Beatriz Beamud
@beatrizbeamud.bsky.social
🧪 Bacteria & Mobile Genetic Elements 💻 Synthetic Biology Group @institutpasteur 👩🔬 PhD @GVAfisabio @i2sysbio
Reposted by 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...
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...
Phage Foundry
phagefoundry.org
November 16, 2025 at 5:58 PM
📣 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...
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...
Reposted by Beatriz Beamud
@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/...
www.pnas.org/doi/10.1073/...
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...
www.pnas.org
October 28, 2025 at 6:36 PM
@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/...
www.pnas.org/doi/10.1073/...
Reposted by Beatriz Beamud
Fascinating preprint. I've always been curious about genome stability of phages.
🧫🦠
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Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community
Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...
www.biorxiv.org
October 13, 2025 at 7:23 AM
Fascinating preprint. I've always been curious about genome stability of phages.
🧫🦠
🧫🦠
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...
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
October 8, 2025 at 8:59 AM
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...
www.nature.com/articles/s41...
Any group would be incredibly lucky to have her!
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!
September 15, 2025 at 6:54 PM
Any group would be incredibly lucky to have her!
Reposted by Beatriz Beamud
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👇
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
September 10, 2025 at 8:17 AM
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👇
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👇
Very well-deserved @dbikard.bsky.social, congratulations!!! 🙌🙌 It's great to learn from the best! 🥳
🎉 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
🧬 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
June 6, 2025 at 7:44 AM
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 ⚡
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
May 15, 2025 at 8:36 AM
Massive effort lead by the amazing @fabbenz.bsky.social to discuss the present and future of CRISPR-based antimicrobials ⚡
Reposted by Beatriz Beamud
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
May 15, 2025 at 6:53 AM
Reposted by Beatriz Beamud
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...
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
April 9, 2025 at 10:10 AM
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...
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...
Reposted by Beatriz Beamud
And here it is, the completed BASEL collection finally published as early access in @plosbiology.org - see the thread for more details. 🤗🧬🎣
April 8, 2025 at 4:59 AM
And here it is, the completed BASEL collection finally published as early access in @plosbiology.org - see the thread for more details. 🤗🧬🎣
Reposted by Beatriz Beamud
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!
The leading region of many conjugative plasmids is depleted in restriction-modification targets https://www.biorxiv.org/content/10.1101/2025.04.03.647016v1
April 4, 2025 at 1:57 PM
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!
Reposted by Beatriz Beamud
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
April 2, 2025 at 4:44 PM
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! ✨
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 💪🏼
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
April 3, 2025 at 6:31 PM
The Hankyphage mistery 🕵️♀️ Puzzling but incredibly fun working with the amazing @sol-uble.bsky.social and the rest of the team on this! ✨