Lightnews — Scholar-powered news

Beatriz Beamud @beatrizbeamud.bsky.social · 22h

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

1

Beatriz Beamud @beatrizbeamud.bsky.social · 22h

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...

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.

www.nature.com

1 1 9

Beatriz Beamud @beatrizbeamud.bsky.social · 23d

Any group would be incredibly lucky to have her!

Sofya Garushyants @garushyants.bsky.social · 23d

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

2

Reposted by Beatriz Beamud

Julie Le Bris @julielebris.bsky.social · 28d

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👇

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...

www.biorxiv.org

2 22 26

Beatriz Beamud @beatrizbeamud.bsky.social · Sep 5

Amazing news!!! Congratulations François!! 🙌🥳

1

Beatriz Beamud @beatrizbeamud.bsky.social · Jun 6

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

European Research Council (ERC) @erc.europa.eu · Jun 5

🎉 Congratulations to David Bikard @pasteur.fr on his 2025 @embo.org Gold Medal win!

🧬 He's pioneering phage-CRISPR tools to edit gut #bacteria in vivo, reshaping the #microbiome from within and opening the door to targeted therapies.

👉 europa.eu/!HQbHTw
👉 europa.eu/!KtWf33

@dbikard.bsky.social

4

Beatriz Beamud @beatrizbeamud.bsky.social · May 15

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

Nature Reviews Bioengineering @natrevbioeng.nature.com · May 14

ICYMI: CRISPR–Cas therapies targeting bacteria

CRISPR–Cas therapies targeting bacteria

Nature Reviews Bioengineering, Published online: 13 May 2025; doi:10.1038/s44222-025-00311-8CRISPR–Cas tools can be designed to kill or modify specific bacteria. This Review explores the engineering of CRISPR–Cas tools and corresponding delivery strategies for the treatment of bacterial infections and modification of the microbiome.

www.nature.com

5 13

Reposted by Beatriz Beamud

Fabienne Benz @fabbenz.bsky.social · May 15

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

Nature Reviews Bioengineering @natrevbioeng.nature.com · May 14

ICYMI: CRISPR–Cas therapies targeting bacteria

CRISPR–Cas therapies targeting bacteria

Nature Reviews Bioengineering, Published online: 13 May 2025; doi:10.1038/s44222-025-00311-8CRISPR–Cas tools can be designed to kill or modify specific bacteria. This Review explores the engineering of CRISPR–Cas tools and corresponding delivery strategies for the treatment of bacterial infections and modification of the microbiome.

www.nature.com

1 35 63

Reposted by Beatriz Beamud

Olaya Rendueles @olayarendueles.bsky.social · Apr 9

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...

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...

doi.org

1 24 37

Reposted by Beatriz Beamud

Alexander Harms @aharms485.bsky.social · Apr 8

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

7 66 130

Reposted by Beatriz Beamud

Manuel Ares-Arroyo @aresarroyom.bsky.social · Apr 4

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!

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Apr 4

The leading region of many conjugative plasmids is depleted in restriction-modification targets https://www.biorxiv.org/content/10.1101/2025.04.03.647016v1

1 7 21

Reposted by Beatriz Beamud

PLOS Biology @plosbiology.org · Apr 2

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

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.

1 10 36

Beatriz Beamud @beatrizbeamud.bsky.social · Apr 3

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

Sol Vendrell @sol-uble.bsky.social · Apr 3

So happy to have published my PhD work! What a funky phage, it was a ride. Big thanks to @beatrizbeamud.bsky.social & @jmouradesousa.bsky.social for bringing their expertise into this story. And my mentors @jmghigolab.bsky.social & @dbikard.bsky.social 💪🏼

PLOS Biology @plosbiology.org · Apr 1

How does the lysogenic-lytic cycle work in intestinal #bacteriophages? @sol-uble.bsky.social @dbikard.bsky.social @jmghigolab.bsky.social &co show that hankyphage produces defective viral particles & identify RepCHP as master repressor of this #phage's lytic cycle @plosbiology.org 🧪 plos.io/41Rr22S

3