social Edze Westra, Simon Lovell, Aras Kadioglu

#mevosky #phagesky

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

www.biorxiv.org/content/10.1...

Check it out! A proper team effort from past and present group members and a great collaboration with @sergemostowylab.bsky.social

El proyecto "Descubrir actividades de resistencia antimicrobiana más allá de la resistencia" de
@sanmillan.bsky.social (#CNB, @csic.es) y @jaescudero.bsky.social (@ucm.es) recibe una ayuda del Programa #Fundamentos de Fundación BBVA.

ℹ️Lee la noticia aquí👇

bit.ly/48cvkp1

Evolutionary rescue accelerates competitive exclusion in a parasite community Environmental stress drives biodiversity loss by altering competitive hierarchies and pushing taxa towards extinction. Parasites and their communities are particularly vulnerable to stress due to envi...

New pre-print: Eco-evolutionary responses of phage to different thermal regimes.

Great work led by Sam Greenrod and fun collaboration with Kayla King's lab.
1/2

www.biorxiv.org/content/10.1...

Now published! www.nature.com/articles/s41...

Very nice collaboration with Hoogenboom ( @ucl.ac.uk ) and Bonev ( @uniofnottingham.bsky.social ) labs.

Evolutionary rescue accelerates competitive exclusion in a parasite community Environmental stress drives biodiversity loss by altering competitive hierarchies and pushing taxa towards extinction. Parasites and their communities are particularly vulnerable to stress due to envi...

Builds on pre-print posted earlier this week and gratuitously reposted here

www.biorxiv.org/content/10.1...
#Phagesky

New pre-print
Competition between phage constrains adaptation to thermal fluctuating temperatures.
More work led by Sam Greenrod in collaboration with @kayla-king.bsky.social lab.
#Phagesky#Microsky

www.biorxiv.org/content/10.1...

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

Now peer-reviewed, improved and published in @microbiologysociety.org Microbiology - thanks to editor and reviewers!

www.microbiologyresearch.org/content/jour...

Vancomycin-resistant enterococci utilise antibiotic-enriched nutrients for intestinal colonisation - Nature Communications Here, the authors show that vancomycin-resistant enterococci grow in the antibiotic-treated gut microbiome by utilising enriched nutrients in the presence of reduced concentrations of inhibitory micro...

So excited to share a new paper from my lab just published in Nature Communications! We showed that vancomycin-resistant enterococci (VRE) occupied distinct intestinal niches in the antibiotic-treated intestine. doi.org/10.1038/s414... Amazing work by first author Olivia King and colleagues!

Simple Sequence Repeats Mediate Phase Variation of the Mucoid Phenotype in Hypervirulent Klebsiella pneumoniae Hypervirulent Klebsiella pneumoniae (HVKp) express a thick mucoid capsular polysaccharide which is essential for virulence and survival in the bloodstream but inhibits epithelial adhesion and invasion...

🎉 Delighted to share the first pre-print from my lab where we demonstrate that intergenic DNA repeats mediate phase variation of the mucoid phenotype in hypervirulent Klebsiella pneumoniae: www.biorxiv.org/content/10.1... #klebclub

We're looking for a technician at Institut Pasteur for experimental work on satellite-phage-bacteria interactions, working directly with @jmouradesousa.bsky.social and myself in the lab of @epcrocha.bsky.social ! ANR funded.

Link to the job emploi.pasteur.fr/offre-de-emp...
Thx for sharing!

Phage "satellites" that produce capsids but have no genes to produce tails have puzzled scientists for a long time. These are abundant as prophages in bacteria, but it was unclear how they can infect without tails

Now, Penadés & co show that they hijack tails from other phages. Incredible!

Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…

Thrilled to share that two of our papers with @jrpenades.bsky.social & GoogleDeepMind
are now out in @cellpress.bsky.social

1️⃣Microbial piracy: tinyurl.com/yvf6t3b3
2️⃣AI co-scientist mirrors experimental science: tinyurl.com/2dym92kj

@imperialcollegeldn.bsky.social
@imperiallifesci.bsky.social

AI mirrors experimental science to uncover a mechanism of gene transfer crucial to bacterial evolution By solving a previously unsolved biological question, the AI co-scientist predicted a complex mechanism of gene transfer and generated hypotheses that opened new research directions, illustrating AI's...

Our second paper with @tcostalab.bsky.social and GoogleDeepMind
reports our experience with Google’s co-scientist: remarkably, the AI independently recapitulated our experimental discovery on cf-PICIs, showcasing AI’s potential to accelerate biology.
www.cell.com/cell/fulltex...

Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization Capsid-forming PICIs (cf-PICIs) produce their own capsids and exploit phage tails from unrelated species to transfer their DNA across bacterial hosts. This tail piracy enables broad dissemination and ...

Thrilled to share our two latest papers with the @tcostalab.bsky.social
lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species.
@imperialcollegeldn.bsky.social
www.cell.com/cell/fulltex...

Lots of heterogeneity in capsule production in Klebsiella and Acinetobacter. Given the pleiotropic impact of capsules, this provides opportunities for multiple types of phenotypical heterogeneity. Check @julielebris.bsky.social thread on our recent publication.

Project - Plasmidlab PLAS-FIGHTER Exploiting plasmid-bacteria interactions to fight

Antimicrobial Resistance (AMR) could cause 10 million deaths by 2050. At PLAS-FIGHTER, we are working to change this!
🔎 We study how plasmids spread resistance to open up new avenues for future containment and diagnostic strategies.
Find out more 👇
plasmidlab.es/project/

#AntibioticResistance

Willing to join us @pasteur.fr for a PhD for a project on how interactions between mobile genetic elements shape bacterial adaptation? Subject to be tailored to candidates with keen interest in evolution, genomics, computational biology, microbiology. Check www.pasteur.fr/en/education...

Pioneer of bacterial genetics: the legacy of Esther Miriam Lederberg Abstract. Esther Miriam Lederberg's brilliant scientific lifework, from the discovery of phage lambda, bacterial conjugation, and replica plating, provided

Thanks to the authors of this piece. I love reading about the work of inspiring pioneers in bacterial genetics. Crazy amount of discoveries!

Pioneer of bacterial genetics: the legacy of Esther Miriam Lederberg
academic.oup.com/genetics/adv...

Lineage-specific defence systems of pandemic Vibrio cholerae | Philosophical Transactions of the Royal Society B: Biological Sciences Cholera remains a significant global health burden. The causative agent responsible for the ongoing cholera pandemic, which began in 1961, is the seventh pandemic El Tor (7PET) lineage of Vibrio chole...

Lineage-specific defence systems of pandemic Vibrio cholerae

Phil. Trans. R. Soc. B by @mblokesch.bsky.social and Kim Seed

royalsocietypublishing.org/doi/10.1098/...

Phage defence-system abundances vary across environments and increase with viral density | Philosophical Transactions of the Royal Society B: Biological Sciences The defence systems bacteria use to protect themselves from their viruses are mechanistically and genetically diverse. Yet the ecological conditions that predict when defences are selected for remain ...

Phage defence-system abundances vary across environments and increase with viral density

Phil. Trans. R. Soc. B by @seanmeaden.bsky.social, Edze Westra and @peterfineran.bsky.social

royalsocietypublishing.org/doi/10.1098/...

Lineage-specific defence systems of pandemic Vibrio cholerae | Philosophical Transactions of the Royal Society B: Biological Sciences Cholera remains a significant global health burden. The causative agent responsible for the ongoing cholera pandemic, which began in 1961, is the seventh pandemic El Tor (7PET) lineage of Vibrio chole...

And as a bonus — a 2nd review in the same special issue, co-authored with Kim Seed! 🧬💥

Lineage-specific defence systems of pandemic Vibrio cholerae
royalsocietypublishing.org/doi/10.1098/...

Thanks to the editors Uri Gophna, Stineke van Houte and Edze Westra for bringing this collection together.

Defence systems encoded by core genomic islands of seventh pandemic Vibrio cholerae | Philosophical Transactions of the Royal Society B: Biological Sciences Vibrio cholerae, the causative agent of cholera, has triggered seven pandemics, with the seventh pandemic emerging in 1961. The success of seventh pandemic El Tor (7PET) V. cholerae as a human pathogen is linked to its acquisition of mobile genetic ...

Excited to share my latest review, now published in the Royal Society theme issue on ‘The ecology and evolution of bacterial immune systems' (available OA):

Defence systems encoded by core genomic islands of seventh pandemic Vibrio cholerae royalsocietypublishing.org/doi/10.1098/...

Some good stuff in here 😊

Preprint: We discovered phage proteins that sequester diverse immune signaling molecules, including cUMP, cCMP, and N7-cADPR

The first viral sponges to inhibit Pycsar and type IV Thoeris

Congrats to talented leading author Romi Hadary! Read her thread to learn more about our findings

Congratulations Rotem Sorek @soreklab.bsky.social on receiving the Gruber prize today in Stockholm