Phages keeping up as treasure troves for biotech! 🧬 Massive congratulations to the whole team for this fantastic application! 👏🎉

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:

New preprint alert!!! 🚀🤓 We are very happy to finally share this with the world — the result of seven years of work and a new tool to study integrons and discover new functions encoded in these bacterial platforms.

If you want to know more, here is a thread 🧵
www.biorxiv.org/content/10.6...

Bacteriophage data on capsular Klebsiella bacteria barcoded library

New paper 🔔

Collaboration
@sullivan-lab.bsky.social
Marissa Gittrich led the work

Klebsiella phage biology has focused almost entirely on capsulated strains, but capsule loss is the #1 resistance mechanism under phage predation. We used a naturally acapsular host to reveal the receptor landscape

➡️ 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? 🤔

🧵👇

Glad to see our latest work out in Nature Microbiology!!

Extremely grateful to everyone involved in the project.

Check it out!! 👇🏻👇🏻

Capturing dynamic phage–pathogen coevolution by clinical surveillance @nature.com @ucberkeleyofficial.bsky.social
www.nature.com/articles/s41...

New preprint out on bioRxiv!

www.biorxiv.org/content/10.6...

Can conjugative plasmids be used to control plasmid and pathogen spread?

Follow me down the rabbit hole that led to this story 🧵

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. 🧵

Thanks a loooot for your daily support 🙏✨

Muchísimas gracias Marian!! A ver si podemos volver a coincidir pronto!!

Thanks a lot!! Hope everything is going well!

I’m incredibly happy to have been awarded an #MSCA Fellowship to join the @sanmillan.bsky.social lab at @csic.es! 🎉🎉

The project includes an exciting secondment at the IRYCIS-RyC hospital! 🏥

Grateful for all the support and the reviewers' recognition of our project in such a competitive call! 🙏

Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive.

Here we explore the conjugative capacity of these mysterious Genomic Islands.

www.biorxiv.org/content/10.6...

Environment and physiology shape antiphage system expression Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of anti...

Bacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed.

In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts.
www.biorxiv.org/content/10.6...

Very proud of @celiaferriolg.bsky.social! Amazing experimental evolution for phage optimization and for host range expansion, allowing us to understand the evolvability of phage RBPs. This work is part of her PhD project at the #EnBivirLab @i2sysbio.es @uv.es @ccbiologiquesuv.bsky.social

📣 New preprint from us at phagefoundry.org 📣
A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort
www.biorxiv.org/content/10.1...

Jumbo phage–mediated transduction of genomic islands | PNAS Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages, and c...

@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎

www.pnas.org/doi/10.1073/...

Fascinating preprint. I've always been curious about genome stability of phages.

🧫🦠

Capsular specificity in temperate phages of Klebsiella pneumoniae is driven by diverse receptor-binding enzymes Understanding host-range determinants in temperate bacteriophages is critical for elucidating phage-host co-evolution and advancing phage therapies.We analysed 3,900 Klebsiella genomes from diverse ec...

Thank you so much, Michael! Prophages are a treasure trove! We were excited to see the recent preprint from @rafalmostowy.bsky.social lab using GWAS, such a great complementary approach!
www.biorxiv.org/content/10.1...

Massive thanks to @concha-eloko.bsky.social @pilardomingoc.bsky.social and @rafa-sanjuan.bsky.social to make it possible!

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...

Any group would be incredibly lucky to have her!

Serotype swapping in Klebsiella spp. by plug-and-play Understanding 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...

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👇

Amazing news!!! Congratulations François!! 🙌🥳

Very well-deserved @dbikard.bsky.social, congratulations!!! 🙌🙌 It's great to learn from the best! 🥳

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

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

Phage therapy for Klebsiella pneumoniae: Understanding bacteria–phage interactions for therapeutic innovations Klebsiella pneumoniae (KP) is a Gram-negative bacterium that commonly resides in the human gastrointestinal tract and can also act as an opportunistic pathogen and cause extra-intestinal infections. K...

Our review on recent advances in #PhageTherapy against Klebsiella pneumoniae is out!
We analyze KP-phage interactions from an eco-evo perspective, summarize many lab and clinical trials, and discuss novel approaches like genetic engineering & machine learning.
#microsky
doi.org/10.1371/jour...

And here it is, the completed BASEL collection finally published as early access in @plosbiology.org - see the thread for more details. 🤗🧬🎣