Beatriz Beamud

📣 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.

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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. 🤗🧬🎣

Do restriction-modification systems shape plasmid sequence composition? A group of plasmid-aficionados, led by Liam Shaw, started to explore this during the 2023 @embo.org Workshop on Plasmids in Trieste. Happy to have contributed to this work and be part of such a great team!

Schematic showing how Hankyphage has multiple mechanisms of generating randomness in its own and its bacterial host genomes. (1) RepCHP-dependent spontaneous induction of prophage, (2) incomplete packaging leading to defective virions and free tails in combination with low-level complete packaging and potential transduction events, (3) intrachromosomal transposition leading to genetic variation in the host genome, and (4) diversity generating retroelements within the phage genome impacting the host range of the phage. Created with BioRender.

The biology and ecological impact of #phages in the mammalian gut are poorly understood. This Primer explores a @plosbiology.org study that provides a glimpse into the disruptive biology of the #Hankyphages, parasites of the ubiquitous Bacteroidaceae. 🧪 Primer: plos.io/3RukgtJ Paper: plos.io/41Rr22S

The Hankyphage mistery 🕵️‍♀️ Puzzling but incredibly fun working with the amazing @sol-uble.bsky.social and the rest of the team on this! ✨